Cell Ontology
type: Ontology
version IRI: cl.owl
preferred_root: cell
description: An ontology of cell types.
contributor: https://orcid.org/0000-0001-5208-3432
contributor: https://orcid.org/0000-0001-9114-8737
contributor: https://orcid.org/0000-0001-9990-8331
contributor: https://orcid.org/0000-0002-2244-7917
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-7073-9172
contributor: https://orcid.org/0000-0002-8688-6599
contributor: https://orcid.org/0000-0002-9900-7880
contributor: https://orcid.org/0000-0003-1980-3228
license: http://creativecommons.org/licenses/by/4.0/
comment: See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, university at buffalo.
version info: 2025-04-10

symbol
type: AnnotationProperty

definition
type: AnnotationProperty
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.

editor note
type: AnnotationProperty
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.

has obsolescence reason
type: AnnotationProperty
definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.

term tracker item
type: AnnotationProperty
definition: An IRI or similar locator for a request or discussion of an ontology term.
comment: The 'tracker item' can associate a tracker with a specific ontology term.

expand expression to
type: AnnotationProperty
definition: A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones

preferred_root
type: AnnotationProperty
definition: Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
label: has ontology root term

term replaced by
type: AnnotationProperty
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
comment: Add as annotation triples in the granting ontology

defined by construct
type: AnnotationProperty
definition: Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
term tracker item: https://github.com/ontodev/robot/issues/963
contributor: https://orcid.org/0000-0002-7356-1779
contributor: https://orcid.org/0000-0002-8688-6599

abbreviation
type: AnnotationProperty
definition: A synonym type for describing abbreviations or initalisms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
sub property of: synonym_type_property

plural form
type: AnnotationProperty
definition: A synonym type for describing pluralization synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
sub property of: synonym_type_property

never in taxon
type: AnnotationProperty
definition: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
defined by construct: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?x owl:disjointWith [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . }

present in taxon
type: AnnotationProperty
definition: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
defined by construct: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) }
comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.

is negative form of
type: AnnotationProperty
creation date: 2018-03-14T00:03:24Z

blood_and_immune_upper_slim
type: AnnotationProperty
date: 2023-03-31T09:17:34Z
comment: a subset of general classes related to blood and the immune system, primarily of hematopoietic origin
sub property of: subset_property

eye_upper_slim
type: AnnotationProperty
comment: a subset of general classes related to specific cell types in the eye.
sub property of: subset_property

general_cell_types_upper_slim
type: AnnotationProperty
comment: a subset of general classes of cell types in the cell ontology.
sub property of: subset_property

kidney_upper_slim
type: AnnotationProperty
date: 2023-11-22T11:18:57Z
comment: a subset of general classes related to specific cell types in the kidney
sub property of: subset_property

preferred term when talking about an instance of this class in Homo sapiens
type: AnnotationProperty
sub property of: synonym_type_property

latin term
type: AnnotationProperty
sub property of: synonym_type_property

plural term
type: AnnotationProperty
sub property of: synonym_type_property

a mis-spelling that is in common use and thus recorded
type: AnnotationProperty
sub property of: synonym_type_property

upper level
type: AnnotationProperty
comment: abstract upper-level terms not directly useful for analysis
sub property of: subset_property

description
type: AnnotationProperty

license
type: AnnotationProperty

title
type: AnnotationProperty

subset_property
type: AnnotationProperty

synonym_type_property
type: AnnotationProperty

consider
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
label: has broad synonym

database_cross_reference
type: AnnotationProperty
definition: An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/123
contributor: https://orcid.org/0000-0002-7356-1779
label: has cross-reference

has_exact_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
label: has exact synonym

has_narrow_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
label: has narrow synonym

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty
definition: An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
label: has related synonym

has_synonym_type
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

see also
type: AnnotationProperty
shorthand: seeAlso

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: BFO_0000003
range: BFO_0000003
property chain axiom: part of
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
in_subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: BFO_0000003
range: BFO_0000003
property chain axiom: part of
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in_subset: ro-eco

occurs in
type: ObjectProperty
inverse of: contains process
domain: BFO_0000003
range: BFO_0000004
property chain axiom: part of
definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

has_not_completed
type: ObjectProperty

lacks_part
type: ObjectProperty
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y

lacks_plasma_membrane_part
type: ObjectProperty
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)

results in distribution of
type: ObjectProperty
database_cross_reference: GOREL:0002003
has_obo_namespace: external
id: results_in_distribution_of
shorthand: results_in_distribution_of
label: results_in_distribution_of

results in fission of
type: ObjectProperty
sub property of: has participant
database_cross_reference: GOREL:0002004
has_obo_namespace: external
id: results_in_fission_of
shorthand: results_in_fission_of
label: results_in_fission_of

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: BFO_0000020
definition: Inverse of characteristic_of
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.

participates in
type: ObjectProperty
inverse of: has participant
domain: BFO_0000002
range: BFO_0000003
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process

has participant
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000002
property chain axiom: has part
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
database_cross_reference: RO:0000057
id: has_participant
shorthand: has_participant

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has quality
type: ObjectProperty
sub property of: has characteristic
range: BFO_0000019
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.

derives from
type: ObjectProperty
inverse of: derives into
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
in_subset: ro-eco

derives into
type: ObjectProperty
definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
in_subset: ro-eco

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/

located in
type: ObjectProperty
type: TransitiveProperty
domain: BFO_0000004
domain: Class
  intersection of: BFO_0000004
  intersection of: Class
    complement of: BFO_0000006
range: BFO_0000004
range: Class
  intersection of: BFO_0000004
  intersection of: Class
    complement of: BFO_0000006
property chain axiom: part of
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
in_subset: valid for go gp2term

Axiom
annotated source: located in
annotated property: domain
annotated target: BFO_0000004
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

Axiom
annotated source: located in
annotated property: range
annotated target: BFO_0000004
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

2D boundary of
type: ObjectProperty
sub property of: mereotopologically related to
inverse of: has 2D boundary
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.

has 2D boundary
type: ObjectProperty
sub property of: mereotopologically related to
domain: BFO_0000040
range: BFO_0000141
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.

innervated_by
type: ObjectProperty
inverse of: innervates
domain: UBERON_0000061
range: UBERON_0000122

has synaptic terminal of
type: ObjectProperty
sub property of: overlaps
inverse of: has synaptic terminal in

bounding layer of
type: ObjectProperty
sub property of: part of
domain: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0002124
range: BFO_0000040
definition: X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
in_subset: ro-eco
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.

occurs across
type: ObjectProperty
sub property of: has part that occurs in
definition: A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
creation date: 2017-07-20T17:19:37Z

before or simultaneous with
type: ObjectProperty
sub property of: temporally related to
in_subset: ro-eco
comment: Primitive instance level timing relation between events

simultaneous with
type: ObjectProperty
sub property of: before or simultaneous with
type: SymmetricProperty
type: TransitiveProperty
definition: x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time.
in_subset: ro-eco
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
in_subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
property chain axiom: starts with
property chain axiom: ends with
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

immediately precedes
type: ObjectProperty
sub property of: precedes
property chain axiom: ends with
property chain axiom: starts with
in_subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

has soma location
type: ObjectProperty
sub property of: overlaps
domain: neuron
range: UBERON_0000465
property chain axiom: part of
definition: Relation between a neuron and a material anatomical entity that its soma is part of.
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)

fasciculates with
type: ObjectProperty
sub property of: overlaps
inverse of: has fasciculating neuron projection
domain: neuron
range: UBERON_0000122
definition: relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.

axon synapses in
type: ObjectProperty
sub property of: has presynaptic terminal in
domain: neuron
property chain axiom: part of
definition: Relation between a neuron and some structure its axon forms (chemical) synapses in.
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))

synapsed by
type: ObjectProperty
sub property of: receives input from
inverse of: synapsed to
range: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron
definition: Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))

has plasma membrane part
type: ObjectProperty
sub property of: has part
domain: UBERON_0000465
range: UBERON_0000465
definition: Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)

has postsynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
inverse of: has presynaptic terminal in
domain: neuron
property chain axiom: part of
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))

has presynaptic terminal in
type: ObjectProperty
sub property of: has synaptic terminal in
domain: neuron
property chain axiom: part of
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)

synapsed to
type: ObjectProperty
sub property of: sends output to
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron
definition: Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
comment: N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))

has synaptic terminal in
type: ObjectProperty
sub property of: overlaps
domain: neuron
property chain axiom: part of
definition: A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
expand expression to: <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: ro-eco

has fasciculating neuron projection
type: ObjectProperty
sub property of: overlaps
domain: UBERON_0000122
range: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron
definition: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.

innervates
type: ObjectProperty
domain: UBERON_0000122
property chain axiom: part of
definition: Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
expand expression to: <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))

continuous with
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
domain: BFO_0000004
range: BFO_0000004
definition: X continuous_with Y if and only if X and Y share a fiat boundary.

shares ancestor with
type: ObjectProperty
sub property of: evolutionarily related to
type: SymmetricProperty
type: TransitiveProperty
definition: two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.
comment: VBO calls this homologous_to

only in taxon
type: ObjectProperty
sub property of: in taxon
definition: x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
editor note: The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
property chain axiom: part of
property chain axiom: has part
property chain axiom: expressed in
property chain axiom: regulates
property chain axiom: capable of
property chain axiom: has developmental contribution from
property chain axiom: results in developmental progression of
property chain axiom: has potential to develop into
property chain axiom: extends_fibers_into
definition: x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
has_narrow_synonym: life cycle stage of
in_subset: ro-eco
comment: Connects a biological entity to its taxon of origin.

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
definition: A is spatially_disjoint_from B if and only if they have no parts in common
editor note: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
expand expression to: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
in_subset: ro-eco

connected to
type: ObjectProperty
sub property of: mereotopologically related to
domain: Restriction
  on property: part of
  some values from: RO_0002577
range: Restriction
  on property: part of
  some values from: RO_0002577
property chain axiom:
  inverse of: connects
property chain axiom: connects
definition: a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b

connects
type: ObjectProperty
sub property of: mereotopologically related to
domain: BFO_0000004
range: Restriction
  on property: part of
  some values from: RO_0002577
definition: c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.

attached to part of
type: ObjectProperty
sub property of: mereotopologically related to
sub property of: biomechanically related to
domain: UBERON_0000061
range: UBERON_0000061
definition: a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.

supplies
type: ObjectProperty
sub property of: connected to
definition: Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
editor note: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure

drains
type: ObjectProperty
sub property of: connected to
definition: Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
editor note: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure

has component
type: ObjectProperty
sub property of: has part
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
in_subset: ro-eco

develops from
type: ObjectProperty
sub property of: has developmental contribution from
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: BFO_0000004
range: BFO_0000004
definition: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
comment: This is the transitive form of the develops from relation

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
definition: inverse of develops from
in_subset: RO_0002259

expressed in
type: ObjectProperty
sub property of: genomically related to
inverse of: expresses
domain: BFO_0000002
domain: Class
  union of: BFO_0000031
  union of: BFO_0000040
range: UBERON_0000465
property chain axiom: part of
definition: x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process

directly develops from
type: ObjectProperty
sub property of: develops from
inverse of: directly develops into
domain: Class
  union of: cell
  union of: UBERON_0010000
range: Class
  union of: cell
  union of: UBERON_0010000
definition: Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
has_exact_synonym: has developmental precursor
comment: TODO - add child relations from DOS

directly develops into
type: ObjectProperty
sub property of: develops into
definition: inverse of directly develops from
in_subset: RO_0002259

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
property chain axiom: ends with
definition: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
property chain axiom: ends with
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
is negative form of: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
property chain axiom: ends with
definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

capable of
type: ObjectProperty
sub property of: capable of part of
domain: BFO_0000004
range: BFO_0000015
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
in_subset: ro-eco

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.

surrounded by
type: ObjectProperty
sub property of: adjacent to
inverse of: surrounds
definition: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: BFO_0000004
range: BFO_0000004
definition: x adjacent to y if and only if x and y share a boundary.
editor note: This relation acts as a join point with BSPO
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

surrounds
type: ObjectProperty
sub property of: adjacent to
definition: inverse of surrounded by
in_subset: RO_0002259

temporally related to
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000003
in_subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

starts
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: starts with
definition: inverse of starts with
in_subset: ro-eco

starts with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in_subset: ro-eco

develops from part of
type: ObjectProperty
sub property of: develops from
property chain axiom: directly develops from
property chain axiom: part of
definition: x develops from part of y if and only if there exists some z such that x develops from z and z is part of y

develops in
type: ObjectProperty
sub property of: developmentally preceded by
domain: UBERON_0001062
property chain axiom: directly develops from
property chain axiom: located in
definition: x develops_in y if x is located in y whilst x is developing

ends
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: ends with
definition: inverse of ends with
in_subset: ro-eco

ends with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in_subset: ro-eco

has start location
type: ObjectProperty
sub property of: has part that occurs in
domain: BFO_0000015
range: BFO_0000004
property chain axiom: starts with
property chain axiom: occurs in
definition: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
in_subset: ro-eco

has end location
type: ObjectProperty
sub property of: has part that occurs in
domain: BFO_0000015
range: BFO_0000004
property chain axiom: ends with
property chain axiom: occurs in
definition: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
in_subset: ro-eco

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: BFO_0000015
property chain axiom: starts with
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: ro-eco

has output
type: ObjectProperty
sub property of: has participant
inverse of: output of
property chain axiom: ends with
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: ro-eco

connecting branch of
type: ObjectProperty
sub property of: connected to
sub property of: in branching relationship with
inverse of: has connecting branch
definition: b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.

has connecting branch
type: ObjectProperty
sub property of: in branching relationship with
definition: inverse of connecting branch of
in_subset: RO_0002259

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
domain: UBERON_0001062
range: UBERON_0001062
property chain axiom: has part
definition: x has developmental contribution from y iff x has some part z such that z develops from y

developmentally contributes to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: part of
definition: inverse of has developmental contribution from
in_subset: RO_0002259

developmentally induced by
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally induces
domain: UBERON_0000465
range: UBERON_0000465
definition: t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T

developmentally induces
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally induce
definition: Inverse of developmentally induced by

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: BFO_0000002
range: BFO_0000002
definition: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
editor note: false
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
in_subset: valid for go gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has_related_synonym: affects
in_subset: valid for go gp2term

developmentally replaces
type: ObjectProperty
sub property of: developmentally preceded by
definition: x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
editor note: This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
definition: Inverse of developmentally preceded by

part of developmental precursor of
type: ObjectProperty
sub property of: developmentally succeeded by
property chain axiom: part of
property chain axiom: directly develops into

expresses
type: ObjectProperty
sub property of: genomically related to
definition: y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.

results in developmental progression of
type: ObjectProperty
sub property of: developmentally related to
domain: GO_0008150
range: UBERON_0001062
definition: p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
editor note: This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.

results in development of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
definition: p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

results in formation of anatomical entity
type: ObjectProperty
sub property of: has output
sub property of: results in developmental progression of
inverse of: formed as result of
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

results in morphogenesis of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
definition: The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

results in maturation of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
definition: The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
definition: p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
in_subset: valid for go annotation extension
in_subset: valid for gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
definition: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
is negative form of: causally upstream of
in_subset: valid for go annotation extension
in_subset: valid for gocam

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: part of
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
editor note: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of

results in acquisition of features of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
range: UBERON_0000061
definition: The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

evolutionarily related to
type: ObjectProperty
definition: A relationship that holds via some environmental process

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.

genomically related to
type: ObjectProperty
domain: BFO_0000002
range: BFO_0000002
definition: holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.

regulates levels of
type: ObjectProperty
sub property of: functionally related to
domain: BFO_0000015
range: BFO_0000040
definition: p regulates levels of c if p regulates some amount (PATO:0000070) of c

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: BFO_0000015
range: BFO_0000015
definition: inverse of regulates
in_subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
in_subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
in_subset: RO_0002259

related via localization to
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000002
definition: A relationship that holds via some process of localization

has target start location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: part of
definition: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

has target end location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: part of
definition: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

results in transport along
type: ObjectProperty
sub property of: related via localization to
definition: Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l

results in transport across
type: ObjectProperty
sub property of: occurs across
sub property of: results in transport to from or in
definition: Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
in_subset: valid for go ontology

results in growth of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure

results in transport to from or in
type: ObjectProperty
sub property of: related via localization to

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
definition: is member of is a mereological relation between a item and a collection.

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
in_subset: RO_0002259
in_subset: ro-eco

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has output
in_subset: RO_0002259
in_subset: ro-eco

formed as result of
type: ObjectProperty
sub property of: output of

has dendrite location
type: ObjectProperty
sub property of: overlaps

attached to
type: ObjectProperty
sub property of: connected to
sub property of: attached to part of
type: SymmetricProperty
definition: a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
in_subset: ro-eco

has muscle origin
type: ObjectProperty
sub property of: attached to
sub property of: biomechanically related to
domain: UBERON_0000061
definition: m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.

Axiom
annotated source: has muscle origin
annotated property: domain
annotated target: UBERON_0000061
comment: We need to import uberon muscle to create a stricter domain constraint

has muscle insertion
type: ObjectProperty
sub property of: attached to
sub property of: biomechanically related to
domain: UBERON_0000061
definition: m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.

Axiom
annotated source: has muscle insertion
annotated property: domain
annotated target: UBERON_0000061
editor note: We need to import uberon muscle into RO to use as a stricter domain constraint

in branching relationship with
type: ObjectProperty
sub property of: mereotopologically related to
domain: BFO_0000040
range: BFO_0000040
definition: A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.

tributary of
type: ObjectProperty
sub property of: connected to
sub property of: in branching relationship with
definition: x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
in_subset: ro-eco

spatially coextensive with
type: ObjectProperty
sub property of: overlaps
property chain axiom: located in
property chain axiom:
  inverse of: located in
definition: x spatially_coextensive_with y if and inly if x and y have the same location

branching part of
type: ObjectProperty
sub property of: part of
sub property of: in branching relationship with
inverse of: has branching part
range: Restriction
  on property: has characteristic
  some values from: PATO_0000402
definition: x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
in_subset: ro-eco

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: UBERON_0001062
range: UBERON_0001062
definition: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
definition: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y

has potential to developmentally induce
type: ObjectProperty
sub property of: has developmental potential involving
definition: x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
comment: This relation has a stronger meaning than merely indicating that X may develop into Y, in that the capability of developing into Y is always present, even if X does not always actually develop into Y. In particular, this means that if Y is restricted to a given taxon T, X is necessarily likewise restricted.

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
definition: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
definition: inverse of upstream of

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
editor note: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yie…

Axiom
annotated source: causally related to
annotated property: definition
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
database_cross_reference: https://en.wikipedia.org/wiki/Causality

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
definition: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
in_subset: valid for go annotation extension
in_subset: valid for gocam

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
property chain axiom: part of
definition: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
has_related_synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
in_subset: RO_0002259

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
editor note: OWL does not allow defining object properties via a Union

contributes to morphology of
type: ObjectProperty
sub property of: overlaps
definition: p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.

composed primarily of
type: ObjectProperty
sub property of: has part
domain: BFO_0000040
range: BFO_0000040
definition: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
in_subset: ro-eco

has part that occurs in
type: ObjectProperty
domain: BFO_0000003
range: BFO_0000004
definition: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
in_subset: ro-eco

receives input from
type: ObjectProperty
sub property of: connected to
inverse of: sends output to
editor note: See notes for inverse relation

sends output to
type: ObjectProperty
sub property of: connected to
editor note: This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.

relation between physical entity and a process or stage
type: ObjectProperty
domain: BFO_0000004
range: BFO_0000003

existence starts during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence starts during or after
property chain axiom: part of
definition: x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).

existence starts with
type: ObjectProperty
sub property of: existence starts during
definition: x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).

existence overlaps
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
definition: x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence starts and ends during
type: ObjectProperty
sub property of: existence starts during
sub property of: existence ends during
definition: x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
has_exact_synonym: exists during
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence ends during or before
property chain axiom: part of
definition: x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends with
type: ObjectProperty
sub property of: existence ends during
definition: x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

transformation of
type: ObjectProperty
sub property of: develops from
type: TransitiveProperty
definition: x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships

immediate transformation of
type: ObjectProperty
sub property of: directly develops from
sub property of: transformation of
definition: x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t

existence starts during or after
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally preceded by
property chain axiom: preceded by
property chain axiom: simultaneous with
definition: x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during or before
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally succeeded by
property chain axiom: precedes
property chain axiom: simultaneous with
definition: x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000003
range: BFO_0000003
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.

depends on
type: ObjectProperty

has skeleton
type: ObjectProperty
sub property of: has part
inverse of: skeleton of
type: AsymmetricProperty
type: IrreflexiveProperty
domain: UBERON_0000061
range: UBERON_0000465
definition: A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.

Axiom
annotated source: has skeleton
annotated property: range
annotated target: UBERON_0000465
editor note: This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.

results in movement of
type: ObjectProperty
sub property of: results in changes to anatomical or cellular structure
definition: Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

biomechanically related to
type: ObjectProperty
sub property of: functionally related to
domain: UBERON_0000061
range: UBERON_0000061
definition: A relation that holds between elements of a musculoskeletal system or its analogs.

has muscle antagonist
type: ObjectProperty
sub property of: biomechanically related to
definition: m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.

has branching part
type: ObjectProperty
sub property of: has part
sub property of: in branching relationship with
type: TransitiveProperty
definition: inverse of branching part of
in_subset: RO_0002259
in_subset: ro-eco

conduit for
type: ObjectProperty
sub property of: overlaps
domain: BFO_0000040
range: BFO_0000040
definition: x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
in_subset: ro-eco

lumen of
type: ObjectProperty
sub property of: part of
range: BFO_0000040
definition: x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
in_subset: ro-eco

luminal space of
type: ObjectProperty
sub property of: lumen of
domain: BFO_0000141
definition: s is luminal space of x iff s is lumen_of x and s is an immaterial entity
in_subset: ro-eco

skeleton of
type: ObjectProperty
sub property of: part of
domain: UBERON_0000061
range: UBERON_0000061
definition: inverse of has skeleton
in_subset: RO_0002259

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p

results in breakdown of
type: ObjectProperty
sub property of: has input
definition: p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p

results in assembly of
type: ObjectProperty
sub property of: results in formation of anatomical entity
sub property of: results in organization of
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

results in disassembly of
type: ObjectProperty
sub property of: results in breakdown of
sub property of: results in organization of

results in organization of
type: ObjectProperty
sub property of: results in changes to anatomical or cellular structure
definition: p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: BFO_0000040
range: BFO_0000015
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'

produces
type: ObjectProperty
inverse of: produced by
domain: BFO_0000040
range: BFO_0000040
property chain axiom:
  inverse of: occurs in
property chain axiom: has output
definition: a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
in_subset: ro-eco
comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.

produced by
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000040
definition: a produced_by b iff some process that occurs_in b has_output a.
in_subset: ro-eco

has primary input or output
type: ObjectProperty
sub property of: has participant
definition: p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
creation date: 2018-12-13T11:26:17Z
in_subset: valid for go ontology

has primary output
type: ObjectProperty
sub property of: has output
sub property of: has primary input or output
definition: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
creation date: 2018-12-13T11:26:32Z
in_subset: valid for go ontology

Axiom
annotated source: has primary output
annotated property: definition
annotated target: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: GOC:dph
database_cross_reference: GOC:kva
database_cross_reference: GOC:pt
comment: PMID:27812932

has primary input
type: ObjectProperty
sub property of: has input
sub property of: has primary input or output
definition: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
creation date: 2018-12-13T11:26:56Z
in_subset: valid for go ontology

Axiom
annotated source: has primary input
annotated property: definition
annotated target: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: GOC:dph
database_cross_reference: GOC:kva
database_cross_reference: GOC:pt
comment: PMID:27812932

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
is negative form of: causally upstream of or within
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
creation date: 2018-03-13T23:55:19Z

has small molecule regulator
type: ObjectProperty
sub property of: has participant
inverse of: is small molecule regulator of
definition: a relation between a process and a continuant, in which the process is regulated by the small molecule continuant
creation date: 2020-04-22T20:27:26Z

has small molecule activator
type: ObjectProperty
sub property of: has small molecule regulator
inverse of: is small molecule activator of
definition: a relation between a process and a continuant, in which the process is activated by the small molecule continuant
creation date: 2020-04-22T20:28:37Z

acts on population of
type: ObjectProperty
sub property of: has participant
definition: p acts on population of c iff c' is a collection, has members of type c, and p has participant c
creation date: 2020-06-08T17:21:33Z
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

is small molecule regulator of
type: ObjectProperty
sub property of: capable of regulating
definition: a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process
creation date: 2020-06-24T13:15:17Z

is small molecule activator of
type: ObjectProperty
sub property of: capable of positively regulating
sub property of: is small molecule regulator of
definition: a relation between a continuant and a process, in which the continuant is a small molecule that activates the process
creation date: 2020-06-24T13:15:26Z

results in fusion of
type: ObjectProperty
sub property of: results in organization of
creation date: 2021-02-26T07:28:29Z
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

has synaptic IO in region
type: ObjectProperty
sub property of: has synaptic terminal in
property chain axiom: part of
definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
creation date: 2020-07-17T09:26:52Z
has_exact_synonym: has synaptic input or output in

has sensory dendrite in
type: ObjectProperty
sub property of: has dendrite location
domain: sensory neuron
property chain axiom: part of
definition: Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.
creation date: 2020-07-20T12:10:09Z
has_exact_synonym: has sensory dendrite location
has_exact_synonym: has sensory terminal in
has_exact_synonym: has sensory terminal location

has characterizing marker set
type: ObjectProperty
domain: cell
definition: A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type.
editor note: C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types.
contributor: https://orcid.org/0000-0001-7258-9596
has_exact_synonym: has marker gene combination
has_exact_synonym: has marker signature set

different in magnitude relative to
type: ObjectProperty
domain: PATO_0000001
range: PATO_0000001
definition: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

Axiom
annotated source: different in magnitude relative to
annotated property: definition
annotated target: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

increased in magnitude relative to
type: ObjectProperty
sub property of: different in magnitude relative to
domain: PATO_0000001
range: PATO_0000001
definition: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.

Axiom
annotated source: increased in magnitude relative to
annotated property: definition
annotated target: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

decreased in magnitude relative to
type: ObjectProperty
sub property of: different in magnitude relative to
domain: PATO_0000001
range: PATO_0000001
definition: q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.

Axiom
annotated source: decreased in magnitude relative to
annotated property: definition
annotated target: q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

has relative magnitude
type: ObjectProperty

has cross section
type: ObjectProperty
definition: s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.

Axiom
annotated source: has cross section
annotated property: definition
annotated target: s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
database_cross_reference: https://orcid.org/0000-0002-6601-2165

has high plasma membrane amount
type: ObjectProperty
sub property of: has plasma membrane part
domain: cell
definition: A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
contributor: https://orcid.org/0000-0003-1617-8244
contributor: https://orcid.org/0000-0003-1940-6740

Axiom
annotated source: has high plasma membrane amount
annotated property: definition
annotated target: A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
database_cross_reference: PMID:19243617

has low plasma membrane amount
type: ObjectProperty
sub property of: has plasma membrane part
domain: cell
definition: A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
contributor: https://orcid.org/0000-0003-1617-8244
contributor: https://orcid.org/0000-0003-1940-6740

Axiom
annotated source: has low plasma membrane amount
annotated property: definition
annotated target: A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
database_cross_reference: PMID:19243617

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
definition: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
contributor: https://orcid.org/0000-0001-9625-1899
contributor: https://orcid.org/0000-0003-2620-0345
creation date: 2021-11-08T12:00:00Z
has_broad_synonym: utilizes

vessel supplies blood to
type: ObjectProperty
sub property of: supplies
domain: UBERON_0001981
range: UBERON_0000061
definition: x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y.
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-02-01T10:09:22Z

vessel drains blood from
type: ObjectProperty
sub property of: drains
domain: UBERON_0001981
range: UBERON_0000061
definition: x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y.
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-02-01T10:09:41Z

results in changes to anatomical or cellular structure
type: ObjectProperty
sub property of: has participant
definition: p has anatomical participant c iff p has participant c, and c is an anatomical entity
creation date: 2018-09-26T01:08:58Z

obsolete has_high_plasma_membrane_amount
type: ObjectProperty
definition: OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1481
term replaced by: has high plasma membrane amount
deprecated: true

Axiom
annotated source: obsolete has_high_plasma_membrane_amount
annotated property: definition
annotated target: OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).
database_cross_reference: PMID:19243617

obsolete has_low_plasma_membrane_amount
type: ObjectProperty
definition: OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1481
term replaced by: has low plasma membrane amount
deprecated: true

Axiom
annotated source: obsolete has_low_plasma_membrane_amount
annotated property: definition
annotated target: OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).
database_cross_reference: PMID:19243617

anteriorly connected to
type: ObjectProperty
sub property of: BSPO_0000099
sub property of: connected to
sub property of: transitively anteriorly connected to
definition: x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
has_obo_namespace: uberon
id: anteriorly_connected_to

Axiom
annotated source: anteriorly connected to
annotated property: definition
annotated target: x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
database_cross_reference: http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern

channel for
type: ObjectProperty
domain: UBERON_0004111
range: UBERON_0000463
has_broad_synonym: carries
has_obo_namespace: uberon
id: channel_for

channels_from
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: uberon
id: channels_from

channels_into
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: uberon
id: channels_into

distally connected to
type: ObjectProperty
sub property of: BSPO_0000100
sub property of: connected to
sub property of: transitively distally connected to
inverse of: proximally connected to
definition: x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
has_obo_namespace: uberon
id: distally_connected_to

Axiom
annotated source: distally connected to
annotated property: definition
annotated target: x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
database_cross_reference: http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern

extends_fibers_into
type: ObjectProperty
sub property of: connected to
type: SymmetricProperty
definition: X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y
has_obo_namespace: uberon
id: extends_fibers_into

Axiom
annotated source: extends_fibers_into
annotated property: definition
annotated target: X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y
database_cross_reference: https://orcid.org/0000-0002-7073-9172

filtered through
type: ObjectProperty
definition: Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
has_obo_namespace: uberon
id: filtered_through
comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed

indirectly_supplies
type: ObjectProperty
type: TransitiveProperty
property chain axiom: has branching part
definition: a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s.
editor note: add to RO
has_obo_namespace: uberon
id: indirectly_supplies

layer part of
type: ObjectProperty
sub property of: part of
has_obo_namespace: uberon
id: layer_part_of

posteriorly connected to
type: ObjectProperty
sub property of: BSPO_0000096
sub property of: connected to
definition: x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
has_obo_namespace: uberon
id: posteriorly_connected_to

Axiom
annotated source: posteriorly connected to
annotated property: definition
annotated target: x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
database_cross_reference: http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern

protects
type: ObjectProperty
has_obo_namespace: uberon
id: protects

proximally connected to
type: ObjectProperty
sub property of: BSPO_0000097
sub property of: connected to
sub property of: transitively proximally connected to
definition: x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
has_obo_namespace: uberon
id: proximally_connected_to

Axiom
annotated source: proximally connected to
annotated property: definition
annotated target: x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
database_cross_reference: http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern

sexually_homologous_to
type: ObjectProperty
sub property of: shares ancestor with
has_obo_namespace: uberon
id: sexually_homologous_to

site_of
type: ObjectProperty
definition: c site_of p if c is the bearer of a disposition that is realized by a process that has p as part.
has_obo_namespace: uberon
has_related_synonym: capable_of_has_part
id: site_of

subdivision of
type: ObjectProperty
has_obo_namespace: uberon
id: subdivision_of
comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B

transitively anteriorly connected to
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: uberon
id: transitively_anteriorly_connected_to

transitively distally connected to
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: uberon
id: transitively_distally_connected_to

transitively proximally connected to
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: uberon
id: transitively_proximally_connected_to

trunk_part_of
type: ObjectProperty
sub property of: part of
has_obo_namespace: uberon
id: trunk_part_of

TAC1
type: Class
subclass of: SO_0000704

STAB1
type: Class
subclass of: SO_0000704

TLL1
type: Class
subclass of: SO_0000704

MSR1
type: Class
subclass of: SO_0000704

TNC
type: Class
subclass of: SO_0000704

ROS1
type: Class
subclass of: SO_0000704

TNIP3
type: Class
subclass of: SO_0000704

HOMER3
type: Class
subclass of: SO_0000704

FCGR2B
type: Class
subclass of: SO_0000704

BPIFB2
type: Class
subclass of: SO_0000704

KCNK2
type: Class
subclass of: SO_0000704

SEMA5B
type: Class
subclass of: SO_0000704

HMOX1
type: Class
subclass of: SO_0000704

PVALB
type: Class
subclass of: SO_0000704

CHGA
type: Class
subclass of: SO_0000704

ACTA2
type: Class
subclass of: SO_0000704

PRR4
type: Class
subclass of: SO_0000704

ST8SIA4
type: Class
subclass of: SO_0000704

PLCH1
type: Class
subclass of: SO_0000704

SMYD1
type: Class
subclass of: SO_0000704

MYB
type: Class
subclass of: SO_0000704

CCN2
type: Class
subclass of: SO_0000704

ONECUT2
type: Class
subclass of: SO_0000704

NPY
type: Class
subclass of: SO_0000704

SFTPA1
type: Class
subclass of: SO_0000704

CHST8
type: Class
subclass of: SO_0000704

F13A1
type: Class
subclass of: SO_0000704

LAMP5
type: Class
subclass of: SO_0000704

HIGD1B
type: Class
subclass of: SO_0000704

AOC3
type: Class
subclass of: SO_0000704

TOP2A
type: Class
subclass of: SO_0000704

GRP
type: Class
subclass of: SO_0000704

HCRTR2
type: Class
subclass of: SO_0000704

SULF1
type: Class
subclass of: SO_0000704

POU2F3
type: Class
subclass of: SO_0000704

NUSAP1
type: Class
subclass of: SO_0000704

LUM
type: Class
subclass of: SO_0000704

RXRG
type: Class
subclass of: SO_0000704

DPT
type: Class
subclass of: SO_0000704

THSD7B
type: Class
subclass of: SO_0000704

VIP
type: Class
subclass of: SO_0000704

TAGLN
type: Class
subclass of: SO_0000704

CHST9
type: Class
subclass of: SO_0000704

GLYATL2
type: Class
subclass of: SO_0000704

SST
type: Class
subclass of: SO_0000704

KIT
type: Class
subclass of: SO_0000704

BSND
type: Class
subclass of: SO_0000704

CXCL5
type: Class
subclass of: SO_0000704

HPGD
type: Class
subclass of: SO_0000704

PCLAF
type: Class
subclass of: SO_0000704

MS4A8
type: Class
subclass of: SO_0000704

MYO5B
type: Class
subclass of: SO_0000704

SCARA5
type: Class
subclass of: SO_0000704

FABP4
type: Class
subclass of: SO_0000704

KCNK3
type: Class
subclass of: SO_0000704

KRT15
type: Class
subclass of: SO_0000704

RRM2
type: Class
subclass of: SO_0000704

THEMIS
type: Class
subclass of: SO_0000704

ANKRD36C
type: Class
subclass of: SO_0000704

CD248
type: Class
subclass of: SO_0000704

GPR149
type: Class
subclass of: SO_0000704

UBE2C
type: Class
subclass of: SO_0000704

ASCL3
type: Class
subclass of: SO_0000704

ADAMTSL1
type: Class
subclass of: SO_0000704

CA8
type: Class
subclass of: SO_0000704

C1orf194
type: Class
subclass of: SO_0000704

ARSJ
type: Class
subclass of: SO_0000704

C6orf58
type: Class
subclass of: SO_0000704

POU3F1
type: Class
subclass of: SO_0000704

DMBT1
type: Class
subclass of: SO_0000704

RELN
type: Class
subclass of: SO_0000704

APOD
type: Class
subclass of: SO_0000704

NPSR1-AS1
type: Class
subclass of: SO_0000704

LYPD2
type: Class
subclass of: SO_0000704

PLCG2
type: Class
subclass of: SO_0000704

PRC1
type: Class
subclass of: SO_0000704

RORB
type: Class
subclass of: SO_0000704

COL5A2
type: Class
subclass of: SO_0000704

AGER
type: Class
subclass of: SO_0000704

SERPINB4
type: Class
subclass of: SO_0000704

MUC5AC
type: Class
subclass of: SO_0000704

LINC00298
type: Class
subclass of: SO_0000704

PEG10
type: Class
subclass of: SO_0000704

LINC00507
type: Class
subclass of: SO_0000704

NS forest marker set of alveolar adventitial fibroblast (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: SCARA5
  intersection of: Restriction
    on property: has part
    some values from: CD248
STATO_0000663: 0.85

NS forest marker set of alveolar type 1 fibroblast cell (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: AOC3
  intersection of: Restriction
    on property: has part
    some values from: LUM
STATO_0000663: 0.70

NS forest marker set of alveolar macrophage (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: MSR1
  intersection of: Restriction
    on property: has part
    some values from: FABP4
STATO_0000663: 0.80

NS forest marker set of CCL3-positive alveolar macrophage (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: TNIP3
  intersection of: Restriction
    on property: has part
    some values from: CXCL5
STATO_0000663: 0.67

NS forest marker set of metallothionein-positive alveolar macrophage (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: HMOX1
  intersection of: Restriction
    on property: has part
    some values from: HPGD
STATO_0000663: 0.41

NS forest marker set of cycling alveolar macrophage (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: NUSAP1
  intersection of: Restriction
    on property: has part
    some values from: PCLAF
  intersection of: Restriction
    on property: has part
    some values from: RRM2
  intersection of: Restriction
    on property: has part
    some values from: UBE2C
STATO_0000663: 0.26

NS forest marker set of pulmonary alveolar type 1 cell (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Restriction
  on property: has part
  some values from: AGER
STATO_0000663: 0.85

NS forest marker set of pulmonary alveolar type 2 cell (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Restriction
  on property: has part
  some values from: SFTPA1
STATO_0000663: 0.95

NS forest marker set of cycling pulmonary alveolar type 2 cell (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: TOP2A
  intersection of: Restriction
    on property: has part
    some values from: PRC1
  intersection of: Restriction
    on property: has part
    some values from: PEG10
STATO_0000663: 0.61

NS forest marker set of bronchial goblet cell (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: ANKRD36C
  intersection of: Restriction
    on property: has part
    some values from: PLCG2
STATO_0000663: 0.55

NS forest marker set of nasal mucosa goblet cell (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: LYPD2
  intersection of: Restriction
    on property: has part
    some values from: MUC5AC
STATO_0000663: 0.81

NS forest marker set of lung interstitial macrophage (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: STAB1
  intersection of: Restriction
    on property: has part
    some values from: FCGR2B
  intersection of: Restriction
    on property: has part
    some values from: F13A1
STATO_0000663: 0.46

NS forest marker set of pulmonary ionocyte (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: BSND
  intersection of: Restriction
    on property: has part
    some values from: ASCL3
STATO_0000663: 0.82

NS forest marker set of multiciliated columnar cell of tracheobronchial tree (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: MS4A8
  intersection of: Restriction
    on property: has part
    some values from: C1orf194
STATO_0000663: 0.86

NS forest marker set of pulmonary neuroendocrine cell (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: CHGA
  intersection of: Restriction
    on property: has part
    some values from: GRP
STATO_0000663: 0.94

NS forest marker set of pulmonary interstitial fibroblast (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: DPT
  intersection of: Restriction
    on property: has part
    some values from: APOD
STATO_0000663: 0.58

NS forest marker set of lung pericyte (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: HIGD1B
  intersection of: Restriction
    on property: has part
    some values from: KCNK3
STATO_0000663: 0.84

NS forest marker set of airway submucosal gland collecting duct epithelial cell (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: GLYATL2
  intersection of: Restriction
    on property: has part
    some values from: DMBT1
STATO_0000663: 0.46

NS forest marker set of mucus secreting cell of bronchus submucosal gland (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Restriction
  on property: has part
  some values from: BPIFB2
STATO_0000663: 0.93

NS forest marker set of serous secreting cell of bronchus submucosal gland (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: PRR4
  intersection of: Restriction
    on property: has part
    some values from: C6orf58
STATO_0000663: 0.75

NS forest marker set of tracheobronchial smooth muscle cell (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: ACTA2
  intersection of: Restriction
    on property: has part
    some values from: TAGLN
STATO_0000663: 0.69

NS forest marker set of respiratory tract suprabasal cell (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: TNC
  intersection of: Restriction
    on property: has part
    some values from: KRT15
  intersection of: Restriction
    on property: has part
    some values from: SERPINB4
STATO_0000663: 0.62

NS forest marker set of brush cell of tracheobronchial tree (Human Lung).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: HOMER3
  intersection of: Restriction
    on property: has part
    some values from: MYB
  intersection of: Restriction
    on property: has part
    some values from: POU2F3
STATO_0000663: 0.56

NS forest marker set of chandelier pvalb GABAergic cortical interneuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: GPR149
  intersection of: Restriction
    on property: has part
    some values from: CA8
STATO_0000663: 0.799748111

NS forest marker set of L2/3 intratelencephalic projecting glutamatergic neuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: ONECUT2
  intersection of: Restriction
    on property: has part
    some values from: COL5A2
STATO_0000663: 0.670149932

NS forest marker set of L4 intratelencephalic projecting glutamatergic neuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: ST8SIA4
  intersection of: Restriction
    on property: has part
    some values from: RORB
STATO_0000663: 0.720108696

NS forest marker set of L5 extratelencephalic projecting glutamatergic cortical neuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: CHST8
  intersection of: Restriction
    on property: has part
    some values from: POU3F1
STATO_0000663: 0.815891473

NS forest marker set of L5 intratelencephalic projecting glutamatergic neuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: KCNK2
  intersection of: Restriction
    on property: has part
    some values from: ARSJ
  intersection of: Restriction
    on property: has part
    some values from: RORB
STATO_0000663: 0.764261336

NS forest marker set of L5/6 near-projecting glutamatergic neuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: TLL1
  intersection of: Restriction
    on property: has part
    some values from: NPSR1-AS1
STATO_0000663: 0.899288218

NS forest marker set of L6 corticothalamic-projecting glutamatergic cortical neuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: SEMA5B
  intersection of: Restriction
    on property: has part
    some values from: SULF1
  intersection of: Restriction
    on property: has part
    some values from: ADAMTSL1
STATO_0000663: 0.631898455

NS forest marker set of L6 intratelencephalic projecting glutamatergic neuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: THEMIS
  intersection of: Restriction
    on property: has part
    some values from: LINC00507
STATO_0000663: 0.641695703

NS forest marker set of L6 intratelencephalic projecting Car3 glutamatergic neuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: SMYD1
  intersection of: Restriction
    on property: has part
    some values from: THEMIS
STATO_0000663: 0.877752028

NS forest marker set of L6b glutamatergic neuron of the primary motor cortex (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: ROS1
  intersection of: Restriction
    on property: has part
    some values from: CCN2
STATO_0000663: 0.819940964

NS forest marker set of lamp5 GABAergic cortical interneuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: KIT
  intersection of: Restriction
    on property: has part
    some values from: LINC00298
STATO_0000663: 0.814687838

NS forest marker set of Lamp5 Lhx6 neuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: LAMP5
  intersection of: Restriction
    on property: has part
    some values from: CHST9
STATO_0000663: 0.821678322

NS forest marker set of PAX6 GABAergic cortical interneuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: HCRTR2
  intersection of: Restriction
    on property: has part
    some values from: RELN
STATO_0000663: 0.724125093

NS forest marker set of pvalb GABAergic cortical interneuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: TAC1
  intersection of: Restriction
    on property: has part
    some values from: PVALB
  intersection of: Restriction
    on property: has part
    some values from: MYO5B
STATO_0000663: 0.691998764

NS forest marker set of sncg GABAergic cortical interneuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: RXRG
  intersection of: Restriction
    on property: has part
    some values from: THSD7B
STATO_0000663: 0.628943702

NS forest marker set of sst GABAergic cortical interneuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: PLCH1
  intersection of: Restriction
    on property: has part
    some values from: SST
STATO_0000663: 0.842367005

NS forest marker set of sst chodl GABAergic cortical interneuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Restriction
  on property: has part
  some values from: NPY
STATO_0000663: 0.894026187

NS forest marker set of VIP GABAergic cortical interneuron (Human Brain).
type: Class
subclass of: SO_0001260
subclass of: Restriction
  on property: has part
  some values from: VIP
STATO_0000663: 0.855531344

cell
type: Class
subclass of: UBERON_0000061
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon_131567
disjoint with: GO_0031012
disjoint with: GO_0032991
disjoint with: GO_0043226
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
database_cross_reference: CALOHA:TS-2035
database_cross_reference: FBbt:00007002
database_cross_reference: FMA:68646
database_cross_reference: GO:0005623
database_cross_reference: KUPO:0000002
database_cross_reference: MESH:D002477
database_cross_reference: VHOG:0001533
database_cross_reference: WBbt:0004017
database_cross_reference: XAO:0003012
database_cross_reference: ZFA:0009000
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: upper level
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).

Axiom
annotated source: cell
annotated property: definition
annotated target: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
database_cross_reference: CARO:mah

Axiom
annotated source: cell
annotated property: database_cross_reference
annotated target: FBbt:00007002
mapping justification: ManualMappingCuration

Axiom
annotated source: cell
annotated property: database_cross_reference
annotated target: ZFA:0009000
mapping justification: UnspecifiedMatching

primary cultured cell
type: Class
subclass of: cultured cell
definition: A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.
database_cross_reference: BTO:0002290
has_exact_synonym: primary cell culture cell
has_exact_synonym: unpassaged cultured cell
has_related_synonym: primary cell line cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Covers cells actively being cultured or stored in a quiescent state for future use.

Axiom
annotated source: primary cultured cell
annotated property: definition
annotated target: A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.
database_cross_reference: ReO:mhb

obsolete immortal cell line cell
type: Class
definition: OBSOLETE: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line.
term replaced by: CLO_0000019
has_exact_synonym: continuous cell line cell
has_exact_synonym: permanent cell line cell
comment: Obsoleted in July 2013 and replaced by the CLO 'immortal cell line cell' class, as a result of CLO-OBI-CL alignment efforts. Covers cells actively being cultured or stored in a quiescent state for future use.
deprecated: true

Axiom
annotated source: obsolete immortal cell line cell
annotated property: definition
annotated target: OBSOLETE: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line.
database_cross_reference: ReO:mhb

obsolete native cell
type: Class
definition: OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
term tracker item: https://github.com/obophenotype/cell-ontology/issues/2124
term replaced by: cell
database_cross_reference: CARO:0000013
has_narrow_synonym: cell in vivo
in_subset: upper level
deprecated: true

Axiom
annotated source: obsolete native cell
annotated property: definition
annotated target: OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
database_cross_reference: CARO:mah

obsolete cell by organism
type: Class
definition: OBSOLETE: A classification of cells by the organisms within which they are contained.
consider: CL:0000000
consider: CL:0000003
consider: CL:0001034
comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its species. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate.
deprecated: true

Axiom
annotated source: obsolete cell by organism
annotated property: definition
annotated target: OBSOLETE: A classification of cells by the organisms within which they are contained.
database_cross_reference: FB:ma

neural crest derived fibroblast
type: Class
equivalent class: Class
  intersection of: fibroblast
  intersection of: Restriction
    on property: develops from
    some values from: migratory neural crest cell
subclass of: fibroblast
subclass of: Restriction
  on property: develops from
  some values from: migratory cranial neural crest cell
definition: Any fibroblast that is derived from the neural crest.
has_exact_synonym: fibroblast neural crest derived
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: neural crest derived fibroblast
annotated property: definition
annotated target: Any fibroblast that is derived from the neural crest.
database_cross_reference: https://orcid.org/0000-0001-5208-3432

neuronal receptor cell
type: Class
equivalent class: Class
  intersection of: sensory receptor cell
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050906
subclass of: sensory neuron
subclass of: sensory receptor cell
definition: Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.
database_cross_reference: ZFA:0009001
has_exact_synonym: neuronal receptor cell (sensu Animalia)
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: neuronal receptor cell
annotated property: definition
annotated target: Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: neuronal receptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009001
mapping justification: UnspecifiedMatching

early embryonic cell (metazoa)
type: Class
subclass of: CL_0002321
definition: A cell found in the embryo before the formation of all the gem layers is complete.
database_cross_reference: ZFA:0009002
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: early embryonic cell (metazoa)
annotated property: definition
annotated target: A cell found in the embryo before the formation of all the gem layers is complete.
database_cross_reference: GOC:tfm

Axiom
annotated source: early embryonic cell (metazoa)
annotated property: database_cross_reference
annotated target: ZFA:0009002
mapping justification: UnspecifiedMatching

migratory cranial neural crest cell
type: Class
subclass of: migratory neural crest cell
definition: Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
database_cross_reference: ZFA:0007091
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: migratory cranial neural crest cell
annotated property: definition
annotated target: Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
database_cross_reference: ZFA:0007091
database_cross_reference: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: migratory cranial neural crest cell
annotated property: database_cross_reference
annotated target: ZFA:0007091
mapping justification: UnspecifiedMatching

obsolete fusiform initial
type: Class
definition: Obsolete. Use PO:0000079 from Plant Ontology instead. An elongated cell with approximately wedge-shaped ends, found in the vascular cambium, which gives rise to the elements of the axial system in the secondary vascular tissues.
term replaced by: PO_0000079
has_related_synonym: xylem initial
has_related_synonym: xylem mother cell
deprecated: true

Axiom
annotated source: obsolete fusiform initial
annotated property: definition
annotated target: Obsolete. Use PO:0000079 from Plant Ontology instead. An elongated cell with approximately wedge-shaped ends, found in the vascular cambium, which gives rise to the elements of the axial system in the secondary vascular tissues.
database_cross_reference: ISBN:0471245208

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
database_cross_reference: MESH:D002478
in_subset: human subset
in_subset: mouse subset
comment: Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture.

Axiom
annotated source: cultured cell
annotated property: definition
annotated target: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
database_cross_reference: ReO:mhb

migratory trunk neural crest cell
type: Class
subclass of: migratory neural crest cell
definition: Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
database_cross_reference: ZFA:0007095
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: migratory trunk neural crest cell
annotated property: definition
annotated target: Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination.
database_cross_reference: ZFA:0007095
database_cross_reference: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: migratory trunk neural crest cell
annotated property: database_cross_reference
annotated target: ZFA:0007095
mapping justification: UnspecifiedMatching

obsolete cell by class
type: Class
consider: CL:0000000
consider: CL:0000003
consider: CL:0001034
comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate.
deprecated: true

obsolete dentine secreting cell
type: Class
consider: CL:0000140
deprecated: true

germ line stem cell
type: Class
equivalent class: Class
  intersection of: germ line cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0017145
subclass of: stem cell
subclass of: germ line cell
definition: A stem cell that is the precursor of gametes.
database_cross_reference: FBbt:00004861
database_cross_reference: ZFA:0005956
has_exact_synonym: germline stem cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: germ line stem cell
annotated property: subClassOf
annotated target: stem cell
is inferred: true

Axiom
annotated source: germ line stem cell
annotated property: definition
annotated target: A stem cell that is the precursor of gametes.
database_cross_reference: doi:10.1016/j.stem.2012.05.016

Axiom
annotated source: germ line stem cell
annotated property: database_cross_reference
annotated target: FBbt:00004861
mapping justification: ManualMappingCuration

Axiom
annotated source: germ line stem cell
annotated property: database_cross_reference
annotated target: ZFA:0005956
mapping justification: UnspecifiedMatching

male germ cell
type: Class
subclass of: germ cell
subclass of: Restriction
  on property: capable of part of
  some values from: GO_0007283
definition: A germ cell that supports male gamete production. In some species, non-germ cells known as Sertoli cells also play a role in spermatogenesis.
description: Male germ cells are specialized cells that give rise to the male gametes and are therefore crucial for sexual reproduction in males. Through a complex process called spermatogenesis in the testes male germ cells undergo several stages of development, each with distinctive morphological and physiological characteristics, eventually differentiating into mature spermatozoa (sperm). Male germ cells are responsible for transferring genetic material from male to offspring as part of sexual reproduction. In the initial stage of their life cycle, they exist as spermatogonial stem cells, which multiply by mitotic division to self-renew and to produce daughter cells. The daughter cells then undergo meiotic division, a process that reduces the number of chromosomes in each cell by half, from diploid to haploid – the formation of spermatids. This is critical for maintaining genetic stability from generation to generation, as it ensures that when an egg and sperm cell unite during fertilization, the resulting offspring will have the correct number of chromosomes. The final phase of spermatogenesis is called spermiogenesis, during which spermatozoa - mature and motile sperm cells – are produced from round spermatids. The matured male germ cells or sperm cells are highly specialized, having a streamlined shape designed for efficient movement towards the female egg. A sperm cell is divided into three main parts, namely the head, midpiece, and tail. The head contains the genetic material, the midpiece contains mitochondria that provide energy, and the tail, termed as the flagellum, propels the sperm cell forward. Each of these parts play significant roles in fertilization. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: FMA:72290
database_cross_reference: MA:0002765
database_cross_reference: VHOG:0001531
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000015
database_cross_reference: ncithesaurus:Spermatogenic_Cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: male germ cell
annotated property: subClassOf
annotated target: germ cell
is inferred: true

Axiom
annotated source: male germ cell
annotated property: definition
annotated target: A germ cell that supports male gamete production. In some species, non-germ cells known as Sertoli cells also play a role in spermatogenesis.
database_cross_reference: PMID:29462262
database_cross_reference: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: male germ cell
annotated property: description
annotated target: Male germ cells are specialized cells that give rise to the male gametes and are therefore crucial for sexual reproduction in males. Through a complex process called spermatogenesis in the testes male germ cells undergo several stages of development, each with distinctive morphological and physiological characteristics, eventually differentiating into mature spermatozoa (sperm). Male germ cells are responsible for transferring genetic material from male to offspring as part of sexual reproduction. In the initial stage of their life cycle, they exist as spermatogonial stem cells, which multiply by mitotic division to self-renew and to produce daughter cells. The daughter cells then undergo meiotic division, a process that reduces the number of chromosomes in each cell by half, from diploid to haploid – the formation of spermatids. This is critical for maintaining genetic stability from generation to generation, as it ensures that when an egg and sperm cell unite during fertilization, the resulting offspring will have the correct number of chromosomes. The final phase of spermatogenesis is called spermiogenesis, during which spermatozoa - mature and motile sperm cells – are produced from round spermatids. The matured male germ cells or sperm cells are highly specialized, having a streamlined shape designed for efficient movement towards the female egg. A sperm cell is divided into three main parts, namely the head, midpiece, and tail. The head contains the genetic material, the midpiece contains mitochondria that provide energy, and the tail, termed as the flagellum, propels the sperm cell forward. Each of these parts play significant roles in fertilization. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1016/S0092-8674(00)81834-6
database_cross_reference: DOI:10.1016/S1534-5807(02)00173-9
database_cross_reference: DOI:10.1242/dev.202046
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK553142/

male germ line stem cell
type: Class
subclass of: germ line stem cell
subclass of: male germ cell
definition: A stem cell that is the precursor of male gametes.
database_cross_reference: FBbt:00004929
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: male germ line stem cell
annotated property: definition
annotated target: A stem cell that is the precursor of male gametes.
database_cross_reference: doi:10.1016/j.stem.2012.05.016

Axiom
annotated source: male germ line stem cell
annotated property: database_cross_reference
annotated target: FBbt:00004929
mapping justification: ManualMappingCuration

spermatocyte
type: Class
equivalent class: Class
  intersection of: male germ cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0048137
subclass of: BFO_0000002
subclass of: male germ cell
subclass of: Restriction
  on property: develops from
  some values from: spermatogonium
subclass of: Restriction
  on property: capable of
  some values from: GO_0048137
definition: A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids.
database_cross_reference: BTO:0001275
database_cross_reference: CALOHA:TS-0951
database_cross_reference: EMAPA:31484
database_cross_reference: FBbt:00004936
database_cross_reference: FMA:84049
database_cross_reference: WBbt:0006799
database_cross_reference: ZFA:0009005
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: spermatocyte
annotated property: definition
annotated target: A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D013090

Axiom
annotated source: spermatocyte
annotated property: database_cross_reference
annotated target: FBbt:00004936
mapping justification: ManualMappingCuration

Axiom
annotated source: spermatocyte
annotated property: database_cross_reference
annotated target: ZFA:0009005
mapping justification: UnspecifiedMatching

spermatid
type: Class
equivalent class: Class
  intersection of: male germ cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001375
  intersection of: Restriction
    on property: capable of
    some values from: GO_0001675
  intersection of: Restriction
    on property: capable of
    some values from: GO_0007288
  intersection of: Restriction
    on property: capable of
    some values from: GO_0007289
subclass of: BFO_0000002
subclass of: male germ cell
subclass of: eukaryotic cell
subclass of: haploid cell
subclass of: Restriction
  on property: develops from
  some values from: secondary spermatocyte
subclass of: Restriction
  on property: capable of
  some values from: GO_0001675
subclass of: Restriction
  on property: capable of
  some values from: GO_0007288
subclass of: Restriction
  on property: capable of
  some values from: GO_0007289
definition: A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa.
database_cross_reference: BTO:0001274
database_cross_reference: CALOHA:TS-0950
database_cross_reference: EMAPA:31486
database_cross_reference: FBbt:00004942
database_cross_reference: FMA:72294
database_cross_reference: WBbt:0006800
database_cross_reference: ZFA:0005769
has_exact_synonym: nematoblast
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: spermatid
annotated property: definition
annotated target: A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa.
database_cross_reference: MESH:D013087

Axiom
annotated source: spermatid
annotated property: database_cross_reference
annotated target: FBbt:00004942
mapping justification: ManualMappingCuration

Axiom
annotated source: spermatid
annotated property: database_cross_reference
annotated target: ZFA:0005769
mapping justification: UnspecifiedMatching

sperm
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: male gamete
subclass of: Restriction
  on property: develops from
  some values from: spermatid
definition: A mature male germ cell that develops from a spermatid.
description: Sperm cells, also known as spermatozoa or male gametes, are highly specialized cells that are pivotal for sexual reproduction in animals. Produced in the male reproductive organs, specifically the testes, sperm cells play an important role in the process of fertilization, where they fuse with a female gamete or egg cell (ovum) to form a zygote, which marks the beginning of a new organism. Sperm cells hold several unique traits that set them apart from other body cells. Structurally, a sperm cell possesses two main structures: the head, containing the nucleus carrying the paternal genetic information, and the flagellum, which generates energy and grants the sperm cell mobility The process of fertilization occurs when one sperm cell successfully penetrates the egg, delivering its genetic information, and ultimately leading to the formation of a new individual combining both paternal and maternal genetic materials. Notably, while hundreds of millions of sperm cells may be released during ejaculation, only one has the opportunity to successfully fertilize the egg, underscoring the highly competitive nature of this biological process. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: BTO:0001277
database_cross_reference: BTO:0002046
database_cross_reference: CALOHA:TS-0949
database_cross_reference: FBbt:00004954
database_cross_reference: FMA:67338
database_cross_reference: WBbt:0006798
database_cross_reference: ZFA:0009006
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000019
has_exact_synonym: sperm cell
has_exact_synonym: spermatozoid
has_exact_synonym: spermatozoon
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: sperm
annotated property: subClassOf
annotated target: male gamete
is inferred: true

Axiom
annotated source: sperm
annotated property: definition
annotated target: A mature male germ cell that develops from a spermatid.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D013094

Axiom
annotated source: sperm
annotated property: description
annotated target: Sperm cells, also known as spermatozoa or male gametes, are highly specialized cells that are pivotal for sexual reproduction in animals. Produced in the male reproductive organs, specifically the testes, sperm cells play an important role in the process of fertilization, where they fuse with a female gamete or egg cell (ovum) to form a zygote, which marks the beginning of a new organism. Sperm cells hold several unique traits that set them apart from other body cells. Structurally, a sperm cell possesses two main structures: the head, containing the nucleus carrying the paternal genetic information, and the flagellum, which generates energy and grants the sperm cell mobility The process of fertilization occurs when one sperm cell successfully penetrates the egg, delivering its genetic information, and ultimately leading to the formation of a new individual combining both paternal and maternal genetic materials. Notably, while hundreds of millions of sperm cells may be released during ejaculation, only one has the opportunity to successfully fertilize the egg, underscoring the highly competitive nature of this biological process. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1080/19420889.2015.1017156
database_cross_reference: DOI:10.1152/physrev.00009.2020
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK26914/

Axiom
annotated source: sperm
annotated property: database_cross_reference
annotated target: FBbt:00004954
mapping justification: ManualMappingCuration

Axiom
annotated source: sperm
annotated property: database_cross_reference
annotated target: ZFA:0009006
mapping justification: UnspecifiedMatching

spermatogonium
type: Class
equivalent class: Class
  intersection of: male germ cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001394
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001501
subclass of: male germ cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001394
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001501
definition: An euploid male germ cell of an early stage of spermatogenesis.
database_cross_reference: BTO:0000958
database_cross_reference: CALOHA:TS-2193
database_cross_reference: EMAPA:31482
database_cross_reference: FBbt:00004934
database_cross_reference: FBbt:00004935
database_cross_reference: FMA:72291
database_cross_reference: ZFA:0009007
has_exact_synonym: spermatogonial cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: spermatogonium
annotated property: definition
annotated target: An euploid male germ cell of an early stage of spermatogenesis.
database_cross_reference: MESH:D013093

Axiom
annotated source: spermatogonium
annotated property: database_cross_reference
annotated target: FBbt:00004934
mapping justification: ManualMappingCuration

Axiom
annotated source: spermatogonium
annotated property: database_cross_reference
annotated target: FBbt:00004935
mapping justification: ManualMappingCuration

Axiom
annotated source: spermatogonium
annotated property: database_cross_reference
annotated target: ZFA:0009007
mapping justification: UnspecifiedMatching

female germ cell
type: Class
equivalent class: Class
  intersection of: germ cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0048477
subclass of: eukaryotic cell
subclass of: germ cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0048477
definition: Female germ cell is a germ cell that supports female gamete production.
database_cross_reference: MA:0000388
database_cross_reference: VHOG:0001530
database_cross_reference: ncithesaurus:Egg
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: female germ cell
annotated property: subClassOf
annotated target: germ cell
is inferred: true

Axiom
annotated source: female germ cell
annotated property: definition
annotated target: Female germ cell is a germ cell that supports female gamete production.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:11023867
database_cross_reference: PMID:20454446

female germ line stem cell
type: Class
equivalent class: Class
  intersection of: female germ cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0017145
subclass of: germ line stem cell
subclass of: female germ cell
definition: A stem cell that is the precursor of female gametes.
database_cross_reference: FBbt:00004873
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: female germ line stem cell
annotated property: subClassOf
annotated target: germ line stem cell
is inferred: true

Axiom
annotated source: female germ line stem cell
annotated property: subClassOf
annotated target: female germ cell
is inferred: true

Axiom
annotated source: female germ line stem cell
annotated property: definition
annotated target: A stem cell that is the precursor of female gametes.
database_cross_reference: doi:10.1016/j.stem.2012.05.016

Axiom
annotated source: female germ line stem cell
annotated property: database_cross_reference
annotated target: FBbt:00004873
mapping justification: ManualMappingCuration

oocyte
type: Class
subclass of: BFO_0000002
subclass of: female germ cell
subclass of: Restriction
  on property: participates in
  some values from: GO_0007143
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon_33208
definition: A female germ cell that has entered meiosis.
database_cross_reference: BTO:0000964
database_cross_reference: CALOHA:TS-0711
database_cross_reference: FBbt:00004886
database_cross_reference: FMA:18644
database_cross_reference: MESH:D009865
database_cross_reference: WBbt:0006797
database_cross_reference: ZFA:0001109
has_related_synonym: oogonium
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: oocyte
annotated property: subClassOf
annotated target: female germ cell
is inferred: true

Axiom
annotated source: oocyte
annotated property: definition
annotated target: A female germ cell that has entered meiosis.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: oocyte
annotated property: database_cross_reference
annotated target: FBbt:00004886
mapping justification: ManualMappingCuration

Axiom
annotated source: oocyte
annotated property: database_cross_reference
annotated target: ZFA:0001109
mapping justification: UnspecifiedMatching

oogonial cell
type: Class
equivalent class: Class
  intersection of: female germ cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0000278
subclass of: BFO_0000002
subclass of: female germ cell
subclass of: Restriction
  on property: develops from
  some values from: primordial germ cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0000278
definition: An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.
database_cross_reference: FMA:83673
database_cross_reference: ZFA:0005878
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: oogonial cell
annotated property: subClassOf
annotated target: female germ cell
is inferred: true

Axiom
annotated source: oogonial cell
annotated property: definition
annotated target: An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: oogonial cell
annotated property: database_cross_reference
annotated target: ZFA:0005878
mapping justification: UnspecifiedMatching

egg cell
type: Class
subclass of: BFO_0000002
subclass of: female gamete
subclass of: Restriction
  on property: participates in
  some values from: GO_0007143
subclass of: Restriction
  on property: develops from
  some values from: oocyte
definition: A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization.
database_cross_reference: BTO:0000369
database_cross_reference: BTO:0003801
database_cross_reference: CALOHA:TS-2191
database_cross_reference: FBbt:00057012
database_cross_reference: FMA:67343
database_cross_reference: MESH:D010063
database_cross_reference: ZFA:0001570
has_exact_synonym: mature oocyte
has_exact_synonym: ovum
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: egg cell
annotated property: subClassOf
annotated target: female gamete
is inferred: true

Axiom
annotated source: egg cell
annotated property: definition
annotated target: A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: egg cell
annotated property: database_cross_reference
annotated target: FBbt:00057012
mapping justification: ManualMappingCuration

Axiom
annotated source: egg cell
annotated property: database_cross_reference
annotated target: ZFA:0001570
mapping justification: UnspecifiedMatching

invertebrate nurse cell
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: polyploid cell
subclass of: CL_4029002
subclass of: Restriction
  on property: develops from
  some values from: cystoblast
definition: A germline cell that contributes to the development of the oocyte by transferring cytoplasm directly to oocyte.
database_cross_reference: BTO:0000953
database_cross_reference: FBbt:00004878
has_related_synonym: nurse cell

Axiom
annotated source: invertebrate nurse cell
annotated property: definition
annotated target: A germline cell that contributes to the development of the oocyte by transferring cytoplasm directly to oocyte.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:15848391

Axiom
annotated source: invertebrate nurse cell
annotated property: database_cross_reference
annotated target: FBbt:00004878
mapping justification: ManualMappingCuration

smooth muscle cell neural crest derived
type: Class
equivalent class: Class
  intersection of: smooth muscle cell
  intersection of: Restriction
    on property: develops from
    some values from: migratory neural crest cell
subclass of: smooth muscle cell
subclass of: Restriction
  on property: develops from
  some values from: migratory cranial neural crest cell
definition: A smooth muscle cell derived from the neural crest.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: smooth muscle cell neural crest derived
annotated property: subClassOf
annotated target: smooth muscle cell
is inferred: true

Axiom
annotated source: smooth muscle cell neural crest derived
annotated property: definition
annotated target: A smooth muscle cell derived from the neural crest.
database_cross_reference: https://orcid.org/0000-0001-5208-3432

CNS neuron (sensu Nematoda and Protostomia)
type: Class
subclass of: BFO_0000002
subclass of: CL_2000029
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001017
subclass of: Restriction
  on property: develops from
  some values from: neuroblast (sensu Nematoda and Protostomia)

neural crest derived neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: develops from
    some values from: migratory neural crest cell
subclass of: BFO_0000002
subclass of: neuron
subclass of: Restriction
  on property: develops from
  some values from: CL_0002676
definition: Any neuron that develops from some migratory neural crest cell.
database_cross_reference: ZFA:0009009
has_exact_synonym: neuron neural crest derived
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: neural crest derived neuron
annotated property: subClassOf
annotated target: neuron
is inferred: true

Axiom
annotated source: neural crest derived neuron
annotated property: definition
annotated target: Any neuron that develops from some migratory neural crest cell.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: neural crest derived neuron
annotated property: database_cross_reference
annotated target: ZFA:0009009
mapping justification: UnspecifiedMatching

glioblast
type: Class
subclass of: BFO_0000002
subclass of: non-terminally differentiated cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: develops from
  some values from: neurectodermal cell
definition: A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes.
database_cross_reference: ZFA:0009010
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: glioblast
annotated property: definition
annotated target: A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes.
database_cross_reference: PMID:37824650
database_cross_reference: Wikipedia:Glioblast

Axiom
annotated source: glioblast
annotated property: database_cross_reference
annotated target: ZFA:0009010
mapping justification: UnspecifiedMatching

neuroblast (sensu Vertebrata)
type: Class
subclass of: non-terminally differentiated cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 7742
definition: A cell that will develop into a neuron often after a migration phase.
database_cross_reference: BTO:0000930
database_cross_reference: FMA:70563
database_cross_reference: ZFA:0009011
has_exact_synonym: neuroblast
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: neuroblast (sensu Vertebrata)
annotated property: definition
annotated target: A cell that will develop into a neuron often after a migration phase.
database_cross_reference: GOC:NV
database_cross_reference: http://en.wikipedia.org/wiki/Neuroblast

Axiom
annotated source: neuroblast (sensu Vertebrata)
annotated property: database_cross_reference
annotated target: ZFA:0009011
mapping justification: UnspecifiedMatching

neuroplacodal cell
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: CL_0002321
subclass of: Restriction
  on property: develops from
  some values from: surface ectodermal cell
definition: A cell of a platelike structure, especially a thickened plate of ectoderm in the early embryo, from which a sense organ develops.
database_cross_reference: ZFA:0009012
has_exact_synonym: neural placode cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: neuroplacodal cell
annotated property: definition
annotated target: A cell of a platelike structure, especially a thickened plate of ectoderm in the early embryo, from which a sense organ develops.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0618947256

Axiom
annotated source: neuroplacodal cell
annotated property: database_cross_reference
annotated target: ZFA:0009012
mapping justification: UnspecifiedMatching

apocrine cell
type: Class
subclass of: exocrine cell
definition: An exocrine cell characterized by loss of part of the cytoplasm during the process of secretion. The secreted substance is accumulated at the apical end and is either budded off through the plasma membrane producing secreted vesicles or dissolved in the cytoplasm that is lost during secretion.
present in taxon: NCBITaxon 9606
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: apocrine cell
annotated property: definition
annotated target: An exocrine cell characterized by loss of part of the cytoplasm during the process of secretion. The secreted substance is accumulated at the apical end and is either budded off through the plasma membrane producing secreted vesicles or dissolved in the cytoplasm that is lost during secretion.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544
database_cross_reference: PMID:25960390

stem cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0017145
subclass of: eukaryotic cell
subclass of: CL_0011115
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon_33208
subclass of: Restriction
  on property: capable of
  some values from: GO_0017145
definition: A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
present in taxon: NCBITaxon 9606
database_cross_reference: CALOHA:TS-2086
database_cross_reference: FMA:63368
database_cross_reference: ZFA:0005957
has_exact_synonym: animal stem cell
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’.

Axiom
annotated source: stem cell
annotated property: definition
annotated target: A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D013234

Axiom
annotated source: stem cell
annotated property: database_cross_reference
annotated target: ZFA:0005957
mapping justification: UnspecifiedMatching

single fate stem cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001400
  intersection of: Restriction
    on property: capable of
    some values from: GO_0017145
subclass of: somatic stem cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001400
definition: A stem cell that self-renews as well as give rise to a single mature cell type.
database_cross_reference: FMA:70569
database_cross_reference: ZFA:0009013
has_exact_synonym: unipotent stem cell
has_exact_synonym: unipotential stem cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: single fate stem cell
annotated property: definition
annotated target: A stem cell that self-renews as well as give rise to a single mature cell type.
database_cross_reference: GOC:tfm

Axiom
annotated source: single fate stem cell
annotated property: database_cross_reference
annotated target: ZFA:0009013
mapping justification: UnspecifiedMatching

epithelial fate stem cell
type: Class
subclass of: single fate stem cell
present in taxon: NCBITaxon 9606
has_exact_synonym: epithelial stem cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: CL_0000988
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002244
  intersection of: Restriction
    on property: capable of
    some values from: GO_0048103
subclass of: somatic stem cell
subclass of: CL_0008001
subclass of: CL_0011026
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002981
subclass of: Restriction
  on property: develops from
  some values from: angioblastic mesenchymal cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0002244
definition: A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000725
database_cross_reference: CALOHA:TS-0448
database_cross_reference: FMA:86475
database_cross_reference: MESH:D006412
database_cross_reference: VHOG:0001485
database_cross_reference: ZFA:0009014
has_exact_synonym: blood forming stem cell
has_exact_synonym: hemopoietic stem cell
has_related_synonym: HSC
has_related_synonym: colony forming unit hematopoietic
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative.

Axiom
annotated source: hematopoietic stem cell
annotated property: definition
annotated target: A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: PMID:19022770
database_cross_reference: http://en.wikipedia.org/wiki/Hematopoietic_stem_cell

Axiom
annotated source: hematopoietic stem cell
annotated property: database_cross_reference
annotated target: ZFA:0009014
mapping justification: UnspecifiedMatching

Axiom
annotated source: hematopoietic stem cell
annotated property: has_related_synonym
annotated target: HSC
has_synonym_type: abbreviation

erythroid progenitor cell
type: Class
subclass of: erythroid lineage cell
subclass of: CL_0000839
subclass of: Restriction
  on property: develops from
  some values from: megakaryocyte-erythroid progenitor cell
definition: A progenitor cell committed to the erythroid lineage.
database_cross_reference: BTO:0004911
database_cross_reference: ZFA:0009015
has_related_synonym: BFU-E
has_related_synonym: CFU-E
has_related_synonym: blast forming unit erythroid
has_related_synonym: burst forming unit erythroid
has_related_synonym: colony forming unit erythroid
has_related_synonym: erythroid stem cell
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: erythroid progenitor cell
annotated property: subClassOf
annotated target: CL_0000839
is inferred: true

Axiom
annotated source: erythroid progenitor cell
annotated property: definition
annotated target: A progenitor cell committed to the erythroid lineage.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0721601464

Axiom
annotated source: erythroid progenitor cell
annotated property: database_cross_reference
annotated target: ZFA:0009015
mapping justification: UnspecifiedMatching

Axiom
annotated source: erythroid progenitor cell
annotated property: has_related_synonym
annotated target: BFU-E
has_synonym_type: abbreviation

Axiom
annotated source: erythroid progenitor cell
annotated property: has_related_synonym
annotated target: CFU-E
has_synonym_type: abbreviation

germ line cell
type: Class
subclass of: cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0022414
definition: A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
database_cross_reference: ZFA:0009016
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: upper level
comment: Originally this term had some plant germ line cell children.

Axiom
annotated source: germ line cell
annotated property: definition
annotated target: A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: germ line cell
annotated property: database_cross_reference
annotated target: ZFA:0009016
mapping justification: UnspecifiedMatching

monoblast
type: Class
equivalent class: Class
  intersection of: CL_0002194
  intersection of: Restriction
    on property: has part
    some values from: CL_0017503
  intersection of: Restriction
    on property: has part
    some values from: GO_0000791
  intersection of: Restriction
    on property: has part
    some values from: GO_0005730
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001012
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030224
subclass of: myeloid cell
subclass of: CL_0002194
subclass of: Restriction
  on property: has part
  some values from: CL_0017503
subclass of: Restriction
  on property: has part
  some values from: GO_0000791
subclass of: Restriction
  on property: has part
  some values from: GO_0005730
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001012
subclass of: Restriction
  on property: develops from
  some values from: CL_0002009
definition: A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus.
database_cross_reference: CALOHA:TS-1195
database_cross_reference: FMA:83553
database_cross_reference: ZFA:0009017
has_related_synonym: CFU-M
has_related_synonym: colony forming unit macrophage
has_related_synonym: colony forming unit monocyte
has_related_synonym: monocyte stem cell
in_subset: human subset
in_subset: mouse subset
comment: Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid.

Axiom
annotated source: monoblast
annotated property: subClassOf
annotated target: CL_0002194
is inferred: true

Axiom
annotated source: monoblast
annotated property: definition
annotated target: A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus.
database_cross_reference: GOC:add
database_cross_reference: PMID:1104740
database_cross_reference: http://en.wikipedia.org/wiki/Monoblast
database_cross_reference: http://www.copewithcytokines.de

Axiom
annotated source: monoblast
annotated property: database_cross_reference
annotated target: ZFA:0009017
mapping justification: UnspecifiedMatching

Axiom
annotated source: monoblast
annotated property: has_related_synonym
annotated target: CFU-M
has_synonym_type: abbreviation

mature eosinophil
type: Class
equivalent class: Class
  intersection of: eosinophil
  intersection of: Restriction
    on property: has part
    some values from: PR_000007152
  intersection of: Restriction
    on property: has part
    some values from: PR_000007857
  intersection of: Restriction
    on property: has part
    some values from: PR_000007858
  intersection of: Restriction
    on property: has part
    some values from: PR_000014046
  intersection of: Restriction
    on property: has part
    some values from: PR_000014047
  intersection of: Restriction
    on property: has part
    some values from: PR_000022006
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: GO_0005634
      intersection of: Restriction
        on property: has characteristic
        some values from: PATO_0001979
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000009129
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002495
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002540
  intersection of: Restriction
    on property: capable of
    some values from: GO_0045730
subclass of: professional antigen presenting cell
subclass of: eosinophil
subclass of: Restriction
  on property: has part
  some values from: PR_000007152
subclass of: Restriction
  on property: has part
  some values from: PR_000007857
subclass of: Restriction
  on property: has part
  some values from: PR_000007858
subclass of: Restriction
  on property: has part
  some values from: PR_000014046
subclass of: Restriction
  on property: has part
  some values from: PR_000014047
subclass of: Restriction
  on property: has part
  some values from: PR_000022006
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: GO_0005634
    intersection of: Restriction
      on property: has characteristic
      some values from: PATO_0001979
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000009129
subclass of: Restriction
  on property: develops from
  some values from: band form eosinophil
subclass of: Restriction
  on property: capable of
  some values from: GO_0002495
subclass of: Restriction
  on property: capable of
  some values from: GO_0002540
subclass of: Restriction
  on property: capable of
  some values from: GO_0045730
definition: A fully differentiated eosinophil, a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Cells are also differentiated from other granulocytes by a small nuclear-to-cytoplasm ratio (1:3). This cell type is CD49d-positive.
editor note: The status of eosinophils as true professional antigen presenting cells is unclear, despite their ability to present exogenous peptides and peptides processed from exogenous proteins (in certain studies) via MHC Class II and activate T cells. Per the equivalence axioms, 'eosinophil' is reasoned to be a subclass of 'professional antigen presenting cell', though the role of eosinophils as such in the body may be limited.
present in taxon: NCBITaxon 9606
has_broad_synonym: polymorphonuclear leucocyte
has_broad_synonym: polymorphonuclear leukocyte
has_exact_synonym: mature eosinocyte
has_exact_synonym: mature eosinophil leucocyte
has_exact_synonym: mature eosinophil leukocyte
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Eosinophils are CD125-positive (IL-5R), GM-CSFR-positive, IL-3R-positive, VLA4-positive. They can also express MHC Class I & II, CD4, CD9, CD11a, CD11b, CD11c, CD13, CD15, CD16, CD17, CD18, CD24, CD25,CD28, CD29, CD32, CD33, CD35, CD37, CD39, CD43, CD44, CD45, CD45RB, CD45RO, CD46, CD47, CD48, CD49d, CD49f, CD50, CD52, CD53, CD54, CD55, CD58, CD59, CD62L, CD63, CD65, CD66, CD69, CD71, CD76, CD80, CD81, CD82, CD86, CD87, CD88, CD89, CD92, CD95, CD97, CD98, CD99, CD100, CD101, CD116, CD117, CD119, CD120, CD123, CD124, CD125, CD131, CD137, CD139, CD148, CD149, CD151, CD153, CD156, CD162, CD161, CD162, CD165, CD174, CD182, CD183, CD191, CD192, CD193, CD196, CD213, IL9R, ad integrin, beta-7 integrin, FceRI, IL13Ra1, TGFbR, PAFR, LTB4R, C3aR, CystLT1R, CystLT2R, fMLPR, CRTH2 (PGD2 receptor), histamine 4R, IDO, KYN, PAR-2, Siglec-8, Siglec-10, LIR1, LIR2, LIR3, LIR7, TLR7, TLR8, and VLA-4. Eosinophils can also secrete CXCL1, eotaxin-1, GM-CSF, IL-2, IL-3, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12, IL-13, IL-16, IL-18, IFN-gamma, LTC4, MIP-1alpha, NGF, PAF, RANTES, substance P, TGF-alpha, TGF-beta, TNF-alpha, and VIP.

Axiom
annotated source: mature eosinophil
annotated property: subClassOf
annotated target: eosinophil
is inferred: true

Axiom
annotated source: mature eosinophil
annotated property: definition
annotated target: A fully differentiated eosinophil, a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Cells are also differentiated from other granulocytes by a small nuclear-to-cytoplasm ratio (1:3). This cell type is CD49d-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: http://www.cap.org

neutrophilic myeloblast
type: Class
equivalent class: Class
  intersection of: CL_0000835
  intersection of: Restriction
    on property: has part
    some values from: PR_000001944
  intersection of: Restriction
    on property: has part
    some values from: PR_000005307
  intersection of: Restriction
    on property: has part
    some values from: PR_000007857
  intersection of: Restriction
    on property: has part
    some values from: PR_000010799
  intersection of: Restriction
    on property: has part
    some values from: PR_000014362
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030223
subclass of: CL_0000834
subclass of: CL_0000835
subclass of: Restriction
  on property: has part
  some values from: PR_000001944
subclass of: Restriction
  on property: has part
  some values from: PR_000005307
subclass of: Restriction
  on property: has part
  some values from: PR_000007857
subclass of: Restriction
  on property: has part
  some values from: PR_000010799
subclass of: Restriction
  on property: has part
  some values from: PR_000014362
subclass of: Restriction
  on property: develops from
  some values from: CL_0000834
definition: A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor.
database_cross_reference: ZFA:0009018
has_related_synonym: neutrophilic granuloblast
in_subset: human subset
in_subset: mouse subset
comment: These cells are CD11b-negative, CD15-negative, CD16-negative, CD35-negative, CD49d-positive, CD68-positive, lactotransferrin-negative, and fMLP receptor-negative. They are found in the Band 3 fraction.

Axiom
annotated source: neutrophilic myeloblast
annotated property: subClassOf
annotated target: CL_0000835
is inferred: true

Axiom
annotated source: neutrophilic myeloblast
annotated property: definition
annotated target: A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:12560239
database_cross_reference: PMID:15514007

Axiom
annotated source: neutrophilic myeloblast
annotated property: database_cross_reference
annotated target: ZFA:0009018
mapping justification: UnspecifiedMatching

mature basophil
type: Class
equivalent class: Class
  intersection of: basophil
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: GO_0005634
      intersection of: Restriction
        on property: has characteristic
        some values from: PATO_0001979
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002349
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002351
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002830
  intersection of: Restriction
    on property: capable of
    some values from: GO_0008015
  intersection of: Restriction
    on property: capable of
    some values from: GO_0032616
  intersection of: Restriction
    on property: capable of
    some values from: GO_0032633
  intersection of: Restriction
    on property: capable of
    some values from: GO_0048295
subclass of: basophil
subclass of: CL_0002274
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: GO_0005634
    intersection of: Restriction
      on property: has characteristic
      some values from: PATO_0001979
subclass of: Restriction
  on property: develops from
  some values from: band form basophil
subclass of: Restriction
  on property: capable of
  some values from: GO_0002349
subclass of: Restriction
  on property: capable of
  some values from: GO_0002351
subclass of: Restriction
  on property: capable of
  some values from: GO_0002830
subclass of: Restriction
  on property: capable of
  some values from: GO_0032616
subclass of: Restriction
  on property: capable of
  some values from: GO_0032633
subclass of: Restriction
  on property: capable of
  some values from: GO_0048295
definition: A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation.
has_broad_synonym: polymorphonuclear leucocyte
has_broad_synonym: polymorphonuclear leukocyte
database_cross_reference: BTO:0001026
database_cross_reference: CALOHA:TS-0688
has_exact_synonym: mature basophil leucocyte
has_exact_synonym: mature basophil leukocyte
in_subset: human subset
in_subset: mouse subset
comment: Mature basophils are also capable of producing IL-3, IL-5, IL-6, IL-8, IL-13, IL-25, CCL22, tslp, vegf, and LTC4.

Axiom
annotated source: mature basophil
annotated property: subClassOf
annotated target: basophil
is inferred: true

Axiom
annotated source: mature basophil
annotated property: definition
annotated target: A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:18466030
database_cross_reference: PMID:19231594
database_cross_reference: PMID:20837449
database_cross_reference: http://www.cap.org

CL_0000044
type: Class
has obsolescence reason: IAO_0000227
term replaced by: common lymphoid progenitor
deprecated: true

obsolete thymus processed stem cell
type: Class
definition: OBSOLETE (was not defined before being made obsolete).
comment: Consider using term 'pro-T cell ; CL:0000827' or the term 'thymocyte ; CL:0000893' or one of its children instead.
deprecated: true

obsolete bursa processed stem cell
type: Class
definition: OBSOLETE (was not defined before being made obsolete).
comment: Consider using term 'pro-B cell ; CL:0000826' or the term 'immature B cell ; CL:0000816 or one of its children instead.
deprecated: true

neural stem cell
type: Class
subclass of: BFO_0000002
subclass of: CL_0002319
subclass of: Restriction
  on property: develops from
  some values from: neurectodermal cell
definition: An undifferentiated neural cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple central nervous system neuronal and glial cell types.
database_cross_reference: BTO:0002881
database_cross_reference: CALOHA:TS-2360
database_cross_reference: FMA:86684
database_cross_reference: ZFA:0009019
has_exact_synonym: NSC
has_exact_synonym: neuronal stem cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: neural stem cell
annotated property: definition
annotated target: An undifferentiated neural cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple central nervous system neuronal and glial cell types.
database_cross_reference: PMID:30639325

Axiom
annotated source: neural stem cell
annotated property: database_cross_reference
annotated target: ZFA:0009019
mapping justification: UnspecifiedMatching

Axiom
annotated source: neural stem cell
annotated property: has_exact_synonym
annotated target: neuronal stem cell
database_cross_reference: PMID:16305818

multi fate stem cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001402
  intersection of: Restriction
    on property: capable of
    some values from: GO_0017145
subclass of: stem cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001402
definition: A stem cell that can give rise to multiple lineages of cells.
database_cross_reference: FMA:84789
database_cross_reference: ZFA:0009020
has_exact_synonym: multi-fate stem cell
has_exact_synonym: multifate stem cell
has_exact_synonym: multipotent cell
has_exact_synonym: multipotent stem cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: multi fate stem cell
annotated property: definition
annotated target: A stem cell that can give rise to multiple lineages of cells.
database_cross_reference: GOC:add

Axiom
annotated source: multi fate stem cell
annotated property: database_cross_reference
annotated target: ZFA:0009020
mapping justification: UnspecifiedMatching

common myeloid progenitor
type: Class
subclass of: CL_0002032
disjoint with: megakaryocyte-erythroid progenitor cell
disjoint with: common lymphoid progenitor
disjoint with: granulocyte monocyte progenitor cell
definition: A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0004730
database_cross_reference: ZFA:0009021
has_exact_synonym: common myeloid precursor
has_related_synonym: CFU-GEMM
has_related_synonym: CFU-S
has_related_synonym: CMP
has_related_synonym: colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte
has_related_synonym: multipotential myeloid stem cell
has_related_synonym: myeloid stem cell
has_related_synonym: pluripotent stem cell (bone marrow)
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059).

Axiom
annotated source: common myeloid progenitor
annotated property: subClassOf
annotated target: CL_0002032
is inferred: true

Axiom
annotated source: common myeloid progenitor
annotated property: definition
annotated target: A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0878932437
database_cross_reference: MESH:D023461

Axiom
annotated source: common myeloid progenitor
annotated property: database_cross_reference
annotated target: ZFA:0009021
mapping justification: UnspecifiedMatching

Axiom
annotated source: common myeloid progenitor
annotated property: has_related_synonym
annotated target: CFU-GEMM
database_cross_reference: ISBN:0878932437
has_synonym_type: abbreviation

Axiom
annotated source: common myeloid progenitor
annotated property: has_related_synonym
annotated target: CFU-S
database_cross_reference: ISBN:0878932437
has_synonym_type: abbreviation

Axiom
annotated source: common myeloid progenitor
annotated property: has_related_synonym
annotated target: CMP
database_cross_reference: ISBN:0878932437
has_synonym_type: abbreviation

Axiom
annotated source: common myeloid progenitor
annotated property: has_related_synonym
annotated target: colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte
database_cross_reference: ISBN:0878932437

Axiom
annotated source: common myeloid progenitor
annotated property: has_related_synonym
annotated target: multipotential myeloid stem cell
database_cross_reference: ISBN:0878932437

Axiom
annotated source: common myeloid progenitor
annotated property: has_related_synonym
annotated target: myeloid stem cell
database_cross_reference: ISBN:0878932437

Axiom
annotated source: common myeloid progenitor
annotated property: has_related_synonym
annotated target: pluripotent stem cell (bone marrow)
database_cross_reference: ISBN:0878932437

megakaryocyte-erythroid progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0002032
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030218
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030219
subclass of: myeloid cell
subclass of: CL_0002032
subclass of: CL_0011026
subclass of: Restriction
  on property: capable of
  some values from: GO_0030218
subclass of: Restriction
  on property: capable of
  some values from: GO_0030219
disjoint with: granulocyte monocyte progenitor cell
disjoint with: CL_0002009
definition: A progenitor cell committed to the megakaryocyte and erythroid lineages.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009022
has_exact_synonym: CFU-EM
has_exact_synonym: CFU-MegE
has_exact_synonym: MEP
has_exact_synonym: Meg/E progenitor
has_exact_synonym: colony forming unit erythroid megakaryocyte
has_exact_synonym: megakaryocyte/erythrocyte progenitor
has_exact_synonym: megakaryocyte/erythroid progenitor cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2.

Axiom
annotated source: megakaryocyte-erythroid progenitor cell
annotated property: subClassOf
annotated target: CL_0002032
is inferred: true

Axiom
annotated source: megakaryocyte-erythroid progenitor cell
annotated property: definition
annotated target: A progenitor cell committed to the megakaryocyte and erythroid lineages.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D055015
database_cross_reference: PMID:16647566
database_cross_reference: http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell

Axiom
annotated source: megakaryocyte-erythroid progenitor cell
annotated property: database_cross_reference
annotated target: ZFA:0009022
mapping justification: UnspecifiedMatching

common lymphoid progenitor
type: Class
equivalent class: Class
  intersection of: CL_0002032
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030098
subclass of: CL_0002032
subclass of: CL_0011026
subclass of: Restriction
  on property: capable of
  some values from: GO_0030098
definition: A oligopotent progenitor cell committed to the lymphoid lineage.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009023
has_exact_synonym: common lymphocyte precursor
has_exact_synonym: common lymphocyte progenitor
has_exact_synonym: common lymphoid precursor
has_related_synonym: CLP
has_related_synonym: ELP
has_related_synonym: committed lymphopoietic stem cell
has_related_synonym: early lymphocyte progenitor
has_related_synonym: lymphoid stem cell
has_related_synonym: lymphopoietic stem cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative.

Axiom
annotated source: common lymphoid progenitor
annotated property: subClassOf
annotated target: CL_0002032
is inferred: true

Axiom
annotated source: common lymphoid progenitor
annotated property: definition
annotated target: A oligopotent progenitor cell committed to the lymphoid lineage.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: PMID:10407577
database_cross_reference: PMID:16551251

Axiom
annotated source: common lymphoid progenitor
annotated property: database_cross_reference
annotated target: ZFA:0009023
mapping justification: UnspecifiedMatching

Axiom
annotated source: common lymphoid progenitor
annotated property: has_related_synonym
annotated target: CLP
has_synonym_type: abbreviation

Axiom
annotated source: common lymphoid progenitor
annotated property: has_related_synonym
annotated target: ELP
has_synonym_type: abbreviation

totipotent stem cell
type: Class
subclass of: somatic stem cell
definition: A stem cell from which all cells of the body can form.
database_cross_reference: FMA:84790
database_cross_reference: MESH:D039901
database_cross_reference: ZFA:0009024
has_exact_synonym: totipotential stem cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: totipotent stem cell
annotated property: definition
annotated target: A stem cell from which all cells of the body can form.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm

Axiom
annotated source: totipotent stem cell
annotated property: database_cross_reference
annotated target: ZFA:0009024
mapping justification: UnspecifiedMatching

CL_0000053
type: Class
has obsolescence reason: IAO_0000227
term replaced by: ameloblast
deprecated: true

bone matrix secreting cell
type: Class
subclass of: secretory cell
in_subset: human subset
in_subset: mouse subset

non-terminally differentiated cell
type: Class
subclass of: CL_0011115
definition: A precursor cell with a limited number of potential fates.
database_cross_reference: BTO:0000125
database_cross_reference: FMA:84782
has_exact_synonym: blast cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: define using PATO mulit-potent or oligopotent?

Axiom
annotated source: non-terminally differentiated cell
annotated property: definition
annotated target: A precursor cell with a limited number of potential fates.
database_cross_reference: SANBI:mhl

myoblast
type: Class
subclass of: muscle precursor cell
definition: A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.
database_cross_reference: BTO:0000222
database_cross_reference: CALOHA:TS-0650
database_cross_reference: FBbt:00005083
database_cross_reference: FMA:70335
database_cross_reference: VHOG:0001529
database_cross_reference: ZFA:0009025
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: myoblast
annotated property: definition
annotated target: A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D032446
database_cross_reference: PMID:21849021

Axiom
annotated source: myoblast
annotated property: database_cross_reference
annotated target: FBbt:00005083
mapping justification: ManualMappingCuration

Axiom
annotated source: myoblast
annotated property: database_cross_reference
annotated target: ZFA:0009025
mapping justification: UnspecifiedMatching

fibroblast
type: Class
subclass of: stromal cell
definition: A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000452
database_cross_reference: CALOHA:TS-0362
database_cross_reference: FMA:63877
database_cross_reference: NCIT:C12482
database_cross_reference: VHOG:0001482
database_cross_reference: ZFA:0009026
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.

Axiom
annotated source: fibroblast
annotated property: definition
annotated target: A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
database_cross_reference: ISBN:0517223651
database_cross_reference: MESH:D005347
database_cross_reference: http://en.wikipedia.org/wiki/Fibroblast

Axiom
annotated source: fibroblast
annotated property: database_cross_reference
annotated target: ZFA:0009026
mapping justification: UnspecifiedMatching

chondroblast
type: Class
subclass of: BFO_0000002
subclass of: non-terminally differentiated cell
subclass of: CL_0002320
subclass of: Restriction
  on property: develops from
  some values from: CL_0007009
subclass of: Restriction
  on property: produces
  some values from: UBERON_0002418
definition: Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell.
database_cross_reference: BTO:0003607
database_cross_reference: FMA:66783
database_cross_reference: ZFA:0009027
has_exact_synonym: chrondoplast
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: chondroblast
annotated property: definition
annotated target: Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell.
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000034
database_cross_reference: ISBN:0618947256

Axiom
annotated source: chondroblast
annotated property: database_cross_reference
annotated target: ZFA:0009027
mapping justification: UnspecifiedMatching

ameloblast
type: Class
subclass of: simple columnar epithelial cell
subclass of: CL_0002077
subclass of: CL_1100001
subclass of: Restriction
  on property: part of
  some values from: UBERON_0005176
subclass of: Restriction
  on property: develops from
  some values from: CL_0007000
subclass of: Restriction
  on property: capable of
  some values from: GO_0097186
subclass of: Restriction
  on property: adjacent to
  some values from: UBERON_0001763
subclass of: Restriction
  on property: produces
  some values from: UBERON_0001752
definition: Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell.
database_cross_reference: BTO:0001663
database_cross_reference: FMA:70576
has_exact_synonym: amelocyte
has_exact_synonym: enamel secreting cell
in_subset: human subset
in_subset: mouse subset
comment: non-encoded relationship from VSAO produces VSAO:0000066

Axiom
annotated source: ameloblast
annotated property: definition
annotated target: Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell.
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000034
database_cross_reference: MESH:D000565

odontoblast
type: Class
subclass of: non-terminally differentiated cell
subclass of: neurecto-epithelial cell
subclass of: CL_0002148
subclass of: CL_0011026
subclass of: Restriction
  on property: part of
  some values from: UBERON_0005176
subclass of: Restriction
  on property: develops from
  some values from: CL_0007003
subclass of: Restriction
  on property: produces
  some values from: UBERON_0001751
definition: Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell.
database_cross_reference: BTO:0001769
database_cross_reference: CALOHA:TS-0696
database_cross_reference: FMA:62999
database_cross_reference: MESH:D009804
database_cross_reference: ZFA:0009029
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: legacy def: One of the cells forming the outer surface of dental pulp that produces tooth dentin.

Axiom
annotated source: odontoblast
annotated property: definition
annotated target: Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell.
database_cross_reference: GO_REF:0000034
database_cross_reference: ISBN:0618947256

Axiom
annotated source: odontoblast
annotated property: database_cross_reference
annotated target: ZFA:0009029
mapping justification: UnspecifiedMatching

cementoblast
type: Class
subclass of: osteoblast
subclass of: secretory cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0005176
subclass of: Restriction
  on property: develops from
  some values from: CL_0007002
subclass of: Restriction
  on property: produces
  some values from: UBERON_0001753
definition: Skeletogenic cell that produces cementum (a bony substance that covers the root of a tooth), is part of the odontogenic papilla, and develops from a precementoblast cell.
database_cross_reference: CALOHA:TS-1164
database_cross_reference: FMA:63002
database_cross_reference: ZFA:0009030
has_exact_synonym: cementum secreting cell
in_subset: human subset
in_subset: mouse subset
comment: Legacy def: A cell of ectomesenchymal origin that aids in the formation the cementum layer on the roots of teeth.

Axiom
annotated source: cementoblast
annotated property: definition
annotated target: Skeletogenic cell that produces cementum (a bony substance that covers the root of a tooth), is part of the odontogenic papilla, and develops from a precementoblast cell.
database_cross_reference: GO_REF:0000034
database_cross_reference: ISBN:0781733901

Axiom
annotated source: cementoblast
annotated property: database_cross_reference
annotated target: ZFA:0009030
mapping justification: UnspecifiedMatching

osteoblast
type: Class
subclass of: non-terminally differentiated cell
subclass of: CL_0002320
subclass of: CL_0011026
subclass of: Restriction
  on property: develops from
  some values from: CL_0007010
subclass of: Restriction
  on property: produces
  some values from: UBERON_0008883
definition: Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell.
database_cross_reference: BTO:0001593
database_cross_reference: CALOHA:TS-0720
database_cross_reference: FMA:66780
database_cross_reference: ZFA:0009031
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: non-encoded relationships from VSAO - capable_of_producing VSAO:0000020

Axiom
annotated source: osteoblast
annotated property: definition
annotated target: Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell.
database_cross_reference: GO_REF:0000034
database_cross_reference: MESH:D010006

Axiom
annotated source: osteoblast
annotated property: database_cross_reference
annotated target: ZFA:0009031
mapping justification: UnspecifiedMatching

obsolete cell by histology
type: Class
definition: OBSOLETE: A classification of cells by their microscopic appearance.
consider: CL:0000000
consider: CL:0000003
consider: CL:0001034
comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its microscopic appearance. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate.
deprecated: true

Axiom
annotated source: obsolete cell by histology
annotated property: definition
annotated target: OBSOLETE: A classification of cells by their microscopic appearance.
database_cross_reference: FB:ma
database_cross_reference: GOC:tfm

ciliated cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: has part
    some values from: GO_0005929
subclass of: eukaryotic cell
subclass of: Restriction
  on property: has part
  some values from: GO_0005929
definition: A cell that has a filiform extrusion of the cell surface.
database_cross_reference: VHOG:0001532
database_cross_reference: XAO:0000031
database_cross_reference: ZFA:0009032
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: ciliated cell
annotated property: definition
annotated target: A cell that has a filiform extrusion of the cell surface.
database_cross_reference: GOC:tfm

Axiom
annotated source: ciliated cell
annotated property: database_cross_reference
annotated target: ZFA:0009032
mapping justification: UnspecifiedMatching

ependymal cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0004670
subclass of: ciliated epithelial cell
subclass of: glial cell
subclass of: neurecto-epithelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0004670
subclass of: Restriction
  on property: directly develops from
  some values from: radial glial cell
definition: A neuroepithelial glial cell, derived from a radial glial cell originating from the neuroectoderm, lines the ventricles of the brain and the central canal of the spinal cord. This cell is characterized by the presence of cilia on its apical surface, which can be motile or non-motile.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0001724
database_cross_reference: FMA:70550
database_cross_reference: ZFA:0009033
has_narrow_synonym: ependymocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: ependymal cell
annotated property: definition
annotated target: A neuroepithelial glial cell, derived from a radial glial cell originating from the neuroectoderm, lines the ventricles of the brain and the central canal of the spinal cord. This cell is characterized by the presence of cilia on its apical surface, which can be motile or non-motile.
database_cross_reference: GOC:tfm
database_cross_reference: JB:jb
database_cross_reference: PMID:34335193
database_cross_reference: PMID:37008045
database_cross_reference: PMID:9550134
database_cross_reference: doi:/10.3389/fncel.2021.703951
database_cross_reference: https://www.britannica.com/science/ependymal-cell

Axiom
annotated source: ependymal cell
annotated property: database_cross_reference
annotated target: ZFA:0009033
mapping justification: UnspecifiedMatching

Axiom
annotated source: ependymal cell
annotated property: has_narrow_synonym
annotated target: ependymocyte
database_cross_reference: doi:10.53347/rID-51713

epithelial cell
type: Class
subclass of: eukaryotic cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000483
disjoint with: leukocyte
definition: A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000414
database_cross_reference: CALOHA:TS-2026
database_cross_reference: CARO:0000077
database_cross_reference: FBbt:00000124
database_cross_reference: FMA:66768
database_cross_reference: WBbt:0003672
database_cross_reference: ZFA:0009034
has_exact_synonym: epitheliocyte
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: epithelial cell
annotated property: definition
annotated target: A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
database_cross_reference: FB:ma
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D004847

Axiom
annotated source: epithelial cell
annotated property: database_cross_reference
annotated target: FBbt:00000124
mapping justification: ManualMappingCuration

Axiom
annotated source: epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009034
mapping justification: UnspecifiedMatching

ciliated epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: has part
    some values from: GO_0005929
subclass of: ciliated cell
subclass of: epithelial cell
definition: An epithelial cell that has a cilia.
database_cross_reference: FMA:70605
database_cross_reference: ZFA:0009035
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: ciliated epithelial cell
annotated property: definition
annotated target: An epithelial cell that has a cilia.
database_cross_reference: GOC:tfm

Axiom
annotated source: ciliated epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009035
mapping justification: UnspecifiedMatching

duct epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000058
subclass of: epithelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000058
definition: An epithelial cell that is part of a duct.
database_cross_reference: ZFA:0009372
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: duct epithelial cell
annotated property: definition
annotated target: An epithelial cell that is part of a duct.
database_cross_reference: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: duct epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009372
mapping justification: UnspecifiedMatching

branched duct epithelial cell
type: Class
subclass of: duct epithelial cell
in_subset: human subset
in_subset: mouse subset

obsolete epithelial cell of gland
type: Class
deprecated: true

blood vessel endothelial cell
type: Class
equivalent class: Class
  intersection of: endothelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001981
subclass of: CL_0002139
subclass of: Restriction
  on property: part of
  some values from: UBERON_0004638
definition: An endothelial cell that lines the vasculature.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009036
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: blood vessel endothelial cell
annotated property: definition
annotated target: An endothelial cell that lines the vasculature.
database_cross_reference: GOC:tfm

Axiom
annotated source: blood vessel endothelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009036
mapping justification: UnspecifiedMatching

non-branched duct epithelial cell
type: Class
subclass of: duct epithelial cell
subclass of: CL_0002078
in_subset: human subset
in_subset: mouse subset

obsolete barrier epithelial cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1149
term replaced by: obsolete barrier cell
deprecated: true

obsolete epithem cell
type: Class
definition: Obsolete. Use PO:0000066 from Plant Ontology instead. A cell that constitutes the mesophyll of a hydathode and is located between the xylem endings and the epidermis. Proposed to be involved in the retrieval of solutes from the xylem sap.
term replaced by: PO_0000066
deprecated: true

Axiom
annotated source: obsolete epithem cell
annotated property: definition
annotated target: Obsolete. Use PO:0000066 from Plant Ontology instead. A cell that constitutes the mesophyll of a hydathode and is located between the xylem endings and the epidermis. Proposed to be involved in the retrieval of solutes from the xylem sap.
database_cross_reference: ISBN:0471245208
database_cross_reference: PMID:12662305

columnar/cuboidal epithelial cell
type: Class
subclass of: epithelial cell
definition: A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009038
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: columnar/cuboidal epithelial cell
annotated property: definition
annotated target: A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
database_cross_reference: GO:0002065
database_cross_reference: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: columnar/cuboidal epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009038
mapping justification: UnspecifiedMatching

squamous epithelial cell
type: Class
subclass of: epithelial cell
database_cross_reference: CALOHA:TS-1249
database_cross_reference: ZFA:0009039
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: squamous epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009039
mapping justification: UnspecifiedMatching

mesothelial cell
type: Class
subclass of: squamous epithelial cell
subclass of: CL_0002078
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001136
definition: A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement.
present in taxon: NCBITaxon 9606
database_cross_reference: FMA:66773
database_cross_reference: ZFA:0009040
has_exact_synonym: mesotheliocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport.

Axiom
annotated source: mesothelial cell
annotated property: definition
annotated target: A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544
database_cross_reference: PMID:26106328

Axiom
annotated source: mesothelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009040
mapping justification: UnspecifiedMatching

Axiom
annotated source: mesothelial cell
annotated property: comment
annotated target: Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport.
database_cross_reference: PMID:26106328

peridermal cell
type: Class
equivalent class: Class
  intersection of: squamous epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0003055
subclass of: squamous epithelial cell
subclass of: epidermal cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0003055
definition: Any squamous epithelial cell that is part of some periderm.
database_cross_reference: ZFA:0009041
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: peridermal cell
annotated property: definition
annotated target: Any squamous epithelial cell that is part of some periderm.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: peridermal cell
annotated property: database_cross_reference
annotated target: ZFA:0009041
mapping justification: UnspecifiedMatching

stratified epithelial cell
type: Class
subclass of: BFO_0000002
subclass of: epithelial cell
subclass of: Restriction
  on property: develops from
  some values from: stratified epithelial stem cell
definition: An epithelial cell, organized into multiple layers, with only the basal layer being in contact with the basement membrane.
database_cross_reference: ZFA:0009042
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: stratified epithelial cell
annotated property: definition
annotated target: An epithelial cell, organized into multiple layers, with only the basal layer being in contact with the basement membrane.
database_cross_reference: Wikipedia:Epithelium
database_cross_reference: doi:/10.1016/B978-0-12-410424-2.00003-2
database_cross_reference: https://www.biologyonline.com/dictionary/stratified-epithelium

Axiom
annotated source: stratified epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009042
mapping justification: UnspecifiedMatching

circulating cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000179
subclass of: eukaryotic cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000179
definition: A cell which moves among different tissues of the body, via blood, lymph, or other medium.
database_cross_reference: ZFA:0009043
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: circulating cell
annotated property: definition
annotated target: A cell which moves among different tissues of the body, via blood, lymph, or other medium.
database_cross_reference: GOC:add

Axiom
annotated source: circulating cell
annotated property: database_cross_reference
annotated target: ZFA:0009043
mapping justification: UnspecifiedMatching

blood cell
type: Class
equivalent class: Class
  intersection of: CL_0000988
  intersection of: Restriction
    on property: capable of
    some values from: GO_0008015
subclass of: CL_0000988
subclass of: Restriction
  on property: capable of
  some values from: GO_0008015
definition: A cell found predominately in the blood.
database_cross_reference: FMA:62844
database_cross_reference: MESH:D001773
database_cross_reference: ZFA:0009044
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: blood cell
annotated property: subClassOf
annotated target: CL_0000988
is inferred: true

Axiom
annotated source: blood cell
annotated property: definition
annotated target: A cell found predominately in the blood.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm

Axiom
annotated source: blood cell
annotated property: database_cross_reference
annotated target: ZFA:0009044
mapping justification: UnspecifiedMatching

epithelial cell of lung
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000115
subclass of: CL_0002632
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000115
definition: An epithelial cell of the lung.
database_cross_reference: BTO:0004299
has_exact_synonym: lung epithelial cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: epithelial cell of lung
annotated property: definition
annotated target: An epithelial cell of the lung.
database_cross_reference: https://orcid.org/0000-0001-5208-3432

epithelial cell of pancreas
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001264
subclass of: CL_0002076
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001264
definition: An epithelial cell of the pancreas.
database_cross_reference: BTO:0000028
database_cross_reference: ZFA:0009045
has_exact_synonym: pancreas epithelial cell
has_exact_synonym: pancreatic epithelial cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: epithelial cell of pancreas
annotated property: definition
annotated target: An epithelial cell of the pancreas.
database_cross_reference: GOC:tfm

Axiom
annotated source: epithelial cell of pancreas
annotated property: database_cross_reference
annotated target: ZFA:0009045
mapping justification: UnspecifiedMatching

T cell
type: Class
equivalent class: Class
  intersection of: lymphocyte
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002456
subclass of: lymphocyte
subclass of: Restriction
  on property: develops from
  some values from: CL_0000827
subclass of: Restriction
  on property: capable of
  some values from: GO_0002456
disjoint with: CL_0000945
definition: A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000782
database_cross_reference: CALOHA:TS-1001
database_cross_reference: FMA:62870
database_cross_reference: MESH:D013601
database_cross_reference: VHOG:0001479
database_cross_reference: ZFA:0009046
has_exact_synonym: T lymphocyte
has_exact_synonym: T-cell
has_exact_synonym: T-lymphocyte
has_related_synonym: immature T cell
has_related_synonym: mature T cell
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: T cell
annotated property: subClassOf
annotated target: lymphocyte
is inferred: true

Axiom
annotated source: T cell
annotated property: definition
annotated target: A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

Axiom
annotated source: T cell
annotated property: database_cross_reference
annotated target: ZFA:0009046
mapping justification: UnspecifiedMatching

obsolete germ line stem cell (sensu Vertebrata)
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1935
term replaced by: germ line stem cell
comment: Obsoleted as there is no need for a term specific for vertebrates.
deprecated: true

obsolete germ line stem cell (sensu Nematoda and Protostomia)
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1935
term replaced by: germ line stem cell
comment: Obsoleted as there is no need for a term specific for nematods and protostomes.
deprecated: true

obsolete male germ line stem cell (sensu Nematoda and Protostomia)
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1935
term replaced by: male germ line stem cell
comment: Obsoleted as there is no need for a term specific for nematods and protostomes.
deprecated: true

obsolete female germ line stem cell (sensu Nematoda and Protostomia)
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1935
term replaced by: female germ line stem cell
comment: Obsoleted as there is no need for a term specific for nematods and protostomes.
deprecated: true

obsolete male germ line stem cell (sensu Vertebrata)
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1935
term replaced by: male germ line stem cell
comment: Obsoleted as there is no need for a term specific for vertebrates.
deprecated: true

obsolete female germ line stem cell (sensu Vertebrata)
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1935
term replaced by: female germ line stem cell
comment: Obsoleted as there is no need for a term specific for vertebrates.
deprecated: true

Kupffer cell
type: Class
equivalent class: Class
  intersection of: CL_0000864
  intersection of: Restriction
    on property: located in
    some values from: UBERON_0001281
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001813
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001925
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002064
  intersection of: Restriction
    on property: capable of
    some values from: GO_0034102
  intersection of: Restriction
    on property: has low plasma membrane amount
    some values from: PR_000001012
subclass of: CL_0000864
subclass of: Restriction
  on property: located in
  some values from: UBERON_0001281
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001813
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001925
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002064
subclass of: Restriction
  on property: capable of
  some values from: GO_0034102
subclass of: Restriction
  on property: has low plasma membrane amount
  some values from: PR_000001012
definition: A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system.
present in taxon: NCBITaxon 9606
description: Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. Kupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: BTO:0000685
database_cross_reference: FMA:14656
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000091
has_exact_synonym: hepatic macrophage
has_exact_synonym: littoral cell of hepatic sinusoid
has_exact_synonym: liver macrophage
has_exact_synonym: macrophagocytus stellatus
has_exact_synonym: stellate cell of von Kupffer
has_exact_synonym: von Kupffer cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Markers: Mouse: F4/80+, CD11b-low, CD68+, sialoadhesin+, CD163/SRCR+; role or process: immune, antigen-presentation, clearance of senescent erythrocytes, iron metabolism. Kupffer cells are also reportedly C3aR-positive, CD14-low, CD54-positive, CD88-positive, and CD284-positive. They are also capable of producing IL-1, IL-6, TNF-alpha, nitric oxide, PGD2, PGE2, PGF2alpha, and TXA2.

Axiom
annotated source: Kupffer cell
annotated property: subClassOf
annotated target: CL_0000864
is inferred: true

Axiom
annotated source: Kupffer cell
annotated property: definition
annotated target: A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0517223651
database_cross_reference: MESH:D007728
database_cross_reference: PMID:15771589
database_cross_reference: PMID:17105582

Axiom
annotated source: Kupffer cell
annotated property: description
annotated target: Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. Kupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1002/cphy.c120026
database_cross_reference: DOI:10.1007/978-1-4939-1311-4_10
database_cross_reference: DOI:10.1016/j.immuni.2022.08.002
database_cross_reference: DOI:10.1038/nri.2017.11
database_cross_reference: DOI:10.1111/j.1478-3231.2006.01342.x

osteoclast
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001474
  intersection of: Restriction
    on property: has part
    some values from: PR_000001850
  intersection of: Restriction
    on property: has part
    some values from: PR_000001937
  intersection of: Restriction
    on property: has part
    some values from: PR_000001944
  intersection of: Restriction
    on property: has part
    some values from: PR_000007597
  intersection of: Restriction
    on property: has part
    some values from: PR_000011178
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001954
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002062
  intersection of: Restriction
    on property: capable of
    some values from: GO_0045453
subclass of: phagocyte (sensu Vertebrata)
subclass of: myeloid leukocyte
subclass of: CL_0001035
subclass of: Restriction
  on property: has part
  some values from: PR_000001850
subclass of: Restriction
  on property: has part
  some values from: PR_000001937
subclass of: Restriction
  on property: has part
  some values from: PR_000001944
subclass of: Restriction
  on property: has part
  some values from: PR_000007597
subclass of: Restriction
  on property: has part
  some values from: PR_000011178
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001954
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002062
subclass of: Restriction
  on property: develops from
  some values from: monocyte
subclass of: Restriction
  on property: capable of
  some values from: GO_0045453
definition: A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive.
description: Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: BTO:0000968
database_cross_reference: CALOHA:TS-0721
database_cross_reference: FMA:66781
database_cross_reference: MESH:D010010
database_cross_reference: ZFA:0009047
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000092
has_related_synonym: chondroclast
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid.

Axiom
annotated source: osteoclast
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: osteoclast
annotated property: subClassOf
annotated target: CL_0001035
is inferred: true

Axiom
annotated source: osteoclast
annotated property: definition
annotated target: A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149
database_cross_reference: PMID:10428500
database_cross_reference: PMID:15055519
database_cross_reference: PMID:17380158

Axiom
annotated source: osteoclast
annotated property: description
annotated target: Osteoclasts, derived from the monocyte/macrophage lineage, play a crucial role in bone remodeling through bone resorption. They are distinguished from other cells by their large size and their unique ability to secrete enzymes and acids that dissolve the calcium phosphate in bone. The formation of osteoclasts is influenced by two primary factors: macrophage colony-stimulating factor (M-CSF) and the ligand-activated receptor (RANKL) of nuclear factor kappa B (NF-κB). Osteoclasts also collaborate with osteoblasts, responsible for new bone formation, to maintain bone health and adapt bone structure. Their coordinated actions allow continuous remodeling while preserving overall bone strength and integrity. Imbalances in osteoclast activity can lead to pathological conditions. For example, excessive activity may contribute to diseases like osteoporosis, periprosthetic osteolysis, bone tumors, and Paget's disease. Other the other hand, osteoclast deficiency ca result in conditions like osteopetrosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.3389/fmed.2017.00234
database_cross_reference: DOI:10.37175/stemedicine.v1i4.57
database_cross_reference: https://www.sciencedirect.com/topics/medicine-and-dentistry/osteoclast

Axiom
annotated source: osteoclast
annotated property: database_cross_reference
annotated target: ZFA:0009047
mapping justification: UnspecifiedMatching

obsolete osteochondroclast
type: Class
definition: OBSOLETE (was not defined before being made obsolete).
comment: Consider using 'osteoclast ; CL:0000092' instead.
deprecated: true

granulocyte
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: has part
    some values from: GO_0030141
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001012
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001332
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001969
  intersection of: Restriction
    on property: capable of
    some values from: GO_0008015
subclass of: blood cell
subclass of: myeloid leukocyte
subclass of: Restriction
  on property: has part
  some values from: GO_0030141
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001012
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001332
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001969
definition: A leukocyte with abundant granules in the cytoplasm.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000539
database_cross_reference: BTO:0001026
database_cross_reference: CALOHA:TS-0422
database_cross_reference: FMA:62854
database_cross_reference: ZFA:0009048
has_exact_synonym: granular leucocyte
has_exact_synonym: granular leukocyte
has_exact_synonym: polymorphonuclear leukocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: granulocyte
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: granulocyte
annotated property: definition
annotated target: A leukocyte with abundant granules in the cytoplasm.
database_cross_reference: GOC:amm
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D006098
database_cross_reference: http://en.wikipedia.org/wiki/Granulocyte

Axiom
annotated source: granulocyte
annotated property: database_cross_reference
annotated target: ZFA:0009048
mapping justification: UnspecifiedMatching

neuron associated cell
type: Class
subclass of: BFO_0000002
subclass of: CL_0002319
subclass of: Restriction
  on property: develops from
  some values from: neurectodermal cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

mature neutrophil
type: Class
equivalent class: Class
  intersection of: neutrophil
  intersection of: Restriction
    on property: has part
    some values from: CL_0017500
  intersection of: Restriction
    on property: has part
    some values from: GO_0070820
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: GO_0005634
      intersection of: Restriction
        on property: has characteristic
        some values from: PATO_0001979
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000009978
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000010543
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000010799
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001256
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001257
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001456
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001483
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001879
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001944
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000007597
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002536
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002690
  intersection of: Restriction
    on property: capable of
    some values from: GO_0006909
  intersection of: Restriction
    on property: capable of
    some values from: GO_0032637
subclass of: phagocyte
subclass of: neutrophil
subclass of: Restriction
  on property: has part
  some values from: CL_0017500
subclass of: Restriction
  on property: has part
  some values from: GO_0070820
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: GO_0005634
    intersection of: Restriction
      on property: has characteristic
      some values from: PATO_0001979
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000009978
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000010543
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000010799
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001256
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001257
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001456
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001483
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001944
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000007597
subclass of: Restriction
  on property: capable of
  some values from: GO_0002536
subclass of: Restriction
  on property: capable of
  some values from: GO_0002690
subclass of: Restriction
  on property: capable of
  some values from: GO_0032637
definition: A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive.
present in taxon: NCBITaxon 9606
has_broad_synonym: poly
has_broad_synonym: polymorphonuclear leucocyte
has_broad_synonym: polymorphonuclear leukocyte
database_cross_reference: BTO:0003473
database_cross_reference: ZFA:0009049
has_exact_synonym: PMN
has_exact_synonym: mature neutrocyte
has_exact_synonym: mature neutrophil leucocyte
has_exact_synonym: mature neutrophil leukocyte
has_exact_synonym: mature neutrophilic leucocyte
has_exact_synonym: mature neutrophilic leukocyte
has_exact_synonym: polymorphonuclear neutrophil
has_exact_synonym: polynuclear neutrophilic leucocyte
has_exact_synonym: polynuclear neutrophilic leukocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Neutrophils are also capable of secreting GRO-alpha, IL-1beta, IL-1ra, IL-3, IL-12, IP-10, MIG, MIP-1alpha, MIP-1beta, TGF-beta, TNF-alpha, VEGF, and anti-microbial peptides. They can positively influence the chemotaxis of basophils, T-cells, monocytes, macrophages, dendritic cells, and other neutrophils. Neutrophils are also CD35-positive, CD64-positive, CD89-positive, CD184-positive, and fMLP receptor-positive Ly-6G-positive (mouse), TLR2-low, TLR4-low, and lineage-negative (CD2, CD3, CD5, CD9, CD19, CD36, CD49d, CD56, CD61, CD235a (glycophorin-A)).

Axiom
annotated source: mature neutrophil
annotated property: subClassOf
annotated target: neutrophil
is inferred: true

Axiom
annotated source: mature neutrophil
annotated property: definition
annotated target: A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D009504
database_cross_reference: PMID:11138776
database_cross_reference: PMID:12560239
database_cross_reference: PMID:15514007
database_cross_reference: PMID:7880385
database_cross_reference: http://www.cap.org

Axiom
annotated source: mature neutrophil
annotated property: database_cross_reference
annotated target: ZFA:0009049
mapping justification: UnspecifiedMatching

mast cell
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: has part
    some values from: GO_0030141
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001865
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001255
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000006169
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002349
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002539
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002660
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002690
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002830
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030210
  intersection of: Restriction
    on property: has high plasma membrane amount
    some values from: PR_000002065
  intersection of: Restriction
    on property: has high plasma membrane amount
    some values from: PR_000007431
subclass of: myeloid leukocyte
subclass of: CL_0002274
subclass of: Restriction
  on property: has part
  some values from: GO_0030141
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001865
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001255
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000006169
subclass of: Restriction
  on property: develops from
  some values from: CL_0000831
subclass of: Restriction
  on property: capable of
  some values from: GO_0002349
subclass of: Restriction
  on property: capable of
  some values from: GO_0002539
subclass of: Restriction
  on property: capable of
  some values from: GO_0002660
subclass of: Restriction
  on property: capable of
  some values from: GO_0002690
subclass of: Restriction
  on property: capable of
  some values from: GO_0002830
subclass of: Restriction
  on property: capable of
  some values from: GO_0030210
subclass of: Restriction
  on property: has high plasma membrane amount
  some values from: PR_000002065
subclass of: Restriction
  on property: has high plasma membrane amount
  some values from: PR_000007431
definition: A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000830
database_cross_reference: CALOHA:TS-0603
database_cross_reference: FMA:66784
has_exact_synonym: histaminocyte
has_exact_synonym: labrocyte
has_exact_synonym: mastocyte
has_related_synonym: tissue basophil
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5.

Axiom
annotated source: mast cell
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: mast cell
annotated property: definition
annotated target: A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:068340007X
database_cross_reference: MESH:D008407
database_cross_reference: PMCID:PMC1312421
database_cross_reference: PMCID:PMC2855166
database_cross_reference: PMID:15153310
database_cross_reference: PMID:16455980
database_cross_reference: PMID:19671378
database_cross_reference: PMID:212366338
database_cross_reference: PMID:9354811

Axiom
annotated source: mast cell
annotated property: has_exact_synonym
annotated target: labrocyte
database_cross_reference: ISBN:0721601464

Axiom
annotated source: mast cell
annotated property: has_exact_synonym
annotated target: mastocyte
database_cross_reference: ISBN:0721601464

Axiom
annotated source: mast cell
annotated property: has_related_synonym
annotated target: tissue basophil
database_cross_reference: ISBN:068340007X

sensory epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050906
subclass of: epithelial cell
subclass of: sensory receptor cell
definition: A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells.
has_broad_synonym: neuroepithelial cell
database_cross_reference: BTO:0004301
database_cross_reference: ZFA:0009050
in_subset: human subset
in_subset: mouse subset
comment: The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710).

Axiom
annotated source: sensory epithelial cell
annotated property: definition
annotated target: A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651
database_cross_reference: ISBN:0721662544

Axiom
annotated source: sensory epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009050
mapping justification: UnspecifiedMatching

interneuron
type: Class
subclass of: CL_2000029
definition: Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0003811
database_cross_reference: FBbt:00005125
database_cross_reference: FMA:67313
database_cross_reference: WBbt:0005113
database_cross_reference: ZFA:0009051
has_related_synonym: CNS interneuron
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: interneuron
annotated property: definition
annotated target: Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D007395

Axiom
annotated source: interneuron
annotated property: database_cross_reference
annotated target: FBbt:00005125
mapping justification: ManualMappingCuration

Axiom
annotated source: interneuron
annotated property: database_cross_reference
annotated target: ZFA:0009051
mapping justification: UnspecifiedMatching

motor neuron
type: Class
subclass of: efferent neuron
definition: An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000312
database_cross_reference: FBbt:00005123
database_cross_reference: FMA:83617
database_cross_reference: WBbt:0005409
database_cross_reference: ZFA:0009052
has_exact_synonym: motoneuron
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: motor neuron
annotated property: definition
annotated target: An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement.
database_cross_reference: MESH:D009046
database_cross_reference: PMID:16875686

Axiom
annotated source: motor neuron
annotated property: database_cross_reference
annotated target: FBbt:00005123
mapping justification: ManualMappingCuration

Axiom
annotated source: motor neuron
annotated property: database_cross_reference
annotated target: ZFA:0009052
mapping justification: UnspecifiedMatching

sensory neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050906
subclass of: afferent neuron
subclass of: Restriction
  on property: capable of
  some values from: GO_0050906
definition: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0001037
database_cross_reference: FBbt:00005124
database_cross_reference: FMA:84649
database_cross_reference: MESH:D011984
database_cross_reference: WBbt:0005759
database_cross_reference: ZFA:0009053
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: sensory neuron
annotated property: definition
annotated target: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
database_cross_reference: ISBN:0721662544

Axiom
annotated source: sensory neuron
annotated property: database_cross_reference
annotated target: FBbt:00005124
mapping justification: ManualMappingCuration

Axiom
annotated source: sensory neuron
annotated property: database_cross_reference
annotated target: ZFA:0009053
mapping justification: UnspecifiedMatching

polymodal neuron
type: Class
subclass of: CL_2000032
definition: A neuron type that respond to multiple stimuli such as mechanical, thermal and chemical. This neuron type is responsible for integrating different types of sensory inputs, allowing organisms to respond appropriately to diverse environmental challenges.
database_cross_reference: ZFA:0009054
has_related_synonym: polymodal sensory neuron
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: polymodal neuron
annotated property: definition
annotated target: A neuron type that respond to multiple stimuli such as mechanical, thermal and chemical. This neuron type is responsible for integrating different types of sensory inputs, allowing organisms to respond appropriately to diverse environmental challenges.
database_cross_reference: PMID:23749412
database_cross_reference: PMID:36381588

Axiom
annotated source: polymodal neuron
annotated property: database_cross_reference
annotated target: ZFA:0009054
mapping justification: UnspecifiedMatching

Axiom
annotated source: polymodal neuron
annotated property: has_related_synonym
annotated target: polymodal sensory neuron
database_cross_reference: PMID:23749412

bipolar neuron
type: Class
equivalent class: Class
  intersection of: interneuron
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0070006
subclass of: interneuron
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0070006
definition: A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.
database_cross_reference: FMA:67282
database_cross_reference: ZFA:0009055
in_subset: BDS subset
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: bipolar neuron
annotated property: definition
annotated target: A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0444009442

Axiom
annotated source: bipolar neuron
annotated property: database_cross_reference
annotated target: ZFA:0009055
mapping justification: UnspecifiedMatching

multipolar neuron
type: Class
subclass of: CL_2000029
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0070026
definition: A neuron with three or more neurites, usually an axon and multiple dendrites.
database_cross_reference: FMA:67287
database_cross_reference: ZFA:0009056
in_subset: BDS subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: multipolar neuron
annotated property: definition
annotated target: A neuron with three or more neurites, usually an axon and multiple dendrites.
database_cross_reference: FMA:67287
database_cross_reference: GOC:tfm

Axiom
annotated source: multipolar neuron
annotated property: database_cross_reference
annotated target: ZFA:0009056
mapping justification: UnspecifiedMatching

pseudounipolar neuron
type: Class
subclass of: CL_2000032
definition: Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma.
database_cross_reference: FMA:67305
database_cross_reference: ZFA:0009057
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pseudounipolar neuron
annotated property: definition
annotated target: Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma.
database_cross_reference: FMA:67305
database_cross_reference: GOC:tfm

Axiom
annotated source: pseudounipolar neuron
annotated property: database_cross_reference
annotated target: ZFA:0009057
mapping justification: UnspecifiedMatching

unipolar neuron
type: Class
subclass of: CL_2000032
definition: Neuron with one neurite that extends from the cell body.
database_cross_reference: FMA:67278
database_cross_reference: ZFA:0009058
in_subset: BDS subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: unipolar neuron
annotated property: definition
annotated target: Neuron with one neurite that extends from the cell body.
database_cross_reference: FMA:67278
database_cross_reference: GOC:nv

Axiom
annotated source: unipolar neuron
annotated property: database_cross_reference
annotated target: ZFA:0009058
mapping justification: UnspecifiedMatching

autonomic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: has soma location
    some values from: UBERON_0002410
subclass of: CL_2000032
subclass of: Restriction
  on property: has soma location
  some values from: UBERON_0002410
definition: A neuron whose cell body is within an autonomic ganglion.
database_cross_reference: FMA:80121
database_cross_reference: ZFA:0009059
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: autonomic neuron
annotated property: definition
annotated target: A neuron whose cell body is within an autonomic ganglion.
database_cross_reference: GOC:tfm

Axiom
annotated source: autonomic neuron
annotated property: database_cross_reference
annotated target: ZFA:0009059
mapping justification: UnspecifiedMatching

cholinergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0014055
subclass of: secretory cell
subclass of: neuron
subclass of: Restriction
  on property: capable of
  some values from: GO_0014055
definition: A neuron that uses acetylcholine as a vesicular neurotransmitter.
database_cross_reference: BTO:0004902
database_cross_reference: FBbt:00007173
database_cross_reference: FMA:84796
database_cross_reference: MESH:D059329
database_cross_reference: WBbt:0006840
database_cross_reference: ZFA:0009060
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cholinergic neuron
annotated property: definition
annotated target: A neuron that uses acetylcholine as a vesicular neurotransmitter.
database_cross_reference: GOC:tfm

Axiom
annotated source: cholinergic neuron
annotated property: database_cross_reference
annotated target: FBbt:00007173
mapping justification: ManualMappingCuration

Axiom
annotated source: cholinergic neuron
annotated property: database_cross_reference
annotated target: ZFA:0009060
mapping justification: UnspecifiedMatching

adrenergic neuron
type: Class
subclass of: CL_4033050
database_cross_reference: MESH:D059331
database_cross_reference: ZFA:0009061
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: adrenergic neuron
annotated property: database_cross_reference
annotated target: ZFA:0009061
mapping justification: UnspecifiedMatching

peptidergic neuron
type: Class
subclass of: neuron
subclass of: Restriction
  on property: capable of
  some values from: GO_0002790
definition: A neuron that uses neuropeptides as transmitters.
database_cross_reference: FBbt:00004101
database_cross_reference: ZFA:0009062
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: peptidergic neuron
annotated property: definition
annotated target: A neuron that uses neuropeptides as transmitters.
database_cross_reference: PMID:23040809
database_cross_reference: doi:10.1016/B978-012589762-4/50021-9

Axiom
annotated source: peptidergic neuron
annotated property: database_cross_reference
annotated target: FBbt:00004101
mapping justification: ManualMappingCuration

Axiom
annotated source: peptidergic neuron
annotated property: database_cross_reference
annotated target: ZFA:0009062
mapping justification: UnspecifiedMatching

obsolete peripheral neuron
type: Class
definition: OBSOLETE A neuron that is part of nerve found outside the central nervous system.
has obsolescence reason: IAO_0000227
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1069
term replaced by: CL_2000032
database_cross_reference: FMA:84664
comment: Merging into CL:2000032.
deprecated: true

Axiom
annotated source: obsolete peripheral neuron
annotated property: definition
annotated target: OBSOLETE A neuron that is part of nerve found outside the central nervous system.
database_cross_reference: ISBN:0721662544

columnar neuron
type: Class
subclass of: CNS neuron (sensu Nematoda and Protostomia)
subclass of: CL_0008028
subclass of: Restriction
  on property: capable of
  some values from: GO_0007601
definition: A neuron of the invertebrate central nervous system. This neuron innervates the central complex (CX) of an invertebrate brain and it forms columnar patterns with its dendrites. It is involved in navigation and spatial processing.
comment: Columnar neurons have been widely studied in Diptera, locusts, honey bees and other insects. In the mammalian brain, a "columnar organisation" is referred to neurons of the neocortex, however these differ from columnar neurons which are found in the insects central nervous system.

Axiom
annotated source: columnar neuron
annotated property: definition
annotated target: A neuron of the invertebrate central nervous system. This neuron innervates the central complex (CX) of an invertebrate brain and it forms columnar patterns with its dendrites. It is involved in navigation and spatial processing.
database_cross_reference: PMID:34696823
database_cross_reference: PMID:37608556

Axiom
annotated source: columnar neuron
annotated property: comment
annotated target: Columnar neurons have been widely studied in Diptera, locusts, honey bees and other insects. In the mammalian brain, a "columnar organisation" is referred to neurons of the neocortex, however these differ from columnar neurons which are found in the insects central nervous system.
database_cross_reference: PMID:18837039
database_cross_reference: PMID:32374034
database_cross_reference: PMID:34696823
database_cross_reference: PMID:37608556
database_cross_reference: PMID:9153131

mononuclear phagocyte
type: Class
equivalent class: Class
  intersection of: phagocyte (sensu Vertebrata)
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001407
subclass of: phagocyte (sensu Vertebrata)
subclass of: CL_0000842
definition: A vertebrate phagocyte with a single nucleus.
present in taxon: NCBITaxon 9606
description: Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it …
database_cross_reference: BTO:0001433
database_cross_reference: ZFA:0009064
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000113
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: mononuclear phagocyte
annotated property: subClassOf
annotated target: phagocyte (sensu Vertebrata)
is inferred: true

Axiom
annotated source: mononuclear phagocyte
annotated property: definition
annotated target: A vertebrate phagocyte with a single nucleus.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

Axiom
annotated source: mononuclear phagocyte
annotated property: description
annotated target: Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it …
database_cross_reference: DOI:10.1016/j.coi.2005.11.008
database_cross_reference: DOI:10.1038/nri3087
database_cross_reference: DOI:10.3389/fimmu.2019.01893

Axiom
annotated source: mononuclear phagocyte
annotated property: database_cross_reference
annotated target: ZFA:0009064
mapping justification: UnspecifiedMatching

surface ectodermal cell
type: Class
equivalent class: Class
  intersection of: ectodermal cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000076
subclass of: ectodermal cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000076
definition: An ectodermal cell that is part of the external ectoderm, forming the outermost layer of the developing embryo. It is characterized by its polarized nature, with distinct apical and basal surfaces (Ferrante Jr., Reinke, & Stanley, 1995). Surface ectodermal cell gives rise to the epidermis, hair follicles, nails, sensory organs, and specialized structures like the apical ectodermal ridge crucial for limb development (Skoufa et al., 2024).
description: Surface ectoderm cells give rise to external structures such as the epidermis, hair, nails, and sweat glands. They are critical during the early stages of embryonic development, where they delineate and create the organism's exterior body plan. Beyond forming the organism's physical exterior, surface ectodermal cells have other significant roles. For instance, these cells lead to the development of the anterior pituitary gland and the enamel of the teeth. They are also integral to the formation of the sensory organs, including the eyes and the ears. In the eyes, they form the cornea and lens epithelium. In the ears, they form the external ear canal and certain parts of the inner ear. Therefore, these cells are instrumental in the development of various sensory systems in an organism. Certain abnormalities or mutations in surface ectodermal cells could lead to medical conditions known as ectodermal dysplasias. These are a group of inherited disorders affecting the development or function of teeth, hair, nails, and sweat glands. Therefore, understanding the formation and function of surface ectodermal cells is also important in identifying and addressing certain genetic disorders and conditions. In summary, surface ectodermal cells are essential in embryonic development, contributing to the creation of the external physical appearance and the sensory organs of an organism. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: FMA:72552
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000114
has_exact_synonym: cell of surface ectoderm
has_exact_synonym: surface ectoderm cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: surface ectodermal cell
annotated property: definition
annotated target: An ectodermal cell that is part of the external ectoderm, forming the outermost layer of the developing embryo. It is characterized by its polarized nature, with distinct apical and basal surfaces (Ferrante Jr., Reinke, & Stanley, 1995). Surface ectodermal cell gives rise to the epidermis, hair follicles, nails, sensory organs, and specialized structures like the apical ectodermal ridge crucial for limb development (Skoufa et al., 2024).
database_cross_reference: PMID:7892198
database_cross_reference: Wikipedia:Surface_ectoderm
database_cross_reference: doi:/10.1101/2024.07.02.601324

Axiom
annotated source: surface ectodermal cell
annotated property: description
annotated target: Surface ectoderm cells give rise to external structures such as the epidermis, hair, nails, and sweat glands. They are critical during the early stages of embryonic development, where they delineate and create the organism's exterior body plan. Beyond forming the organism's physical exterior, surface ectodermal cells have other significant roles. For instance, these cells lead to the development of the anterior pituitary gland and the enamel of the teeth. They are also integral to the formation of the sensory organs, including the eyes and the ears. In the eyes, they form the cornea and lens epithelium. In the ears, they form the external ear canal and certain parts of the inner ear. Therefore, these cells are instrumental in the development of various sensory systems in an organism. Certain abnormalities or mutations in surface ectodermal cells could lead to medical conditions known as ectodermal dysplasias. These are a group of inherited disorders affecting the development or function of teeth, hair, nails, and sweat glands. Therefore, understanding the formation and function of surface ectodermal cells is also important in identifying and addressing certain genetic disorders and conditions. In summary, surface ectodermal cells are essential in embryonic development, contributing to the creation of the external physical appearance and the sensory organs of an organism. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1038/srep32007
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK539836/
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK563130

Axiom
annotated source: surface ectodermal cell
annotated property: has_exact_synonym
annotated target: surface ectoderm cell
database_cross_reference: doi:/10.1101/2024.07.02.601324

endothelial cell
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: Restriction
  on property: develops from
  some values from: mesodermal cell
definition: An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0001176
database_cross_reference: CALOHA:TS-0278
database_cross_reference: FMA:66772
database_cross_reference: ZFA:0009065
has_exact_synonym: endotheliocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard].

Axiom
annotated source: endothelial cell
annotated property: definition
annotated target: An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D042783
database_cross_reference: PMID:21275341
database_cross_reference: http://en.wikipedia.org/wiki/Endothelial_cell
database_cross_reference: https://sourceforge.net/tracker/

Axiom
annotated source: endothelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009065
mapping justification: UnspecifiedMatching

pioneer neuron
type: Class
subclass of: neuron
definition: Pioneer neurons establish a pathway in the developing central nervous system and then undergo programmed cell death once the adult axons, which follow them, have made connections with the target site. Thus, they are a transient cell type involved in axon guidance.
database_cross_reference: FBbt:00005128
database_cross_reference: ZFA:0009066
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pioneer neuron
annotated property: definition
annotated target: Pioneer neurons establish a pathway in the developing central nervous system and then undergo programmed cell death once the adult axons, which follow them, have made connections with the target site. Thus, they are a transient cell type involved in axon guidance.
database_cross_reference: GOC:cvs
database_cross_reference: GOC:tfm

Axiom
annotated source: pioneer neuron
annotated property: database_cross_reference
annotated target: FBbt:00005128
mapping justification: ManualMappingCuration

Axiom
annotated source: pioneer neuron
annotated property: database_cross_reference
annotated target: ZFA:0009066
mapping justification: UnspecifiedMatching

CNS neuron (sensu Vertebrata)
type: Class
subclass of: CL_2000029
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001017
database_cross_reference: ZFA:0009067
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: CNS neuron (sensu Vertebrata)
annotated property: database_cross_reference
annotated target: ZFA:0009067
mapping justification: UnspecifiedMatching

basket cell
type: Class
equivalent class: Class
  intersection of: interneuron
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0070002
  intersection of: Restriction
    on property: capable of
    some values from: GO_0061534
subclass of: CL_0011005
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0070002
definition: Basket cells are inhibitory GABAergic interneurons of the brain. In general, dendrites of basket cells are free branching and contain smooth spines. Axons are highly branched. The branched axonal arborizations give rise to basket-like structures that surround the soma of the target cell. Basket cells form axo-somatic synapses, meaning their synapses target somas of other cells.
contributor: https://orcid.org/0000-0002-2825-0621
database_cross_reference: ZFA:0009068
in_subset: BDS subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: basket cell
annotated property: definition
annotated target: Basket cells are inhibitory GABAergic interneurons of the brain. In general, dendrites of basket cells are free branching and contain smooth spines. Axons are highly branched. The branched axonal arborizations give rise to basket-like structures that surround the soma of the target cell. Basket cells form axo-somatic synapses, meaning their synapses target somas of other cells.
database_cross_reference: WikipediaVersioned:Basket_cell&oldid=951703880

Axiom
annotated source: basket cell
annotated property: database_cross_reference
annotated target: ZFA:0009068
mapping justification: UnspecifiedMatching

cerebellar Golgi cell
type: Class
subclass of: CL_4023057
definition: Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004.
database_cross_reference: MESH:D000080906
database_cross_reference: ZFA:0009069
has_exact_synonym: Golgi cell
has_exact_synonym: Golgi neuron
has_exact_synonym: cerebellar Golgi neuron
has_exact_synonym: cerebellum Golgi cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cerebellar Golgi cell
annotated property: definition
annotated target: Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004.
database_cross_reference: NIFSTD:sao1415726815

Axiom
annotated source: cerebellar Golgi cell
annotated property: database_cross_reference
annotated target: ZFA:0009069
mapping justification: UnspecifiedMatching

granule cell
type: Class
subclass of: CL_2000029
definition: A neuron of the vertebrate central nervous system that is small in size. This general class includes small neurons in the granular layer of the cerebellar cortex, cerebral cortex neurons that are not pyramidal cells and small neurons without axons found in the olfactory bulb.
database_cross_reference: BTO:0003393
database_cross_reference: ZFA:0009070
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: granule cell
annotated property: definition
annotated target: A neuron of the vertebrate central nervous system that is small in size. This general class includes small neurons in the granular layer of the cerebellar cortex, cerebral cortex neurons that are not pyramidal cells and small neurons without axons found in the olfactory bulb.
database_cross_reference: granule+cell

Axiom
annotated source: granule cell
annotated property: database_cross_reference
annotated target: ZFA:0009070
mapping justification: UnspecifiedMatching

Purkinje cell
type: Class
subclass of: GABAergic neuron
subclass of: CL_1001611
subclass of: Restriction
  on property: has soma location
  some values from: UBERON_0002979
definition: An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress.
description: Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction …
database_cross_reference: BTO:0001011
database_cross_reference: CALOHA:TS-0845
database_cross_reference: FMA:67969
database_cross_reference: ZFA:0009071
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000121
has_exact_synonym: Purkinje neuron
has_exact_synonym: cerebellar Purkinje cell
has_related_synonym: PC
has_related_synonym: PN
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Some of the neurodegenerative disorders that causes loss and degeration of Purkinje cells are Spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), Fetal alcohol syndrome (Laurent Servais et al., 2016), Dandy-Walker malformation (Alexander Atamian et al., 2024).

Axiom
annotated source: Purkinje cell
annotated property: definition
annotated target: An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress.
database_cross_reference: MESH:D011689
database_cross_reference: PMID:12907269
database_cross_reference: PMID:14568361
database_cross_reference: PMID:31424738
database_cross_reference: PMID:33288911
database_cross_reference: PMID:38168772

Axiom
annotated source: Purkinje cell
annotated property: description
annotated target: Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction …
database_cross_reference: DOI:10.1007/s12311-018-0985-7
database_cross_reference: DOI:10.1038/nrn3886
database_cross_reference: DOI:10.7554/eLife.63668
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK545154/
database_cross_reference: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell

Axiom
annotated source: Purkinje cell
annotated property: database_cross_reference
annotated target: ZFA:0009071
mapping justification: UnspecifiedMatching

Axiom
annotated source: Purkinje cell
annotated property: has_exact_synonym
annotated target: Purkinje neuron
database_cross_reference: PMID:28821816

Axiom
annotated source: Purkinje cell
annotated property: has_exact_synonym
annotated target: cerebellar Purkinje cell
database_cross_reference: https://doi.org/10.1016/j.proghi.2004.07.002

Axiom
annotated source: Purkinje cell
annotated property: has_related_synonym
annotated target: PC
database_cross_reference: PMID:38168772
has_synonym_type: abbreviation

Axiom
annotated source: Purkinje cell
annotated property: has_related_synonym
annotated target: PN
database_cross_reference: PMID:28821816
has_synonym_type: abbreviation

Axiom
annotated source: Purkinje cell
annotated property: comment
annotated target: Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Some of the neurodegenerative disorders that causes loss and degeration of Purkinje cells are Spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), Fetal alcohol syndrome (Laurent Servais et al., 2016), Dandy-Walker malformation (Alexander Atamian et al., 2024).
database_cross_reference: PMID:17535929
database_cross_reference: PMID:27215193
database_cross_reference: PMID:37426070
database_cross_reference: https://doi.org/10.1016/j.stem.2023.11.013

stellate neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0070010
subclass of: CL_2000029
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0070010
definition: A neuron that has dendritic processes radiating from the cell body forming a star-like shape.
database_cross_reference: BTO:0002316
database_cross_reference: ZFA:0009072
in_subset: BDS subset
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: stellate neuron
annotated property: definition
annotated target: A neuron that has dendritic processes radiating from the cell body forming a star-like shape.
database_cross_reference: ISBN:9780123973481

Axiom
annotated source: stellate neuron
annotated property: database_cross_reference
annotated target: ZFA:0009072
mapping justification: UnspecifiedMatching

neuron associated cell (sensu Vertebrata)
type: Class
subclass of: neuron associated cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: develops from
  some values from: migratory neural crest cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

obsolete glial cell (sensu Nematoda and Protostomia)
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/715
comment: This is a grouping class that is no longer needed or wanted.
deprecated: true

glial cell
type: Class
subclass of: neuron associated cell
definition: A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
present in taxon: NCBITaxon 9606
description: Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease a…
database_cross_reference: BTO:0002606
database_cross_reference: CALOHA:TS-0415
database_cross_reference: FBbt:00005144
database_cross_reference: FMA:54536
database_cross_reference: ZFA:0009073
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000125
has_exact_synonym: neuroglial cell
has_related_synonym: neuroglia
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571

Axiom
annotated source: glial cell
annotated property: definition
annotated target: A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
database_cross_reference: MESH:D009457

Axiom
annotated source: glial cell
annotated property: description
annotated target: Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease a…
database_cross_reference: DOI:10.1002/glia.24343
database_cross_reference: DOI:10.1038/nn1988
database_cross_reference: DOI:10.1101/cshperspect.a020602
database_cross_reference: DOI:10.1126/science.aat0473
database_cross_reference: DOI:10.3389/fncel.2017.00024

Axiom
annotated source: glial cell
annotated property: database_cross_reference
annotated target: FBbt:00005144
mapping justification: ManualMappingCuration

Axiom
annotated source: glial cell
annotated property: database_cross_reference
annotated target: ZFA:0009073
mapping justification: UnspecifiedMatching

macroglial cell
type: Class
subclass of: glial cell
subclass of: Restriction
  on property: develops from
  some values from: glioblast (sensu Vertebrata)
definition: A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together.
database_cross_reference: BTO:0000771
database_cross_reference: CALOHA:TS-2027
database_cross_reference: FMA:54538
database_cross_reference: ZFA:0009074
has_exact_synonym: macrogliocyte
has_related_synonym: macroglia
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: macroglial cell
annotated property: definition
annotated target: A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: macroglial cell
annotated property: database_cross_reference
annotated target: ZFA:0009074
mapping justification: UnspecifiedMatching

Axiom
annotated source: macroglial cell
annotated property: has_related_synonym
annotated target: macroglia
database_cross_reference: doi:10.1152/physrev.2001.81.2.871
has_synonym_type: plural form

astrocyte
type: Class
subclass of: macroglial cell
definition: A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000099
database_cross_reference: CALOHA:TS-0060
database_cross_reference: FMA:54537
database_cross_reference: ZFA:0009075
has_exact_synonym: astrocytic glia
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive.

Axiom
annotated source: astrocyte
annotated property: definition
annotated target: A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury.
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D001253
database_cross_reference: PMID:11746784
database_cross_reference: PMID:12162730
database_cross_reference: PMID:12898703
database_cross_reference: PMID:20942978
database_cross_reference: http://en.wikipedia.org/wiki/Astrocyte

Axiom
annotated source: astrocyte
annotated property: database_cross_reference
annotated target: ZFA:0009075
mapping justification: UnspecifiedMatching

oligodendrocyte
type: Class
subclass of: macroglial cell
subclass of: CL_4023154
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001017
subclass of: Restriction
  on property: develops from
  some values from: CL_0002453
definition: A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000962
database_cross_reference: CALOHA:TS-0709
database_cross_reference: FMA:54540
database_cross_reference: ZFA:0009076
has_exact_synonym: OLs
has_related_synonym: oligodendroglia
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Oligodendrocytes are reportedly MDP-positive and CD4-negative.

Axiom
annotated source: oligodendrocyte
annotated property: subClassOf
annotated target: macroglial cell
is inferred: true

Axiom
annotated source: oligodendrocyte
annotated property: definition
annotated target: A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system.
database_cross_reference: MESH:D009836
database_cross_reference: http://en.wikipedia.org/wiki/Oligodendrocyte

Axiom
annotated source: oligodendrocyte
annotated property: database_cross_reference
annotated target: ZFA:0009076
mapping justification: UnspecifiedMatching

Axiom
annotated source: oligodendrocyte
annotated property: has_exact_synonym
annotated target: OLs
database_cross_reference: PMID:8734446

microglial cell
type: Class
equivalent class: Class
  intersection of: glial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001017
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001012
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001813
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002064
  intersection of: Restriction
    on property: capable of
    some values from: GO_0045087
subclass of: glial cell
subclass of: CL_0000878
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001012
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001813
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002064
subclass of: Restriction
  on property: develops from
  some values from: mesodermal cell
subclass of: Restriction
  on property: develops from
  some values from: Class
    intersection of: stem cell
    intersection of: Restriction
      on property: part of
      some values from: UBERON_0001040
subclass of: Restriction
  on property: capable of
  some values from: GO_0045087
definition: A transcriptomically distinct central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive.
present in taxon: NCBITaxon 9606
description: Microglial cells, sometimes referred to as microglia, are a type of glial cell that primarily exist within the central nervous system (CNS), notably in the brain and the spinal cord. Classified among the resident immune cells, microglial cells represent about 10% of all cells found within the CNS. These cells are derived from progenitor cells in the yolk sac, which differentiates them from other types of glial cells (such as astrocytes and oligodendrocytes) that are derived from neuroectodermal cell lineages. The primary role of microglial cells is to act as the first and main active form of immune defense in the CNS. They express a vast repertoire of pattern recognition receptors, which allow them to sense and eliminate microbes invading the CNS parenchyma. They represent one of the macrophage populations of the CNS and are responsible for phagocytosis (engulfing and destroying cellular waste or pathogens) in the neural environment. Microglial cells are particularly responsive to pathogens and injuries and change their morphology in reaction to inflammation or insult: In the normal state they are characterized by a ramified shape with small processes; in response to stimuli, some microglia mature and change to an amoeboid shape. Beyond their macrophagic activity, they also perform synaptic pruning during brain development, eliminate unnecessarily produced neurons, and facilitate tissue regeneration and repair. they play integral roles in regulating neural development and supporting cell survival and are important for maintaining tissue homeostasis. While their protective role generally benefits the brain, their over-activation can occasionally lead to neuro-inflammatory diseases, underlining the importance of balanced microglial cell functions. They have been extensively studied for their association with neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. (This extended description was generated by ChatGPT and revi…
has_broad_synonym: brain macrophage
database_cross_reference: BTO:0000078
database_cross_reference: BTO:0000962
database_cross_reference: FMA:54539
database_cross_reference: ZFA:0009077
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000129
has_exact_synonym: brain-resident macrophage
has_exact_synonym: hortega cells
has_exact_synonym: microgliocyte
has_related_synonym: MF.microglia.CNS
has_related_synonym: microglia
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Unlike macroglial cells, microglial cells arise from hematopoietic stem cells in the yolk sac during early embryogenesis that populate the central nervous system. They derive from embryonic mesoderm and are not from neuroectoderm where glioblast develops from. Markers: Mouse: CD11b+, F4/80+, CD68+. They represent ~12% of the cells in the CNS, but they are not uniformly distributed within the CNS. A normal adult mouse brain has approximately 3.5x10e6 microglia. Microglia are also reportedly CD3-negative, CD4-positive, CD8-negative, CD11b-positive, CD11c-high, CD14-negative, CD19-negative, CD45-low, CD56-negative, CD163-negative, CD200R-positive, CD281-positive, CD282-positive, CD283-positive, CD284-positive, CD285-positive, CD286-positive, CD287-positive, CD288-positive, CD289-positive, Gr1-negative, nestin-positive, and PU.1-positive.

Axiom
annotated source: microglial cell
annotated property: definition
annotated target: A transcriptomically distinct central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: MESH:D017628
database_cross_reference: PMID:11517395
database_cross_reference: PMID:12430718
database_cross_reference: PMID:14561199
database_cross_reference: PMID:14612429
database_cross_reference: PMID:16177057
database_cross_reference: PMID:19461673
database_cross_reference: PMID:2089275
database_cross_reference: http://en.wikipedia.org/wiki/Microglia

Axiom
annotated source: microglial cell
annotated property: description
annotated target: Microglial cells, sometimes referred to as microglia, are a type of glial cell that primarily exist within the central nervous system (CNS), notably in the brain and the spinal cord. Classified among the resident immune cells, microglial cells represent about 10% of all cells found within the CNS. These cells are derived from progenitor cells in the yolk sac, which differentiates them from other types of glial cells (such as astrocytes and oligodendrocytes) that are derived from neuroectodermal cell lineages. The primary role of microglial cells is to act as the first and main active form of immune defense in the CNS. They express a vast repertoire of pattern recognition receptors, which allow them to sense and eliminate microbes invading the CNS parenchyma. They represent one of the macrophage populations of the CNS and are responsible for phagocytosis (engulfing and destroying cellular waste or pathogens) in the neural environment. Microglial cells are particularly responsive to pathogens and injuries and change their morphology in reaction to inflammation or insult: In the normal state they are characterized by a ramified shape with small processes; in response to stimuli, some microglia mature and change to an amoeboid shape. Beyond their macrophagic activity, they also perform synaptic pruning during brain development, eliminate unnecessarily produced neurons, and facilitate tissue regeneration and repair. they play integral roles in regulating neural development and supporting cell survival and are important for maintaining tissue homeostasis. While their protective role generally benefits the brain, their over-activation can occasionally lead to neuro-inflammatory diseases, underlining the importance of balanced microglial cell functions. They have been extensively studied for their association with neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. (This extended description was generated by ChatGPT and revi…
database_cross_reference: DOI:10.1016/j.cell.2019.08.053
database_cross_reference: DOI:10.1016/j.conb.2022.102674
database_cross_reference: DOI:10.1016/j.tins.2021.11.001
database_cross_reference: DOI:10.1038/nri3086
database_cross_reference: DOI:10.3389/fnins.2021.742065

Axiom
annotated source: microglial cell
annotated property: database_cross_reference
annotated target: ZFA:0009077
mapping justification: UnspecifiedMatching

Axiom
annotated source: microglial cell
annotated property: has_exact_synonym
annotated target: hortega cells
database_cross_reference: http://www.copewithcytokines.de/

Axiom
annotated source: microglial cell
annotated property: has_exact_synonym
annotated target: microgliocyte
database_cross_reference: http://www.copewithcytokines.de/

Axiom
annotated source: microglial cell
annotated property: has_related_synonym
annotated target: microglia
database_cross_reference: doi:10.1038/s41598-020-66092-9
has_synonym_type: plural form

Axiom
annotated source: microglial cell
annotated property: comment
annotated target: Unlike macroglial cells, microglial cells arise from hematopoietic stem cells in the yolk sac during early embryogenesis that populate the central nervous system. They derive from embryonic mesoderm and are not from neuroectoderm where glioblast develops from. Markers: Mouse: CD11b+, F4/80+, CD68+. They represent ~12% of the cells in the CNS, but they are not uniformly distributed within the CNS. A normal adult mouse brain has approximately 3.5x10e6 microglia. Microglia are also reportedly CD3-negative, CD4-positive, CD8-negative, CD11b-positive, CD11c-high, CD14-negative, CD19-negative, CD45-low, CD56-negative, CD163-negative, CD200R-positive, CD281-positive, CD282-positive, CD283-positive, CD284-positive, CD285-positive, CD286-positive, CD287-positive, CD288-positive, CD289-positive, Gr1-negative, nestin-positive, and PU.1-positive.
database_cross_reference: PMID:23616747

neuron associated cell (sensu Nematoda and Protostomia)
type: Class
subclass of: neuron associated cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon_33317

gut endothelial cell
type: Class
equivalent class: Class
  intersection of: endothelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001555
subclass of: endothelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001555
subclass of: Restriction
  on property: develops from
  some values from: endodermal cell
definition: An endothelial cell that lines the blood and lymphatic vessels of the digestive tract. This cell forms the gut–vascular barrier (GVB) through tight junctions and crosstalk with pericytes and enteric glial cells, regulating the passage of nutrients and immune cells while restricting microbial translocation into the bloodstream.
description: Gut endothelial cells are a crucial component of the endothelium, a thin layer of single cells that line the interior surface of blood vessels and lymphatic vessels, including those in the digestive system or "gut". These cells plays an integral role in various physiological and metabolic functions, actively participating in nutrient absorption, host defense, and vascular homeostasis in the gut. The primary function of gut endothelial cells lies in their ability to control the passage of materials and the transit of white blood cells into and out of the bloodstream. They achieve this through the formation of a semi-permeable barrier, in which permeability is regulated by tight junctions; complex structures that bring the cells together, sealing the space between them. This ensures a controlled, selective passage of nutrients, ions, and water from the bloodstream into the gut and vice versa, helping maintain homeostasis and overall health. Gut endothelial cells also play a significant role in angiogenesis and serve as a critical regulator of the gut immune responses playing a modulative role in gut immune homeostasis and inflammatory responses. In addition, they generate nitric oxide, a potent vasodilator, which helps in maintaining vascular tonus, preventing platelet and leukocyte adhesion, and decreasing smooth muscle proliferation. These multi-faceted roles make gut endothelial cells indispensable for the normal functioning of the gut and overall health. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: ZFA:0009078
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000131
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: gut endothelial cell
annotated property: definition
annotated target: An endothelial cell that lines the blood and lymphatic vessels of the digestive tract. This cell forms the gut–vascular barrier (GVB) through tight junctions and crosstalk with pericytes and enteric glial cells, regulating the passage of nutrients and immune cells while restricting microbial translocation into the bloodstream.
database_cross_reference: PMID:26564856

Axiom
annotated source: gut endothelial cell
annotated property: description
annotated target: Gut endothelial cells are a crucial component of the endothelium, a thin layer of single cells that line the interior surface of blood vessels and lymphatic vessels, including those in the digestive system or "gut". These cells plays an integral role in various physiological and metabolic functions, actively participating in nutrient absorption, host defense, and vascular homeostasis in the gut. The primary function of gut endothelial cells lies in their ability to control the passage of materials and the transit of white blood cells into and out of the bloodstream. They achieve this through the formation of a semi-permeable barrier, in which permeability is regulated by tight junctions; complex structures that bring the cells together, sealing the space between them. This ensures a controlled, selective passage of nutrients, ions, and water from the bloodstream into the gut and vice versa, helping maintain homeostasis and overall health. Gut endothelial cells also play a significant role in angiogenesis and serve as a critical regulator of the gut immune responses playing a modulative role in gut immune homeostasis and inflammatory responses. In addition, they generate nitric oxide, a potent vasodilator, which helps in maintaining vascular tonus, preventing platelet and leukocyte adhesion, and decreasing smooth muscle proliferation. These multi-faceted roles make gut endothelial cells indispensable for the normal functioning of the gut and overall health. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1038/nri2171
database_cross_reference: DOI:10.1111/bph.14527
database_cross_reference: DOI:10.3390/ijms23073698
database_cross_reference: DOI:10.3748/wjg.v17.i5.578
database_cross_reference: DOI:full/10.15252/emmm.202114121

Axiom
annotated source: gut endothelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009078
mapping justification: UnspecifiedMatching

corneal endothelial cell
type: Class
subclass of: endothelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001985
subclass of: Restriction
  on property: develops from
  some values from: migratory cranial neural crest cell
definition: An hexagonal, flattened, mitochondria-rich endothelial cell that forms a monolayer on the posterior surface of the cornea (the corneal endothelium). Corneal endothelial cells are derived from the neural crest and are responsible for keeping the cornea transparent by maintaining the tissue in a semi-dry state through the action of their ionic pumps and tight junction barrier.
present in taxon: NCBITaxon 9606
database_cross_reference: CALOHA:TS-0172
database_cross_reference: FMA:70614
database_cross_reference: ZFA:0009079
in_subset: cellxgene subset
in_subset: eye_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: corneal endothelial cell
annotated property: definition
annotated target: An hexagonal, flattened, mitochondria-rich endothelial cell that forms a monolayer on the posterior surface of the cornea (the corneal endothelium). Corneal endothelial cells are derived from the neural crest and are responsible for keeping the cornea transparent by maintaining the tissue in a semi-dry state through the action of their ionic pumps and tight junction barrier.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:21976958
database_cross_reference: PMID:23284695
database_cross_reference: PMID:34741068
database_cross_reference: PMID:36769303

Axiom
annotated source: corneal endothelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009079
mapping justification: UnspecifiedMatching

neurectodermal cell
type: Class
subclass of: ectodermal cell
definition: Ectoderm destined to be nervous tissue.
database_cross_reference: ZFA:0009080
has_exact_synonym: neurectoderm cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: neurectodermal cell
annotated property: definition
annotated target: Ectoderm destined to be nervous tissue.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:068340007X

Axiom
annotated source: neurectodermal cell
annotated property: database_cross_reference
annotated target: ZFA:0009080
mapping justification: UnspecifiedMatching

mesenchymal stem cell
type: Class
subclass of: multi fate stem cell
subclass of: CL_0002320
definition: A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs.
database_cross_reference: BTO:0002625
database_cross_reference: BTO:0003298
database_cross_reference: FMA:70546
database_cross_reference: ZFA:0009081
has_narrow_synonym: bone marrow stromal cells
has_narrow_synonym: colony-forming unit-fibroblast
has_narrow_synonym: marrow stromal cells
has_related_synonym: BMSC
has_related_synonym: CFU-F
has_related_synonym: MSC
has_related_synonym: mesenchymal precursor cell
has_related_synonym: mesenchymal progenitor cells
has_related_synonym: mesenchymal stem cell
has_related_synonym: mesenchymal stromal cell
has_related_synonym: mesenchymal stromal cells
has_related_synonym: stem cells, mesenchymal
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2.

Axiom
annotated source: mesenchymal stem cell
annotated property: subClassOf
annotated target: CL_0002320
is inferred: true

Axiom
annotated source: mesenchymal stem cell
annotated property: definition
annotated target: A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs.
database_cross_reference: FB:ma
database_cross_reference: GOC:dsd
database_cross_reference: PMCID:PMC2613570
database_cross_reference: PMID:10102814
database_cross_reference: PMID:16923606
database_cross_reference: PMID:17986482
database_cross_reference: PMID:19960544
database_cross_reference: http://en.wikipedia.org/wiki/Mesenchymal_stem_cell
database_cross_reference: http://www.copewithcytokines.de/cope.cgi

Axiom
annotated source: mesenchymal stem cell
annotated property: database_cross_reference
annotated target: ZFA:0009081
mapping justification: UnspecifiedMatching

Axiom
annotated source: mesenchymal stem cell
annotated property: has_narrow_synonym
annotated target: marrow stromal cells
database_cross_reference: PMID:11378515

Axiom
annotated source: mesenchymal stem cell
annotated property: has_related_synonym
annotated target: BMSC
has_synonym_type: abbreviation

Axiom
annotated source: mesenchymal stem cell
annotated property: has_related_synonym
annotated target: CFU-F
has_synonym_type: abbreviation

Axiom
annotated source: mesenchymal stem cell
annotated property: has_related_synonym
annotated target: MSC
database_cross_reference: PMID:11378515
has_synonym_type: abbreviation

Axiom
annotated source: mesenchymal stem cell
annotated property: has_related_synonym
annotated target: mesenchymal progenitor cells
database_cross_reference: MESH:D044982
has_synonym_type: plural form

Axiom
annotated source: mesenchymal stem cell
annotated property: has_related_synonym
annotated target: mesenchymal stromal cells
has_synonym_type: plural form

Axiom
annotated source: mesenchymal stem cell
annotated property: has_related_synonym
annotated target: stem cells, mesenchymal
database_cross_reference: MESH:D044982
has_synonym_type: plural form

fibrocyte
type: Class
equivalent class: Class
  intersection of: stromal cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002495
  intersection of: Restriction
    on property: capable of
    some values from: GO_0045766
subclass of: stromal cell
subclass of: Restriction
  on property: develops from
  some values from: fibroblast
subclass of: Restriction
  on property: capable of
  some values from: GO_0002495
subclass of: Restriction
  on property: capable of
  some values from: GO_0045766
definition: An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes.
database_cross_reference: FMA:63879
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Cultured human fibrocytes are MHCI-positive, MHCII-positive, CD1a-negative, CD3-negative, CD4-negative, CD8-negative, CD10-negative, CD11b-positive, CD13-positive, CD14-negative, CD16-negative, CD18-positive, CD19-negative, CD25-negative, CD29-positive, CD32-positive, CD33-negative, CD34-positive, CD38-negative, CD40-positive, CD44-negative, CD45RO-positive, CD49a-positive, CD49b-positive, CD49c-negative, CD49d-negative, CD49e-positive, CD49f-negative, CD56-negative, CD58-positive, CD61-positive, CD64-positive, CD70-negative, CD71-positive, CD80-positive, CD83-negative, CD86-positive, CD103-negative, CD105-positive, CD181-positive, CD182-negative, CD183-positive, CD184-positive, CD185-negative, CD186-negative, CD191-positive, CD192-negative, CD193-positive, CD194-positive, CD195-positive, CD196-negative, CD197-positive, CD199-positive, desmin-negative, F4/80-positive, Gr1-positive, LSP-1-positive, MHCI-positive, MHCII-positive, alpha-SMA-negative, TCRab-negative, TCRgd-negative, and vimentin-positive. Fibrocytes are also capable of secreting angiogenin, bFGF, CCL2, CCL3, CCL4, CCL8, CXCL1, type I collagen, type III collagen, CTGF, fibronectin, GM-CSF, IL-1a, IL-6, IL-8, IL-10, M-CSF, MMP-9, PDGF-A, TGF-alpha, TGF-beta1, TNF-alpha, and VEGF-A.

Axiom
annotated source: fibrocyte
annotated property: subClassOf
annotated target: stromal cell
is inferred: true

Axiom
annotated source: fibrocyte
annotated property: definition
annotated target: An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes.
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0412046911
database_cross_reference: ISBN:0517223651
database_cross_reference: PMID:11641248
database_cross_reference: PMID:15010326
database_cross_reference: PMID:17607298
database_cross_reference: PMID:18222966
database_cross_reference: PMID:8790603
database_cross_reference: PMID:9551999
database_cross_reference: http://en.wikipedia.org/wiki/Fibrocyte

adipocyte
type: Class
subclass of: BFO_0000002
subclass of: stuff accumulating cell
subclass of: CL_0002320
subclass of: Restriction
  on property: develops from
  some values from: mesenchymal stem cell
definition: A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000443
database_cross_reference: CALOHA:TS-0012
database_cross_reference: FMA:63880
database_cross_reference: ZFA:0009082
has_exact_synonym: adipose cell
has_exact_synonym: fat cell
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: adipocyte
annotated property: definition
annotated target: A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.
database_cross_reference: MESH:D017667

Axiom
annotated source: adipocyte
annotated property: database_cross_reference
annotated target: ZFA:0009082
mapping justification: UnspecifiedMatching

osteocyte
type: Class
subclass of: BFO_0000002
subclass of: CL_0001035
subclass of: CL_0002320
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002481
subclass of: Restriction
  on property: develops from
  some values from: CL_0001040
definition: A mature osteoblast that has become embedded in the bone matrix. They occupy a small cavity, called lacuna, in the matrix and are connected to adjacent osteocytes via protoplasmic projections called canaliculi.
has_broad_synonym: bone cell
database_cross_reference: BTO:0002038
database_cross_reference: CALOHA:TS-1167
database_cross_reference: FMA:66779
database_cross_reference: VSAO:0000124
database_cross_reference: ZFA:0009083
in_subset: human subset
in_subset: mouse subset
comment: VSAO relationship simplified OBO_REL:integral_part_of VSAO:0000118

Axiom
annotated source: osteocyte
annotated property: definition
annotated target: A mature osteoblast that has become embedded in the bone matrix. They occupy a small cavity, called lacuna, in the matrix and are connected to adjacent osteocytes via protoplasmic projections called canaliculi.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D010011

Axiom
annotated source: osteocyte
annotated property: database_cross_reference
annotated target: ZFA:0009083
mapping justification: UnspecifiedMatching

chondrocyte
type: Class
subclass of: glycosaminoglycan secreting cell
subclass of: collagen secreting cell
subclass of: Restriction
  on property: located in
  some values from: UBERON_0002418
subclass of: Restriction
  on property: develops from
  some values from: chondroblast
definition: Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell.
database_cross_reference: BTO:0000249
database_cross_reference: CALOHA:TS-0138
database_cross_reference: FMA:66782
database_cross_reference: ZFA:0009084
has_exact_synonym: cartilage cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: chondrocyte
annotated property: definition
annotated target: Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell.
database_cross_reference: GO_REF:0000034
database_cross_reference: MESH:D019902

Axiom
annotated source: chondrocyte
annotated property: database_cross_reference
annotated target: ZFA:0009084
mapping justification: UnspecifiedMatching

CL_0000139
type: Class
has obsolescence reason: IAO_0000227
term replaced by: ameloblast
deprecated: true

odontocyte
type: Class
subclass of: BFO_0000002
subclass of: CL_0002320
subclass of: Restriction
  on property: develops from
  some values from: odontoblast
subclass of: Restriction
  on property: develops from
  some values from: mesenchymal stem cell
subclass of: Restriction
  on property: produces
  some values from: UBERON_0001751
definition: Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell.
database_cross_reference: ZFA:0009086
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: odontocyte
annotated property: definition
annotated target: Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell.
database_cross_reference: GO_REF:0000034

Axiom
annotated source: odontocyte
annotated property: database_cross_reference
annotated target: ZFA:0009086
mapping justification: UnspecifiedMatching

cementocyte
type: Class
subclass of: osteocyte
subclass of: Restriction
  on property: part of
  some values from: UBERON_0005176
subclass of: Restriction
  on property: develops from
  some values from: cementoblast
definition: An osteocytelike cell with numerous processes, trapped in a lacuna in the cement of the tooth.
database_cross_reference: FMA:63003
database_cross_reference: ZFA:0009087
in_subset: human subset
in_subset: mouse subset
comment: CHECK: wikipedia says that cementocytes no longer produce cementum, but the phenoscape def is: Skeletogenic cell that produces cementum, is part of the odontogenic papilla, and is a transformation of a cementoblast cell (no change to existing def).

Axiom
annotated source: cementocyte
annotated property: definition
annotated target: An osteocytelike cell with numerous processes, trapped in a lacuna in the cement of the tooth.
database_cross_reference: ISBN:0781733901

Axiom
annotated source: cementocyte
annotated property: database_cross_reference
annotated target: ZFA:0009087
mapping justification: UnspecifiedMatching

hyalocyte
type: Class
subclass of: stromal cell
definition: A cell occurring in the peripheral part of the vitreous body of the eye that may be responsible for production of hyaluronic acid and collagen.
database_cross_reference: BTO:0004271
database_cross_reference: FMA:70620
has_related_synonym: vitreous cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: hyalocyte
annotated property: definition
annotated target: A cell occurring in the peripheral part of the vitreous body of the eye that may be responsible for production of hyaluronic acid and collagen.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:19073178

guidepost cell
type: Class
subclass of: neuron associated cell (sensu Nematoda and Protostomia)

obsolete cell by function
type: Class
definition: OBSOLETE: A classification of cells by their primary end goal or behavior.
consider: CL:0000000
consider: CL:0000003
consider: CL:0001034
comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its function or behavior. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate.
deprecated: true

Axiom
annotated source: obsolete cell by function
annotated property: definition
annotated target: OBSOLETE: A classification of cells by their primary end goal or behavior.
database_cross_reference: FB:ma

professional antigen presenting cell
type: Class
equivalent class: Class
  intersection of: leukocyte
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002504
subclass of: leukocyte
subclass of: Restriction
  on property: capable of
  some values from: GO_0002504
definition: A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response.
database_cross_reference: ZFA:0009088
has_related_synonym: APC
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells.

Axiom
annotated source: professional antigen presenting cell
annotated property: definition
annotated target: A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0781735149

Axiom
annotated source: professional antigen presenting cell
annotated property: database_cross_reference
annotated target: ZFA:0009088
mapping justification: UnspecifiedMatching

Axiom
annotated source: professional antigen presenting cell
annotated property: has_related_synonym
annotated target: APC
has_synonym_type: abbreviation

simple columnar epithelial cell
type: Class
subclass of: columnar/cuboidal epithelial cell
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009089
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: simple columnar epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009089
mapping justification: UnspecifiedMatching

pigment cell
type: Class
subclass of: stuff accumulating cell
definition: A pigment cell is a cell that contains pigment granules.
database_cross_reference: VHOG:0001678
database_cross_reference: ZFA:0009090
has_exact_synonym: chromatocyte
has_exact_synonym: chromatophore
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pigment cell
annotated property: definition
annotated target: A pigment cell is a cell that contains pigment granules.
database_cross_reference: GOC:tfm

Axiom
annotated source: pigment cell
annotated property: database_cross_reference
annotated target: ZFA:0009090
mapping justification: UnspecifiedMatching

melanocyte
type: Class
equivalent class: Class
  intersection of: pigment cell
  intersection of: Restriction
    on property: has part
    some values from: GO_0042470
  intersection of: Restriction
    on property: develops from
    some values from: melanoblast
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: has part
  some values from: GO_0042470
subclass of: Restriction
  on property: develops from
  some values from: melanoblast
definition: A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.
present in taxon: NCBITaxon 9606
description: Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: BTO:0000847
database_cross_reference: CALOHA:TS-0613
database_cross_reference: FMA:70545
database_cross_reference: MESH:D008544
database_cross_reference: VHOG:0001679
database_cross_reference: ZFA:0009091
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000148
has_narrow_synonym: melanophore
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: melanocyte
annotated property: definition
annotated target: A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.
database_cross_reference: SANBI:mhl

Axiom
annotated source: melanocyte
annotated property: description
annotated target: Melanocytes are specialized cells prevalently found in the skin, but also present in the hair follicles, eyes, inner ear, bones, heart, and brain. Their primary function is the synthesis of melanin, a pigment responsible for coloration of skin, hair, and eyes. The presence and distribution of this pigment play a crucial role in the body's defense mechanism against harmful ultraviolet radiation. In addition to melanin production, melanocytes also engage in a variety of other biological functions. They play a fundamental role in the immune response, owing to their ability to present antigens to T cells. Furthermore, they contribute to the maintenance of the skin's homeostasis by regulating processes such as extracellular matrix remodeling and cytokine production. A balance in melanocyte function is pivotal, as dysfunctions often result in dermatological disorders. For instance, the loss of melanocytes or reduction in their function may lead to hypopigmentation conditions such as vitiligo, whereas an abnormal increase could result in hyperpigmentation disorders or melanoma, a dangerous type of skin cancer. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1002/med.21754
database_cross_reference: DOI:10.1038/nrc.2016.37
database_cross_reference: DOI:10.1111/j.1751-1097.2007.00226.x
database_cross_reference: DOI:10.3390/ijms21249769
database_cross_reference: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/melanocyte

Axiom
annotated source: melanocyte
annotated property: database_cross_reference
annotated target: ZFA:0009091
mapping justification: UnspecifiedMatching

visual pigment cell
type: Class
subclass of: pigment cell
has_broad_synonym: pigment cell
in_subset: human subset
in_subset: mouse subset

glandular secretory epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: secretory cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002530
subclass of: CL_1100001
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002530
definition: An epithelial cell, located in a gland, that is specialised for the synthesis and secretion of specific biomolecules, such as hormones, or mucous.
database_cross_reference: CALOHA:TS-2085
database_cross_reference: FMA:86494
has_exact_synonym: glandular epithelial cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: glandular secretory epithelial cell
annotated property: definition
annotated target: An epithelial cell, located in a gland, that is specialised for the synthesis and secretion of specific biomolecules, such as hormones, or mucous.
database_cross_reference: GOC:tfm
database_cross_reference: ORCID:0000-0002-7073-9172

secretory cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0032940
subclass of: cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0032940
definition: A cell that specializes in controlled release of one or more substances.
database_cross_reference: BTO:0003659
database_cross_reference: FMA:86916
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: secretory cell
annotated property: definition
annotated target: A cell that specializes in controlled release of one or more substances.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

exocrine cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002365
subclass of: secretory cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002365
definition: A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.
database_cross_reference: FMA:16014
database_cross_reference: ZFA:0009092
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: exocrine cell
annotated property: definition
annotated target: A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.
database_cross_reference: ISBN:0198547684

Axiom
annotated source: exocrine cell
annotated property: database_cross_reference
annotated target: ZFA:0009092
mapping justification: UnspecifiedMatching

glycosaminoglycan secreting cell
type: Class
subclass of: extracellular matrix secreting cell
subclass of: carbohydrate secreting cell
definition: A cell that secretes glycosaminoglycans.
database_cross_reference: ZFA:0009093
has_exact_synonym: GAG secreting cell
has_narrow_synonym: hyaluronic acid secreting cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: glycosaminoglycan secreting cell
annotated property: definition
annotated target: A cell that secretes glycosaminoglycans.
database_cross_reference: GOC:tfm

Axiom
annotated source: glycosaminoglycan secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009093
mapping justification: UnspecifiedMatching

protein secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0009306
subclass of: secretory cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0009306
definition: Any secretory cell that is capable of some protein secretion.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: protein secreting cell
annotated property: definition
annotated target: Any secretory cell that is capable of some protein secretion.
database_cross_reference: FBC:Autogenerated

peptic cell
type: Class
subclass of: exocrine cell
subclass of: protein secreting cell
subclass of: CL_0002659
subclass of: Restriction
  on property: part of
  some values from: UBERON_0010038
definition: An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by a basally located nucleus, abundant rough endoplasmic reticulum, and large apical secretory granules. It produces and secretes pepsinogen, the inactive precursor of the digestive enzyme pepsin.
database_cross_reference: FMA:62902
has_exact_synonym: chief cell of stomach
has_exact_synonym: gastric chief cell
has_exact_synonym: pepsinogen secreting cell
has_exact_synonym: zymogenic cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: peptic cell
annotated property: definition
annotated target: An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by a basally located nucleus, abundant rough endoplasmic reticulum, and large apical secretory granules. It produces and secretes pepsinogen, the inactive precursor of the digestive enzyme pepsin.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:21907708
database_cross_reference: PMID:30571046
database_cross_reference: Wikipedia:Gastric_chief_cell

Axiom
annotated source: peptic cell
annotated property: has_exact_synonym
annotated target: gastric chief cell
database_cross_reference: Wikipedia:Chief_cell

Axiom
annotated source: peptic cell
annotated property: has_exact_synonym
annotated target: zymogenic cell
database_cross_reference: Wikipedia:Chief_cell

obsolete antibody secreting cell
type: Class
definition: OBSOLETE: A cell of the lymphoid series that can react with antigen to produce specific cell products called antibodies. Various cell subpopulations, often B cells, can be defined, based on the different classes of immunoglobulins that they synthesize.
comment: Consider using 'B cell ; CL:0000236' or one of its children instead.
deprecated: true

surfactant secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0043129
subclass of: secretory cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0043129
definition: A cell that specializes in secretion of surfactant in the alveoli of the lung.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: surfactant secreting cell
annotated property: subClassOf
annotated target: secretory cell
is inferred: true

Axiom
annotated source: surfactant secreting cell
annotated property: definition
annotated target: A cell that specializes in secretion of surfactant in the alveoli of the lung.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

club cell
type: Class
subclass of: surfactant secreting cell
subclass of: CL_0002202
subclass of: CL_0008055
subclass of: CL_0011026
subclass of: Restriction
  on property: has plasma membrane part
  some values from: GO_0005902
definition: A non-mucous, epithelial secretory cell that is part of the tracheobronchial tree. A club cell has short microvilli but no cilia. A club cell is able to multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium and it also protects the tracheobronchial epithelium.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0004811
database_cross_reference: FMA:14119
has_exact_synonym: Clara cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: club cell
annotated property: definition
annotated target: A non-mucous, epithelial secretory cell that is part of the tracheobronchial tree. A club cell has short microvilli but no cilia. A club cell is able to multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium and it also protects the tracheobronchial epithelium.
database_cross_reference: DOI:10.1183/09031936.00146609
database_cross_reference: DOI:10.1378/chest.12-2762
database_cross_reference: GOC:tfm
database_cross_reference: PMID:28128362
database_cross_reference: PMID:29874100
database_cross_reference: PMID:7905712

seromucus secreting cell
type: Class
subclass of: secretory cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

goblet cell
type: Class
subclass of: mucus secreting cell
subclass of: CL_1100001
subclass of: Restriction
  on property: has part
  some values from: GO_0005902
subclass of: Restriction
  on property: has part
  some values from: GO_0098594
definition: A specialized, columnar, mucus secreting epithelial cell shaped like a flask or goblet. A narrow basal end contains the nucleus while the apical end is swollen by the accumulation of mucus laden secretory granules. Short microvilli project from the apical plasma membrane.
description: Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some sub…
database_cross_reference: BTO:0001540
database_cross_reference: FMA:13148
database_cross_reference: ZFA:0009094
database_cross_reference: http://en.wikipedia.org/wiki/Goblet_cell
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000160
has_exact_synonym: chalice cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: goblet cell
annotated property: definition
annotated target: A specialized, columnar, mucus secreting epithelial cell shaped like a flask or goblet. A narrow basal end contains the nucleus while the apical end is swollen by the accumulation of mucus laden secretory granules. Short microvilli project from the apical plasma membrane.
database_cross_reference: MESH:D020397
database_cross_reference: http://en.wikipedia.org/wiki/Goblet_cell

Axiom
annotated source: goblet cell
annotated property: description
annotated target: Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some sub…
database_cross_reference: DOI:10.1016/S1357-2725(02)00083-3
database_cross_reference: DOI:10.1038/s41575-022-00675-x
database_cross_reference: DOI:10.1165/ajrcmb.25.5.f218
database_cross_reference: DOI:10.1242/bio.20121701
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK553208/

Axiom
annotated source: goblet cell
annotated property: database_cross_reference
annotated target: ZFA:0009094
mapping justification: UnspecifiedMatching

obsolete acid secreting cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/427
consider: parietal cell
deprecated: true

parietal cell
type: Class
subclass of: exocrine cell
subclass of: CL_0002659
subclass of: Restriction
  on property: part of
  some values from: UBERON_0010038
subclass of: Restriction
  on property: has part
  some values from: GO_0005902
subclass of: Restriction
  on property: capable of
  some values from: GO_0001696
definition: An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by its pyramidal shape, abundant mitochondria, and a complex network of secretory canaliculi lined with microvilli. It secretes hydrochloric acid into the stomach lumen and produces intrinsic factor, essential for vitamin B12 absorption.
database_cross_reference: BTO:0001780
database_cross_reference: FMA:62901
has_exact_synonym: gastric parietal cell
has_exact_synonym: oxyntic cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function.

Axiom
annotated source: parietal cell
annotated property: definition
annotated target: An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by its pyramidal shape, abundant mitochondria, and a complex network of secretory canaliculi lined with microvilli. It secretes hydrochloric acid into the stomach lumen and produces intrinsic factor, essential for vitamin B12 absorption.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651
database_cross_reference: PMID:31613538
database_cross_reference: PMID:31670611

Axiom
annotated source: parietal cell
annotated property: has_exact_synonym
annotated target: gastric parietal cell
database_cross_reference: PMID:29263912

Axiom
annotated source: parietal cell
annotated property: has_exact_synonym
annotated target: oxyntic cell
database_cross_reference: Wikipedia:Parietal_cell

Axiom
annotated source: parietal cell
annotated property: comment
annotated target: Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function.
database_cross_reference: PMID:29263912
database_cross_reference: PMID:31613538

endocrine cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: capable of
    some values from: Class
      intersection of: GO_0046879
      intersection of: Restriction
        on property: has target end location
        some values from: UBERON_0001009
subclass of: secretory cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000949
subclass of: Restriction
  on property: capable of
  some values from: Class
    intersection of: GO_0046879
    intersection of: Restriction
      on property: has target end location
      some values from: UBERON_0001009
definition: A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.
present in taxon: NCBITaxon 9606
database_cross_reference: FMA:83809
database_cross_reference: ZFA:0009096
has_exact_synonym: endocrinocyte
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: endocrine cell
annotated property: definition
annotated target: A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.
database_cross_reference: MESH:D055098

Axiom
annotated source: endocrine cell
annotated property: database_cross_reference
annotated target: ZFA:0009096
mapping justification: UnspecifiedMatching

enteroendocrine cell
type: Class
subclass of: endocrine cell
subclass of: CL_1100001
definition: An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas.
description: Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body. (This extended description was generated by Chat…
database_cross_reference: BTO:0003865
database_cross_reference: FMA:62930
database_cross_reference: MESH:D019858
database_cross_reference: ZFA:0009097
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000164
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: enteroendocrine cell
annotated property: definition
annotated target: An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas.
database_cross_reference: GOC:tfm
database_cross_reference: SANBI:mhl

Axiom
annotated source: enteroendocrine cell
annotated property: description
annotated target: Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body. (This extended description was generated by Chat…
database_cross_reference: DOI:10.1038/s41574-019-0168-8
database_cross_reference: DOI:10.1111/j.1463-1326.2011.01438.x
database_cross_reference: DOI:10.1196/annals.1294.001
database_cross_reference: DOI:10.1210/endrev/bnaa018
database_cross_reference: DOI:10.7554/elife.78512

Axiom
annotated source: enteroendocrine cell
annotated property: database_cross_reference
annotated target: ZFA:0009097
mapping justification: UnspecifiedMatching

neuroendocrine cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0046879
subclass of: endocrine cell
subclass of: efferent neuron
subclass of: neurecto-epithelial cell
subclass of: CL_1100001
definition: A neuron that is capable of some hormone secretion in response to neuronal signals.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0002691
database_cross_reference: FBbt:00005130
database_cross_reference: FMA:83810
database_cross_reference: ZFA:0009098
has_related_synonym: neurosecretory cell
has_related_synonym: neurosecretory neuron
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements. The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron.

Axiom
annotated source: neuroendocrine cell
annotated property: definition
annotated target: A neuron that is capable of some hormone secretion in response to neuronal signals.
database_cross_reference: MESH:D055099

Axiom
annotated source: neuroendocrine cell
annotated property: database_cross_reference
annotated target: FBbt:00005130
mapping justification: ManualMappingCuration

Axiom
annotated source: neuroendocrine cell
annotated property: database_cross_reference
annotated target: ZFA:0009098
mapping justification: UnspecifiedMatching

Axiom
annotated source: neuroendocrine cell
annotated property: comment
annotated target: The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements. The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron.
database_cross_reference: PMID:5342440
database_cross_reference: https://www.clinicalkey.com/#!/content/book/3-s2.0-B9780323555968000073

chromaffin cell
type: Class
subclass of: neural crest derived neuron
subclass of: amine precursor uptake and decarboxylation cell
definition: A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system.
description: Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: BTO:0000259
database_cross_reference: FMA:69263
database_cross_reference: ZFA:0009099
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000166
has_exact_synonym: phaeochromocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: chromaffin cell
annotated property: definition
annotated target: A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system.
database_cross_reference: MESH:D019439

Axiom
annotated source: chromaffin cell
annotated property: description
annotated target: Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1002/cphy.c190003
database_cross_reference: DOI:10.1016/j.biocel.2016.02.003
database_cross_reference: DOI:10.3389/fendo.2018.00711
database_cross_reference: DOI:10.3389/fimmu.2022.977175
database_cross_reference: DOI:10.3389/fimmu.2022.977175/full

Axiom
annotated source: chromaffin cell
annotated property: database_cross_reference
annotated target: ZFA:0009099
mapping justification: UnspecifiedMatching

peptide hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030072
subclass of: secretory cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0030072
definition: Any secretory cell that is capable of some peptide hormone secretion.
database_cross_reference: ZFA:0009100
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: peptide hormone secreting cell
annotated property: definition
annotated target: Any secretory cell that is capable of some peptide hormone secretion.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: peptide hormone secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009100
mapping justification: UnspecifiedMatching

insulin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030073
subclass of: protein secreting cell
subclass of: peptide hormone secreting cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0030073
definition: Any secretory cell that is capable of some insulin secretion.
database_cross_reference: BTO:0000783
database_cross_reference: ZFA:0009101
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: insulin secreting cell
annotated property: definition
annotated target: Any secretory cell that is capable of some insulin secretion.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: insulin secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009101
mapping justification: UnspecifiedMatching

type B pancreatic cell
type: Class
equivalent class: Class
  intersection of: enteroendocrine cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000006
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030073
subclass of: insulin secreting cell
subclass of: CL_0008024
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000006
subclass of: Restriction
  on property: develops from
  some values from: CL_0002351
definition: A cell that secretes insulin and is located towards the center of the islets of Langerhans.
present in taxon: NCBITaxon 9606
has_broad_synonym: beta cell
database_cross_reference: BTO:0000783
database_cross_reference: EV:0200009
database_cross_reference: FMA:70586
database_cross_reference: MA:0002419
database_cross_reference: ZFA:0009102
database_cross_reference: ncithesaurus:Beta_Cell
has_exact_synonym: B-cell of pancreatic islet
has_exact_synonym: beta cell of pancreatic islet
has_exact_synonym: insulin-secreting cell
has_exact_synonym: pancreatic B cell
has_exact_synonym: pancreatic B-cell
has_exact_synonym: pancreatic beta cell
has_exact_synonym: pancreatic islet core
has_exact_synonym: type B enteroendocrine cell
has_related_synonym: beta cell islet
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression.

Axiom
annotated source: type B pancreatic cell
annotated property: subClassOf
annotated target: insulin secreting cell
is inferred: true

Axiom
annotated source: type B pancreatic cell
annotated property: definition
annotated target: A cell that secretes insulin and is located towards the center of the islets of Langerhans.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651
database_cross_reference: http://en.wikipedia.org/wiki/Pancreatic_b_cell

Axiom
annotated source: type B pancreatic cell
annotated property: has_broad_synonym
annotated target: beta cell
database_cross_reference: ZFA:0009102

Axiom
annotated source: type B pancreatic cell
annotated property: database_cross_reference
annotated target: ZFA:0009102
mapping justification: UnspecifiedMatching

Axiom
annotated source: type B pancreatic cell
annotated property: has_exact_synonym
annotated target: B-cell of pancreatic islet
database_cross_reference: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: has_exact_synonym
annotated target: beta cell of pancreatic islet
database_cross_reference: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: has_exact_synonym
annotated target: insulin-secreting cell
database_cross_reference: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: has_exact_synonym
annotated target: pancreatic B-cell
database_cross_reference: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: has_exact_synonym
annotated target: pancreatic beta cell
database_cross_reference: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: has_exact_synonym
annotated target: pancreatic islet core
database_cross_reference: MA:0002419

Axiom
annotated source: type B pancreatic cell
annotated property: has_exact_synonym
annotated target: type B enteroendocrine cell
database_cross_reference: FMA:70586

Axiom
annotated source: type B pancreatic cell
annotated property: has_related_synonym
annotated target: beta cell islet
database_cross_reference: MA:0002419

glucagon secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0070091
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0070091
definition: A cell that secretes glucagon.
database_cross_reference: FMA:84045
database_cross_reference: ZFA:0009103
has_exact_synonym: glucagon-secreting cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: glucagon secreting cell
annotated property: definition
annotated target: A cell that secretes glucagon.
database_cross_reference: GOC:tfm

Axiom
annotated source: glucagon secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009103
mapping justification: UnspecifiedMatching

pancreatic A cell
type: Class
equivalent class: Class
  intersection of: CL_0002067
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000006
subclass of: CL_0002067
subclass of: CL_0008024
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000006
subclass of: Restriction
  on property: develops from
  some values from: CL_0002351
definition: A type A enteroendocrine cell found in the periphery of the islets of Langerhans that secretes glucagon.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000990
database_cross_reference: FMA:70585
database_cross_reference: MESH:D050416
database_cross_reference: ZFA:0009104
has_exact_synonym: alpha cell of islet of Langerhans
has_exact_synonym: pancreatic alpha cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: pancreatic A cell
annotated property: definition
annotated target: A type A enteroendocrine cell found in the periphery of the islets of Langerhans that secretes glucagon.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: pancreatic A cell
annotated property: database_cross_reference
annotated target: ZFA:0009104
mapping justification: UnspecifiedMatching

somatostatin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0070253
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0070253
definition: Any secretory cell that is capable of some somatostatin secretion.
database_cross_reference: ZFA:0009105
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: somatostatin secreting cell
annotated property: definition
annotated target: Any secretory cell that is capable of some somatostatin secretion.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: somatostatin secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009105
mapping justification: UnspecifiedMatching

pancreatic D cell
type: Class
equivalent class: Class
  intersection of: type D enteroendocrine cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001264
subclass of: type D enteroendocrine cell
subclass of: CL_0008024
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000006
subclass of: Restriction
  on property: develops from
  some values from: CL_0002351
definition: A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000803
database_cross_reference: FMA:70587
database_cross_reference: ZFA:0005743
has_exact_synonym: D-cell of pancreatic islet
has_exact_synonym: delta cell of islet
has_exact_synonym: delta cell of pancreatic islet
has_exact_synonym: pancreatic D-cell
has_exact_synonym: pancreatic delta cell
has_exact_synonym: somatostatin-secreting pancreatic cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: pancreatic D cell
annotated property: definition
annotated target: A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin.
database_cross_reference: FMA:0517223651
database_cross_reference: GOC:tfm

Axiom
annotated source: pancreatic D cell
annotated property: database_cross_reference
annotated target: ZFA:0005743
mapping justification: UnspecifiedMatching

steroid hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0035929
subclass of: secretory cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0035929
definition: Any secretory cell that is capable of some steroid hormone secretion.
database_cross_reference: ZFA:0009106
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: steroid hormone secreting cell
annotated property: definition
annotated target: Any secretory cell that is capable of some steroid hormone secretion.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: steroid hormone secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009106
mapping justification: UnspecifiedMatching

luteal cell
type: Class
subclass of: progesterone secreting cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002512
definition: A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0003939
database_cross_reference: FMA:18688
has_exact_synonym: corpus luteum cell
has_exact_synonym: lutein cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: luteal cell
annotated property: definition
annotated target: A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells.
database_cross_reference: MESH:D008184
database_cross_reference: PMID:31849844

Axiom
annotated source: luteal cell
annotated property: has_exact_synonym
annotated target: corpus luteum cell
database_cross_reference: PMID:16790079

ecdysteroid secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0045457
subclass of: steroid hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0045457
definition: Any secretory cell that is capable of some ecdysteroid secretion.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: ecdysteroid secreting cell
annotated property: definition
annotated target: Any secretory cell that is capable of some ecdysteroid secretion.
database_cross_reference: FBC:Autogenerated

testosterone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0035936
subclass of: secretory cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0035936
definition: Any secretory cell that is capable of some testosterone secretion.
database_cross_reference: ZFA:0009107
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: testosterone secreting cell
annotated property: definition
annotated target: Any secretory cell that is capable of some testosterone secretion.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: testosterone secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009107
mapping justification: UnspecifiedMatching

Leydig cell
type: Class
subclass of: BFO_0000002
subclass of: testosterone secreting cell
subclass of: CL_4030031
subclass of: Restriction
  on property: part of
  some values from: UBERON_0005212
subclass of: Restriction
  on property: develops from
  some values from: CL_0009091
definition: A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis.
description: Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biol…
has_broad_synonym: interstitial cell
database_cross_reference: BTO:0000755
database_cross_reference: CALOHA:TS-1150
database_cross_reference: EMAPA:29655
database_cross_reference: FMA:72297
database_cross_reference: MESH:D007985
database_cross_reference: ZFA:0009108
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000178
has_exact_synonym: interstitial cell of Leydig
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Note that the Amphibian Anatomy Ontology (AA) has a class 'leydig cells' but this is unrelated

Axiom
annotated source: Leydig cell
annotated property: definition
annotated target: A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:12050120

Axiom
annotated source: Leydig cell
annotated property: description
annotated target: Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biol…
database_cross_reference: DOI:10.1016/j.coemr.2019.03.001
database_cross_reference: DOI:10.1093/biolre/ioy059
database_cross_reference: DOI:10.1210/clinem/dgaa603
database_cross_reference: DOI:10.3389/fendo.2014.00006
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors.

Axiom
annotated source: Leydig cell
annotated property: database_cross_reference
annotated target: ZFA:0009108
mapping justification: UnspecifiedMatching

progesterone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0042701
subclass of: steroid hormone secreting cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0042701
definition: Any secretory cell that is capable of some progesterone secretion.
database_cross_reference: ZFA:0009109
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: progesterone secreting cell
annotated property: definition
annotated target: Any secretory cell that is capable of some progesterone secretion.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: progesterone secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009109
mapping justification: UnspecifiedMatching

estradiol secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0035938
subclass of: steroid hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0035938
definition: A steroid hormone secreting cell that secretes estradiol.
database_cross_reference: ZFA:0009110
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: estradiol secreting cell
annotated property: definition
annotated target: A steroid hormone secreting cell that secretes estradiol.
database_cross_reference: https://orcid.org/0000-0001-5208-3432

Axiom
annotated source: estradiol secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009110
mapping justification: UnspecifiedMatching

obsolete metabolising cell
type: Class
definition: A cell whose primary function is intermediary metabolism.
term tracker item: https://github.com/obophenotype/cell-ontology/issues/720
comment: Removing this grouping class, because the groupings are incomplete and too hard to maintain.
deprecated: true

Axiom
annotated source: obsolete metabolising cell
annotated property: definition
annotated target: A cell whose primary function is intermediary metabolism.
database_cross_reference: FB:ma

hepatocyte
type: Class
subclass of: BFO_0000002
subclass of: epithelial cell
subclass of: endopolyploid cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002107
subclass of: Restriction
  on property: develops from
  some values from: CL_0005026
subclass of: Restriction
  on property: capable of
  some values from: GO_0006699
subclass of: Restriction
  on property: capable of
  some values from: GO_0098754
definition: The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
present in taxon: NCBITaxon 9606
description: Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform…
database_cross_reference: BTO:0000575
database_cross_reference: CALOHA:TS-0454
database_cross_reference: FMA:14515
database_cross_reference: ZFA:0009111
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000182
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive.

Axiom
annotated source: hepatocyte
annotated property: definition
annotated target: The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0412046911
database_cross_reference: MESH:D022781
database_cross_reference: PMID:19717280
database_cross_reference: http://en.wikipedia.org/wiki/Hepatocyte

Axiom
annotated source: hepatocyte
annotated property: description
annotated target: Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform…
database_cross_reference: DOI:10.1016/j.biocel.2011.11.011
database_cross_reference: DOI:10.1055/s-2007-1007096
database_cross_reference: DOI:10.1083/jcb.201903090
database_cross_reference: DOI:10.1111/j.1439-0396.2007.00752.x

Axiom
annotated source: hepatocyte
annotated property: database_cross_reference
annotated target: ZFA:0009111
mapping justification: UnspecifiedMatching

contractile cell
type: Class
subclass of: cell
definition: A cell whose primary function is to shorten.
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: contractile cell
annotated property: definition
annotated target: A cell whose primary function is to shorten.
database_cross_reference: FB:ma

CL_0000184
type: Class
has obsolescence reason: IAO_0000227
term replaced by: pericyte
deprecated: true

myoepithelial cell
type: Class
subclass of: columnar/cuboidal epithelial cell
subclass of: contractile cell
definition: Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament.
database_cross_reference: BTO:0002309
database_cross_reference: CALOHA:TS-2379
database_cross_reference: FMA:67799
database_cross_reference: ZFA:0009113
has_exact_synonym: basket epithelial cell
has_exact_synonym: myoepitheliocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: myoepithelial cell
annotated property: definition
annotated target: Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: myoepithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009113
mapping justification: UnspecifiedMatching

myofibroblast cell
type: Class
subclass of: contractile cell
subclass of: CL_0002320
definition: An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell.
present in taxon: NCBITaxon 9606
has_exact_synonym: MFB
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Myofibroblasts are alpha-SMA-positive, CD34-negative, CD45-negative. They are reportedly capable of secreting IL-1beta, IL-6, and TNF-alpha.

Axiom
annotated source: myofibroblast cell
annotated property: definition
annotated target: An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell.
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D058628
database_cross_reference: PMID:19800625
database_cross_reference: PMID:20630469
database_cross_reference: PMID:22387320

Axiom
annotated source: myofibroblast cell
annotated property: has_exact_synonym
annotated target: MFB
database_cross_reference: PMID:8731193

muscle cell
type: Class
subclass of: BFO_0000002
subclass of: contractile cell
subclass of: eukaryotic cell
subclass of: electrically responsive cell
subclass of: Restriction
  on property: develops from
  some values from: myoblast
definition: A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
database_cross_reference: BTO:0000888
database_cross_reference: BTO:0000902
database_cross_reference: CALOHA:TS-2032
database_cross_reference: FBbt:00005074
database_cross_reference: FMA:67328
database_cross_reference: WBbt:0003675
database_cross_reference: ZFA:0009114
has_exact_synonym: muscle fiber
has_exact_synonym: myocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: muscle cell
annotated property: definition
annotated target: A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
database_cross_reference: MESH:D032342

Axiom
annotated source: muscle cell
annotated property: database_cross_reference
annotated target: FBbt:00005074
mapping justification: ManualMappingCuration

Axiom
annotated source: muscle cell
annotated property: database_cross_reference
annotated target: ZFA:0009114
mapping justification: UnspecifiedMatching

cell of skeletal muscle
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001134
subclass of: eukaryotic cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001134
definition: A somatic cell located in skeletal muscle.
present in taxon: NCBITaxon 9606
description: Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: BTO:0004392
database_cross_reference: CALOHA:TS-2158
database_cross_reference: FMA:9727
database_cross_reference: ZFA:0009115
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000188
has_exact_synonym: skeletal muscle cell
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: cell of skeletal muscle
annotated property: definition
annotated target: A somatic cell located in skeletal muscle.
database_cross_reference: GOC:tfm

Axiom
annotated source: cell of skeletal muscle
annotated property: description
annotated target: Skeletal muscle cells, or myocytes, are essential for the musculoskeletal system, featuring a striated appearance from tightly packed sarcomeres. These elongated, multi-nucleated cells convert ATP into mechanical energ and are key for voluntary movement and posture. They also are responsible for maintaining body temperature, storing nutrients, and stabilizing joints. Skeletal muscle cells organize themselves tightly into bundles to form muscle fibers. Embedded within each of these cells are thousands of myofibrils, which are made up of the contractile proteins, actin (the thin filament), and myosin (the thick filament). Contraction of a skeletal muscle cell occurs when these myofibrils shorten, a process driven by the sliding of actin and myosin filaments over each other in a mechanism famously known as the sliding filament theory. Additionally, skeletal muscle cells exhibit a high degree of plasticity, which allows for their adaptation in response to alterations in functional demands or damages. They have an innate regenerative capacity due to the presence of satellite cells—quiescent muscle stem cells that reside within the muscle fibers. Upon muscle injury, these satellite cells become activated, proliferate, and differentiate into new muscle cells, thereby contributing to the repair and growth of injured skeletal muscle. With this, skeletal muscle cells serve not only a pivotal biomechanical function but also possess a great capacity for self-healing and regeneration. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1002/cphy.c160033
database_cross_reference: DOI:10.3390/biology10101056
database_cross_reference: https://www.nature.com/scitable/topicpage/the-sliding-filament-theory-of-muscle-contraction-14567666/
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK537139
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK9961/

Axiom
annotated source: cell of skeletal muscle
annotated property: database_cross_reference
annotated target: ZFA:0009115
mapping justification: UnspecifiedMatching

slow muscle cell
type: Class
subclass of: CL_0008046
subclass of: Restriction
  on property: develops from
  some values from: CL_0000857
definition: A muscle cell that develops tension more slowly than a fast-twitch fiber.
description: Slow muscle cells, as the name implies, are a type of muscle cell well known for their slow contractile speed. They are also referred to as type I, slow-twitch, or red muscles because of their high myoglobin content which gives them a dark, reddish appearance. These cells are predominantly found in the postural muscles of the body, such as those in the back and lower limbs. A defining characteristic of slow muscle cells is their significant resistance to fatigue. This is largely due to their efficient oxidative metabolism, which allows them to continuously contract over extended periods without succumbing to fatigue. This extraordinary endurance is facilitated by a high concentration of mitochondria, which enables the efficient use of oxygen for energy production, and capillaries, which supplies the necessary oxygen and nutrients. Additionally, these cells have an abundant supply of myoglobin, a protein that stores and transports oxygen within the muscle cell, further supporting their aerobic metabolism. The primary role of slow muscle cells in the human body is to provide sustained, low-intensity contractions over a prolonged period. They are responsible for maintaining posture and providing stability, rather than delivering short, powerful bursts of activity. They play a pivotal role in supporting various physical activities such as standing, walking, or any form of exercise that requires endurance over speed. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: ZFA:0009116
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000189
has_related_synonym: slow muscle fiber
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: slow muscle cell
annotated property: definition
annotated target: A muscle cell that develops tension more slowly than a fast-twitch fiber.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0323052908

Axiom
annotated source: slow muscle cell
annotated property: description
annotated target: Slow muscle cells, as the name implies, are a type of muscle cell well known for their slow contractile speed. They are also referred to as type I, slow-twitch, or red muscles because of their high myoglobin content which gives them a dark, reddish appearance. These cells are predominantly found in the postural muscles of the body, such as those in the back and lower limbs. A defining characteristic of slow muscle cells is their significant resistance to fatigue. This is largely due to their efficient oxidative metabolism, which allows them to continuously contract over extended periods without succumbing to fatigue. This extraordinary endurance is facilitated by a high concentration of mitochondria, which enables the efficient use of oxygen for energy production, and capillaries, which supplies the necessary oxygen and nutrients. Additionally, these cells have an abundant supply of myoglobin, a protein that stores and transports oxygen within the muscle cell, further supporting their aerobic metabolism. The primary role of slow muscle cells in the human body is to provide sustained, low-intensity contractions over a prolonged period. They are responsible for maintaining posture and providing stability, rather than delivering short, powerful bursts of activity. They play a pivotal role in supporting various physical activities such as standing, walking, or any form of exercise that requires endurance over speed. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1093/ptj/81.11.1810
database_cross_reference: DOI:10.1186/s13578-015-0054-6
database_cross_reference: DOI:10.3389/fphys.2021.747214
database_cross_reference: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/slow-muscle-fiber

Axiom
annotated source: slow muscle cell
annotated property: database_cross_reference
annotated target: ZFA:0009116
mapping justification: UnspecifiedMatching

Axiom
annotated source: slow muscle cell
annotated property: has_related_synonym
annotated target: slow muscle fiber
database_cross_reference: ISBN:0815316208

fast muscle cell
type: Class
subclass of: CL_0008046
subclass of: Restriction
  on property: develops from
  some values from: CL_0000858
definition: A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron.
description: Fast muscle cells, also known as type II muscle fibers, are a particular type of muscle cell that specializes in conducting rapid, high-intensity contractions. These cells are primarily found within skeletal muscle groups that are directly involved in gross motor activities, such as running, jumping, or lifting heavy weights. The designation "fast" refers to their speed of contraction in response to neural stimuli, which is significantly quicker when compared to other muscle cell types such as slow-twitch or type I muscle fibers. The primary function of fast muscle cells revolves around their role in anaerobic metabolism, which provides the energy needed for short, forceful bursts of power. They contain a high concentration of glycolytic enzymes that facilitate this process, leading to a swift break down of glucose to generate ATP (adenosine triphosphate), the primary energy currency in biological systems. On the downside, the byproduct of this very rapid, anaerobic metabolic process is lactic acid, which can build up and cause muscle fatigue. Fast muscle cells can be further classified into two subtypes based on their metabolic characteristics: type IIa and type IIb/x. Type IIa cells, also known as fast oxidative-glycolytic fibers, possess a good oxygen supply and can function in both anaerobic and aerobic conditions, exhibiting moderate resistance to fatigue. On the other hand, type IIb/x cells, also known as fast glycolytic fibers, primarily rely on anaerobic metabolism and tire out a lot quicker. Both these subtypes can adapt to changing demands due to exercise and conditioning, highlighting the plasticity that is a key characteristic of these versatile muscle cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: ZFA:0009117
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000190
has_exact_synonym: glycolytic muscle fiber
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: fast muscle cell
annotated property: definition
annotated target: A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0323052908

Axiom
annotated source: fast muscle cell
annotated property: description
annotated target: Fast muscle cells, also known as type II muscle fibers, are a particular type of muscle cell that specializes in conducting rapid, high-intensity contractions. These cells are primarily found within skeletal muscle groups that are directly involved in gross motor activities, such as running, jumping, or lifting heavy weights. The designation "fast" refers to their speed of contraction in response to neural stimuli, which is significantly quicker when compared to other muscle cell types such as slow-twitch or type I muscle fibers. The primary function of fast muscle cells revolves around their role in anaerobic metabolism, which provides the energy needed for short, forceful bursts of power. They contain a high concentration of glycolytic enzymes that facilitate this process, leading to a swift break down of glucose to generate ATP (adenosine triphosphate), the primary energy currency in biological systems. On the downside, the byproduct of this very rapid, anaerobic metabolic process is lactic acid, which can build up and cause muscle fatigue. Fast muscle cells can be further classified into two subtypes based on their metabolic characteristics: type IIa and type IIb/x. Type IIa cells, also known as fast oxidative-glycolytic fibers, possess a good oxygen supply and can function in both anaerobic and aerobic conditions, exhibiting moderate resistance to fatigue. On the other hand, type IIb/x cells, also known as fast glycolytic fibers, primarily rely on anaerobic metabolism and tire out a lot quicker. Both these subtypes can adapt to changing demands due to exercise and conditioning, highlighting the plasticity that is a key characteristic of these versatile muscle cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1152/japplphysiol.00636.2019
database_cross_reference: DOI:10.3389/fcell.2018.00125
database_cross_reference: DOI:10.4161/org.4.3.6312
database_cross_reference: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/fast-muscle-fiber

Axiom
annotated source: fast muscle cell
annotated property: database_cross_reference
annotated target: ZFA:0009117
mapping justification: UnspecifiedMatching

CL_0000191
type: Class
has obsolescence reason: IAO_0000227
term replaced by: smooth muscle cell
deprecated: true

smooth muscle cell
type: Class
subclass of: CL_0008000
subclass of: CL_0008007
subclass of: Restriction
  on property: develops from
  some values from: smooth muscle myoblast
definition: A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).
present in taxon: NCBITaxon 9606
description: Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has_broad_synonym: non-striated muscle cell
database_cross_reference: BTO:0004576
database_cross_reference: CALOHA:TS-2159
database_cross_reference: FMA:14072
database_cross_reference: ZFA:0009118
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000192
has_exact_synonym: SMCs
has_exact_synonym: myocytes, smooth muscle
has_exact_synonym: smooth muscle fiber
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: smooth muscle cell
annotated property: definition
annotated target: A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).
database_cross_reference: MESH:D032389
database_cross_reference: PMID:9315361
database_cross_reference: http://en.wikipedia.org/wiki/Smooth_muscle_cell

Axiom
annotated source: smooth muscle cell
annotated property: description
annotated target: Smooth muscle cells are a specialized type of muscle cells that are primarily found within the walls of hollow organs such as the intestine, stomach, bladder, uterus, and blood vessels. These cells are an essential component of the autonomic nervous system controling involuntary movements within the body. Smooth muscle cells play a vital role in many physiological processes due to their unique functionality. They can contract and relax in a slow, sustained, and controlled manner to help modulate the size and shape of the lumens of the organs they surround. For example, in the digestive system, coordinated contraction and relaxation of smooth muscle cells propels food along the gastrointestinal tract - a process known as peristalsis. In the blood vessels, the smooth muscle cells, by contracting or relaxing, either constrict or dilate the vessels, which in turn, help regulate blood flow and pressure. On a cellular level, smooth muscle cells possess a single, centrally located nucleus and contain an arranged network of actin and myosin filaments, which are the proteins responsible for muscle contraction. Unlike their counterparts in skeletal or cardiac muscles, these cells lack specific contact points for these filaments, hence the lack of visible striations. Furthermore, the contraction of smooth muscle cells is regulated by hormones and neurotransmitters, such as acetylcholine and norepinephrine, adding an additional layer of complex regulation to these highly specialized cells. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1093/ptj/81.11.1810
database_cross_reference: https://training.seer.cancer.gov/anatomy/muscular/types.html
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK10854/
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK526125
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK556137/

Axiom
annotated source: smooth muscle cell
annotated property: database_cross_reference
annotated target: ZFA:0009118
mapping justification: UnspecifiedMatching

Axiom
annotated source: smooth muscle cell
annotated property: has_exact_synonym
annotated target: SMCs
database_cross_reference: PMID:9315361

Axiom
annotated source: smooth muscle cell
annotated property: has_exact_synonym
annotated target: myocytes, smooth muscle
database_cross_reference: MESH:D032389

cardiac muscle cell (sensu Arthopoda)
type: Class
equivalent class: Class
  intersection of: cardiac muscle cell
  intersection of: Restriction
    on property: develops from
    some values from: cardioblast (sensu Arthropoda)
subclass of: cardiac muscle cell
subclass of: Restriction
  on property: develops from
  some values from: cardioblast (sensu Arthropoda)
definition: A striated muscle cell of an arthropod heart that participates in heart contraction.

Axiom
annotated source: cardiac muscle cell (sensu Arthopoda)
annotated property: definition
annotated target: A striated muscle cell of an arthropod heart that participates in heart contraction.
database_cross_reference: MESH:D032383

obsolete nodal cardiac cell
type: Class
comment: Consider CL:0002072.
deprecated: true

obsolete Purkinje fiber
type: Class
deprecated: true

insect flight muscle cell
type: Class
subclass of: CL_0008003
definition: A muscle cell that is involved in the mechanism of insect flight. This encompasses both, cells that power flight and cells that control flight.
database_cross_reference: FBbt:00003360
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: insect flight muscle cell
annotated property: definition
annotated target: A muscle cell that is involved in the mechanism of insect flight. This encompasses both, cells that power flight and cells that control flight.
database_cross_reference: doi:10.2142/biophysics.7.21

Axiom
annotated source: insect flight muscle cell
annotated property: database_cross_reference
annotated target: FBbt:00003360
mapping justification: ManualMappingCuration

sensory receptor cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001032
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050906
subclass of: eukaryotic cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001032
subclass of: Restriction
  on property: capable of
  some values from: GO_0050906
definition: A cell that is capable of detection of a stimulus involved in sensory perception.
database_cross_reference: MESH:D011984
has_exact_synonym: receptor cell
in_subset: human subset
in_subset: mouse subset

pain receptor cell
type: Class
subclass of: neuronal receptor cell
definition: The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings.
database_cross_reference: ZFA:0009119
has_exact_synonym: nociceptor
has_exact_synonym: nocireceptor
in_subset: human subset
in_subset: mouse subset
comment: Editor note: request detection of stimulus involved in sensory perception of pain; add develops_from relationship

Axiom
annotated source: pain receptor cell
annotated property: definition
annotated target: The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings.
database_cross_reference: MESH:D009619

Axiom
annotated source: pain receptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009119
mapping justification: UnspecifiedMatching

Axiom
annotated source: pain receptor cell
annotated property: has_exact_synonym
annotated target: nociceptor

Axiom
annotated source: pain receptor cell
annotated property: has_exact_synonym
annotated target: nocireceptor

mechanoreceptor cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050974
subclass of: sensory neuron
subclass of: Restriction
  on property: capable of
  some values from: GO_0050974
definition: A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
database_cross_reference: ZFA:0009120
has_related_synonym: mechanoreceptor
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: mechanoreceptor cell
annotated property: definition
annotated target: A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
database_cross_reference: MESH:D008465

Axiom
annotated source: mechanoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009120
mapping justification: UnspecifiedMatching

Axiom
annotated source: mechanoreceptor cell
annotated property: has_related_synonym
annotated target: mechanoreceptor
database_cross_reference: MP:0000972

touch receptor cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050976
subclass of: mechanoreceptor cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0050976
definition: Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception of touch.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: touch receptor cell
annotated property: definition
annotated target: Any neuron that is capable of some detection of mechanical stimulus involved in sensory perception of touch.
database_cross_reference: FBC:Autogenerated

CL_0000201
type: Class
has obsolescence reason: IAO_0000227
term replaced by: auditory hair cell
deprecated: true

auditory hair cell
type: Class
subclass of: CL_0000855
subclass of: Restriction
  on property: capable of
  some values from: GO_0050910
definition: A mechanoreceptor cell of the auditory or vestibular system that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system.
database_cross_reference: ZFA:0009121
has_related_synonym: auditory receptor cell
in_subset: human subset
in_subset: mouse subset
comment: In mammals these cells are located in the organ of Corti.

Axiom
annotated source: auditory hair cell
annotated property: definition
annotated target: A mechanoreceptor cell of the auditory or vestibular system that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system.
database_cross_reference: MESH:D006198
database_cross_reference: WikipediaVersioned:Hair_cell&oldid=1045345915

Axiom
annotated source: auditory hair cell
annotated property: database_cross_reference
annotated target: ZFA:0009121
mapping justification: UnspecifiedMatching

gravity sensitive cell
type: Class
equivalent class: Class
  intersection of: neuronal receptor cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0070999
subclass of: neuronal receptor cell
subclass of: mechanoreceptor cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0070999
definition: Any neuronal receptor cell that is capable of some detection of mechanical stimulus involved in sensory perception of gravity.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: gravity sensitive cell
annotated property: definition
annotated target: Any neuronal receptor cell that is capable of some detection of mechanical stimulus involved in sensory perception of gravity.
database_cross_reference: FBC:Autogenerated

acceleration receptive cell
type: Class
subclass of: neuronal receptor cell
in_subset: human subset
in_subset: mouse subset

thermoreceptor cell
type: Class
equivalent class: Class
  intersection of: neuronal receptor cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050960
subclass of: neuronal receptor cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0050960
definition: A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain.
database_cross_reference: ZFA:0009123
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: thermoreceptor cell
annotated property: definition
annotated target: A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D013823
database_cross_reference: MP:0000971

Axiom
annotated source: thermoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009123
mapping justification: UnspecifiedMatching

chemoreceptor cell
type: Class
equivalent class: Class
  intersection of: sensory receptor cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050907
subclass of: sensory receptor cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0050907
definition: A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood.
database_cross_reference: ZFA:0009124
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: chemoreceptor cell
annotated property: definition
annotated target: A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood.
database_cross_reference: MESH:D002628

Axiom
annotated source: chemoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009124
mapping justification: UnspecifiedMatching

olfactory receptor cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050911
subclass of: neuronal receptor cell
subclass of: chemoreceptor cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0005725
subclass of: Restriction
  on property: capable of
  some values from: GO_0050911
definition: Any neuron that is capable of some detection of chemical stimulus involved in sensory perception of smell.
database_cross_reference: BTO:0004185
database_cross_reference: FMA:67860
database_cross_reference: MESH:D018034
database_cross_reference: Wikipedia:Olfactory_receptor_neuron
database_cross_reference: ZFA:0009125
has_exact_synonym: Schultze's cell
has_exact_synonym: odorant receptor cell
has_exact_synonym: olfactory receptor neuron
has_exact_synonym: olfactory sensory neuron
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: olfactory receptor cell
annotated property: definition
annotated target: Any neuron that is capable of some detection of chemical stimulus involved in sensory perception of smell.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: olfactory receptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009125
mapping justification: UnspecifiedMatching

pH receptor cell
type: Class
subclass of: chemoreceptor cell
in_subset: human subset
in_subset: mouse subset

taste receptor cell
type: Class
equivalent class: Class
  intersection of: chemoreceptor cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050912
subclass of: sensory epithelial cell
subclass of: chemoreceptor cell
subclass of: CL_0002076
subclass of: Restriction
  on property: capable of
  some values from: GO_0050912
definition: A specialized cell involved in gustatory sensory perception.
database_cross_reference: FMA:67910
database_cross_reference: ZFA:0009126
has_exact_synonym: taste bud cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: taste receptor cell
annotated property: definition
annotated target: A specialized cell involved in gustatory sensory perception.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0618947256

Axiom
annotated source: taste receptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009126
mapping justification: UnspecifiedMatching

photoreceptor cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050908
subclass of: sensory neuron
subclass of: CL_0008028
subclass of: Restriction
  on property: capable of
  some values from: GO_0050908
definition: A cell specialized in detecting light stimuli that are involved in visual perception.
database_cross_reference: BTO:0001060
database_cross_reference: CALOHA:TS-0868
database_cross_reference: FBbt:00004211
database_cross_reference: FMA:86740
database_cross_reference: ZFA:0009127
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: photoreceptor cell
annotated property: definition
annotated target: A cell specialized in detecting light stimuli that are involved in visual perception.
database_cross_reference: MESH:D010786

Axiom
annotated source: photoreceptor cell
annotated property: database_cross_reference
annotated target: FBbt:00004211
mapping justification: ManualMappingCuration

Axiom
annotated source: photoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009127
mapping justification: UnspecifiedMatching

electrically active cell
type: Class
subclass of: cell
definition: A cell whose function is determined by the generation or the reception of an electric signal.
database_cross_reference: ZFA:0009128
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: electrically active cell
annotated property: definition
annotated target: A cell whose function is determined by the generation or the reception of an electric signal.
database_cross_reference: FB:ma

Axiom
annotated source: electrically active cell
annotated property: database_cross_reference
annotated target: ZFA:0009128
mapping justification: UnspecifiedMatching

obsolete absorptive cell
type: Class
definition: OBSOLETE. A cell that takes up and metabolizes substances.
term tracker item: https://github.com/obophenotype/cell-ontology/issues/2271
present in taxon: NCBITaxon 9606
in_subset: cellxgene subset
in_subset: human reference atlas
comment: It has no child terms. Consider using 'gut absorptive cell'.
deprecated: true

Axiom
annotated source: obsolete absorptive cell
annotated property: definition
annotated target: OBSOLETE. A cell that takes up and metabolizes substances.
database_cross_reference: CL:CVS

obsolete lining cell
type: Class
definition: OBSOLETE. A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.
term tracker item: https://github.com/obophenotype/cell-ontology/issues/3014
has_exact_synonym: boundary cell
comment: Obsoleted term because redundant
deprecated: true

Axiom
annotated source: obsolete lining cell
annotated property: definition
annotated target: OBSOLETE. A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.
database_cross_reference: JB:jb

synovial cell
type: Class
subclass of: CL_0002078
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002217
definition: A cell located in the synovial joint.
database_cross_reference: CALOHA:TS-0995
database_cross_reference: ZFA:0009131
has_exact_synonym: synoviocyte
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: synovial cell
annotated property: subClassOf
annotated target: CL_0002078
is inferred: true

Axiom
annotated source: synovial cell
annotated property: database_cross_reference
annotated target: ZFA:0009131
mapping justification: UnspecifiedMatching

obsolete barrier cell
type: Class
definition: OBSOLETE. A cell whose primary function is to prevent the transport of stuff across compartments.
term tracker item: https://github.com/obophenotype/cell-ontology/issues/3012
comment: Not needed term
deprecated: true

Axiom
annotated source: obsolete barrier cell
annotated property: definition
annotated target: OBSOLETE. A cell whose primary function is to prevent the transport of stuff across compartments.
database_cross_reference: JB:jb

Sertoli cell
type: Class
equivalent class: Class
  intersection of: supporting cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001343
subclass of: androgen binding protein secreting cell
subclass of: supporting cell
subclass of: CL_0002625
subclass of: CL_1100001
definition: A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier.
database_cross_reference: BTO:0001238
database_cross_reference: CALOHA:TS-0922
database_cross_reference: FMA:72298
database_cross_reference: VHOG:0001348
database_cross_reference: ZFA:0009133
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: Sertoli cell
annotated property: subClassOf
annotated target: supporting cell
is inferred: true

Axiom
annotated source: Sertoli cell
annotated property: definition
annotated target: A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier.
database_cross_reference: MESH:D012708

Axiom
annotated source: Sertoli cell
annotated property: database_cross_reference
annotated target: ZFA:0009133
mapping justification: UnspecifiedMatching

obsolete insulating cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/3013
comment: obsoleted because the term is not needed
deprecated: true

myelinating Schwann cell
type: Class
subclass of: CL_0002573
subclass of: CL_4023154
subclass of: Restriction
  on property: develops from
  some values from: CL_0002377
definition: A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons.
has_broad_synonym: Schwann cell
has_broad_synonym: peripheral neuroglial cell
database_cross_reference: CALOHA:TS-0898
database_cross_reference: FMA:62121
database_cross_reference: ZFA:0009135
has_exact_synonym: neurilemmal cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: myelinating Schwann cell
annotated property: definition
annotated target: A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons.
database_cross_reference: GOC:cvs
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D012583

Axiom
annotated source: myelinating Schwann cell
annotated property: database_cross_reference
annotated target: ZFA:0009135
mapping justification: UnspecifiedMatching

motile cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0048870
subclass of: cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0048870
definition: A cell that moves by its own activities.
database_cross_reference: ZFA:0009136
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: motile cell
annotated property: definition
annotated target: A cell that moves by its own activities.
database_cross_reference: FB:ma

Axiom
annotated source: motile cell
annotated property: database_cross_reference
annotated target: ZFA:0009136
mapping justification: UnspecifiedMatching

obsolete cell by lineage
type: Class
consider: CL:0000000
consider: CL:0000003
consider: CL:0001034
comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell in a multicellular organiam, apart from a zygote, can potentially be classified by its lineage. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate.
deprecated: true

ectodermal cell
type: Class
subclass of: eukaryotic cell
subclass of: CL_0002321
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000924
definition: A cell of the outer of the three germ layers of the embryo.
database_cross_reference: FMA:72549
database_cross_reference: ZFA:0009137
has_exact_synonym: ectoderm cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: ectodermal cell
annotated property: definition
annotated target: A cell of the outer of the three germ layers of the embryo.
database_cross_reference: MESH:D004475

Axiom
annotated source: ectodermal cell
annotated property: database_cross_reference
annotated target: ZFA:0009137
mapping justification: UnspecifiedMatching

mesodermal cell
type: Class
subclass of: eukaryotic cell
subclass of: CL_0002321
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000926
definition: A cell of the middle germ layer of the embryo.
description: Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: FMA:72554
database_cross_reference: ZFA:0009138
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000222
has_exact_synonym: mesoblast
has_exact_synonym: mesoderm cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: mesodermal cell
annotated property: definition
annotated target: A cell of the middle germ layer of the embryo.
database_cross_reference: MESH:D008648

Axiom
annotated source: mesodermal cell
annotated property: description
annotated target: Mesodermal cells are pluripotent and the most abundant in the human body. They contribute to the development of several structures such as the skeletal muscles, bones, heart and blood vessels, kidneys, gonads, connective tissues, and certain layers of the skin. Hence, the mesoderm is often regarded as an active and diverse layer due to its role in forming many bodily structures. In embryonic development, these cells are instrumental, contributing to the body's structures through a carefully coordinated sequence of morphogenetic movements. This process forms the complex multicellular architecture of tissues and organs from a simple ball of cells. Without the function of mesodermal cells, the body's integral structures and systems would cease to form correctly, leading to developmental disorders such as axial mesodermal dysplasia complex (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1016/j.ceb.2019.07.012
database_cross_reference: DOI:10.5535/arm.2016.40.1.162
database_cross_reference: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mesoderm

Axiom
annotated source: mesodermal cell
annotated property: database_cross_reference
annotated target: ZFA:0009138
mapping justification: UnspecifiedMatching

endodermal cell
type: Class
subclass of: eukaryotic cell
subclass of: CL_0002321
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000925
definition: A cell of the inner of the three germ layers of the embryo.
database_cross_reference: FMA:72555
database_cross_reference: ZFA:0009139
has_exact_synonym: endoderm cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: endodermal cell
annotated property: definition
annotated target: A cell of the inner of the three germ layers of the embryo.
database_cross_reference: MESH:D004707

Axiom
annotated source: endodermal cell
annotated property: database_cross_reference
annotated target: ZFA:0009139
mapping justification: UnspecifiedMatching

obsolete cell by nuclear number
type: Class
definition: OBSOLETE: A classification of cells by the number of their nuclei.
consider: CL:0000000
consider: CL:0000003
consider: CL:0001034
comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its nuclear number (note that this term was previously used as a parent class of enucleate cell). If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate.
deprecated: true

Axiom
annotated source: obsolete cell by nuclear number
annotated property: definition
annotated target: OBSOLETE: A classification of cells by the number of their nuclei.
database_cross_reference: FB:ma
database_cross_reference: GOC:tfm

anucleate cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001405
subclass of: cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001405
disjoint with: CL_0002242
definition: A cell that lacks a nucleus.
database_cross_reference: FMA:68647
has_exact_synonym: non-nucleated cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: anucleate cell
annotated property: definition
annotated target: A cell that lacks a nucleus.
database_cross_reference: FB:ma

single nucleate cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001407
subclass of: eukaryotic cell
subclass of: CL_0002242
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001407
definition: A cell with a single nucleus.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: single nucleate cell
annotated property: definition
annotated target: A cell with a single nucleus.
database_cross_reference: FB:ma
database_cross_reference: GOC:tfm

binucleate cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001406
subclass of: multinucleate cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001406
definition: Any cell that has characteristic some binucleate.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: binucleate cell
annotated property: definition
annotated target: Any cell that has characteristic some binucleate.
database_cross_reference: FBC:Autogenerated

multinucleate cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001908
subclass of: eukaryotic cell
subclass of: CL_0002242
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001908
definition: A cell with more than one nucleus.
has_exact_synonym: multinucleated cells
has_exact_synonym: polynuclear cells
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: multinucleate cell
annotated property: definition
annotated target: A cell with more than one nucleus.
database_cross_reference: FB:ma
database_cross_reference: Wikipedia:Multinucleate

Axiom
annotated source: multinucleate cell
annotated property: has_exact_synonym
annotated target: multinucleated cells
database_cross_reference: Wikipedia:Multinucleate

Axiom
annotated source: multinucleate cell
annotated property: has_exact_synonym
annotated target: polynuclear cells
database_cross_reference: Wikipedia:Multinucleate

obsolete lymphoblast
type: Class
definition: OBSOLETE (was not defined before being made obsolete).
comment: Refers to an activated mature lymphocyte phenotype rather than a distinct cell type; consider using 'lymphocyte ; CL:0000542' or one of its children instead.
deprecated: true

obsolete T lymphoblast
type: Class
definition: OBSOLETE (was not defined before being made obsolete).
comment: Refers to an activated mature T lymphocyte phenotype rather than a distinct cell type; consider using 'T cell ; CL:0000084' or one of its children instead.
deprecated: true

obsolete B lymphoblast
type: Class
definition: OBSOLETE (was not defined before being made obsolete).
comment: Refers to an activated mature B lymphocyte phenotype rather than a distinct cell type; consider using 'B cell ; CL:0000236' or one of its children instead.
deprecated: true

erythrocyte
type: Class
equivalent class: Class
  intersection of: erythroid lineage cell
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0005840
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001945
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0002039
  intersection of: Restriction
    on property: capable of
    some values from: GO_0008015
  intersection of: Restriction
    on property: capable of
    some values from: GO_0015671
subclass of: blood cell
subclass of: oxygen accumulating cell
subclass of: erythroid lineage cell
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0005840
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001945
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0002039
subclass of: Restriction
  on property: develops from
  some values from: reticulocyte
definition: A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000424
database_cross_reference: CALOHA:TS-0290
database_cross_reference: FMA:81100
has_exact_synonym: RBC
has_exact_synonym: red blood cell
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: erythrocyte
annotated property: subClassOf
annotated target: erythroid lineage cell
is inferred: true

Axiom
annotated source: erythrocyte
annotated property: definition
annotated target: A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D004912

platelet
type: Class
subclass of: blood cell
subclass of: anucleate cell
subclass of: serotonin secreting cell
subclass of: myeloid cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001874
subclass of: Restriction
  on property: develops from
  some values from: megakaryocyte
subclass of: Restriction
  on property: capable of part of
  some values from: GO_0007596
definition: A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000132
database_cross_reference: CALOHA:TS-0803
database_cross_reference: FMA:62851
has_exact_synonym: anucleate thrombocyte
has_exact_synonym: blood platelet
has_exact_synonym: enucleate thrombocyte
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF.

Axiom
annotated source: platelet
annotated property: subClassOf
annotated target: myeloid cell
is inferred: true

Axiom
annotated source: platelet
annotated property: definition
annotated target: A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D001792
database_cross_reference: PMID:11110672
database_cross_reference: PMID:16987572
database_cross_reference: PMID:17204662
database_cross_reference: PMID:17479180
database_cross_reference: PMID:20414831
database_cross_reference: http://en.wikipedia.org/wiki/Platelet

phagocyte
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0006909
subclass of: motile cell
subclass of: stuff accumulating cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0006909
definition: Any cell capable of ingesting particulate matter via phagocytosis.
database_cross_reference: BTO:0001044
database_cross_reference: FMA:83806
database_cross_reference: MESH:D010586
database_cross_reference: ZFA:0009140
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: phagocyte
annotated property: definition
annotated target: Any cell capable of ingesting particulate matter via phagocytosis.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0721601464

Axiom
annotated source: phagocyte
annotated property: database_cross_reference
annotated target: ZFA:0009140
mapping justification: UnspecifiedMatching

macrophage
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002504
  intersection of: Restriction
    on property: capable of
    some values from: GO_0006909
  intersection of: Restriction
    on property: capable of
    some values from: GO_0031268
subclass of: mononuclear phagocyte
subclass of: professional antigen presenting cell
subclass of: myeloid leukocyte
subclass of: Restriction
  on property: develops from
  some values from: monocyte
subclass of: Restriction
  on property: capable of
  some values from: GO_0031268
definition: A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000801
database_cross_reference: CALOHA:TS-0587
database_cross_reference: FMA:63261
database_cross_reference: FMA:83585
database_cross_reference: MESH:D008264
database_cross_reference: ZFA:0009141
has_exact_synonym: histiocyte
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid.

Axiom
annotated source: macrophage
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: macrophage
annotated property: definition
annotated target: A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: PMID:16213494
database_cross_reference: PMID:1919437

Axiom
annotated source: macrophage
annotated property: database_cross_reference
annotated target: ZFA:0009141
mapping justification: UnspecifiedMatching

B cell
type: Class
equivalent class: Class
  intersection of: CL_0000945
  intersection of: Restriction
    on property: capable of
    some values from: GO_0019724
subclass of: CL_0000945
subclass of: Restriction
  on property: capable of
  some values from: GO_0019724
definition: A lymphocyte of B lineage that is capable of B cell mediated immunity.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000776
database_cross_reference: CALOHA:TS-0068
database_cross_reference: FMA:62869
database_cross_reference: MESH:D001402
database_cross_reference: VHOG:0001480
database_cross_reference: ZFA:0009142
has_exact_synonym: B lymphocyte
has_exact_synonym: B-cell
has_exact_synonym: B-lymphocyte
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: B cell
annotated property: subClassOf
annotated target: CL_0000945
is inferred: true

Axiom
annotated source: B cell
annotated property: definition
annotated target: A lymphocyte of B lineage that is capable of B cell mediated immunity.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149

Axiom
annotated source: B cell
annotated property: database_cross_reference
annotated target: ZFA:0009142
mapping justification: UnspecifiedMatching

keratinizing barrier epithelial cell
type: Class
subclass of: stratified squamous epithelial cell
subclass of: keratin accumulating cell
subclass of: CL_0002077
subclass of: Restriction
  on property: develops from
  some values from: surface ectodermal cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

non keratinizing barrier epithelial cell
type: Class
subclass of: stratified squamous epithelial cell
in_subset: human subset
in_subset: mouse subset

brush border epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: has part
    some values from: GO_0005903
subclass of: columnar/cuboidal epithelial cell
subclass of: Restriction
  on property: has part
  some values from: GO_0005903
definition: An epithelial cell characterized by the presence of a brush border on its apical surface, which increases the surface area for absorption.
database_cross_reference: ajpgi.00005.2011
database_cross_reference: PMID:25422372
database_cross_reference: ZFA:0009143
in_subset: human subset
in_subset: mouse subset
comment: All brush border cells are columnar-cuboidal. The formal logical definition of this term asserts this. Brush border epithelial cells are predominantly found lining the small intestine and the proximal tubules of the kidneys.

Axiom
annotated source: brush border epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009143
mapping justification: UnspecifiedMatching

stratified squamous epithelial cell
type: Class
equivalent class: Class
  intersection of: stratified epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0006915
subclass of: squamous epithelial cell
subclass of: stratified epithelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0006915
definition: A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009144
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: stratified squamous epithelial cell
annotated property: definition
annotated target: A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus.
database_cross_reference: PMID:30422572
database_cross_reference: Wikipedia:Epithelium
database_cross_reference: Wikipedia:Stratified_squamous_epithelium

Axiom
annotated source: stratified squamous epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009144
mapping justification: UnspecifiedMatching

stratified cuboidal epithelial cell
type: Class
equivalent class: Class
  intersection of: stratified epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0010077
subclass of: columnar/cuboidal epithelial cell
subclass of: stratified epithelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0010077
definition: A stratified epithelial cell that is part of cuboidal epithelium, characterized by multiple layers of cuboidal cells forming the apical layer. This provides a protective lining for ducts in large glands, such as sweat glands.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009145
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: stratified cuboidal epithelial cell
annotated property: definition
annotated target: A stratified epithelial cell that is part of cuboidal epithelium, characterized by multiple layers of cuboidal cells forming the apical layer. This provides a protective lining for ducts in large glands, such as sweat glands.
database_cross_reference: PMID:30422572
database_cross_reference: Wikipedia:Stratified_cuboidal_epithelium

Axiom
annotated source: stratified cuboidal epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009145
mapping justification: UnspecifiedMatching

Merkel cell
type: Class
subclass of: neuron associated cell (sensu Vertebrata)
subclass of: keratinocyte
subclass of: neurecto-epithelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002025
definition: A modified epidermal cell located in the stratum basale. They are found mostly in areas where sensory perception is acute. Merkel cells are closely associated with an expanded terminal bulb of an afferent myelinated nerve fiber.
present in taxon: NCBITaxon 9606
database_cross_reference: FMA:70548
database_cross_reference: ZFA:0009146
has_exact_synonym: Merkel's cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: Merkel cell
annotated property: subClassOf
annotated target: keratinocyte
database_cross_reference: PMID:19782676

Axiom
annotated source: Merkel cell
annotated property: definition
annotated target: A modified epidermal cell located in the stratum basale. They are found mostly in areas where sensory perception is acute. Merkel cells are closely associated with an expanded terminal bulb of an afferent myelinated nerve fiber.
database_cross_reference: MESH:D018862

Axiom
annotated source: Merkel cell
annotated property: database_cross_reference
annotated target: ZFA:0009146
mapping justification: UnspecifiedMatching

obsolete glial cell (sensu Vertebrata)
type: Class
definition: A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Form the myelin insulation of nervous pathways, guide neuronal migration during development, and exchange metabolites with neurons. Neuroglia have high-affinity transmitter uptake systems, voltage-dependent and transmitter-gated ion channels, and can release transmitters, but their role in signaling (as in many other functions) is unclear.
term tracker item: https://github.com/obophenotype/cell-ontology/issues/715
comment: This is a grouping class that is no longer needed or wanted.
deprecated: true

Axiom
annotated source: obsolete glial cell (sensu Vertebrata)
annotated property: definition
annotated target: A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Form the myelin insulation of nervous pathways, guide neuronal migration during development, and exchange metabolites with neurons. Neuroglia have high-affinity transmitter uptake systems, voltage-dependent and transmitter-gated ion channels, and can release transmitters, but their role in signaling (as in many other functions) is unclear.
database_cross_reference: MESH:D009457

transitional epithelial cell
type: Class
subclass of: epithelial cell
definition: A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium.
present in taxon: NCBITaxon 9606
database_cross_reference: FMA:66778
database_cross_reference: ZFA:0009148
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: transitional epithelial cell
annotated property: definition
annotated target: A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: transitional epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009148
mapping justification: UnspecifiedMatching

obsolete passage cell
type: Class
definition: Obsolete. Use PO:0000353 from Plant Ontology instead. Cell in exodermis or endodermis that remains thin walled when the associated cells develop thick secondary walls. Has casparian strip in endodermis.
term replaced by: PO_0000353
deprecated: true

Axiom
annotated source: obsolete passage cell
annotated property: definition
annotated target: Obsolete. Use PO:0000353 from Plant Ontology instead. Cell in exodermis or endodermis that remains thin walled when the associated cells develop thick secondary walls. Has casparian strip in endodermis.
database_cross_reference: ISBN:0471245208

Mauthner neuron
type: Class
subclass of: interneuron
database_cross_reference: ZFA:0009149
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: Mauthner neuron
annotated property: database_cross_reference
annotated target: ZFA:0009149
mapping justification: UnspecifiedMatching

Rohon-Beard neuron
type: Class
subclass of: primary sensory neuron (sensu Teleostei)
definition: Type of neuron that is a primary mechanosensory cell, with peripheral neurites innervating the skin with free nerve endings.
database_cross_reference: AAO:0010316
database_cross_reference: EFO:0003711
database_cross_reference: VHOG:0001484
database_cross_reference: ZFA:0009150
has_exact_synonym: Rohon Beard cell
has_exact_synonym: Rohon-Beard cell
has_related_synonym: RB neuron

Axiom
annotated source: Rohon-Beard neuron
annotated property: definition
annotated target: Type of neuron that is a primary mechanosensory cell, with peripheral neurites innervating the skin with free nerve endings.
database_cross_reference: VHOG:0001484

Axiom
annotated source: Rohon-Beard neuron
annotated property: database_cross_reference
annotated target: ZFA:0009150
mapping justification: UnspecifiedMatching

Axiom
annotated source: Rohon-Beard neuron
annotated property: has_exact_synonym
annotated target: Rohon Beard cell
database_cross_reference: VHOG:0001484

Axiom
annotated source: Rohon-Beard neuron
annotated property: has_related_synonym
annotated target: RB neuron
database_cross_reference: VHOG:0001484

obsolete microsporocyte
type: Class
definition: Obsolete. Use PO:0020047 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and forms four haploid (1n) microspores; also called microspore mother cell and, in seed plants, pollen mother cell.
term replaced by: PO_0020047
has_exact_synonym: pollen mother cell
has_exact_synonym: primary sporogenous cell
deprecated: true

Axiom
annotated source: obsolete microsporocyte
annotated property: definition
annotated target: Obsolete. Use PO:0020047 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and forms four haploid (1n) microspores; also called microspore mother cell and, in seed plants, pollen mother cell.
database_cross_reference: ISBN:0471245208

hatching gland cell
type: Class
subclass of: secretory cell
database_cross_reference: ZFA:0009151
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: hatching gland cell
annotated property: database_cross_reference
annotated target: ZFA:0009151
mapping justification: UnspecifiedMatching

obsolete megaspore
type: Class
definition: Obsolete. Use PO:0020019 from Plant Ontology instead. A haploid (1n) spore developing into a female gametophyte in heterosporous plants.
term replaced by: PO_0020019
deprecated: true

Axiom
annotated source: obsolete megaspore
annotated property: definition
annotated target: Obsolete. Use PO:0020019 from Plant Ontology instead. A haploid (1n) spore developing into a female gametophyte in heterosporous plants.
database_cross_reference: ISBN:0471245208

extramedullary cell
type: Class
subclass of: sensory neuron
database_cross_reference: ZFA:0009152
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: extramedullary cell
annotated property: database_cross_reference
annotated target: ZFA:0009152
mapping justification: UnspecifiedMatching

obsolete microspore
type: Class
definition: Obsolete. Use PO:0020048 from Plant Ontology instead. A haploid (1n) spore developing into a male gametophyte in heterosporous plants; the uninucleate pollen grain in seed plants.
term replaced by: PO_0020048
deprecated: true

Axiom
annotated source: obsolete microspore
annotated property: definition
annotated target: Obsolete. Use PO:0020048 from Plant Ontology instead. A haploid (1n) spore developing into a male gametophyte in heterosporous plants; the uninucleate pollen grain in seed plants.
database_cross_reference: ISBN:0471245208

eurydendroid cell
type: Class
subclass of: efferent neuron
database_cross_reference: ZFA:0009153
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: eurydendroid cell
annotated property: database_cross_reference
annotated target: ZFA:0009153
mapping justification: UnspecifiedMatching

obsolete egg cell
type: Class
definition: Obsolete. Use PO:0020094 from Plant Ontology instead. The female gamete of plants.
term replaced by: PO_0020094
has_exact_synonym: female gametophyte egg cell
deprecated: true

Axiom
annotated source: obsolete egg cell
annotated property: definition
annotated target: Obsolete. Use PO:0020094 from Plant Ontology instead. The female gamete of plants.
database_cross_reference: TAIR:lr

eukaryotic cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: in taxon
    some values from: NCBITaxon 2759
subclass of: cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 2759
disjoint with: prokaryotic cell
definition: Any cell that in taxon some Eukaryota.
database_cross_reference: MESH:D005057
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: eukaryotic cell
annotated property: definition
annotated target: Any cell that in taxon some Eukaryota.
database_cross_reference: FBC:Autogenerated

uric acid accumulating cell
type: Class
subclass of: stuff accumulating cell
in_subset: human subset
in_subset: mouse subset

Eumycetozoan cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: in taxon
    some values from: NCBITaxon_142796
subclass of: eukaryotic cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon_142796
definition: Any cell that in taxon some Eumycetozoa.

Axiom
annotated source: Eumycetozoan cell
annotated property: definition
annotated target: Any cell that in taxon some Eumycetozoa.
database_cross_reference: FBC:Autogenerated

obsolete fiber tracheid
type: Class
definition: Obsolete. Use PO:0000355 from Plant Ontology instead. A fiber like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit like apertures.
term replaced by: PO_0000355
deprecated: true

Axiom
annotated source: obsolete fiber tracheid
annotated property: definition
annotated target: Obsolete. Use PO:0000355 from Plant Ontology instead. A fiber like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit like apertures.
database_cross_reference: ISBN:0471245208

obsolete aggregate cell
type: Class
term replaced by: DDANAT_0000403
deprecated: true

obsolete mucilage cell
type: Class
definition: Obsolete. Use PO:0000373 from Plant Ontology instead. Cell containing mucilages or gums or similar carbohydrate material characterized by the property of swelling in water.
term replaced by: PO_0000373
deprecated: true

Axiom
annotated source: obsolete mucilage cell
annotated property: definition
annotated target: Obsolete. Use PO:0000373 from Plant Ontology instead. Cell containing mucilages or gums or similar carbohydrate material characterized by the property of swelling in water.
database_cross_reference: ISBN:0471245208

obsolete anterior cell
type: Class
consider: http://purl.obolibrary.org/obo/DDANAT_0000002
consider: false
comment: Obsoleted becuase this term has an overly general name, no definition, and by it's classification appears to refer to a very specific cell type in dictystelium. If needed, the term should be in DDANAT - probably as a subclass of http://purl.obolibrary.org/obo/DDANAT_0000002
deprecated: true

obsolete guard mother cell
type: Class
definition: Obsolete. Use PO:0000351 from Plant Ontology instead. An epidermal cell that divides to produce the guard cells.
term replaced by: PO_0000351
deprecated: true

Axiom
annotated source: obsolete guard mother cell
annotated property: definition
annotated target: Obsolete. Use PO:0000351 from Plant Ontology instead. An epidermal cell that divides to produce the guard cells.
database_cross_reference: ISBN:0471245208

obsolete vegetative cell (sensu Mycetozoa)
type: Class
term replaced by: DDANAT_0000002
deprecated: true

obsolete phloem initial
type: Class
definition: Obsolete. Use PO:0000400 from Plant Ontology instead. A cambial cell on the phloem side of the cambial zone that is the source of one or more cells arising by periclinal divisions and differentiating into phloem elements with or without additional divisions in various planes.
term replaced by: PO_0000400
has_exact_synonym: phloem mother cell
deprecated: true

Axiom
annotated source: obsolete phloem initial
annotated property: definition
annotated target: Obsolete. Use PO:0000400 from Plant Ontology instead. A cambial cell on the phloem side of the cambial zone that is the source of one or more cells arising by periclinal divisions and differentiating into phloem elements with or without additional divisions in various planes.
database_cross_reference: ISBN:0471245208

obsolete anterior like cell
type: Class
term replaced by: DDANAT_0000404
deprecated: true

obsolete meristemoid
type: Class
definition: Obsolete. Use PO:0004011 from Plant Ontology instead. A cell constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells.
term replaced by: PO_0004011
deprecated: true

Axiom
annotated source: obsolete meristemoid
annotated property: definition
annotated target: Obsolete. Use PO:0004011 from Plant Ontology instead. A cell constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells.
database_cross_reference: ISBN:0471245208

obsolete prespore cell
type: Class
term replaced by: DDANAT_0000405
deprecated: true

obsolete sieve element
type: Class
definition: Obsolete. Consult Plant Ontology instead. The cell in the phloem tissue concerned with mainly longitudinal conduction of food materials. Classified into sieve cell and sieve tube member.
deprecated: true

Axiom
annotated source: obsolete sieve element
annotated property: definition
annotated target: Obsolete. Consult Plant Ontology instead. The cell in the phloem tissue concerned with mainly longitudinal conduction of food materials. Classified into sieve cell and sieve tube member.
database_cross_reference: ISBN:0471245208

obsolete prestalk cell
type: Class
term replaced by: DDANAT_0000406
deprecated: true

obsolete subsidiary cell
type: Class
definition: Obsolete. Use PO:0000284 from Plant Ontology instead. An epidermal cell associated with a stoma and at least morphologically distinguishable from the epidermal cells composing the groundmass of the tissue.
term replaced by: PO_0000284
deprecated: true

Axiom
annotated source: obsolete subsidiary cell
annotated property: definition
annotated target: Obsolete. Use PO:0000284 from Plant Ontology instead. An epidermal cell associated with a stoma and at least morphologically distinguishable from the epidermal cells composing the groundmass of the tissue.
database_cross_reference: ISBN:047124520

obsolete prestalk A cell
type: Class
term replaced by: DDANAT_0000408
deprecated: true

obsolete cambial initial
type: Class
definition: OBSOLETE, use term from Plant Ontology. A cell localized in the vascular cambium or phellogen. Its periclinal division can contribute cells either to the outside or to the inside of the axis; in vascular cambium, classified into fusiform initials (source of axial cells of xylem and phloem) and ray initials (source of the ray cells).
comment: replaced_by PO:0000295
deprecated: true

Axiom
annotated source: obsolete cambial initial
annotated property: definition
annotated target: OBSOLETE, use term from Plant Ontology. A cell localized in the vascular cambium or phellogen. Its periclinal division can contribute cells either to the outside or to the inside of the axis; in vascular cambium, classified into fusiform initials (source of axial cells of xylem and phloem) and ray initials (source of the ray cells).
database_cross_reference: ISBN:0471245208

obsolete prestalk AB cell
type: Class
term replaced by: DDANAT_0000410
deprecated: true

CL_0000274
type: Class
has obsolescence reason: IAO_0000227
term replaced by: obsolete fusiform initial
deprecated: true

obsolete prestalk B cell
type: Class
term replaced by: DDANAT_0000409
deprecated: true

obsolete sclerenchyma cell
type: Class
definition: Obsolete. Use PO:0000077 from Plant Ontology instead. Cell variable in form and size, being more or less thick, often lignified, secondary walls. Belongs to the category of subcells and may or may not be devoid of protoplast at maturity.
term replaced by: PO_0000077
deprecated: true

Axiom
annotated source: obsolete sclerenchyma cell
annotated property: definition
annotated target: Obsolete. Use PO:0000077 from Plant Ontology instead. Cell variable in form and size, being more or less thick, often lignified, secondary walls. Belongs to the category of subcells and may or may not be devoid of protoplast at maturity.
database_cross_reference: ISBN:0471245208

obsolete prestalk I cell
type: Class
definition: OBSOLETE: Initial population of prestalk cells that activate the ecmA promoter at the mound stage and that presumably further differentiate into pstA and pstO cells.
term replaced by: DDANAT_0000406
comment: This cell type does not exist in Dictyostelium. it has been long deleted in their anatomy ontology.
deprecated: true

Axiom
annotated source: obsolete prestalk I cell
annotated property: definition
annotated target: OBSOLETE: Initial population of prestalk cells that activate the ecmA promoter at the mound stage and that presumably further differentiate into pstA and pstO cells.
database_cross_reference: DictyBase:DDB

obsolete central cell
type: Class
definition: Obsolete. Use PO:0020090 from Plant Ontology instead. OBSOLETED, use term from Plant Ontology. A cell containing the two polar nuclei which, after double fertilization, will develop into the endosperm.
term replaced by: PO_0020090
deprecated: true

Axiom
annotated source: obsolete central cell
annotated property: definition
annotated target: Obsolete. Use PO:0020090 from Plant Ontology instead. OBSOLETED, use term from Plant Ontology. A cell containing the two polar nuclei which, after double fertilization, will develop into the endosperm.
database_cross_reference: TAIR:lr

obsolete prestalk 0 cell
type: Class
term replaced by: DDANAT_0000407
deprecated: true

obsolete generative cell
type: Class
definition: Obsolete. Use PO:0020097 from Plant Ontology instead. The cell that will give rise to the generative nuclei which will participate in fertilization.
term replaced by: PO_0020097
deprecated: true

Axiom
annotated source: obsolete generative cell
annotated property: definition
annotated target: Obsolete. Use PO:0020097 from Plant Ontology instead. The cell that will give rise to the generative nuclei which will participate in fertilization.
database_cross_reference: TAIR:lr

obsolete pstAB/ALC
type: Class
term replaced by: DDANAT_0000411
deprecated: true

obsolete trichome
type: Class
definition: Obsolete. Use PO:0000282 from Plant Ontology instead. An outgrowth from the epidermis. Trichomes vary in size and complexity and include hairs, scales, and other structures and may be glandular. In Arabidopsis, patterning of trichome development is not random but does not appear to be lineage-based like stomata.
term replaced by: PO_0000282
deprecated: true

Axiom
annotated source: obsolete trichome
annotated property: definition
annotated target: Obsolete. Use PO:0000282 from Plant Ontology instead. An outgrowth from the epidermis. Trichomes vary in size and complexity and include hairs, scales, and other structures and may be glandular. In Arabidopsis, patterning of trichome development is not random but does not appear to be lineage-based like stomata.
database_cross_reference: ISBN:0471245208
database_cross_reference: PMID:10938806

obsolete pstO/ALC
type: Class
term replaced by: DDANAT_0000412
deprecated: true

obsolete companion cell
type: Class
definition: Obsolete. Use PO:0000071 from Plant Ontology instead. A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member.
term replaced by: PO_0000071
deprecated: true

Axiom
annotated source: obsolete companion cell
annotated property: definition
annotated target: Obsolete. Use PO:0000071 from Plant Ontology instead. A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member.
database_cross_reference: ISBN:0879015322

obsolete stalk cell
type: Class
term replaced by: DDANAT_0000413
deprecated: true

hyphal cell
type: Class
subclass of: fungal cell
definition: A cell of a filament of a fungal mycelium.

Axiom
annotated source: hyphal cell
annotated property: definition
annotated target: A cell of a filament of a fungal mycelium.
database_cross_reference: ISBN:08199377X

eye photoreceptor cell
type: Class
equivalent class: Class
  intersection of: photoreceptor cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000970
subclass of: neuronal receptor cell
subclass of: photoreceptor cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000970
definition: Any photoreceptor cell that is part of some eye.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009154
in_subset: cellxgene subset
in_subset: eye_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: eye photoreceptor cell
annotated property: definition
annotated target: Any photoreceptor cell that is part of some eye.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: eye photoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009154
mapping justification: UnspecifiedMatching

obsolete synergid
type: Class
definition: Obsolete. Use PO:0000191 from Plant Ontology instead. A cell in the micropylar end of the embryo sac associated with the egg in the egg apparatus of angiosperms. Plays a vital role in fertilization.
term replaced by: PO_0000191
deprecated: true

Axiom
annotated source: obsolete synergid
annotated property: definition
annotated target: Obsolete. Use PO:0000191 from Plant Ontology instead. A cell in the micropylar end of the embryo sac associated with the egg in the egg apparatus of angiosperms. Plays a vital role in fertilization.
database_cross_reference: ISBN:047125208

obsolete chemotactic amoeboid cell (sensu Mycetozoa)
type: Class
term replaced by: DDANAT_0000402
deprecated: true

obsolete xylem fiber cell
type: Class
definition: Obsolete. Use PO:0000274 from Plant Ontology instead. A fiber of the xylem tissue, Two types are recognized in the secondary xylem: fiber tracheids and libriform fibers.
term replaced by: PO_0000274
deprecated: true

Axiom
annotated source: obsolete xylem fiber cell
annotated property: definition
annotated target: Obsolete. Use PO:0000274 from Plant Ontology instead. A fiber of the xylem tissue, Two types are recognized in the secondary xylem: fiber tracheids and libriform fibers.
database_cross_reference: ISBN:0471245208

obsolete spore (sensu Mycetozoa)
type: Class
term replaced by: DDANAT_0000414
deprecated: true

obsolete guard cell
type: Class
definition: Obsolete. Use PO:0000293 from Plant Ontology instead. One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor.
term replaced by: PO_0000293
has_exact_synonym: stomatal guard cell
deprecated: true

Axiom
annotated source: obsolete guard cell
annotated property: definition
annotated target: Obsolete. Use PO:0000293 from Plant Ontology instead. One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor.
database_cross_reference: ISBN:0471245208

structural cell
type: Class
subclass of: cell
definition: A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism.
database_cross_reference: ZFA:0005745
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: structural cell
annotated property: definition
annotated target: A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism.
database_cross_reference: TAIR:sr

Axiom
annotated source: structural cell
annotated property: database_cross_reference
annotated target: ZFA:0005745
mapping justification: UnspecifiedMatching

obsolete sieve cell
type: Class
definition: Obsolete. Consult Plant Ontology instead. A type of sieve element that has relatively undifferentiated sieve areas (with narrow pores), rather uniform in structure on all walls; that is, there are no sieve plates. Typical of gymnosperms and lower vascular plants.
deprecated: true

Axiom
annotated source: obsolete sieve cell
annotated property: definition
annotated target: Obsolete. Consult Plant Ontology instead. A type of sieve element that has relatively undifferentiated sieve areas (with narrow pores), rather uniform in structure on all walls; that is, there are no sieve plates. Typical of gymnosperms and lower vascular plants.
database_cross_reference: ISBN:0471245208

somatotropin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030252
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0030252
definition: A peptide hormone secreting cell that produces growth hormone, somatotropin.
database_cross_reference: ZFA:0009155
has_exact_synonym: growth hormone secreting cell
has_exact_synonym: somatotrophin secreting cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: somatotropin secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that produces growth hormone, somatotropin.
database_cross_reference: GOC:tfm
database_cross_reference: SANBI:mhl

Axiom
annotated source: somatotropin secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009155
mapping justification: UnspecifiedMatching

obsolete vegetative cell
type: Class
definition: Obsolete. Use PO:0020099 from Plant Ontology instead. Cell type formed after the first mitotic division of the microgametophye, The nucleus of this cell migrates to the tip of the pollen tube after germination and disintegrates when the pollen tube penetrates the nucellus.
term replaced by: PO_0020099
deprecated: true

Axiom
annotated source: obsolete vegetative cell
annotated property: definition
annotated target: Obsolete. Use PO:0020099 from Plant Ontology instead. Cell type formed after the first mitotic division of the microgametophye, The nucleus of this cell migrates to the tip of the pollen tube after germination and disintegrates when the pollen tube penetrates the nucellus.
database_cross_reference: ISBN:0140514031
database_cross_reference: TAIR:lr

obsolete socket cell
type: Class
definition: Obsolete. Use PO:0000115 from Plant Ontology instead. A cell that surrounds a trichome and provides support for the trichome.
term replaced by: PO_0000115
deprecated: true

Axiom
annotated source: obsolete socket cell
annotated property: definition
annotated target: Obsolete. Use PO:0000115 from Plant Ontology instead. A cell that surrounds a trichome and provides support for the trichome.
database_cross_reference: PMID:10938806

obsolete xylem element
type: Class
definition: Obsolete. Use PO:0000273 from Plant Ontology instead. A cell composing the xylem.
term replaced by: PO_0000273
deprecated: true

Axiom
annotated source: obsolete xylem element
annotated property: definition
annotated target: Obsolete. Use PO:0000273 from Plant Ontology instead. A cell composing the xylem.
database_cross_reference: ISBN:0471245208

obsolete trichoblast
type: Class
definition: OBSOLETED. Commonly used for a cell in root epidermis that gives rise to a root hair. The daughter cell produced by the asymmetric division of a root epidermal cell that gives rise to a root hair.
comment: Obsoleted. Use trichoblast from the plant ontology (PO:0000262).
deprecated: true

Axiom
annotated source: obsolete trichoblast
annotated property: definition
annotated target: OBSOLETED. Commonly used for a cell in root epidermis that gives rise to a root hair. The daughter cell produced by the asymmetric division of a root epidermal cell that gives rise to a root hair.
database_cross_reference: ISBN:0471245208

gamete
type: Class
equivalent class: Class
  intersection of: germ cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001375
  intersection of: Restriction
    on property: capable of
    some values from: GO_0009566
subclass of: haploid cell
subclass of: germ cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0009566
definition: A mature sexual reproductive cell having a single set of unpaired chromosomes.
description: Gametes are reproductive cells essential for sexual reproduction in eukaryotic organisms, including humans, animals, and many plants. These cells are haploid, containing half the genome or only one set of chromosomes, which is a contrast to the diploid state (two sets of chromosomes) found in most cells in a multicellular organism. This reduction in genetic material is crucial since it allows for the re-establishment of the diploid number of chromosomes when two gametes merge to form a diploid zygote during fertilization. There are two major types of gametes in animals: sperm cells in males and egg (or ova) in females. These gametes contribute equally to the genetic makeup of the offspring but are morphologically and functionally distinct. Sperm cells (or spermatozoa) are characterized by their motility, small size, and large quantities; they are produced continuously in vast numbers through a process called spermatogenesis in the male gonads or testes. Female gametes are much larger, fewer in numbers, and are not motile; they undergo a development process known as oogenesis, which takes place within the ovaries. The egg also contributes most of the cytoplasm and organelles (including mitochondria) to the zygote that are required for initial cell division stages after fertilization. Gametes have a primary role in sexual reproduction and genetic variation, which aids in evolution. The formation of gametes involves a special type of cell division called meiosis that introduces genetic diversity via the process of recombination and independent assortment. Following the fusion of male and female gametes, the combination of paternal and maternal genetic material in the zygote allows for genetic recombination, which is a fundamental source of genetic variation and, thus, evolution. Therefore, gametes not only are critical to the inception of new individuals but also contribute to species survival and evolution. (This extended description was generated by ChatGPT and revie…
database_cross_reference: CALOHA:TS-0395
database_cross_reference: FBbt:00005412
database_cross_reference: FMA:18649
database_cross_reference: ZFA:0009156
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000300
has_exact_synonym: haploid nucleated cell
has_related_synonym: haploid germ cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: gamete
annotated property: subClassOf
annotated target: germ cell
is inferred: true

Axiom
annotated source: gamete
annotated property: definition
annotated target: A mature sexual reproductive cell having a single set of unpaired chromosomes.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: gamete
annotated property: description
annotated target: Gametes are reproductive cells essential for sexual reproduction in eukaryotic organisms, including humans, animals, and many plants. These cells are haploid, containing half the genome or only one set of chromosomes, which is a contrast to the diploid state (two sets of chromosomes) found in most cells in a multicellular organism. This reduction in genetic material is crucial since it allows for the re-establishment of the diploid number of chromosomes when two gametes merge to form a diploid zygote during fertilization. There are two major types of gametes in animals: sperm cells in males and egg (or ova) in females. These gametes contribute equally to the genetic makeup of the offspring but are morphologically and functionally distinct. Sperm cells (or spermatozoa) are characterized by their motility, small size, and large quantities; they are produced continuously in vast numbers through a process called spermatogenesis in the male gonads or testes. Female gametes are much larger, fewer in numbers, and are not motile; they undergo a development process known as oogenesis, which takes place within the ovaries. The egg also contributes most of the cytoplasm and organelles (including mitochondria) to the zygote that are required for initial cell division stages after fertilization. Gametes have a primary role in sexual reproduction and genetic variation, which aids in evolution. The formation of gametes involves a special type of cell division called meiosis that introduces genetic diversity via the process of recombination and independent assortment. Following the fusion of male and female gametes, the combination of paternal and maternal genetic material in the zygote allows for genetic recombination, which is a fundamental source of genetic variation and, thus, evolution. Therefore, gametes not only are critical to the inception of new individuals but also contribute to species survival and evolution. (This extended description was generated by ChatGPT and revie…
database_cross_reference: DOI:10.1038/s41586-020-2347-0
database_cross_reference: DOI:10.3389/fcell.2022.1040708
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK10008/
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK553142/

Axiom
annotated source: gamete
annotated property: database_cross_reference
annotated target: FBbt:00005412
mapping justification: ManualMappingCuration

Axiom
annotated source: gamete
annotated property: database_cross_reference
annotated target: ZFA:0009156
mapping justification: UnspecifiedMatching

pole cell
type: Class
subclass of: primordial germ cell
definition: A primordial germ cell of insects. Such cells form at the posterior pole of the early embryo.
database_cross_reference: FBbt:00000092
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pole cell
annotated property: definition
annotated target: A primordial germ cell of insects. Such cells form at the posterior pole of the early embryo.
database_cross_reference: doi:10.1017/CBO9780511818202.015

Axiom
annotated source: pole cell
annotated property: database_cross_reference
annotated target: FBbt:00000092
mapping justification: ManualMappingCuration

obsolete IgM B cell
type: Class
definition: OBSOLETE (was not defined before being made obsolete).
comment: Not a differentiation state per se; consider using 'B cell ; CL:0000236' or one of its children instead.
deprecated: true

obsolete IgG B cell
type: Class
definition: OBSOLETE (was not defined before being made obsolete).
comment: Not a differentiation state per se, and IgG isotypes vary by species; consider using 'B cell ; CL:0000236' or one of its children instead.
deprecated: true

obsolete IgA B cell
type: Class
definition: OBSOLETE (was not defined before being made obsolete).
comment: Not a differentiation state per se, and IgA isotypes vary by species. Consider using 'B cell ; CL:0000236' or one of its children instead.
deprecated: true

obsolete IgE B cell
type: Class
definition: OBSOLETE (was not defined before being made obsolete).
comment: Not a differentiation state per se; consider using 'B cell ; CL:0000236' or one of its children instead.
deprecated: true

crystallin accumulating cell
type: Class
subclass of: stuff accumulating cell
has_exact_synonym: lens cell
in_subset: eye_upper_slim
in_subset: human subset
in_subset: mouse subset

tracheal epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0003126
subclass of: CL_0002202
subclass of: Restriction
  on property: part of
  some values from: UBERON_0003126
subclass of: Restriction
  on property: develops from
  some values from: tracheoblast
definition: An epithelial cell found in the trachea.
database_cross_reference: FMA:74793
has_exact_synonym: tracheocyte
in_subset: human subset
in_subset: mouse subset
comment: This class is for the vertebrate tracheal structure. For the analagous insect cell type, see 'respiratory tube epithelial cell'

Axiom
annotated source: tracheal epithelial cell
annotated property: subClassOf
annotated target: CL_0002202
is inferred: true

Axiom
annotated source: tracheal epithelial cell
annotated property: definition
annotated target: An epithelial cell found in the trachea.
database_cross_reference: GOC:tfm

metal ion accumulating cell
type: Class
subclass of: stuff accumulating cell
in_subset: human subset
in_subset: mouse subset

copper accumulating cell
type: Class
subclass of: metal ion accumulating cell
has_exact_synonym: cuprophilic cell
in_subset: human subset
in_subset: mouse subset

iron accumulating cell
type: Class
subclass of: metal ion accumulating cell
in_subset: human subset
in_subset: mouse subset

keratin accumulating cell
type: Class
subclass of: stuff accumulating cell
database_cross_reference: ZFA:0009157
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: keratin accumulating cell
annotated property: database_cross_reference
annotated target: ZFA:0009157
mapping justification: UnspecifiedMatching

keratinocyte
type: Class
equivalent class: Class
  intersection of: keratinizing barrier epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001003
subclass of: keratinizing barrier epithelial cell
subclass of: epidermal cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001003
subclass of: Restriction
  on property: capable of
  some values from: GO_0002775
subclass of: Restriction
  on property: capable of
  some values from: GO_0002776
subclass of: Restriction
  on property: capable of
  some values from: GO_0090023
definition: An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000667
database_cross_reference: CALOHA:TS-0500
database_cross_reference: FMA:62879
database_cross_reference: ZFA:0009158
has_exact_synonym: keratinized cell of epidermis
has_exact_synonym: malpighian cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Keratinocytes are reportedly CDw210a-negative, CDw210b-positive, CD281-positive, CD282-positive, CD285-positive, IL22Ra1-positive, Human keratinocytes are reportedly capable of secreting BD-2, BD-3, hCAP-18, CXCL1, CXCL5, CXCL8, elafin, MMP-3, NGAL, PDGF-A, S100A7, S100A8, and S100A9. Transcription factors: STAT3-positive.

Axiom
annotated source: keratinocyte
annotated property: subClassOf
annotated target: keratinizing barrier epithelial cell
is inferred: true

Axiom
annotated source: keratinocyte
annotated property: subClassOf
annotated target: epidermal cell
is inferred: true

Axiom
annotated source: keratinocyte
annotated property: definition
annotated target: An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell.
database_cross_reference: GOC:dsd
database_cross_reference: MESH:D015603
database_cross_reference: PMID:15582983
database_cross_reference: PMID:15749908
database_cross_reference: PMID:19727116
database_cross_reference: http://en.wikipedia.org/wiki/Keratinocyte

Axiom
annotated source: keratinocyte
annotated property: database_cross_reference
annotated target: ZFA:0009158
mapping justification: UnspecifiedMatching

serous secreting cell
type: Class
subclass of: seromucus secreting cell
definition: Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid.
database_cross_reference: BTO:0003687
database_cross_reference: FMA:62511
has_exact_synonym: serous cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: serous secreting cell
annotated property: definition
annotated target: Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651
database_cross_reference: ISBN:0721662544

milk secreting cell
type: Class
subclass of: secretory cell
in_subset: human subset
in_subset: mouse subset

tear secreting cell
type: Class
subclass of: exocrine cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001817
definition: A cell secreting tears, the fluid secreted by the lacrimal glands. This fluid moistens the conjunctiva and cornea.
has_exact_synonym: tears secreting cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: tear secreting cell
annotated property: definition
annotated target: A cell secreting tears, the fluid secreted by the lacrimal glands. This fluid moistens the conjunctiva and cornea.
database_cross_reference: MESH:D013666

obsolete ray initial
type: Class
definition: Obsolete. Use PO:0000082 from Plant Ontology instead. A meristemic ray cell in the vascular cambium that gives rise to ray cells of the secondary xylem and secondary phloem.
term replaced by: PO_0000082
deprecated: true

Axiom
annotated source: obsolete ray initial
annotated property: definition
annotated target: Obsolete. Use PO:0000082 from Plant Ontology instead. A meristemic ray cell in the vascular cambium that gives rise to ray cells of the secondary xylem and secondary phloem.
database_cross_reference: ISBN:0471245208

sebocyte
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001821
subclass of: glandular secretory epithelial cell
subclass of: exocrine cell
subclass of: epidermal cell
subclass of: CL_0002308
subclass of: CL_2000021
definition: An epithelial cell that is part of a sebaceous gland. This cell produces and secretes sebum, an oily, lipid-rich substance, through holocrine secretion where the entire cell ruptures to release its contents.
present in taxon: NCBITaxon 9606
has_exact_synonym: sebum secreting cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: sebocyte
annotated property: definition
annotated target: An epithelial cell that is part of a sebaceous gland. This cell produces and secretes sebum, an oily, lipid-rich substance, through holocrine secretion where the entire cell ruptures to release its contents.
database_cross_reference: MESH:D012629
database_cross_reference: PMID:19944183

sweat secreting cell
type: Class
subclass of: glandular secretory epithelial cell
definition: A cell secreting sweat, the fluid excreted by the sweat glands of mammals. It consists of water containing sodium chloride, phosphate, urea, ammonia, and other waste products.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: sweat secreting cell
annotated property: definition
annotated target: A cell secreting sweat, the fluid excreted by the sweat glands of mammals. It consists of water containing sodium chloride, phosphate, urea, ammonia, and other waste products.
database_cross_reference: MESH:D013542

mucus secreting cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0070254
subclass of: seromucus secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0070254
definition: Any cell that is capable of some mucus secretion.
database_cross_reference: BTO:0003689
database_cross_reference: ZFA:0009159
has_exact_synonym: mucous cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: mucus secreting cell
annotated property: definition
annotated target: Any cell that is capable of some mucus secretion.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: mucus secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009159
mapping justification: UnspecifiedMatching

obsolete megasporocyte
type: Class
definition: Obsolete. Use PO:0000431 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores; also called megaspore mother cell.
term replaced by: PO_0000431
has_exact_synonym: archesporial cell
has_exact_synonym: megaspore mother cell
deprecated: true

Axiom
annotated source: obsolete megasporocyte
annotated property: definition
annotated target: Obsolete. Use PO:0000431 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores; also called megaspore mother cell.
database_cross_reference: ISBN:0471245208

obsolete seminal fluid secreting cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1149
term replaced by: secretory cell
consider: CL_1001597
deprecated: true

pulmonary alveolar epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0004821
subclass of: epithelial cell of lung
subclass of: Restriction
  on property: part of
  some values from: UBERON_0004821
definition: An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates.
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-09-02T08:27:21Z
database_cross_reference: BTO:0000395
database_cross_reference: CALOHA:TS-2168
database_cross_reference: FMA:62499
database_cross_reference: MESH:D056809
has_exact_synonym: alveolar epithelial cell
has_exact_synonym: alveolus of lung epithelial cell
has_exact_synonym: epithelial cell of alveolus of lung
has_exact_synonym: pneumocyte
has_exact_synonym: pneumonocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pulmonary alveolar epithelial cell
annotated property: definition
annotated target: An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:20054144
database_cross_reference: PMID:29463737

Axiom
annotated source: pulmonary alveolar epithelial cell
annotated property: has_exact_synonym
annotated target: pneumocyte
database_cross_reference: PMID:32491474

lysozyme secreting cell
type: Class
subclass of: protein secreting cell
in_subset: human subset
in_subset: mouse subset

metanephric mesenchyme stem cell
type: Class
subclass of: BFO_0000002
subclass of: mesenchymal stem cell
subclass of: Restriction
  on property: develops from
  some values from: mesodermal cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

stuff accumulating cell
type: Class
subclass of: cell
definition: A cell that is specialised to accumulate a particular substance(s).
in_subset: human subset
in_subset: mouse subset
in_subset: upper level

Axiom
annotated source: stuff accumulating cell
annotated property: definition
annotated target: A cell that is specialised to accumulate a particular substance(s).
database_cross_reference: FB:ma

glycogen accumulating cell
type: Class
subclass of: stuff accumulating cell
in_subset: human subset
in_subset: mouse subset

extracellular matrix secreting cell
type: Class
subclass of: stromal cell
database_cross_reference: ZFA:0009162
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: extracellular matrix secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009162
mapping justification: UnspecifiedMatching

obsolete myelin accumulating cell
type: Class
has obsolescence reason: IAO_0000227
term replaced by: CL_4023154
comment: see: https://github.com/obophenotype/cell-ontology/issues/161
deprecated: true

oxygen accumulating cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0015671
subclass of: cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0015671
definition: Any cell that is capable of some oxygen transport.
database_cross_reference: ZFA:0009164
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: oxygen accumulating cell
annotated property: definition
annotated target: Any cell that is capable of some oxygen transport.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: oxygen accumulating cell
annotated property: database_cross_reference
annotated target: ZFA:0009164
mapping justification: UnspecifiedMatching

obsolete collenchymal cell
type: Class
definition: Obsolete. Use PO:0000075 from Plant Ontology instead. An elongated living cell with unevenly thickened nonlignified primary walls.
term replaced by: PO_0000075
deprecated: true

Axiom
annotated source: obsolete collenchymal cell
annotated property: definition
annotated target: Obsolete. Use PO:0000075 from Plant Ontology instead. An elongated living cell with unevenly thickened nonlignified primary walls.
database_cross_reference: ISBN:0471245208

obsolete tracheid
type: Class
definition: Obsolete. Use PO:0000301 from Plant Ontology instead. A tracheary element of the xylem that has no perforations, as contrasted with a vessel member. May occur in primary and in secondary xylem. May have any kind of secondary wall thickening found in tracheary elements.
term replaced by: PO_0000301
deprecated: true

Axiom
annotated source: obsolete tracheid
annotated property: definition
annotated target: Obsolete. Use PO:0000301 from Plant Ontology instead. A tracheary element of the xylem that has no perforations, as contrasted with a vessel member. May occur in primary and in secondary xylem. May have any kind of secondary wall thickening found in tracheary elements.
database_cross_reference: ISBN:0471245208

obsolete atrichoblast
type: Class
definition: OBSOLETE, use term from Plant Ontology. A cell formed after asymmetric division of root epidermal cell that does not give rise to a root hair.
term replaced by: PO_0020090
has_related_synonym: non-hair cell
deprecated: true

Axiom
annotated source: obsolete atrichoblast
annotated property: definition
annotated target: OBSOLETE, use term from Plant Ontology. A cell formed after asymmetric division of root epidermal cell that does not give rise to a root hair.
database_cross_reference: ISBN:0387987819

migratory neural crest cell
type: Class
subclass of: motile cell
subclass of: CL_0011012
subclass of: CL_0011026
subclass of: Restriction
  on property: develops from
  some values from: CL_0007004
definition: A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.
database_cross_reference: FMA:86667
database_cross_reference: ZFA:0007086
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: migratory neural crest cell
annotated property: definition
annotated target: A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.
database_cross_reference: doi:10.1016/j.stem.2015.02.017

Axiom
annotated source: migratory neural crest cell
annotated property: database_cross_reference
annotated target: ZFA:0007086
mapping justification: UnspecifiedMatching

vegetative cell (sensu Fungi)
type: Class
subclass of: fungal cell
database_cross_reference: BTO:0002307
database_cross_reference: FAO:0000032
has_related_synonym: yeast-form

mesenchyme condensation cell
type: Class
subclass of: CL_0008019
definition: A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.
database_cross_reference: ZFA:0009166
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: mesenchyme condensation cell
annotated property: definition
annotated target: A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:5025404

Axiom
annotated source: mesenchyme condensation cell
annotated property: database_cross_reference
annotated target: ZFA:0009166
mapping justification: UnspecifiedMatching

adrenal medulla chromaffin cell
type: Class
equivalent class: Class
  intersection of: chromaffin cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001236
subclass of: biogenic amine secreting cell
subclass of: CL_1000426
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001236
subclass of: Restriction
  on property: develops from
  some values from: migratory trunk neural crest cell
definition: A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation.
database_cross_reference: FMA:69262
database_cross_reference: ZFA:0009167
has_exact_synonym: medullary chromaffin cell of adrenal gland
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: adrenal medulla chromaffin cell
annotated property: definition
annotated target: A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation.
database_cross_reference: GOC:tfm
database_cross_reference: http://www.britannica.com/EBchecked/topic/6405/adrenal-gland

Axiom
annotated source: adrenal medulla chromaffin cell
annotated property: database_cross_reference
annotated target: ZFA:0009167
mapping justification: UnspecifiedMatching

Axiom
annotated source: adrenal medulla chromaffin cell
annotated property: has_exact_synonym
annotated target: medullary chromaffin cell of adrenal gland
database_cross_reference: FMA:69262

CL_0000337
type: Class
has obsolescence reason: IAO_0000227
term replaced by: neuroblast (sensu Vertebrata)
deprecated: true

neuroblast (sensu Nematoda and Protostomia)
type: Class
subclass of: neural stem cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon_33317
definition: A neural precursor of the central nervous system.
has_broad_synonym: neuroblast
database_cross_reference: FBbt:00005146
in_subset: cellxgene subset

Axiom
annotated source: neuroblast (sensu Nematoda and Protostomia)
annotated property: definition
annotated target: A neural precursor of the central nervous system.
database_cross_reference: PMID:1295739

Axiom
annotated source: neuroblast (sensu Nematoda and Protostomia)
annotated property: database_cross_reference
annotated target: FBbt:00005146
mapping justification: ManualMappingCuration

glioblast (sensu Vertebrata)
type: Class
subclass of: glioblast
subclass of: neuron associated cell (sensu Vertebrata)
subclass of: CL_0011026
definition: An early neural cell developing from the early ependymal cell of the neural tube.
database_cross_reference: FMA:70564
database_cross_reference: ZFA:0009169
has_exact_synonym: spongioblast
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: glioblast (sensu Vertebrata)
annotated property: definition
annotated target: An early neural cell developing from the early ependymal cell of the neural tube.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0618947256

Axiom
annotated source: glioblast (sensu Vertebrata)
annotated property: database_cross_reference
annotated target: ZFA:0009169
mapping justification: UnspecifiedMatching

glioblast (sensu Nematoda and Protostomia)
type: Class
subclass of: glioblast
subclass of: neuron associated cell (sensu Nematoda and Protostomia)
definition: A precursor of the central nervous system that gives rise to glial cells only.
database_cross_reference: FBbt:00005145

Axiom
annotated source: glioblast (sensu Nematoda and Protostomia)
annotated property: definition
annotated target: A precursor of the central nervous system that gives rise to glial cells only.
database_cross_reference: doi:10.1002/glia.21162

Axiom
annotated source: glioblast (sensu Nematoda and Protostomia)
annotated property: database_cross_reference
annotated target: FBbt:00005145
mapping justification: ManualMappingCuration

pigment cell (sensu Nematoda and Protostomia)
type: Class
subclass of: pigment cell
never in taxon: NCBITaxon_33511

pigment cell (sensu Vertebrata)
type: Class
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 7742
definition: Any animal cell containing pigment granules.
database_cross_reference: ZFA:0009170
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pigment cell (sensu Vertebrata)
annotated property: definition
annotated target: Any animal cell containing pigment granules.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: pigment cell (sensu Vertebrata)
annotated property: database_cross_reference
annotated target: ZFA:0009170
mapping justification: UnspecifiedMatching

visual pigment cell (sensu Vertebrata)
type: Class
equivalent class: Class
  intersection of: pigment cell (sensu Vertebrata)
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050908
subclass of: visual pigment cell
subclass of: pigment cell (sensu Vertebrata)
subclass of: Restriction
  on property: capable of
  some values from: GO_0050908
definition: A pigment cell that is capable of detecting light stimulus that is involved in visual perception.
database_cross_reference: FMA:63846
database_cross_reference: ZFA:0009171
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: visual pigment cell (sensu Vertebrata)
annotated property: subClassOf
annotated target: pigment cell (sensu Vertebrata)
is inferred: true

Axiom
annotated source: visual pigment cell (sensu Vertebrata)
annotated property: definition
annotated target: A pigment cell that is capable of detecting light stimulus that is involved in visual perception.
database_cross_reference: GOC:tfm

Axiom
annotated source: visual pigment cell (sensu Vertebrata)
annotated property: database_cross_reference
annotated target: ZFA:0009171
mapping justification: UnspecifiedMatching

obsolete non-visual cell (sensu Vertebrata)
type: Class
deprecated: true

dental papilla cell
type: Class
subclass of: BFO_0000002
subclass of: CL_0008019
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001763
subclass of: Restriction
  on property: develops from
  some values from: migratory cranial neural crest cell
definition: A mesenchymal cell that is part of a small mass of condensed mesenchyme in the enamel organ; it differentiates into the dentin and dental pulp.
database_cross_reference: ZFA:0009173
in_subset: human subset
in_subset: mouse subset
comment: Merge with odontoblast?

Axiom
annotated source: dental papilla cell
annotated property: definition
annotated target: A mesenchymal cell that is part of a small mass of condensed mesenchyme in the enamel organ; it differentiates into the dentin and dental pulp.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: dental papilla cell
annotated property: database_cross_reference
annotated target: ZFA:0009173
mapping justification: UnspecifiedMatching

hair follicle dermal papilla cell
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000412
subclass of: mesenchymal stem cell
subclass of: CL_0011026
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000412
subclass of: Restriction
  on property: develops from
  some values from: migratory neural crest cell
definition: A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling.
in_subset: human subset
in_subset: mouse subset
comment: Are these really all stem cells?

Axiom
annotated source: hair follicle dermal papilla cell
annotated property: subClassOf
annotated target: mesenchymal stem cell
is inferred: true

Axiom
annotated source: hair follicle dermal papilla cell
annotated property: definition
annotated target: A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:9893172

scleral cell
type: Class
equivalent class: Class
  intersection of: structural cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001773
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: structural cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001773
subclass of: Restriction
  on property: develops from
  some values from: migratory cranial neural crest cell
definition: A cell of the sclera of the eye.
database_cross_reference: ZFA:0009174
in_subset: eye_upper_slim
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: scleral cell
annotated property: definition
annotated target: A cell of the sclera of the eye.
database_cross_reference: GOC:add

Axiom
annotated source: scleral cell
annotated property: database_cross_reference
annotated target: ZFA:0009174
mapping justification: UnspecifiedMatching

choroidal cell of the eye
type: Class
equivalent class: Class
  intersection of: structural cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001776
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: structural cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001776
subclass of: Restriction
  on property: develops from
  some values from: migratory cranial neural crest cell
definition: A structural cell that is part of optic choroid.
database_cross_reference: ZFA:0009175
in_subset: eye_upper_slim
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: choroidal cell of the eye
annotated property: definition
annotated target: A structural cell that is part of optic choroid.
database_cross_reference: GOC:add

Axiom
annotated source: choroidal cell of the eye
annotated property: database_cross_reference
annotated target: ZFA:0009175
mapping justification: UnspecifiedMatching

extraembryonic cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000478
subclass of: eukaryotic cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000478
definition: Any cell that is part of some extraembryonic structure.
database_cross_reference: ZFA:0009176
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: extraembryonic cell
annotated property: definition
annotated target: Any cell that is part of some extraembryonic structure.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: extraembryonic cell
annotated property: database_cross_reference
annotated target: ZFA:0009176
mapping justification: UnspecifiedMatching

amnioserosal cell
type: Class
equivalent class: Class
  intersection of: extraembryonic cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0010302
subclass of: extraembryonic cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0010302
definition: Any extraembryonic cell that is part of some amnioserosa.

Axiom
annotated source: amnioserosal cell
annotated property: definition
annotated target: Any extraembryonic cell that is part of some amnioserosa.
database_cross_reference: FBC:Autogenerated

trophoblast cell
type: Class
subclass of: BFO_0000002
subclass of: extraembryonic cell
subclass of: Restriction
  on property: develops from
  some values from: CL_1000274
definition: An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development.
description: Trophoblast cells, originating from the blastocyst's outer layer, are highly specialized and pivotal for embryo development. Their crucial roles include facilitating implantation and contributing to the formation of the placenta, an essential organ for fetal nutrition, gas exchange, and waste removal during pregnancy. These cells play a crucial role in implantation by adhering to the uterus lining. Post-implantation, some trophoblast cells differentiate, forming syncytiotrophoblasts. These multi-nucleated cells absorb nutrients, release waste, and secrete hormones, including human chorionic gonadotropin (hCG), sustaining pregnancy. Trophoblast cells also play a crucial role in immune tolerance, preventing the maternal immune system from treating the fetus as foreign. This balance is vital for a healthy pregnancy. Dysfunctional trophoblast cells may lead to complications like miscarriages or preeclampsia, emphasizing their importance in both embryology and reproductive medicine. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: FMA:83028
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000351
has_exact_synonym: trophoblastic cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: trophoblast cell
annotated property: subClassOf
annotated target: extraembryonic cell
is inferred: true

Axiom
annotated source: trophoblast cell
annotated property: definition
annotated target: An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D014327
database_cross_reference: PMID:37630754
database_cross_reference: doi:10.1007/978-3-030-84725-8

Axiom
annotated source: trophoblast cell
annotated property: description
annotated target: Trophoblast cells, originating from the blastocyst's outer layer, are highly specialized and pivotal for embryo development. Their crucial roles include facilitating implantation and contributing to the formation of the placenta, an essential organ for fetal nutrition, gas exchange, and waste removal during pregnancy. These cells play a crucial role in implantation by adhering to the uterus lining. Post-implantation, some trophoblast cells differentiate, forming syncytiotrophoblasts. These multi-nucleated cells absorb nutrients, release waste, and secrete hormones, including human chorionic gonadotropin (hCG), sustaining pregnancy. Trophoblast cells also play a crucial role in immune tolerance, preventing the maternal immune system from treating the fetus as foreign. This balance is vital for a healthy pregnancy. Dysfunctional trophoblast cells may lead to complications like miscarriages or preeclampsia, emphasizing their importance in both embryology and reproductive medicine. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1016/j.jri.2023.103811
database_cross_reference: DOI:10.1530/JOE-17-0402
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK53245

Axiom
annotated source: trophoblast cell
annotated property: has_exact_synonym
annotated target: trophoblastic cell
database_cross_reference: doi:10.1007/978-3-030-84725-8

epiblast cell
type: Class
subclass of: totipotent stem cell
definition: A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: epiblast cell
annotated property: definition
annotated target: A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0618947256

blastoderm cell
type: Class
subclass of: early embryonic cell (metazoa)
definition: An undifferentiated cell produced by early cleavages of the fertilized egg (zygote).
database_cross_reference: BTO:0001473
database_cross_reference: FMA:72551
database_cross_reference: ZFA:0009177
has_exact_synonym: blastomere
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: blastoderm cell
annotated property: definition
annotated target: An undifferentiated cell produced by early cleavages of the fertilized egg (zygote).
database_cross_reference: MESH:D001756

Axiom
annotated source: blastoderm cell
annotated property: database_cross_reference
annotated target: ZFA:0009177
mapping justification: UnspecifiedMatching

blastemal cell
type: Class
subclass of: multi fate stem cell
database_cross_reference: ZFA:0009178
database_cross_reference: ncithesaurus:Blastemal_Cell
has_exact_synonym: blastema cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: blastemal cell
annotated property: database_cross_reference
annotated target: ZFA:0009178
mapping justification: UnspecifiedMatching

multi-potent skeletal muscle stem cell
type: Class
equivalent class: Class
  intersection of: multi fate stem cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001134
subclass of: multi fate stem cell
subclass of: cell of skeletal muscle
definition: A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell.
database_cross_reference: FMA:86767
database_cross_reference: ZFA:0009179
in_subset: human subset
in_subset: mouse subset
comment: Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo.

Axiom
annotated source: multi-potent skeletal muscle stem cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

Axiom
annotated source: multi-potent skeletal muscle stem cell
annotated property: definition
annotated target: A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell.
database_cross_reference: PMID:18282570

Axiom
annotated source: multi-potent skeletal muscle stem cell
annotated property: database_cross_reference
annotated target: ZFA:0009179
mapping justification: UnspecifiedMatching

hair matrix stem cell
type: Class
subclass of: single fate stem cell
in_subset: human subset
in_subset: mouse subset

stratified epithelial stem cell
type: Class
subclass of: epithelial fate stem cell
database_cross_reference: ZFA:0009180
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: stratified epithelial stem cell
annotated property: database_cross_reference
annotated target: ZFA:0009180
mapping justification: UnspecifiedMatching

sphincter associated smooth muscle cell
type: Class
equivalent class: Class
  intersection of: smooth muscle cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0004590
subclass of: smooth muscle cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0004590
definition: A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning.
description: Smooth muscle cells, as a broader category, are non-striated, involuntary muscle cells that usually exhibit contractions and dilation to facilitate numerous physiological functions. Sphincter associated smooth muscle cells are a specific type of smooth muscle cell that are primarily associated with the functioning of various anatomical sphincters in the human body. The traits that distinguishes sphincter associated smooth muscle cells from other smooth muscle cells are their location and specialized function in sphincter mechanisms. Sphincter associated smooth muscle cells play a pivotal role in regulating the opening and closure of the bodily sphincters. These sphincters can be found at multiple locations within the body including the gastrointestinal tract (namely the esophagus, stomach, small intestine, and rectum), the urinary tract, and the circulatory system. Upon receiving signals from the autonomous nervous system, these cells contract or relax to modulate the aperture of sphincters, thus controlling the movement of substances through them. Due to their precise and vital functional role, any dysfunction or dysregulation in these cells can lead to serious medical conditions, such as gastroesophageal reflux or urinary incontinence. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000358
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: sphincter associated smooth muscle cell
annotated property: subClassOf
annotated target: smooth muscle cell
is inferred: true

Axiom
annotated source: sphincter associated smooth muscle cell
annotated property: definition
annotated target: A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning.
database_cross_reference: GOC:cjm

Axiom
annotated source: sphincter associated smooth muscle cell
annotated property: description
annotated target: Smooth muscle cells, as a broader category, are non-striated, involuntary muscle cells that usually exhibit contractions and dilation to facilitate numerous physiological functions. Sphincter associated smooth muscle cells are a specific type of smooth muscle cell that are primarily associated with the functioning of various anatomical sphincters in the human body. The traits that distinguishes sphincter associated smooth muscle cells from other smooth muscle cells are their location and specialized function in sphincter mechanisms. Sphincter associated smooth muscle cells play a pivotal role in regulating the opening and closure of the bodily sphincters. These sphincters can be found at multiple locations within the body including the gastrointestinal tract (namely the esophagus, stomach, small intestine, and rectum), the urinary tract, and the circulatory system. Upon receiving signals from the autonomous nervous system, these cells contract or relax to modulate the aperture of sphincters, thus controlling the movement of substances through them. Due to their precise and vital functional role, any dysfunction or dysregulation in these cells can lead to serious medical conditions, such as gastroesophageal reflux or urinary incontinence. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK482438/
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK532857/
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK557452/

vascular associated smooth muscle cell
type: Class
equivalent class: Class
  intersection of: smooth muscle cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002049
subclass of: smooth muscle cell
subclass of: CL_4033054
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002049
definition: A smooth muscle cell associated with the vasculature.
present in taxon: NCBITaxon 9606
description: Vascular associated smooth muscle cells (VSMCs) are specialized cells that constitute a major component of the blood vessel wall in the circulatory system. They derive their name from the predominantly smooth appearance under microscopic examination, as opposed to the striated appearance of cardiac and skeletal muscles. A principal function of VSMCs is to regulate vascular tone, which directly dictates blood pressure and blood flow distribution across various body parts. This is achieved through coordinated contraction and relaxation of the muscles in response to a variety of extracellular signals. When a blood vessel is exposed to stimuli like pressure or injury, VSMCs contract, resulting in vasoconstriction and ultimately, an increase in blood pressure. Conversely, in response to vasodilators, these cells relax, leading to vasodilation and a consequent decrease in blood pressure. VSMCs are also involved in vascular remodeling, a process where blood vessels adapt their structure to long-term changes in hemodynamic conditions or disease states. In diseases like atherosclerosis and hypertension, an aberrant proliferative and synthetic phenotype of VSMCs contributes to the formation of plaques, leading to vessel hardening or even occlusion. Recent research has further implicated these cells in immune responses, recognizing their function in leukocyte recruitment and inflammation, factors that are largely instrumental in vascular pathologies. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: ZFA:0009181
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000359
has_exact_synonym: VSMC
has_exact_synonym: vascular smooth muscle cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: vascular associated smooth muscle cell
annotated property: subClassOf
annotated target: smooth muscle cell
is inferred: true

Axiom
annotated source: vascular associated smooth muscle cell
annotated property: definition
annotated target: A smooth muscle cell associated with the vasculature.
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm

Axiom
annotated source: vascular associated smooth muscle cell
annotated property: description
annotated target: Vascular associated smooth muscle cells (VSMCs) are specialized cells that constitute a major component of the blood vessel wall in the circulatory system. They derive their name from the predominantly smooth appearance under microscopic examination, as opposed to the striated appearance of cardiac and skeletal muscles. A principal function of VSMCs is to regulate vascular tone, which directly dictates blood pressure and blood flow distribution across various body parts. This is achieved through coordinated contraction and relaxation of the muscles in response to a variety of extracellular signals. When a blood vessel is exposed to stimuli like pressure or injury, VSMCs contract, resulting in vasoconstriction and ultimately, an increase in blood pressure. Conversely, in response to vasodilators, these cells relax, leading to vasodilation and a consequent decrease in blood pressure. VSMCs are also involved in vascular remodeling, a process where blood vessels adapt their structure to long-term changes in hemodynamic conditions or disease states. In diseases like atherosclerosis and hypertension, an aberrant proliferative and synthetic phenotype of VSMCs contributes to the formation of plaques, leading to vessel hardening or even occlusion. Recent research has further implicated these cells in immune responses, recognizing their function in leukocyte recruitment and inflammation, factors that are largely instrumental in vascular pathologies. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1093/cvr/cvs135
database_cross_reference: DOI:10.1093/cvr/cvy023
database_cross_reference: DOI:10.1161/ATVBAHA.118.311229
database_cross_reference: DOI:10.3389/fimmu.2020.599415
database_cross_reference: DOI:10.3390/ijms20225694

Axiom
annotated source: vascular associated smooth muscle cell
annotated property: database_cross_reference
annotated target: ZFA:0009181
mapping justification: UnspecifiedMatching

morula cell
type: Class
subclass of: early embryonic cell (metazoa)
subclass of: eukaryotic cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000085
definition: A cell of the early embryo at the developmental stage in which the blastomeres, resulting from repeated mitotic divisions of the fertilized ovum (zygote), form a compact cell mass.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: morula cell
annotated property: definition
annotated target: A cell of the early embryo at the developmental stage in which the blastomeres, resulting from repeated mitotic divisions of the fertilized ovum (zygote), form a compact cell mass.
database_cross_reference: MESH:D009028

gastrula cell
type: Class
subclass of: early embryonic cell (metazoa)
subclass of: Restriction
  on property: part of
  some values from: UBERON_0004734
definition: A cell of the embryo in the early stage following the blastula, characterized by morphogenetic cell movements, cell differentiation, and the formation of the three germ layers.
database_cross_reference: ZFA:0009182
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: gastrula cell
annotated property: definition
annotated target: A cell of the embryo in the early stage following the blastula, characterized by morphogenetic cell movements, cell differentiation, and the formation of the three germ layers.
database_cross_reference: MESH:D005775

Axiom
annotated source: gastrula cell
annotated property: database_cross_reference
annotated target: ZFA:0009182
mapping justification: UnspecifiedMatching

epidermal cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0007376
subclass of: CL_0002159
subclass of: Restriction
  on property: part of
  some values from: UBERON_0007376
definition: An epithelial cell of the integument (the outer layer of an organism).
database_cross_reference: BTO:0001470
database_cross_reference: CALOHA:TS-0283
database_cross_reference: FMA:62411
database_cross_reference: MESH:D000078404
database_cross_reference: ZFA:0009183
has_exact_synonym: cell of epidermis
has_narrow_synonym: epithelial cell of skin
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: epidermal cell
annotated property: definition
annotated target: An epithelial cell of the integument (the outer layer of an organism).
database_cross_reference: Flybase:dsj
database_cross_reference: MA:ma

Axiom
annotated source: epidermal cell
annotated property: database_cross_reference
annotated target: ZFA:0009183
mapping justification: UnspecifiedMatching

Axiom
annotated source: epidermal cell
annotated property: has_exact_synonym
annotated target: cell of epidermis
database_cross_reference: FMA:62411

Axiom
annotated source: epidermal cell
annotated property: has_narrow_synonym
annotated target: epithelial cell of skin
database_cross_reference: FMA:62411

obsolete axial cell
type: Class
definition: Obsolete. Use PO:0000081 from Plant Ontology instead. OBSOLETE, use term from the Plant Ontology. A secondary vascular cell that develops from the fusiform cambial initials and oriented with their longest diameter parallel with the main axis of stem or root. These cells make up the axial system, also known as vertical or longitudinal system.
term replaced by: PO_0000081
deprecated: true

Axiom
annotated source: obsolete axial cell
annotated property: definition
annotated target: Obsolete. Use PO:0000081 from Plant Ontology instead. OBSOLETE, use term from the Plant Ontology. A secondary vascular cell that develops from the fusiform cambial initials and oriented with their longest diameter parallel with the main axis of stem or root. These cells make up the axial system, also known as vertical or longitudinal system.
database_cross_reference: ISBN:0471245208

obsolete ray cell
type: Class
definition: Obsolete. Consult Plant Ontology. A cell that develops from the ray initial and composes all rays (panels of tissue variable in height and width, formed by the ray initials in the vascular cambium and extending radially in the secondary xylem and secondary phloem) in the secondary vascular tissues.
deprecated: true

Axiom
annotated source: obsolete ray cell
annotated property: definition
annotated target: Obsolete. Consult Plant Ontology. A cell that develops from the ray initial and composes all rays (panels of tissue variable in height and width, formed by the ray initials in the vascular cambium and extending radially in the secondary xylem and secondary phloem) in the secondary vascular tissues.
database_cross_reference: ISBN:0471245208

animal zygote
type: Class
equivalent class: Class
  intersection of: CL_0010017
  intersection of: Restriction
    on property: in taxon
    some values from: NCBITaxon_33208
subclass of: early embryonic cell (metazoa)
subclass of: eukaryotic cell
subclass of: CL_0010017
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon_33208
definition: Diploid cell produced by the fusion of sperm cell nucleus and egg cell.
has_broad_synonym: zygote
database_cross_reference: BTO:0000854
database_cross_reference: EHDAA2:0004546
database_cross_reference: FMA:72395
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: animal zygote
annotated property: definition
annotated target: Diploid cell produced by the fusion of sperm cell nucleus and egg cell.
database_cross_reference: ISBN:0471245208

obsolete sperm cell (sensu Viridiplantae)
type: Class
definition: Obsolete. Use PO:0000084 from Plant Ontology instead. Male gamete, part of male germ unit.
term replaced by: PO_0000084
has_related_synonym: gametophyte sperm cell
has_related_synonym: male gametophyte sperm cell
has_related_synonym: pollen germ cell
deprecated: true

Axiom
annotated source: obsolete sperm cell (sensu Viridiplantae)
annotated property: definition
annotated target: Obsolete. Use PO:0000084 from Plant Ontology instead. Male gamete, part of male germ unit.
database_cross_reference: ISBN:0471245208

sheath cell (sensu Nematoda)
type: Class
subclass of: supporting cell (sensu Nematoda)
has_related_synonym: glial cell (sensu Nematoda)
in_subset: human subset
in_subset: mouse subset

obsolete myrosin cell
type: Class
definition: Obsolete. Use PO:0000352 from Plant Ontology instead. Cell containing glucosinolates ('mustard oil glucosides') and myrosinases, enzymes hydrolyzing the glucosinolates. Occurs in eleven dicotyledon families, the two largest of which are the Brassicaceae and Euphorbiaceae.
term replaced by: PO_0000352
deprecated: true

Axiom
annotated source: obsolete myrosin cell
annotated property: definition
annotated target: Obsolete. Use PO:0000352 from Plant Ontology instead. Cell containing glucosinolates ('mustard oil glucosides') and myrosinases, enzymes hydrolyzing the glucosinolates. Occurs in eleven dicotyledon families, the two largest of which are the Brassicaceae and Euphorbiaceae.
database_cross_reference: ISBN:0471245208

CL_0000369
type: Class
has obsolescence reason: IAO_0000227
term replaced by: CL_0002372
deprecated: true

obsolete transfer cell
type: Class
definition: Obsolete. Use PO:0000078 from Plant Ontology instead. Parenchyma cell with the wall ingrowth (or invaginations) that increase the surface of the plasmalemma. Appears to be specialized for short-distance transfer of solutes.
term replaced by: PO_0000078
has_related_synonym: intermediary cell
deprecated: true

Axiom
annotated source: obsolete transfer cell
annotated property: definition
annotated target: Obsolete. Use PO:0000078 from Plant Ontology instead. Parenchyma cell with the wall ingrowth (or invaginations) that increase the surface of the plasmalemma. Appears to be specialized for short-distance transfer of solutes.
database_cross_reference: ISBN:0471245208

protoplast
type: Class
subclass of: experimentally modified cell in vitro
definition: The cell protoplasm after removal of the cell wall.
never in taxon: NCBITaxon_33208
database_cross_reference: MESH:D011523

Axiom
annotated source: protoplast
annotated property: definition
annotated target: The cell protoplasm after removal of the cell wall.
database_cross_reference: ISBN:08199377X

tormogen cell
type: Class
subclass of: epidermal cell (sensu Arthropoda)
definition: An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization that forms a socket around the base of a cuticular specialization produced by a trichogen cell.
has_broad_synonym: socket cell
database_cross_reference: FBbt:00005171

Axiom
annotated source: tormogen cell
annotated property: definition
annotated target: An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization that forms a socket around the base of a cuticular specialization produced by a trichogen cell.
database_cross_reference: ISBN:978-0801481253

Axiom
annotated source: tormogen cell
annotated property: has_broad_synonym
annotated target: socket cell
database_cross_reference: ISBN:978-0801481253

Axiom
annotated source: tormogen cell
annotated property: database_cross_reference
annotated target: FBbt:00005171
mapping justification: ManualMappingCuration

histoblast
type: Class
subclass of: CL_0011026
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon_50557
definition: A progenitor cell found in the larval epidermis of insects and that gives rise to the adult abdominal epidermis.
database_cross_reference: FBbt:00001789

Axiom
annotated source: histoblast
annotated property: definition
annotated target: A progenitor cell found in the larval epidermis of insects and that gives rise to the adult abdominal epidermis.
database_cross_reference: doi:10.1016/j.cub.2022.01.045

Axiom
annotated source: histoblast
annotated property: database_cross_reference
annotated target: FBbt:00001789
mapping justification: ManualMappingCuration

trichogen cell
type: Class
subclass of: epidermal cell (sensu Arthropoda)
definition: An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization, often in the form of a hair, bristle, peg or scale. The base of this specialization is often surrounded by a socket produced by a closely associated tormogen cell.
has_broad_synonym: hair cell
database_cross_reference: BTO:0004744
database_cross_reference: FBbt:00005169

Axiom
annotated source: trichogen cell
annotated property: definition
annotated target: An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization, often in the form of a hair, bristle, peg or scale. The base of this specialization is often surrounded by a socket produced by a closely associated tormogen cell.
database_cross_reference: ISBN:978-0801481253

Axiom
annotated source: trichogen cell
annotated property: database_cross_reference
annotated target: FBbt:00005169
mapping justification: ManualMappingCuration

obsolete osteoprogenitor cell
type: Class
term replaced by: CL_0007010
database_cross_reference: BTO:0002051
deprecated: true

humidity receptor cell
type: Class
subclass of: neuronal receptor cell
in_subset: human subset
in_subset: mouse subset

tracheoblast
type: Class
subclass of: branched duct epithelial cell
in_subset: human subset
in_subset: mouse subset

supporting cell (sensu Nematoda and Protostomia)
type: Class
subclass of: supporting cell
has_exact_synonym: support cell (sensu Nematoda and Protostomia)
in_subset: human subset
in_subset: mouse subset

sensory processing neuron
type: Class
subclass of: CL_2000029
subclass of: Restriction
  on property: capable of
  some values from: GO_0050893
database_cross_reference: ZFA:0009185
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: sensory processing neuron
annotated property: database_cross_reference
annotated target: ZFA:0009185
mapping justification: UnspecifiedMatching

thecogen cell
type: Class
subclass of: supporting cell (sensu Nematoda and Protostomia)
definition: The support cell that makes the thecogen dendritic cap - a cuticle-like matrix around the tip of the eo-dendrite and which encloses the soma of the eo-neuron.
database_cross_reference: FBbt:00005173
has_exact_synonym: fly sheath cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: thecogen cell
annotated property: definition
annotated target: The support cell that makes the thecogen dendritic cap - a cuticle-like matrix around the tip of the eo-dendrite and which encloses the soma of the eo-neuron.
database_cross_reference: Fbbt:00005173

Axiom
annotated source: thecogen cell
annotated property: database_cross_reference
annotated target: FBbt:00005173
mapping justification: ManualMappingCuration

obsolete neurosecretory neuron
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1784
term replaced by: neuroendocrine cell
comment: 'neuroendocrine cell' (which has exact synonym "neurosecretory cell") and 'neurosecretory neuron' may all refer to the same cell type.
deprecated: true

scolopale cell
type: Class
subclass of: eukaryotic cell
subclass of: supporting cell (sensu Nematoda and Protostomia)
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001038
definition: A cell that is part of a scolopidium and surrounds the dendrite of a scolopidial neuron.
database_cross_reference: FBbt:00005219
has_exact_synonym: scolopidial sheath cell

Axiom
annotated source: scolopale cell
annotated property: definition
annotated target: A cell that is part of a scolopidium and surrounds the dendrite of a scolopidial neuron.
database_cross_reference: doi:10.1016/B978-012369493-5.50012-2
database_cross_reference: doi:10.1017/CBO9780511818202.024

Axiom
annotated source: scolopale cell
annotated property: database_cross_reference
annotated target: FBbt:00005219
mapping justification: ManualMappingCuration

Axiom
annotated source: scolopale cell
annotated property: has_exact_synonym
annotated target: scolopidial sheath cell
database_cross_reference: ISBN:978-087969828-7

nephrogenic mesenchyme stem cell
type: Class
subclass of: mesenchymal stem cell
subclass of: CL_0011026
subclass of: Restriction
  on property: develops from
  some values from: mesenchymal stem cell
database_cross_reference: ZFA:0009187
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: nephrogenic mesenchyme stem cell
annotated property: database_cross_reference
annotated target: ZFA:0009187
mapping justification: UnspecifiedMatching

ligament cell
type: Class
subclass of: supporting cell
database_cross_reference: ZFA:0009188
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: ligament cell
annotated property: database_cross_reference
annotated target: ZFA:0009188
mapping justification: UnspecifiedMatching

prohemocyte (sensu Nematoda and Protostomia)
type: Class
subclass of: CL_0008001
definition: A precursor of mature hemocytes.
never in taxon: NCBITaxon_33511
database_cross_reference: FBbt:00005062

Axiom
annotated source: prohemocyte (sensu Nematoda and Protostomia)
annotated property: definition
annotated target: A precursor of mature hemocytes.
database_cross_reference: doi:10.1016/B978-012369493-5.50008-0

Axiom
annotated source: prohemocyte (sensu Nematoda and Protostomia)
annotated property: database_cross_reference
annotated target: FBbt:00005062
mapping justification: ManualMappingCuration

obsolete attachment cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/3016
comment: The obsoleted term is redundant
deprecated: true

hemocyte (sensu Arthropoda)
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: blood cell (sensu Nematoda and Protostomia)
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 6656
subclass of: Restriction
  on property: develops from
  some values from: prohemocyte (sensu Nematoda and Protostomia)
definition: A blood cell of the circulatory system of arthropods.
database_cross_reference: FBbt:00005063

Axiom
annotated source: hemocyte (sensu Arthropoda)
annotated property: definition
annotated target: A blood cell of the circulatory system of arthropods.
database_cross_reference: doi:10.1016/B978-012369493-5.50008-0

Axiom
annotated source: hemocyte (sensu Arthropoda)
annotated property: database_cross_reference
annotated target: FBbt:00005063
mapping justification: ManualMappingCuration

tendon cell
type: Class
equivalent class: Class
  intersection of: fibrocyte
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000043
subclass of: fibrocyte
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000043
definition: An elongated fibrocyte that is part of a tendon. The cytoplasm is stretched between the collagen fibres of the tendon. They have a central cell nucleus with a prominent nucleolus. Tendon cells have a well-developed rough endoplasmic reticulum and they are responsible for synthesis and turnover of tendon fibres and ground substance.
database_cross_reference: ZFA:0009189
has_exact_synonym: muscle attachment cell
has_related_synonym: tenocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: tendon cell
annotated property: subClassOf
annotated target: fibrocyte
is inferred: true

Axiom
annotated source: tendon cell
annotated property: definition
annotated target: An elongated fibrocyte that is part of a tendon. The cytoplasm is stretched between the collagen fibres of the tendon. They have a central cell nucleus with a prominent nucleolus. Tendon cells have a well-developed rough endoplasmic reticulum and they are responsible for synthesis and turnover of tendon fibres and ground substance.
database_cross_reference: GOC:NV
database_cross_reference: GOC:tfm
database_cross_reference: PMID:957445

Axiom
annotated source: tendon cell
annotated property: database_cross_reference
annotated target: ZFA:0009189
mapping justification: UnspecifiedMatching

socket cell (sensu Nematoda)
type: Class
subclass of: supporting cell (sensu Nematoda)
subclass of: cuticle secreting cell
in_subset: human subset
in_subset: mouse subset

blood cell (sensu Nematoda and Protostomia)
type: Class
subclass of: blood cell
never in taxon: NCBITaxon_33511

obsolete podocyte (sensu Diptera)
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1949
term replaced by: plasmatocyte
comment: Obsoleted as podocytes are not a distinct cell type from plasmatocytes.
deprecated: true

crystal cell
type: Class
subclass of: hemocyte (sensu Arthropoda)
subclass of: Restriction
  on property: develops from
  some values from: procrystal cell
definition: A hemocyte that synthesizes and secretes melanins as part of the antimicrobial immune response. It is characterized morphologically by crystal inclusions of phenoloxidases in its cytoplasm, hence its name.

Axiom
annotated source: crystal cell
annotated property: definition
annotated target: A hemocyte that synthesizes and secretes melanins as part of the antimicrobial immune response. It is characterized morphologically by crystal inclusions of phenoloxidases in its cytoplasm, hence its name.
database_cross_reference: doi:10.1016/B978-012369493-5.50008-0

electrically responsive cell
type: Class
subclass of: electrically active cell
definition: A cell whose function is determined by its response to an electric signal.
database_cross_reference: ZFA:0009190
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: electrically responsive cell
annotated property: definition
annotated target: A cell whose function is determined by its response to an electric signal.
database_cross_reference: FB:ma

Axiom
annotated source: electrically responsive cell
annotated property: database_cross_reference
annotated target: ZFA:0009190
mapping justification: UnspecifiedMatching

plasmatocyte
type: Class
subclass of: hemocyte (sensu Arthropoda)
subclass of: Restriction
  on property: capable of
  some values from: GO_0035010
definition: A phagocytic hemocyte, responsible for the engulfment of small particles, microbes, and apoptotic tissue debris. It may also secretes antimicrobial peptides and contribute to the production and secretion of proteins of the hemolymph.
database_cross_reference: FBbt:00001685
has_related_synonym: macrophage
in_subset: cellxgene subset

Axiom
annotated source: plasmatocyte
annotated property: definition
annotated target: A phagocytic hemocyte, responsible for the engulfment of small particles, microbes, and apoptotic tissue debris. It may also secretes antimicrobial peptides and contribute to the production and secretion of proteins of the hemolymph.
database_cross_reference: https://doi.org/10.1016/B978-012369493-5.50008-0

Axiom
annotated source: plasmatocyte
annotated property: database_cross_reference
annotated target: FBbt:00001685
mapping justification: ManualMappingCuration

procrystal cell
type: Class
subclass of: prohemocyte (sensu Nematoda and Protostomia)
definition: A precursor of mature crystal cells.
database_cross_reference: FBbt:00001689

Axiom
annotated source: procrystal cell
annotated property: definition
annotated target: A precursor of mature crystal cells.
database_cross_reference: doi:10.1016/B978-012369493-5.50008-0

Axiom
annotated source: procrystal cell
annotated property: database_cross_reference
annotated target: FBbt:00001689
mapping justification: ManualMappingCuration

lamellocyte
type: Class
subclass of: hemocyte (sensu Arthropoda)
definition: A hemocyte found in immuno-stimulated larvae.
database_cross_reference: FBbt:00001687

Axiom
annotated source: lamellocyte
annotated property: definition
annotated target: A hemocyte found in immuno-stimulated larvae.
database_cross_reference: doi:10.1016/B978-012369493-5.50008-0

Axiom
annotated source: lamellocyte
annotated property: database_cross_reference
annotated target: FBbt:00001687
mapping justification: ManualMappingCuration

ganglion interneuron
type: Class
equivalent class: Class
  intersection of: interneuron
  intersection of: Restriction
    on property: has soma location
    some values from: UBERON_0000045
subclass of: interneuron
subclass of: Restriction
  on property: has soma location
  some values from: UBERON_0000045
definition: Any interneuron that has its soma located in some ganglion.
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: ganglion interneuron
annotated property: subClassOf
annotated target: interneuron
is inferred: true

Axiom
annotated source: ganglion interneuron
annotated property: definition
annotated target: Any interneuron that has its soma located in some ganglion.
database_cross_reference: FBC:Autogenerated

obsolete polygonal cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1949
term replaced by: prohemocyte (sensu Nematoda and Protostomia)
comment: Obsoleted as this is actually the same thing as prohemocytes.
deprecated: true

obsolete phloem element
type: Class
definition: Obsolete. Consult Plant Ontology instead. OBSOLETED, not defined prior to obsoletion.
deprecated: true

Axiom
annotated source: obsolete phloem element
annotated property: definition
annotated target: Obsolete. Consult Plant Ontology instead. OBSOLETED, not defined prior to obsoletion.
database_cross_reference: GOC:tfm

obsolete pavement cell
type: Class
definition: Obsolete. Use PO:0000332 from Plant Ontology instead. An epidermal cell with a characteristic convoluted anticlinal cell wall that gives a jigsaw like appearance to the lamina.
term replaced by: PO_0000332
deprecated: true

Axiom
annotated source: obsolete pavement cell
annotated property: definition
annotated target: Obsolete. Use PO:0000332 from Plant Ontology instead. An epidermal cell with a characteristic convoluted anticlinal cell wall that gives a jigsaw like appearance to the lamina.
database_cross_reference: ISBN:087694289

obsolete macrophage (sensu Diptera)
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1949
term replaced by: plasmatocyte
comment: Obsoleted as plasmatocytes are the macrophages (phagocytic cells) of Diptera.
deprecated: true

obsolete CNS interneuron
type: Class
definition: OBSOLETE. An interneuron that has its cell body in a central nervous system.
term tracker item: https://github.com/obophenotype/cell-ontology/issues/2869
term replaced by: interneuron
present in taxon: NCBITaxon 9606
in_subset: cellxgene subset
in_subset: human reference atlas
comment: Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system.
deprecated: true

Axiom
annotated source: obsolete CNS interneuron
annotated property: definition
annotated target: OBSOLETE. An interneuron that has its cell body in a central nervous system.
database_cross_reference: doi:10.1016/B978-0-12-817424-1.00001-X

CL_0000403
type: Class
has obsolescence reason: IAO_0000227
term replaced by: CL_0000850
deprecated: true

electrically signaling cell
type: Class
subclass of: electrically active cell
definition: A cell that initiates an electrical signal and passes that signal to another cell.
database_cross_reference: ZFA:0009193
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: electrically signaling cell
annotated property: definition
annotated target: A cell that initiates an electrical signal and passes that signal to another cell.
database_cross_reference: FB:ma

Axiom
annotated source: electrically signaling cell
annotated property: database_cross_reference
annotated target: ZFA:0009193
mapping justification: UnspecifiedMatching

obsolete neuroepidermoblast
type: Class
term tracker item: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/issues/1621
comment: Obsoleted as the term seems completely unused in the literature.
deprecated: true

CNS short range interneuron
type: Class
subclass of: interneuron
database_cross_reference: ZFA:0009194
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: CNS short range interneuron
annotated property: database_cross_reference
annotated target: ZFA:0009194
mapping justification: UnspecifiedMatching

scolopidial ligament cell
type: Class
subclass of: eukaryotic cell
subclass of: supporting cell (sensu Nematoda and Protostomia)
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001038
definition: A cell that anchors the cell body of a scolopidial neuron to the integument.
database_cross_reference: FBbt:00005221

Axiom
annotated source: scolopidial ligament cell
annotated property: definition
annotated target: A cell that anchors the cell body of a scolopidial neuron to the integument.
database_cross_reference: doi:10.1016/B978-0-12-408088-1.00002-6
database_cross_reference: doi:10.1023/a:1018564904170

Axiom
annotated source: scolopidial ligament cell
annotated property: database_cross_reference
annotated target: FBbt:00005221
mapping justification: ManualMappingCuration

male gamete
type: Class
equivalent class: Class
  intersection of: male germ cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001375
  intersection of: Restriction
    on property: capable of
    some values from: GO_0009566
subclass of: male germ cell
subclass of: gamete
definition: Any male germ cell that has characteristic some haploid and is capable of some fertilization.
description: The male gamete, also known as a sperm cell, is a highly specialized cell type critical to sexual reproduction. Sperm are produced during a process called spermatogenesis within the male reproductive organ, specifically the testes. They are haploid cells, carrying the genetic material from the male parent, and fuse with the ovum, the female gamete, to form a diploid zygote during fertilization, thereby initiating gestation and the development of a new organism. The male gamete is distinguished by its morphology, notably its elongated shape which is geared towards locomotion. One of the primary characteristics of a male gamete is its flagellum, or tail, which propels the cell towards the female gamete. It additionally contains an elongated head region housing the nucleus, where the genetic material is stored. The anterior section of the head, the acrosome, releases enzymes essential for penetrating the protective layers of the ovum during the fertilization process. The function of male gametes does not cease upon fertilization. In addition to delivering the paternal set of chromosomes, fusion of the sperm cell with the ovum causes an increase in cytosolic Ca2+ which then activates the female egg cell to undergo the so-called cortical reaction during which the egg’s zona pellucida is changed so fusion with additional sperm is prevented. The Ca2+ signal also initiates the development of the zygote and eventual formation of an embryo. Male gametes also contribute towards forming the placenta, which supplies nutrients and removes waste products during gestation. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: BTO:0001277
database_cross_reference: CALOHA:TS-0949
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000408
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: male gamete
annotated property: subClassOf
annotated target: male germ cell
is inferred: true

Axiom
annotated source: male gamete
annotated property: subClassOf
annotated target: gamete
is inferred: true

Axiom
annotated source: male gamete
annotated property: definition
annotated target: Any male germ cell that has characteristic some haploid and is capable of some fertilization.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: male gamete
annotated property: description
annotated target: The male gamete, also known as a sperm cell, is a highly specialized cell type critical to sexual reproduction. Sperm are produced during a process called spermatogenesis within the male reproductive organ, specifically the testes. They are haploid cells, carrying the genetic material from the male parent, and fuse with the ovum, the female gamete, to form a diploid zygote during fertilization, thereby initiating gestation and the development of a new organism. The male gamete is distinguished by its morphology, notably its elongated shape which is geared towards locomotion. One of the primary characteristics of a male gamete is its flagellum, or tail, which propels the cell towards the female gamete. It additionally contains an elongated head region housing the nucleus, where the genetic material is stored. The anterior section of the head, the acrosome, releases enzymes essential for penetrating the protective layers of the ovum during the fertilization process. The function of male gametes does not cease upon fertilization. In addition to delivering the paternal set of chromosomes, fusion of the sperm cell with the ovum causes an increase in cytosolic Ca2+ which then activates the female egg cell to undergo the so-called cortical reaction during which the egg’s zona pellucida is changed so fusion with additional sperm is prevented. The Ca2+ signal also initiates the development of the zygote and eventual formation of an embryo. Male gametes also contribute towards forming the placenta, which supplies nutrients and removes waste products during gestation. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1016/j.semcdb.2016.04.009
database_cross_reference: DOI:10.1242/dev.202046
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK26843/
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK553142/

obsolete scolopidial sheath cell
type: Class
term replaced by: scolopale cell
comment: Obsoleted as this refers to the same cell type as 'scolopale cell'.
deprecated: true

CNS long range interneuron
type: Class
subclass of: interneuron
database_cross_reference: ZFA:0009195
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: CNS long range interneuron
annotated property: database_cross_reference
annotated target: ZFA:0009195
mapping justification: UnspecifiedMatching

Caenorhabditis hypodermal cell
type: Class
subclass of: epithelial cell
subclass of: multinucleate cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 6237
definition: An epithelial cell of the hypodermis of Caenorhabditis.
has_broad_synonym: roundworm hypodermal cell
database_cross_reference: WBbt:0007846
database_cross_reference: ZFA:0009196
comment: This term was originally added to CL for parity with the Worm anatomy ontology, which is dedicated to C elegans. It is not clear if it makes sense to try and generalize the concept and include in CL, and this term may be obsoleted in future. Note there is no similarity to the hypodermis in vertebrates.

Axiom
annotated source: Caenorhabditis hypodermal cell
annotated property: definition
annotated target: An epithelial cell of the hypodermis of Caenorhabditis.
database_cross_reference: GOC:tfm
database_cross_reference: http://www.wormatlas.org/hermaphrodite/hypodermis/mainframe.htm

Axiom
annotated source: Caenorhabditis hypodermal cell
annotated property: database_cross_reference
annotated target: ZFA:0009196
mapping justification: UnspecifiedMatching

polyploid cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001377
subclass of: cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001377
definition: A cell that contains more than two haploid sets of chromosomes.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: polyploid cell
annotated property: definition
annotated target: A cell that contains more than two haploid sets of chromosomes.
database_cross_reference: FB:ma
database_cross_reference: PMID:32646579
database_cross_reference: https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy

haploid cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001375
subclass of: cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001375
definition: A cell whose nucleus contains a single haploid genome.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: haploid cell
annotated property: definition
annotated target: A cell whose nucleus contains a single haploid genome.
database_cross_reference: FB:ma
database_cross_reference: GOC:tfm

obsolete cell by ploidy
type: Class
definition: OBSOLETE: A classification of cells by the number of haploid genome equivalents of their nucleus or nuclei.
consider: CL:0000000
consider: CL:0000003
consider: CL:0000255
consider: CL:0001034
comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell with chromosomes can be classified by its ploidy. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), eukaryotic cell (CL:0000255) or cell in vitro (CL:0001034) as appropriate.
deprecated: true

Axiom
annotated source: obsolete cell by ploidy
annotated property: definition
annotated target: OBSOLETE: A classification of cells by the number of haploid genome equivalents of their nucleus or nuclei.
database_cross_reference: FB:ma
database_cross_reference: GOC:tfm

diploid cell
type: Class
subclass of: cell
definition: A cell whose nucleus has two haploid genomes.
database_cross_reference: FMA:72300
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: diploid cell
annotated property: definition
annotated target: A cell whose nucleus has two haploid genomes.
database_cross_reference: FB:ma

polytene cell
type: Class
subclass of: polyploid cell
in_subset: human subset
in_subset: mouse subset

endopolyploid cell
type: Class
subclass of: polyploid cell
in_subset: human subset
in_subset: mouse subset

arcade cell
type: Class
subclass of: epithelial cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 6237
definition: An epithelial cell found in C. elegans that firmly hold the outer body wall and the lips to the inner cylinder of the pharynx in a manner that keeps these organs from breaking apart, while still giving each organ freedom of movement during feeding.
database_cross_reference: WBbt:0005793

Axiom
annotated source: arcade cell
annotated property: definition
annotated target: An epithelial cell found in C. elegans that firmly hold the outer body wall and the lips to the inner cylinder of the pharynx in a manner that keeps these organs from breaking apart, while still giving each organ freedom of movement during feeding.
database_cross_reference: GOC:tfm
database_cross_reference: http://www.wormatlas.org/ver1/handbook/hypodermis/hypsupportother.htm#arcadecells

seam cell
type: Class
subclass of: epithelial fate stem cell
definition: An epithelial fate stem cell found in flatworms.
database_cross_reference: BTO:0003039
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: seam cell
annotated property: definition
annotated target: An epithelial fate stem cell found in flatworms.
database_cross_reference: GOC:tfm
database_cross_reference: http://www.wormatlas.org/hermaphrodite/seam%20cells/mainframe.htm

syncytial epithelial cell
type: Class
subclass of: epithelial cell
subclass of: CL_4052002
definition: An epithelial cell that forms a syncytium, which is a multinucleated cell resulting from the fusion of multiple cells.
database_cross_reference: Wikipedia:Syncytium
in_subset: human subset
in_subset: mouse subset

coelomocyte
type: Class
subclass of: circulating cell
subclass of: phagocyte (sensu Nematoda and Protostomia)
definition: A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids.
database_cross_reference: BTO:0002856
database_cross_reference: WBbt:0005751

Axiom
annotated source: coelomocyte
annotated property: definition
annotated target: A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

mitogenic signaling cell
type: Class
subclass of: cell
definition: A cell whose primary function is to cause growth by stimulating cell division in its immediate cellular environment.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: mitogenic signaling cell
annotated property: definition
annotated target: A cell whose primary function is to cause growth by stimulating cell division in its immediate cellular environment.
database_cross_reference: FB:ma

tip cell
type: Class
subclass of: mitogenic signaling cell
in_subset: human subset
in_subset: mouse subset

excretory cell
type: Class
subclass of: cell
definition: A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids.
database_cross_reference: WBbt:0005812
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: excretory cell
annotated property: definition
annotated target: A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:19783135

pore cell
type: Class
subclass of: cuticle secreting cell
definition: Forms the terminal part of the cuticle-lined excretory duct of C. elegans.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pore cell
annotated property: definition
annotated target: Forms the terminal part of the cuticle-lined excretory duct of C. elegans.
database_cross_reference: JB:jb

obsolete scaffold cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/708
comment: This is a cell used in tissue engineering and is out of scope for CL.
deprecated: true

GLR cell
type: Class
subclass of: CL_0002320
definition: A scaffolding cell type found in C. elegans, this cell plays a supportive role to the muscle arms. May also have an endocrine role.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: GLR cell
annotated property: definition
annotated target: A scaffolding cell type found in C. elegans, this cell plays a supportive role to the muscle arms. May also have an endocrine role.
database_cross_reference: GOC:tfm
database_cross_reference: http://wormatlas.psc.edu/hermaphrodite/muscleGLR/mainframe.htm

yolk cell
type: Class
subclass of: stuff accumulating cell
subclass of: extraembryonic cell
database_cross_reference: ZFA:0000084
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: yolk cell
annotated property: database_cross_reference
annotated target: ZFA:0000084
mapping justification: UnspecifiedMatching

imaginal disc cell
type: Class
subclass of: simple columnar epithelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000939
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon_50557
definition: A columnar epithelial cell that is part of an insect imaginal disc.
database_cross_reference: FBbt:00007108
comment: This term does not encompass all the cell types that may be found in an epithelial disc (such as the peripodial or adepithelial cells), only the cells that form the disc epithelium proper.

Axiom
annotated source: imaginal disc cell
annotated property: definition
annotated target: A columnar epithelial cell that is part of an insect imaginal disc.
database_cross_reference: doi:10.1007/s00412-016-0595-4

Axiom
annotated source: imaginal disc cell
annotated property: database_cross_reference
annotated target: FBbt:00007108
mapping justification: ManualMappingCuration

xanthophore cell
type: Class
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: develops from
  some values from: CL_0005002
definition: A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red.
database_cross_reference: ZFA:0009198
has_related_synonym: xanthophore
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: xanthophore cell
annotated property: definition
annotated target: A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red.
database_cross_reference: SANBI:mhl

Axiom
annotated source: xanthophore cell
annotated property: database_cross_reference
annotated target: ZFA:0009198
mapping justification: UnspecifiedMatching

iridophore
type: Class
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: develops from
  some values from: CL_0005001
definition: A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platelets or iridisomes. The color-generating components produce a silver, gold, or iridescent color.
database_cross_reference: ZFA:0009199
has_related_synonym: guanophore
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: iridophore
annotated property: definition
annotated target: A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platelets or iridisomes. The color-generating components produce a silver, gold, or iridescent color.
database_cross_reference: SANBI:mhl

Axiom
annotated source: iridophore
annotated property: database_cross_reference
annotated target: ZFA:0009199
mapping justification: UnspecifiedMatching

reticular cell
type: Class
subclass of: fibroblast
definition: A fibroblast that synthesizes collagen and uses it to produce reticular fibers, thus providing structural support. Reticular cells are found in many organs, including the spleen, lymph nodes and kidneys. Subtypes of reticular cells include epithelial, mesenchymal, and fibroblastic reticular cells. Fibroblastic reticular cells are involved in directing B cells and T cells to specific regions within a tissue, whereas epithelial and mesenchymal reticular cells are associated with certain areas of the brain.
present in taxon: NCBITaxon 9606
database_cross_reference: FMA:62877
database_cross_reference: ZFA:0009200
has_exact_synonym: reticulum cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: reticular cell
annotated property: definition
annotated target: A fibroblast that synthesizes collagen and uses it to produce reticular fibers, thus providing structural support. Reticular cells are found in many organs, including the spleen, lymph nodes and kidneys. Subtypes of reticular cells include epithelial, mesenchymal, and fibroblastic reticular cells. Fibroblastic reticular cells are involved in directing B cells and T cells to specific regions within a tissue, whereas epithelial and mesenchymal reticular cells are associated with certain areas of the brain.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651
database_cross_reference: http://en.wikipedia.org/wiki/Reticular_cell

Axiom
annotated source: reticular cell
annotated property: database_cross_reference
annotated target: ZFA:0009200
mapping justification: UnspecifiedMatching

obsolete functional megaspore
type: Class
definition: Obsolete. Use PO:0000244 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that will undergo megagametogenesis.
term replaced by: PO_0000244
deprecated: true

Axiom
annotated source: obsolete functional megaspore
annotated property: definition
annotated target: Obsolete. Use PO:0000244 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that will undergo megagametogenesis.
database_cross_reference: TAIR:lr

eccrine cell
type: Class
subclass of: CL_1100001
definition: A secretory cell that discharges its product without loss of cytoplasm.
present in taxon: NCBITaxon 9606
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: eccrine cell
annotated property: definition
annotated target: A secretory cell that discharges its product without loss of cytoplasm.
database_cross_reference: ISBN:0198547684

alkali secreting cell
type: Class
subclass of: secretory cell
database_cross_reference: ZFA:0009201
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: alkali secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009201
mapping justification: UnspecifiedMatching

vaginal lubricant secreting cell
type: Class
subclass of: secretory cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000996
in_subset: human subset
in_subset: mouse subset

gonadtroph
type: Class
subclass of: luteinizing hormone secreting cell
subclass of: basophil cell of pars distalis of adenohypophysis
definition: A rounded cell that is usually situated next to sinusoids; secretes follicular stimulating hormone (FSH) and luteinizing hormone (LH).
database_cross_reference: BTO:0002482
database_cross_reference: FMA:83100
database_cross_reference: ZFA:0009202
has_exact_synonym: delta basophil
has_exact_synonym: follicle stimulating hormone secreting cell
has_exact_synonym: gonadotrope
has_exact_synonym: gonadotrope cell
has_exact_synonym: gonadotroph
has_exact_synonym: gonadotropic cell
has_exact_synonym: pituitary delta cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: gonadtroph
annotated property: definition
annotated target: A rounded cell that is usually situated next to sinusoids; secretes follicular stimulating hormone (FSH) and luteinizing hormone (LH).
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651
database_cross_reference: http://en.wikipedia.org/wiki/Gonadotroph

Axiom
annotated source: gonadtroph
annotated property: database_cross_reference
annotated target: ZFA:0009202
mapping justification: UnspecifiedMatching

luteinizing hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0032275
subclass of: secretory cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0032275
definition: A peptide hormone secreting cell pituitary that produces luteinizing hormone.
database_cross_reference: ZFA:0009203
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: luteinizing hormone secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell pituitary that produces luteinizing hormone.
database_cross_reference: GOC:tfm

Axiom
annotated source: luteinizing hormone secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009203
mapping justification: UnspecifiedMatching

prolactin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0070459
subclass of: protein secreting cell
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0070459
definition: A peptide hormone cell that secretes prolactin.
database_cross_reference: ZFA:0009204
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: prolactin secreting cell
annotated property: definition
annotated target: A peptide hormone cell that secretes prolactin.
database_cross_reference: GOC:tfm
database_cross_reference: SANBI:mhl

Axiom
annotated source: prolactin secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009204
mapping justification: UnspecifiedMatching

melanocyte stimulating hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0036160
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0036160
definition: A cell of the intermediate pituitary that produces melanocyte stimulating hormone.
database_cross_reference: BTO:0002277
database_cross_reference: ZFA:0009205
has_exact_synonym: melanotrope
has_exact_synonym: melanotroph
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: melanocyte stimulating hormone secreting cell
annotated property: definition
annotated target: A cell of the intermediate pituitary that produces melanocyte stimulating hormone.
database_cross_reference: SANBI:mhl

Axiom
annotated source: melanocyte stimulating hormone secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009205
mapping justification: UnspecifiedMatching

follicle stem cell (sensu Arthropoda)
type: Class
subclass of: epithelial fate stem cell
subclass of: Restriction
definition: A stem cell that gives rise to the follicle cells that surround the oocyte in female arthropods.
has_broad_synonym: somatic stem cell
database_cross_reference: FBbt:00004903

Axiom
annotated source: follicle stem cell (sensu Arthropoda)
annotated property: definition
annotated target: A stem cell that gives rise to the follicle cells that surround the oocyte in female arthropods.
database_cross_reference: doi:10.1016/B978-012369493-5.50005-5
database_cross_reference: doi:10.1038/s41467-020-19361-0
database_cross_reference: doi:10.1242/dev.121.11.3797

Axiom
annotated source: follicle stem cell (sensu Arthropoda)
annotated property: has_broad_synonym
annotated target: somatic stem cell
database_cross_reference: doi:10.1016/j.devcel.2005.08.012

Axiom
annotated source: follicle stem cell (sensu Arthropoda)
annotated property: database_cross_reference
annotated target: FBbt:00004903
mapping justification: ManualMappingCuration

follicular dendritic cell
type: Class
subclass of: dendritic cell
definition: A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0004267
database_cross_reference: FMA:83037
database_cross_reference: MESH:D020566
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Due to its unique lineage and distinct function, this is not a type of dendritic cell; CL:0000451.

Axiom
annotated source: follicular dendritic cell
annotated property: definition
annotated target: A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response.
database_cross_reference: ISBN:127520252

calcitonin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0036161
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0036161
definition: Any secretory cell that is capable of some calcitonin secretion.
database_cross_reference: ZFA:0009206
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: calcitonin secreting cell
annotated property: definition
annotated target: Any secretory cell that is capable of some calcitonin secretion.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: calcitonin secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009206
mapping justification: UnspecifiedMatching

obliquely striated muscle cell
type: Class
equivalent class: Class
  intersection of: muscle cell
  intersection of: Restriction
    on property: has part
    some values from: GO_0030017
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0002479
subclass of: striated muscle cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0002479
definition: A muscle cell in which the fibers are organised into sarcomeres but in which adjacent myofibrils are offset from each other, producing an oblique banding pattern.
in_subset: human subset
in_subset: mouse subset
comment: Examples include the somatic muscles of nemotodes and cephalopods.

Axiom
annotated source: obliquely striated muscle cell
annotated property: definition
annotated target: A muscle cell in which the fibers are organised into sarcomeres but in which adjacent myofibrils are offset from each other, producing an oblique banding pattern.
database_cross_reference: GOC:DOS
database_cross_reference: PMID:8720463

apoptosis fated cell
type: Class
subclass of: cell
in_subset: human subset
in_subset: mouse subset

chief cell of parathyroid gland
type: Class
subclass of: CL_1001593
subclass of: Restriction
  on property: part of
  some values from: UBERON_0011197
subclass of: Restriction
  on property: capable of
  some values from: GO_0035898
definition: An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone.
database_cross_reference: BTO:0004712
database_cross_reference: CALOHA:TS-2140
database_cross_reference: FMA:69078
has_exact_synonym: parathyroid chief cell
has_exact_synonym: parathyroid gland chief cell
has_exact_synonym: parathyroid hormone secreting cell
has_exact_synonym: principal cell of parathyroid gland
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: chief cell of parathyroid gland
annotated property: definition
annotated target: An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone.
database_cross_reference: FMA:69078
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651

carbohydrate secreting cell
type: Class
subclass of: secretory cell
in_subset: human subset
in_subset: mouse subset

white adipocyte
type: Class
subclass of: adipocyte
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001347
subclass of: Restriction
  on property: develops from
  some values from: CL_0002334
definition: An adipocyte with light coloration and few mitochondria. It contains a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole.
database_cross_reference: CALOHA:TS-1119
database_cross_reference: FMA:83434
has_exact_synonym: white adipose cell
has_related_synonym: white fat cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: white adipocyte
annotated property: definition
annotated target: An adipocyte with light coloration and few mitochondria. It contains a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D052438

brown adipocyte
type: Class
subclass of: adipocyte
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001348
subclass of: Restriction
  on property: develops from
  some values from: CL_0002335
definition: A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation.
database_cross_reference: CALOHA:TS-0099
database_cross_reference: FMA:83435
has_exact_synonym: brown adipose cell
has_exact_synonym: brown fat cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: brown adipocyte
annotated property: definition
annotated target: A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation.
database_cross_reference: MESH:D002001

CL_0000450
type: Class
has obsolescence reason: IAO_0000227
term replaced by: adipocyte
deprecated: true

dendritic cell
type: Class
equivalent class: Class
  intersection of: leukocyte
  intersection of: Restriction
    on property: has part
    some values from: GO_0042613
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001003
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001407
  intersection of: Restriction
    on property: capable of
    some values from: GO_0001816
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002504
  intersection of: Restriction
    on property: capable of
    some values from: GO_0019882
  intersection of: Restriction
    on property: capable of
    some values from: GO_0045580
subclass of: mononuclear phagocyte
subclass of: professional antigen presenting cell
subclass of: Restriction
  on property: has part
  some values from: GO_0042613
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001003
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: capable of
  some values from: GO_0001816
subclass of: Restriction
  on property: capable of
  some values from: GO_0045580
disjoint with: lymphocyte
definition: A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0002042
database_cross_reference: CALOHA:TS-0194
database_cross_reference: FMA:83036
database_cross_reference: MESH:D003713
database_cross_reference: ZFA:0009209
has_related_synonym: interdigitating cell
has_related_synonym: veiled cell
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: dendritic cell
annotated property: definition
annotated target: A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).
database_cross_reference: GOC:add
database_cross_reference: ISBN:0781735149

Axiom
annotated source: dendritic cell
annotated property: database_cross_reference
annotated target: ZFA:0009209
mapping justification: UnspecifiedMatching

thyroid hormone secreting cell
type: Class
subclass of: endocrine cell
database_cross_reference: ZFA:0009210
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: thyroid hormone secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009210
mapping justification: UnspecifiedMatching

Langerhans cell
type: Class
equivalent class: Class
  intersection of: CL_0000990
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001293
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002828
subclass of: myeloid leukocyte
subclass of: CL_0000990
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001293
subclass of: Restriction
  on property: develops from
  some values from: myeloid cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0002828
definition: Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000705
database_cross_reference: CALOHA:TS-2375
database_cross_reference: FMA:63072
database_cross_reference: MESH:D007801
has_exact_synonym: LC
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Originally described in the dendritic cell ontology (DC_CL:0000021 )(PMID:19243617). These cells are also CD1a-high, CD14-negative, CD207-positive (langerin), CD324-positive (E-cadherin), and DCIR-positive. They reside in the epidermis.

Axiom
annotated source: Langerhans cell
annotated property: subClassOf
annotated target: CL_0000990
is inferred: true

Axiom
annotated source: Langerhans cell
annotated property: definition
annotated target: Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus.
database_cross_reference: GOC:add
database_cross_reference: GOC:amm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0721601464
database_cross_reference: ISBN:0781735149
database_cross_reference: PMCID:PMC2346585
database_cross_reference: PMID:17850486

epinephrine secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0048242
subclass of: biogenic amine secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0048242
definition: A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types.
database_cross_reference: ZFA:0009211
has_exact_synonym: adrenaline secreting cell
has_exact_synonym: epinephrin secreting cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: epinephrine secreting cell
annotated property: definition
annotated target: A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:12438093

Axiom
annotated source: epinephrine secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009211
mapping justification: UnspecifiedMatching

Axiom
annotated source: epinephrine secreting cell
annotated property: has_exact_synonym
annotated target: adrenaline secreting cell
database_cross_reference: GO:0048242

obsolete starch sheath cell
type: Class
definition: Obsolete. Use PO:0004531 from Plant Ontology instead. A cell characterized by conspicuous and rather stable accumulation of starch.
term replaced by: PO_0004531
deprecated: true

Axiom
annotated source: obsolete starch sheath cell
annotated property: definition
annotated target: Obsolete. Use PO:0004531 from Plant Ontology instead. A cell characterized by conspicuous and rather stable accumulation of starch.
database_cross_reference: ISBN:044174520

mineralocorticoid secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0035931
subclass of: steroid hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0035931
definition: Any secretory cell that is capable of some mineralocorticoid secretion.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: mineralocorticoid secreting cell
annotated property: definition
annotated target: Any secretory cell that is capable of some mineralocorticoid secretion.
database_cross_reference: FBC:Autogenerated

biogenic amine secreting cell
type: Class
subclass of: secretory cell
database_cross_reference: ZFA:0009212
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: biogenic amine secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009212
mapping justification: UnspecifiedMatching

serotonin secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0001820
subclass of: biogenic amine secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0001820
definition: A cell type that secretes 5-Hydroxytryptamine (serotonin).
database_cross_reference: ZFA:0009213
has_exact_synonym: 5-HT secreting cell
has_exact_synonym: 5-Hydroxytryptamine secreting cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: serotonin secreting cell
annotated property: definition
annotated target: A cell type that secretes 5-Hydroxytryptamine (serotonin).
database_cross_reference: GOC:tfm
database_cross_reference: PMID:19630576

Axiom
annotated source: serotonin secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009213
mapping justification: UnspecifiedMatching

noradrenergic cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0048243
subclass of: biogenic amine secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0048243
definition: A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme.
database_cross_reference: ZFA:0009214
has_exact_synonym: noradrenaline secreting cell
has_exact_synonym: norepinephrin secreting cell
has_exact_synonym: norepinephrine secreting cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: noradrenergic cell
annotated property: definition
annotated target: A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:068340007X

Axiom
annotated source: noradrenergic cell
annotated property: database_cross_reference
annotated target: ZFA:0009214
mapping justification: UnspecifiedMatching

glucocorticoid secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0035933
subclass of: steroid hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0035933
definition: Any secretory cell that is capable of some glucocorticoid secretion.
database_cross_reference: ZFA:0009215
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: glucocorticoid secreting cell
annotated property: definition
annotated target: Any secretory cell that is capable of some glucocorticoid secretion.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: glucocorticoid secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009215
mapping justification: UnspecifiedMatching

CL_0000461
type: Class
has obsolescence reason: IAO_0000227
term replaced by: kidney granular cell
deprecated: true

adepithelial cell
type: Class
subclass of: muscle precursor cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon_50557
definition: A cell of mesodermal origin that is closely associated with the epithelium of an imaginal disc. It is a precursor of some of the insect's adult muscles.
database_cross_reference: FBbt:00003219

Axiom
annotated source: adepithelial cell
annotated property: definition
annotated target: A cell of mesodermal origin that is closely associated with the epithelium of an imaginal disc. It is a precursor of some of the insect's adult muscles.
database_cross_reference: doi:10.1016/S0925-4773(97)00654-0

Axiom
annotated source: adepithelial cell
annotated property: database_cross_reference
annotated target: FBbt:00003219
mapping justification: ManualMappingCuration

epidermal cell (sensu Arthropoda)
type: Class
subclass of: epidermal cell
subclass of: neurecto-epithelial cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 6656
subclass of: Restriction
  on property: develops from
  some values from: epidermoblast
definition: An epidermal cell that secretes chitinous cuticle from its apical side.
database_cross_reference: FBbt:00007325
comment: While insect epidermis is generally columnar/cuboidal, there are certainly well studied cases where it is not (e.g.- Rhodnius prolixus when starved). So it would be safer to add this as a differentium for particular species where this is known. -DSJ.

Axiom
annotated source: epidermal cell (sensu Arthropoda)
annotated property: definition
annotated target: An epidermal cell that secretes chitinous cuticle from its apical side.
database_cross_reference: FlyBase:ds
database_cross_reference: ISBN:ISBN:978-0801481253

Axiom
annotated source: epidermal cell (sensu Arthropoda)
annotated property: database_cross_reference
annotated target: FBbt:00007325
mapping justification: ManualMappingCuration

epidermoblast
type: Class
subclass of: non-terminally differentiated cell
subclass of: neurecto-epithelial cell
subclass of: Restriction
  on property: develops from
  some values from: surface ectodermal cell
definition: An epidermal progenitor cell that arises from neuroectoderm and in turn gives rise to the epidermal sheath of ventral and cephalic regions.
database_cross_reference: FBbt:00004994
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: epidermoblast
annotated property: definition
annotated target: An epidermal progenitor cell that arises from neuroectoderm and in turn gives rise to the epidermal sheath of ventral and cephalic regions.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:7576311

Axiom
annotated source: epidermoblast
annotated property: database_cross_reference
annotated target: FBbt:00004994
mapping justification: ManualMappingCuration

cardioblast (sensu Arthropoda)
type: Class
subclass of: CL_0010021
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 6656
definition: A precursor of the cells that form the dorsal vessel of arthropods.
database_cross_reference: FBbt:00001666

Axiom
annotated source: cardioblast (sensu Arthropoda)
annotated property: definition
annotated target: A precursor of the cells that form the dorsal vessel of arthropods.
database_cross_reference: doi:10.1007/BF00360522

Axiom
annotated source: cardioblast (sensu Arthropoda)
annotated property: database_cross_reference
annotated target: FBbt:00001666
mapping justification: ManualMappingCuration

CL_0000466
type: Class
has obsolescence reason: IAO_0000227
term replaced by: cardiac muscle cell (sensu Arthopoda)
deprecated: true

adrenocorticotropic hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0051458
subclass of: peptide hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0051458
definition: A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin.
database_cross_reference: ZFA:0009216
has_exact_synonym: ACTH secreting cell
has_exact_synonym: adrenocorticotrophic hormone secreting cell
has_exact_synonym: corticotrophin hormone secreting cell
has_exact_synonym: corticotropin hormone secreting cell
has_exact_synonym: corticotropin secreting cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: adrenocorticotropic hormone secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin.
database_cross_reference: GOC:tfm
database_cross_reference: SANBI:mhl

Axiom
annotated source: adrenocorticotropic hormone secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009216
mapping justification: UnspecifiedMatching

Axiom
annotated source: adrenocorticotropic hormone secreting cell
annotated property: has_exact_synonym
annotated target: ACTH secreting cell
database_cross_reference: GO:0051458

Axiom
annotated source: adrenocorticotropic hormone secreting cell
annotated property: has_exact_synonym
annotated target: corticotropin secreting cell
database_cross_reference: GO:0051458

neuroglioblast (sensu Nematoda and Protostomia)
type: Class
subclass of: neural stem cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon_33317
definition: A precursor of the central nervous system that gives rise to both neurons and glial cells.
database_cross_reference: FBbt:00005147
has_exact_synonym: neuro-glioblast
has_exact_synonym: neuroglioblast

Axiom
annotated source: neuroglioblast (sensu Nematoda and Protostomia)
annotated property: definition
annotated target: A precursor of the central nervous system that gives rise to both neurons and glial cells.
database_cross_reference: doi:10.1002/glia.21162

Axiom
annotated source: neuroglioblast (sensu Nematoda and Protostomia)
annotated property: database_cross_reference
annotated target: FBbt:00005147
mapping justification: ManualMappingCuration

ganglion mother cell
type: Class
subclass of: CL_0011020
subclass of: Restriction
  on property: develops from
  some values from: neuroblast (sensu Nematoda and Protostomia)
definition: A neural progenitor cell that is the daughter of a neuroblast (sensu arthopoda). The progeny of ganglion mother cells develop into neurons, glia and (occasionally) epithelial cells.
database_cross_reference: FBbt:00005149

Axiom
annotated source: ganglion mother cell
annotated property: database_cross_reference
annotated target: FBbt:00005149
mapping justification: ManualMappingCuration

digestive enzyme secreting cell
type: Class
subclass of: protein secreting cell
database_cross_reference: ZFA:0009217
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: digestive enzyme secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009217
mapping justification: UnspecifiedMatching

CL_0000471
type: Class
has obsolescence reason: IAO_0000227
term replaced by: somatotropin secreting cell
deprecated: true

obsolete chlorenchyma cell
type: Class
definition: Obsolete. Use PO:0000076 from Plant Ontology instead. OBSOLETE, use term from Plant Ontology. Parenchyma cells containing chloroplasts; a component of leaf mesophyll and other green parenchyma tissue.
term replaced by: PO_0000076
deprecated: true

Axiom
annotated source: obsolete chlorenchyma cell
annotated property: definition
annotated target: Obsolete. Use PO:0000076 from Plant Ontology instead. OBSOLETE, use term from Plant Ontology. Parenchyma cells containing chloroplasts; a component of leaf mesophyll and other green parenchyma tissue.
database_cross_reference: ISBN:0471245208

OBSOLETE defensive cell
type: Class
definition: OBSOLETE: A cell whose primary function is to protect the organism.
term tracker item: https://github.com/obophenotype/cell-ontology/pull/3056
comment: Unsustainable functional grouping term of dubious utility.
deprecated: true

pericardial nephrocyte
type: Class
subclass of: phagocyte (sensu Nematoda and Protostomia)
subclass of: CL_0002520
definition: An insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel.
database_cross_reference: FBbt:00005058
has_narrow_synonym: pericardial cell

Axiom
annotated source: pericardial nephrocyte
annotated property: definition
annotated target: An insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel.
database_cross_reference: FBbt:00003184
database_cross_reference: GO:0061320
database_cross_reference: GOC:tfm
database_cross_reference: PMID:19783135

Axiom
annotated source: pericardial nephrocyte
annotated property: database_cross_reference
annotated target: FBbt:00005058
mapping justification: ManualMappingCuration

Axiom
annotated source: pericardial nephrocyte
annotated property: has_narrow_synonym
annotated target: pericardial cell
database_cross_reference: FBbt:00005058
database_cross_reference: GO:0061320

obsolete degenerate megaspore
type: Class
definition: Obsolete. Use PO:0000245 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that do not participate in megagametogenesis.
term replaced by: PO_0000245
deprecated: true

Axiom
annotated source: obsolete degenerate megaspore
annotated property: definition
annotated target: Obsolete. Use PO:0000245 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that do not participate in megagametogenesis.
database_cross_reference: TAIR:lr

thyrotroph
type: Class
subclass of: basophil cell of pars distalis of adenohypophysis
subclass of: Restriction
  on property: capable of
  some values from: GO_0070460
definition: A basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin. This cell type is elongated, polygonal and lie in clusters towards the adenohypophyseal center.
database_cross_reference: FMA:83099
database_cross_reference: MESH:D052684
database_cross_reference: ZFA:0009218
has_exact_synonym: beta-basophil
has_exact_synonym: thyroid stimulating hormone secreting cell
has_exact_synonym: thyrotrope
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: thyrotroph
annotated property: definition
annotated target: A basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin. This cell type is elongated, polygonal and lie in clusters towards the adenohypophyseal center.
database_cross_reference: ISBN:0517223651
database_cross_reference: SANBI:mhl

Axiom
annotated source: thyrotroph
annotated property: database_cross_reference
annotated target: ZFA:0009218
mapping justification: UnspecifiedMatching

follicle cell of egg chamber
type: Class
subclass of: BFO_0000002
subclass of: follicular epithelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000992
subclass of: Restriction
  on property: develops from
  some values from: follicle stem cell (sensu Arthropoda)
definition: A somatic epithelial cell of the insect egg chamber.
has_broad_synonym: follicle cell
has_broad_synonym: ovarian follicle cell
database_cross_reference: FBbt:00004904

Axiom
annotated source: follicle cell of egg chamber
annotated property: database_cross_reference
annotated target: FBbt:00004904
mapping justification: ManualMappingCuration

oxytocin stimulating hormone secreting cell
type: Class
subclass of: peptide hormone secreting cell
definition: A peptide hormone secreting cell that secretes oxytocin stimulating hormone
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: oxytocin stimulating hormone secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that secretes oxytocin stimulating hormone
database_cross_reference: GO:tfm

vasopressin stimulating hormone secreting cell
type: Class
subclass of: peptide hormone secreting cell
definition: A peptide hormone secreting cell that secretes vasopressin stimulating hormone
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: vasopressin stimulating hormone secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that secretes vasopressin stimulating hormone
database_cross_reference: GO:tfm

secretin stimulating hormone secreting cell
type: Class
subclass of: peptide hormone secreting cell
definition: A peptide hormone secreting cell that secretes secretin stimulating hormone
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: secretin stimulating hormone secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that secretes secretin stimulating hormone
database_cross_reference: GO:tfm

cholecystokin stimulating hormone secreting cell
type: Class
subclass of: peptide hormone secreting cell
definition: A peptide hormone secreting cell that secretes cholecystokin stimulating hormone.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cholecystokin stimulating hormone secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that secretes cholecystokin stimulating hormone.
database_cross_reference: GO:tfm

juvenile hormone secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0045443
subclass of: secretory cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0045443
definition: An endocrine cell that secretes juvenile hormone.
database_cross_reference: FBbt:00058020
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: juvenile hormone secreting cell
annotated property: definition
annotated target: An endocrine cell that secretes juvenile hormone.
database_cross_reference: GO:tfm

Axiom
annotated source: juvenile hormone secreting cell
annotated property: database_cross_reference
annotated target: FBbt:00058020
mapping justification: ManualMappingCuration

bombesin stimulating hormone secreting cell
type: Class
subclass of: peptide hormone secreting cell
definition: A peptide hormone secreting cell that secretes bombesin stimulating hormone.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: bombesin stimulating hormone secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that secretes bombesin stimulating hormone.
database_cross_reference: GO:tfm
database_cross_reference: https://orcid.org/0000-0001-5208-3432

connective tissue type mast cell
type: Class
equivalent class: Class
  intersection of: mast cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002384
subclass of: mast cell
subclass of: CL_0002320
definition: Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent.
present in taxon: NCBITaxon 9606
has_exact_synonym: MC(TC)
has_exact_synonym: MCTC
has_exact_synonym: TC mast cells
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: They are CD88-positive. The cytoplasmic granules contain high levels of histamine and heparin (mouse) or major neutral proteases, tryptase, chymase, carboxypeptidase A, and cathepsin G (humans). Reportedly, they cannot produce leukotrienes (LTC4) and IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype.

Axiom
annotated source: connective tissue type mast cell
annotated property: subClassOf
annotated target: mast cell
is inferred: true

Axiom
annotated source: connective tissue type mast cell
annotated property: definition
annotated target: Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: PMID:19923473
database_cross_reference: PMID:9354811

mucosal type mast cell
type: Class
equivalent class: Class
  intersection of: mast cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001961
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002540
subclass of: mast cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001961
subclass of: Restriction
  on property: capable of
  some values from: GO_0002540
definition: Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype.
present in taxon: NCBITaxon 9606
has_exact_synonym: MC(T)
has_exact_synonym: MCT
has_exact_synonym: T mast cells
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: They are CD88-negative. The cytoplasmic granules contain low levels of histamine and high levels of chondroitin sulfate (mouse) or major neutral proteases and tryptase (humans). Additionally, they can produce leukotrienes (LTC4), IL-5, IL-6, and low levels of IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype.

Axiom
annotated source: mucosal type mast cell
annotated property: subClassOf
annotated target: mast cell
is inferred: true

Axiom
annotated source: mucosal type mast cell
annotated property: definition
annotated target: Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: PMID:19923473
database_cross_reference: PMID:9354811

garland cell
type: Class
subclass of: binucleate cell
subclass of: phagocyte (sensu Nematoda and Protostomia)
subclass of: CL_0002520
definition: A large binucleate cell that forms a 'garland' around the anterior end of the proventriculus (cardia) at its junction with the esophagus in both adults and larvae flies. Each cell is surrounded by a basement membrane and there are numerous micro-invaginations (lacunae) extending from the surface into the cytoplasm. At the mouth of each lacuna is a doubled filament forming a specialised filtration system (diaphragm). The filtrate is endocytosed from the lacunae.
has_broad_synonym: garland nephrocyte
database_cross_reference: BTO:0004596
database_cross_reference: FBbt:00005059

Axiom
annotated source: garland cell
annotated property: definition
annotated target: A large binucleate cell that forms a 'garland' around the anterior end of the proventriculus (cardia) at its junction with the esophagus in both adults and larvae flies. Each cell is surrounded by a basement membrane and there are numerous micro-invaginations (lacunae) extending from the surface into the cytoplasm. At the mouth of each lacuna is a doubled filament forming a specialised filtration system (diaphragm). The filtrate is endocytosed from the lacunae.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:19783135
database_cross_reference: fbbt:00005059

Axiom
annotated source: garland cell
annotated property: has_broad_synonym
annotated target: garland nephrocyte
database_cross_reference: GO:0061321

Axiom
annotated source: garland cell
annotated property: database_cross_reference
annotated target: FBbt:00005059
mapping justification: ManualMappingCuration

oenocyte
type: Class
subclass of: secretory cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 6656
definition: A secretory cell of ectodermal origin. This cell may have important functions in fatty acid and hydrocarbon metabolism and is metabolically linked to the fat body and tracheae. This cell is exclusive of arthropods.
database_cross_reference: FBbt:00004995
comment: Oenocytes are highly variable in size, shape, cluster formation and anatomical location. In adults, oenocytes tend to be smaller but more numerous than in larvae. While oenocytes have been found in arachnids and crustaceans, they have been most abundantly described in insects.

Axiom
annotated source: oenocyte
annotated property: definition
annotated target: A secretory cell of ectodermal origin. This cell may have important functions in fatty acid and hydrocarbon metabolism and is metabolically linked to the fat body and tracheae. This cell is exclusive of arthropods.
database_cross_reference: GOC:bf
database_cross_reference: PMID:11171397
database_cross_reference: PMID:24397521
database_cross_reference: PMID:34208190
database_cross_reference: https://www.merriam-webster.com/dictionary/oenocyte

Axiom
annotated source: oenocyte
annotated property: database_cross_reference
annotated target: FBbt:00004995
mapping justification: ManualMappingCuration

Axiom
annotated source: oenocyte
annotated property: comment
annotated target: Oenocytes are highly variable in size, shape, cluster formation and anatomical location. In adults, oenocytes tend to be smaller but more numerous than in larvae. While oenocytes have been found in arachnids and crustaceans, they have been most abundantly described in insects.
database_cross_reference: PMID:24397521
database_cross_reference: PMID:34208190

visible light photoreceptor cell
type: Class
equivalent class: Class
  intersection of: photoreceptor cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0009584
subclass of: photoreceptor cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0009584
definition: A photoreceptor cell that detects visible light.
database_cross_reference: ZFA:0009219
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: visible light photoreceptor cell
annotated property: definition
annotated target: A photoreceptor cell that detects visible light.
database_cross_reference: GOC:tfm

Axiom
annotated source: visible light photoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009219
mapping justification: UnspecifiedMatching

scotopic photoreceptor cell
type: Class
subclass of: photoreceptor cell
in_subset: human subset
in_subset: mouse subset

photopic photoreceptor cell
type: Class
subclass of: visible light photoreceptor cell
database_cross_reference: ZFA:0009220
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: photopic photoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009220
mapping justification: UnspecifiedMatching

obsolete cytotoxic T cell
type: Class
definition: OBSOLETE: A cell responsible for spontaneous cytotoxicity of a variety of tumor cells without prior immunization. These natural killer cells are found in non-immune humans and experimental animals and are thought by some to be the same as killer cells (killing by antibody-dependent cell cytotoxicity), but they can also kill in the absence of antibody.
comment: This term had an incorrect definition and was overly broad. Consider using 'cytotoxic T cell ; CL:0000910' (in most cases) or another lymphocyte cell type if cytotoxicity is shown to be part of the cell's phenotype in a particular experimental situation.
deprecated: true

CD4-positive helper T cell
type: Class
equivalent class: Class
  intersection of: CD4-positive, alpha-beta T cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0001816
subclass of: CD4-positive, alpha-beta T cell
subclass of: Restriction
  on property: develops from
  some values from: CL_0000896
subclass of: Restriction
  on property: capable of
  some values from: GO_0001816
subclass of: Restriction
  on property: output of
  some values from: GO_0030217
definition: A CD4-positive, alpha-beta T cell that cooperates with other lymphocytes via direct contact or cytokine release to initiate a variety of immune functions.
present in taxon: NCBITaxon 9606
database_cross_reference: CALOHA:TS-1146
database_cross_reference: FMA:70572
has_exact_synonym: CD4-positive T-helper cell
has_exact_synonym: CD4-positive helper T lymphocyte
has_exact_synonym: CD4-positive helper T-cell
has_exact_synonym: CD4-positive helper T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: CD4-positive helper T cell
annotated property: subClassOf
annotated target: CD4-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD4-positive helper T cell
annotated property: definition
annotated target: A CD4-positive, alpha-beta T cell that cooperates with other lymphocytes via direct contact or cytokine release to initiate a variety of immune functions.
database_cross_reference: GOC:add
database_cross_reference: GOC:pam
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149
database_cross_reference: MESH:D006377

obsolete regulatory T cell
type: Class
definition: OBSOLETE: Subpopulation of CD4+ cells which induce CD8+ suppressor T cells to suppress antibody production by B cells. They also stimulate other cellular immune responses.
comment: This term was defined too narrowly; consider using the term 'regulatory T cell ; CL:0000815' instead.
deprecated: true

UV sensitive photoreceptor cell
type: Class
equivalent class: Class
  intersection of: photoreceptor cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0009589
subclass of: photoreceptor cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0009589
definition: A photoreceptor cell that detects ultraviolet light.
database_cross_reference: ZFA:0009221
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: UV sensitive photoreceptor cell
annotated property: definition
annotated target: A photoreceptor cell that detects ultraviolet light.
database_cross_reference: GOC:tfm

Axiom
annotated source: UV sensitive photoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009221
mapping justification: UnspecifiedMatching

blue sensitive photoreceptor cell
type: Class
subclass of: photopic photoreceptor cell
definition: A photoreceptor cell that is sensitive to blue light.
database_cross_reference: ZFA:0009222
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: blue sensitive photoreceptor cell
annotated property: definition
annotated target: A photoreceptor cell that is sensitive to blue light.
database_cross_reference: GO:tfm

Axiom
annotated source: blue sensitive photoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009222
mapping justification: UnspecifiedMatching

green sensitive photoreceptor cell
type: Class
subclass of: photopic photoreceptor cell
definition: A photoreceptor cell that is sensitive to green light.
database_cross_reference: ZFA:0009223
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: green sensitive photoreceptor cell
annotated property: definition
annotated target: A photoreceptor cell that is sensitive to green light.
database_cross_reference: GO:tfm

Axiom
annotated source: green sensitive photoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009223
mapping justification: UnspecifiedMatching

red sensitive photoreceptor cell
type: Class
subclass of: photopic photoreceptor cell
definition: A photoreceptor cell that is sensitive to red light.
database_cross_reference: ZFA:0009224
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: red sensitive photoreceptor cell
annotated property: definition
annotated target: A photoreceptor cell that is sensitive to red light.
database_cross_reference: GO:tfm

Axiom
annotated source: red sensitive photoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009224
mapping justification: UnspecifiedMatching

inhibitory interneuron
type: Class
subclass of: interneuron
definition: An interneuron (also called relay neuron, association neuron or local circuit neuron) is a multipolar neuron which connects afferent neurons and efferent neurons in neural pathways. Like motor neurons, interneuron cell bodies are always located in the central nervous system (CNS).
database_cross_reference: FMA:84776
database_cross_reference: ZFA:0009225
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: inhibitory interneuron
annotated property: definition
annotated target: An interneuron (also called relay neuron, association neuron or local circuit neuron) is a multipolar neuron which connects afferent neurons and efferent neurons in neural pathways. Like motor neurons, interneuron cell bodies are always located in the central nervous system (CNS).
database_cross_reference: GOC:tfm
database_cross_reference: http://en.wikipedia.org/wiki/Interneuron

Axiom
annotated source: inhibitory interneuron
annotated property: database_cross_reference
annotated target: ZFA:0009225
mapping justification: UnspecifiedMatching

stromal cell
type: Class
subclass of: BFO_0000002
subclass of: CL_0002320
subclass of: Restriction
  on property: develops from
  some values from: mesenchymal stem cell
definition: A connective tissue cell of an organ found in the loose connective tissue.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0002064
database_cross_reference: FMA:83624
database_cross_reference: ZFA:0009226
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: stromal cell
annotated property: definition
annotated target: A connective tissue cell of an organ found in the loose connective tissue.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D017154

Axiom
annotated source: stromal cell
annotated property: database_cross_reference
annotated target: ZFA:0009226
mapping justification: UnspecifiedMatching

follicular epithelial cell
type: Class
subclass of: epithelial cell
definition: An epithelial somatic cell associated with a maturing oocyte.
in_subset: human subset
in_subset: mouse subset

granulosa cell
type: Class
subclass of: BFO_0000002
subclass of: steroid hormone secreting cell
subclass of: CL_0002174
subclass of: Restriction
  on property: develops from
  some values from: CL_4033066
definition: A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors.
description: Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: BTO:0000542
database_cross_reference: CALOHA:TS-0729
database_cross_reference: FMA:18718
database_cross_reference: ZFA:0009227
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000501
has_exact_synonym: granulosa cell of ovary
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: granulosa cell
annotated property: definition
annotated target: A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors.
database_cross_reference: MESH:D006107

Axiom
annotated source: granulosa cell
annotated property: description
annotated target: Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1016/j.ejogrb.2004.01.010
database_cross_reference: DOI:10.1093/humrep/del408
database_cross_reference: DOI:10.1093/humupd/6.3.279
database_cross_reference: DOI:10.1210/jcem-28-3-355
database_cross_reference: DOI:10.3389/fendo.2019.00832/full

Axiom
annotated source: granulosa cell
annotated property: database_cross_reference
annotated target: ZFA:0009227
mapping justification: UnspecifiedMatching

type D enteroendocrine cell
type: Class
subclass of: enteroendocrine cell
subclass of: neuroendocrine cell
subclass of: somatostatin secreting cell
definition: A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin.
description: Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: FMA:62935
database_cross_reference: ZFA:0009228
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000502
has_exact_synonym: D cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: type D enteroendocrine cell
annotated property: definition
annotated target: A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin.
database_cross_reference: MESH:D019864

Axiom
annotated source: type D enteroendocrine cell
annotated property: description
annotated target: Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1016/j.pharmthera.2015.05.007
database_cross_reference: DOI:10.1038/s41574-018-0020-6
database_cross_reference: DOI:10.1093/annonc/mdh216
database_cross_reference: https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell

Axiom
annotated source: type D enteroendocrine cell
annotated property: database_cross_reference
annotated target: ZFA:0009228
mapping justification: UnspecifiedMatching

theca cell
type: Class
subclass of: CL_0002132
subclass of: CL_0002174
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000155
definition: A specialized stromal cell that forms the theca layer outside the basal lamina lining the ovarian follicle, appearing during the secondary follicle stage.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0002850
database_cross_reference: ZFA:0009229
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: theca cell
annotated property: definition
annotated target: A specialized stromal cell that forms the theca layer outside the basal lamina lining the ovarian follicle, appearing during the secondary follicle stage.
database_cross_reference: MESH:D013799
database_cross_reference: PMID:15833266
database_cross_reference: PMID:36758341

Axiom
annotated source: theca cell
annotated property: database_cross_reference
annotated target: ZFA:0009229
mapping justification: UnspecifiedMatching

enterochromaffin-like cell
type: Class
subclass of: enteroendocrine cell
subclass of: CL_0002274
definition: A enteroendocrine cell part of the glands of the gastric mucosa. They produce histamine and peptides such as chromogranins. This cell type respond to gastrin by releasing histamine which acts as a paracrine stimulator of the release of hydrochloric acid from the gastric parietal cells.
database_cross_reference: BTO:0002692
has_exact_synonym: ECL
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Consider enterochromaffin cell (CL:0002065). For several years this cell type was "enterochromaffin cell" despite a MESH dbxref and a free text definition that clearly meant enterochromaffin-like cell.

Axiom
annotated source: enterochromaffin-like cell
annotated property: definition
annotated target: A enteroendocrine cell part of the glands of the gastric mucosa. They produce histamine and peptides such as chromogranins. This cell type respond to gastrin by releasing histamine which acts as a paracrine stimulator of the release of hydrochloric acid from the gastric parietal cells.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D019861

substance P secreting cell
type: Class
subclass of: peptide hormone secreting cell
definition: A peptide hormone secreting cell that secretes substance P.
database_cross_reference: ZFA:0009230
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: substance P secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that secretes substance P.
database_cross_reference: GO:tfm

Axiom
annotated source: substance P secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009230
mapping justification: UnspecifiedMatching

enkephalin secreting cell
type: Class
subclass of: endorphin secreting cell
definition: An endorphine cell that secretes enkephalin.
database_cross_reference: ZFA:0009231
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: enkephalin secreting cell
annotated property: definition
annotated target: An endorphine cell that secretes enkephalin.
database_cross_reference: GO:tfm

Axiom
annotated source: enkephalin secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009231
mapping justification: UnspecifiedMatching

endorphin secreting cell
type: Class
subclass of: peptide hormone secreting cell
definition: A peptide hormone secreting cell that secretes endorphin.
database_cross_reference: ZFA:0009232
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: endorphin secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that secretes endorphin.
database_cross_reference: GO:tfm

Axiom
annotated source: endorphin secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009232
mapping justification: UnspecifiedMatching

type G enteroendocrine cell
type: Class
subclass of: enteroendocrine cell
subclass of: neuroendocrine cell
subclass of: enkephalin secreting cell
subclass of: gastrin secreting cell
definition: An endocrine cell found in the stomach and duodenum and is responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli.
database_cross_reference: BTO:0004108
database_cross_reference: FMA:67609
has_exact_synonym: G cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: type G enteroendocrine cell
annotated property: definition
annotated target: An endocrine cell found in the stomach and duodenum and is responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651
database_cross_reference: MESH:D019863
database_cross_reference: PMID:10700044
database_cross_reference: PMID:35674015
database_cross_reference: PMID:37240181

gastrin secreting cell
type: Class
subclass of: peptide hormone secreting cell
definition: A peptide hormone secreting cell that secretes gastrin.
present in taxon: NCBITaxon 9606
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: gastrin secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that secretes gastrin.
database_cross_reference: GO:tfm

paneth cell
type: Class
subclass of: glandular secretory epithelial cell
subclass of: lysozyme secreting cell
subclass of: CL_0002563
subclass of: Restriction
  on property: part of
  some values from: UBERON_0011184
subclass of: Restriction
  on property: has part
  some values from: GO_0005773
subclass of: Restriction
  on property: has part
  some values from: GO_0005902
subclass of: Restriction
  on property: develops from
  some values from: CL_4047017
definition: An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix.
description: Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. In addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: BTO:0000993
database_cross_reference: FMA:62897
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000510
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: paneth cell
annotated property: definition
annotated target: An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651
database_cross_reference: MESH:D019879
database_cross_reference: PMID:29184701
database_cross_reference: PMID:32308658
database_cross_reference: PMID:33484640

Axiom
annotated source: paneth cell
annotated property: description
annotated target: Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. In addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1007/s00018-002-8412-z
database_cross_reference: DOI:10.1038/nature09637
database_cross_reference: DOI:10.1038/nrmicro2546
database_cross_reference: DOI:10.1146/annurev-physiol-030212-183744
database_cross_reference: DOI:10.3389/fimmu.2020.00587

androgen binding protein secreting cell
type: Class
subclass of: protein secreting cell
definition: A peptide hormone secreting cell that secretes androgen binding protein.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: androgen binding protein secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that secretes androgen binding protein.
database_cross_reference: GO:tfm

obsolete paracrine cell
type: Class
consider: secretory cell
comment: The term paracrine describes a role of a secreted hormone. There are a vast number of cell types that could fit this description, however it is difficult to know every case where a secreted hormone has paracrine effects.
deprecated: true

cardiac muscle myoblast
type: Class
equivalent class: Class
  intersection of: myoblast
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001133
  intersection of: Restriction
    on property: develops into
    some values from: cardiac muscle cell
subclass of: CL_0002494
subclass of: CL_0010021
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001133
definition: A precursor cell destined to differentiate into cardiac muscle cell.
database_cross_reference: FMA:84797
database_cross_reference: ZFA:0009234
has_exact_synonym: cardiac muscle progenitor cell
has_exact_synonym: cardiomyocyte progenitor cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cardiac muscle myoblast
annotated property: definition
annotated target: A precursor cell destined to differentiate into cardiac muscle cell.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D032386

Axiom
annotated source: cardiac muscle myoblast
annotated property: database_cross_reference
annotated target: ZFA:0009234
mapping justification: UnspecifiedMatching

smooth muscle myoblast
type: Class
equivalent class: Class
  intersection of: myoblast
  intersection of: Restriction
    on property: develops into
    some values from: smooth muscle cell
subclass of: myoblast
subclass of: Restriction
  on property: develops into
  some values from: smooth muscle cell
definition: A precursor cell destined to differentiate into smooth muscle myocytes.
description: A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: FMA:84798
database_cross_reference: ZFA:0009235
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000514
has_exact_synonym: myoblast, smooth muscle
has_related_synonym: satellite cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: smooth muscle myoblast
annotated property: definition
annotated target: A precursor cell destined to differentiate into smooth muscle myocytes.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D032390

Axiom
annotated source: smooth muscle myoblast
annotated property: description
annotated target: A precursor to the smooth muscle cell, the smooth muscle myoblast, is integral to various body systems, including the cardiovascular, gastrointestinal, and respiratory systems. Smooth muscle myoblasts arise from the differentiation of mesenchymal stem cells, a process tightly regulated by specific genetic factors and environmental signals. Their role extends to myogenesis, particularly in the formation of muscular tissue, especially during embryonic development. Smooth muscle myoblasts possess distinctive cellular characteristics. In contrast to skeletal muscle myoblasts, they do not fuse to create multinucleated fibers. Instead, they differentiate into individual, uninucleated smooth muscle cells. This differentiation unfolds in two distinct phases: proliferation, marked by rapid division to increase cell numbers, and differentiation, involving structural and functional transformation into mature smooth muscle cells. This intricate process is intricately mediated by various signaling molecules and transcription factors. Functionally, smooth muscle myoblasts and the mature muscle cells they generate play pivotal roles in various physiological processes. Smooth muscle cells orchestrate involuntary muscle responses and are integral to body systems that regulate blood flow, propel food along the digestive tract, and control airflow in the respiratory tract. These diverse functions underscore the significance of smooth muscle myoblasts in the body's growth, maintenance, and overall function. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1074/jbc.RA118.001739
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK544225/
database_cross_reference: https://www.sciencedirect.com/topics/medicine-and-dentistry/smooth-muscle

Axiom
annotated source: smooth muscle myoblast
annotated property: database_cross_reference
annotated target: ZFA:0009235
mapping justification: UnspecifiedMatching

Axiom
annotated source: smooth muscle myoblast
annotated property: has_exact_synonym
annotated target: myoblast, smooth muscle
database_cross_reference: MESH:D032390

skeletal muscle myoblast
type: Class
equivalent class: Class
  intersection of: myoblast
  intersection of: Restriction
    on property: develops into
    some values from: CL_0008002
subclass of: myoblast
subclass of: CL_0011026
subclass of: Restriction
  on property: develops from
  some values from: multi-potent skeletal muscle stem cell
subclass of: Restriction
  on property: develops into
  some values from: CL_0008002
definition: A myoblast that differentiates into skeletal muscle fibers.
database_cross_reference: FMA:84799
database_cross_reference: ZFA:0009236
has_exact_synonym: skeletal myoblast
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: skeletal muscle myoblast
annotated property: definition
annotated target: A myoblast that differentiates into skeletal muscle fibers.
database_cross_reference: SANBI:mhl

Axiom
annotated source: skeletal muscle myoblast
annotated property: database_cross_reference
annotated target: ZFA:0009236
mapping justification: UnspecifiedMatching

perineuronal satellite cell
type: Class
subclass of: neuron associated cell (sensu Vertebrata)
subclass of: Restriction
  on property: develops from
  some values from: glioblast (sensu Vertebrata)
definition: A non-neuronal cell that surrounds the neuronal cell bodies of the ganglia.
present in taxon: NCBITaxon 9606
database_cross_reference: FMA:54550
database_cross_reference: ZFA:0009237
has_exact_synonym: perineural satellite cell
has_exact_synonym: perineuronal satellite oligodendroglial cell
has_exact_synonym: satellite oligodendrocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: perineuronal satellite cell
annotated property: definition
annotated target: A non-neuronal cell that surrounds the neuronal cell bodies of the ganglia.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D027161

Axiom
annotated source: perineuronal satellite cell
annotated property: database_cross_reference
annotated target: ZFA:0009237
mapping justification: UnspecifiedMatching

macrophage derived foam cell
type: Class
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: CL_0000891
subclass of: Restriction
  on property: develops from
  some values from: macrophage
definition: A type of foam cell derived from a macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions.
has_exact_synonym: lipophage
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: macrophage derived foam cell
annotated property: definition
annotated target: A type of foam cell derived from a macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions.
database_cross_reference: GOC:add
database_cross_reference: PMID:20213546

phagocyte (sensu Vertebrata)
type: Class
subclass of: phagocyte
subclass of: eukaryotic cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 7742
definition: A phagocyte in vertebrates that is able to phagocytosis.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: phagocyte (sensu Vertebrata)
annotated property: definition
annotated target: A phagocyte in vertebrates that is able to phagocytosis.
database_cross_reference: GOC:tfm

phagocyte (sensu Nematoda and Protostomia)
type: Class
subclass of: phagocyte
definition: A phagocyte from organisms in the Nematoda or Protostomia clades.
never in taxon: NCBITaxon_33511

Axiom
annotated source: phagocyte (sensu Nematoda and Protostomia)
annotated property: definition
annotated target: A phagocyte from organisms in the Nematoda or Protostomia clades.
database_cross_reference: GOC:tfm

prokaryotic cell
type: Class
subclass of: cell
never in taxon: NCBITaxon 2759
database_cross_reference: MESH:D011387

fungal cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: in taxon
    some values from: NCBITaxon 4751
subclass of: eukaryotic cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 4751
definition: Any cell that in taxon some Fungi.

Axiom
annotated source: fungal cell
annotated property: definition
annotated target: Any cell that in taxon some Fungi.
database_cross_reference: FBC:Autogenerated

obsolete spore
type: Class
definition: OBSOLETE: The reproductive structure of bacteria, fungi and cryptograms.
deprecated: true

Axiom
annotated source: obsolete spore
annotated property: definition
annotated target: OBSOLETE: The reproductive structure of bacteria, fungi and cryptograms.
database_cross_reference: ISBN:08199377X

mononuclear cytotrophoblast cell
type: Class
subclass of: trophoblast cell
definition: A cell from the inner layer of the trophoblast of the early mammalian embryo that gives rise to the outer surface and villi of the chorion. Mononuclear crytoblasts fuse to give rise to a multinuclear cytotrophoblast.
present in taxon: NCBITaxon 9606
database_cross_reference: FMA:83042
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: mononuclear cytotrophoblast cell
annotated property: definition
annotated target: A cell from the inner layer of the trophoblast of the early mammalian embryo that gives rise to the outer surface and villi of the chorion. Mononuclear crytoblasts fuse to give rise to a multinuclear cytotrophoblast.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0323052908

spheroplast
type: Class
subclass of: protoplast
definition: A cell, usually of bacteria or yeast, which has partially lost its cell wall.
has_exact_synonym: sphaeroplast

Axiom
annotated source: spheroplast
annotated property: definition
annotated target: A cell, usually of bacteria or yeast, which has partially lost its cell wall.
database_cross_reference: MESH:D013104

syncytiotrophoblast cell
type: Class
equivalent class: Class
  intersection of: trophoblast cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001908
subclass of: trophoblast cell
subclass of: CL_4052002
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000371
definition: A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy.
present in taxon: NCBITaxon 9606
database_cross_reference: FMA:83043
has_exact_synonym: syncytial trophoblast cell
has_exact_synonym: syncytiotrophoblastic cell
has_related_synonym: plasmidotrophoblast cell
has_related_synonym: syntrophoblast cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: syncytiotrophoblast cell
annotated property: definition
annotated target: A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0323052908

Axiom
annotated source: syncytiotrophoblast cell
annotated property: has_exact_synonym
annotated target: syncytial trophoblast cell
database_cross_reference: PMID:11787150

Axiom
annotated source: syncytiotrophoblast cell
annotated property: has_exact_synonym
annotated target: syncytiotrophoblastic cell
database_cross_reference: PMID:21733368

afferent neuron
type: Class
subclass of: neuron
definition: A neuron which conveys sensory information centrally from the periphery.
present in taxon: NCBITaxon 9606
database_cross_reference: FMA:87653
database_cross_reference: ZFA:0009238
has_exact_synonym: input neuron
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: afferent neuron
annotated property: definition
annotated target: A neuron which conveys sensory information centrally from the periphery.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D009475

Axiom
annotated source: afferent neuron
annotated property: database_cross_reference
annotated target: ZFA:0009238
mapping justification: UnspecifiedMatching

efferent neuron
type: Class
subclass of: neuron
definition: A neuron which sends impulses peripherally to activate muscles or secretory cells.
database_cross_reference: ZFA:0009239
has_exact_synonym: output neuron
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: efferent neuron
annotated property: definition
annotated target: A neuron which sends impulses peripherally to activate muscles or secretory cells.
database_cross_reference: MESH:D009476

Axiom
annotated source: efferent neuron
annotated property: database_cross_reference
annotated target: ZFA:0009239
mapping justification: UnspecifiedMatching

nitrergic neuron
type: Class
subclass of: neuron
definition: A nerve cell where transmission is mediated by nitric oxide.
database_cross_reference: FMA:84792
database_cross_reference: ZFA:0009240
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: nitrergic neuron
annotated property: definition
annotated target: A nerve cell where transmission is mediated by nitric oxide.
database_cross_reference: MESH:D026602

Axiom
annotated source: nitrergic neuron
annotated property: database_cross_reference
annotated target: ZFA:0009240
mapping justification: UnspecifiedMatching

pigmented epithelial cell
type: Class
subclass of: neurecto-epithelial cell
database_cross_reference: ZFA:0009241
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pigmented epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009241
mapping justification: UnspecifiedMatching

primary neuron (sensu Teleostei)
type: Class
subclass of: BFO_0000002
subclass of: CL_2000029
subclass of: Restriction
  on property: has soma location
  some values from: UBERON_0002240
definition: A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed.
database_cross_reference: ZFA:0009242

Axiom
annotated source: primary neuron (sensu Teleostei)
annotated property: definition
annotated target: A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed.
database_cross_reference: PMID:1842357
database_cross_reference: doi:10.1242/dev.108.1.121

Axiom
annotated source: primary neuron (sensu Teleostei)
annotated property: database_cross_reference
annotated target: ZFA:0009242
mapping justification: UnspecifiedMatching

primary sensory neuron (sensu Teleostei)
type: Class
equivalent class: Class
  intersection of: sensory neuron
  intersection of: primary neuron (sensu Teleostei)
subclass of: sensory neuron
subclass of: primary neuron (sensu Teleostei)
definition: A primary neuron (sensu Teleostei) that has a sensory function.
in_subset: cellxgene subset

Axiom
annotated source: primary sensory neuron (sensu Teleostei)
annotated property: definition
annotated target: A primary neuron (sensu Teleostei) that has a sensory function.
database_cross_reference: PMID:1842357

CAP motoneuron
type: Class
subclass of: primary motor neuron (sensu Teleostei)
definition: A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates the lateral surface of ventral axial muscles
database_cross_reference: ZFA:0009243
has_exact_synonym: CaP motorneuron
has_related_synonym: cap cell
has_related_synonym: caudal primary motor neuron

Axiom
annotated source: CAP motoneuron
annotated property: definition
annotated target: A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates the lateral surface of ventral axial muscles
database_cross_reference: PMID:17971221
database_cross_reference: PMID:35431796

Axiom
annotated source: CAP motoneuron
annotated property: database_cross_reference
annotated target: ZFA:0009243
mapping justification: UnspecifiedMatching

Axiom
annotated source: CAP motoneuron
annotated property: has_exact_synonym
annotated target: CaP motorneuron
database_cross_reference: PMID:3746410

Axiom
annotated source: CAP motoneuron
annotated property: has_related_synonym
annotated target: cap cell
database_cross_reference: PMID:17971221

Axiom
annotated source: CAP motoneuron
annotated property: has_related_synonym
annotated target: caudal primary motor neuron
database_cross_reference: PMID:18077593

primary motor neuron (sensu Teleostei)
type: Class
subclass of: primary neuron (sensu Teleostei)
subclass of: CL_0011001
definition: A primary neuron (sensu Teleostei) that has a motor function.
database_cross_reference: ZFA:0009244

Axiom
annotated source: primary motor neuron (sensu Teleostei)
annotated property: definition
annotated target: A primary neuron (sensu Teleostei) that has a motor function.
database_cross_reference: PMID:1842357

Axiom
annotated source: primary motor neuron (sensu Teleostei)
annotated property: database_cross_reference
annotated target: ZFA:0009244
mapping justification: UnspecifiedMatching

primary interneuron (sensu Teleostei)
type: Class
subclass of: primary neuron (sensu Teleostei)
subclass of: CL_0005000
definition: A primary neuron (sensu Teleostei) that is neither a sensory neuron or a motor neuron.
database_cross_reference: ZFA:0009245

Axiom
annotated source: primary interneuron (sensu Teleostei)
annotated property: definition
annotated target: A primary neuron (sensu Teleostei) that is neither a sensory neuron or a motor neuron.
database_cross_reference: PMID:1842357

Axiom
annotated source: primary interneuron (sensu Teleostei)
annotated property: database_cross_reference
annotated target: ZFA:0009245
mapping justification: UnspecifiedMatching

secondary neuron (sensu Teleostei)
type: Class
subclass of: CL_2000029
subclass of: UBERON_0010313
subclass of: Restriction
  on property: has soma location
  some values from: UBERON_0002240
definition: A neuron of teleosts that develops later than a primary neuron, typically during the larval stages.
database_cross_reference: ZFA:0009246

Axiom
annotated source: secondary neuron (sensu Teleostei)
annotated property: definition
annotated target: A neuron of teleosts that develops later than a primary neuron, typically during the larval stages.
database_cross_reference: PMID:1842357
database_cross_reference: doi:10.1242/dev.108.1.121

Axiom
annotated source: secondary neuron (sensu Teleostei)
annotated property: database_cross_reference
annotated target: ZFA:0009246
mapping justification: UnspecifiedMatching

secondary motor neuron (sensu Teleostei)
type: Class
equivalent class: Class
  intersection of: motor neuron
  intersection of: secondary neuron (sensu Teleostei)
subclass of: secondary neuron (sensu Teleostei)
subclass of: CL_0011001
definition: A secondary neuron (sensu Teleostei) that has a motor function.
database_cross_reference: ZFA:0009247

Axiom
annotated source: secondary motor neuron (sensu Teleostei)
annotated property: definition
annotated target: A secondary neuron (sensu Teleostei) that has a motor function.
database_cross_reference: PMID:1842357

Axiom
annotated source: secondary motor neuron (sensu Teleostei)
annotated property: database_cross_reference
annotated target: ZFA:0009247
mapping justification: UnspecifiedMatching

obsolete antipodal cell
type: Class
definition: Obsolete. Use PO:0020093 from Plant Ontology instead. OBSOLETE, use term from plant ontology. A cell located at the chalazal end of the mature embryo sac in angiosperms.
term replaced by: PO_0020093
deprecated: true

Axiom
annotated source: obsolete antipodal cell
annotated property: definition
annotated target: Obsolete. Use PO:0020093 from Plant Ontology instead. OBSOLETE, use term from plant ontology. A cell located at the chalazal end of the mature embryo sac in angiosperms.
database_cross_reference: ISBN:047125208

obsolete epidermal initial
type: Class
definition: Obsolete. Use PO:0000349 from Plant Ontology instead. A relatively unspecialized cell that will give rise to specialized cell types of the epidermis.
term replaced by: PO_0000349
deprecated: true

Axiom
annotated source: obsolete epidermal initial
annotated property: definition
annotated target: Obsolete. Use PO:0000349 from Plant Ontology instead. A relatively unspecialized cell that will give rise to specialized cell types of the epidermis.
database_cross_reference: TAIR:lr

obsolete idioblast
type: Class
definition: OBSOLETE: A cell in a tissue that markedly differs in form, size, or contents from other cells in the same tissue.
deprecated: true

Axiom
annotated source: obsolete idioblast
annotated property: definition
annotated target: OBSOLETE: A cell in a tissue that markedly differs in form, size, or contents from other cells in the same tissue.
database_cross_reference: ISBN:0471245208

neuron
type: Class
subclass of: electrically responsive cell
subclass of: electrically signaling cell
subclass of: CL_0002319
subclass of: Restriction
  on property: capable of
  some values from: GO_0019226
definition: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000938
database_cross_reference: CALOHA:TS-0683
database_cross_reference: FBbt:00005106
database_cross_reference: FMA:54527
database_cross_reference: VHOG:0001483
database_cross_reference: WBbt:0003679
database_cross_reference: ZFA:0009248
has_exact_synonym: nerve cell
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.

Axiom
annotated source: neuron
annotated property: definition
annotated target: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
database_cross_reference: MESH:D009474
database_cross_reference: http://en.wikipedia.org/wiki/Neuron

Axiom
annotated source: neuron
annotated property: database_cross_reference
annotated target: FBbt:00005106
mapping justification: ManualMappingCuration

Axiom
annotated source: neuron
annotated property: database_cross_reference
annotated target: ZFA:0009248
mapping justification: UnspecifiedMatching

melanoblast
type: Class
subclass of: non-terminally differentiated cell
subclass of: CL_0011026
subclass of: Restriction
  on property: develops from
  some values from: migratory neural crest cell
definition: A cell that originates from the neural crest and differentiates into a pigment cell.
database_cross_reference: BTO:0003217
database_cross_reference: FMA:83377
database_cross_reference: ZFA:0009249
in_subset: human subset
in_subset: mouse subset
comment: Derived from UBERON:0002342 neural crest.

Axiom
annotated source: melanoblast
annotated property: definition
annotated target: A cell that originates from the neural crest and differentiates into a pigment cell.
database_cross_reference: GOC:tfm
database_cross_reference: SANBI:mhl

Axiom
annotated source: melanoblast
annotated property: database_cross_reference
annotated target: ZFA:0009249
mapping justification: UnspecifiedMatching

lymphocyte
type: Class
equivalent class: Class
  intersection of: leukocyte
  intersection of: Restriction
    on property: has part
    some values from: CL_0017500
  intersection of: Restriction
    on property: has part
    some values from: GO_0000792
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001407
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0040072
subclass of: CL_0000842
subclass of: Restriction
  on property: has part
  some values from: CL_0017500
subclass of: Restriction
  on property: has part
  some values from: GO_0000792
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0040072
subclass of: Restriction
  on property: develops from
  some values from: common lymphoid progenitor
disjoint with: myeloid leukocyte
definition: A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000775
database_cross_reference: CALOHA:TS-0583
database_cross_reference: FMA:62863
database_cross_reference: MESH:D008214
database_cross_reference: VHOG:0001535
database_cross_reference: ZFA:0009250
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)

Axiom
annotated source: lymphocyte
annotated property: definition
annotated target: A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0683073696
database_cross_reference: ISBN:0781735149

Axiom
annotated source: lymphocyte
annotated property: database_cross_reference
annotated target: ZFA:0009250
mapping justification: UnspecifiedMatching

obsolete sieve tube member
type: Class
definition: Obsolete. Use PO:0000289 from Plant Ontology instead. One of the series of cellular components of a sieve tube. It shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores). Also sieve tube element and the obsolete sieve tube segment.
term replaced by: PO_0000289
has_exact_synonym: sieve tube element
deprecated: true

Axiom
annotated source: obsolete sieve tube member
annotated property: definition
annotated target: Obsolete. Use PO:0000289 from Plant Ontology instead. One of the series of cellular components of a sieve tube. It shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores). Also sieve tube element and the obsolete sieve tube segment.
database_cross_reference: ISBN:0471245208

slowly adapting mechanoreceptor cell
type: Class
subclass of: mechanoreceptor cell
in_subset: human subset
in_subset: mouse subset

T-helper 1 cell
type: Class
equivalent class: Class
  intersection of: CD4-positive helper T cell
  intersection of: Restriction
    on property: has part
    some values from: PR_000001835
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001202
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001207
  intersection of: Restriction
    on property: capable of
    some values from: GO_0032609
subclass of: CD4-positive helper T cell
subclass of: Restriction
  on property: has part
  some values from: PR_000001835
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001202
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001207
subclass of: Restriction
  on property: capable of
  some values from: GO_0032609
definition: A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0001678
database_cross_reference: FMA:84382
has_exact_synonym: T helper cells type 1
has_exact_synonym: T(H)-1 cell
has_exact_synonym: Th1 CD4+ T cell
has_exact_synonym: Th1 T cell
has_exact_synonym: Th1 T lymphocyte
has_exact_synonym: Th1 T-cell
has_exact_synonym: Th1 T-lymphocyte
has_exact_synonym: Th1 cell
has_exact_synonym: helper T cell type 1
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: This cell type is compatible with the HIPC Lyoplate markers for 'Th1 CD4+ T cell', but its logical definition includes additional known characteristics of T-helper 1 T cells.

Axiom
annotated source: T-helper 1 cell
annotated property: subClassOf
annotated target: CD4-positive helper T cell
is inferred: true

Axiom
annotated source: T-helper 1 cell
annotated property: definition
annotated target: A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma.
database_cross_reference: GOC:add
database_cross_reference: GOC:pam
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: PMID:19375293
database_cross_reference: PMID:20303875
database_cross_reference: PMID:22343568

Axiom
annotated source: T-helper 1 cell
annotated property: has_exact_synonym
annotated target: T helper cells type 1
database_cross_reference: PMID:9419219

Axiom
annotated source: T-helper 1 cell
annotated property: has_exact_synonym
annotated target: Th1 CD4+ T cell
database_cross_reference: PMID:22343568

T-helper 2 cell
type: Class
equivalent class: Class
  intersection of: CD4-positive helper T cell
  intersection of: Restriction
    on property: has part
    some values from: PR_000001941
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001202
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001207
  intersection of: Restriction
    on property: capable of
    some values from: GO_0032633
subclass of: CD4-positive helper T cell
subclass of: CL_0001051
subclass of: Restriction
  on property: has part
  some values from: PR_000001941
subclass of: Restriction
  on property: capable of
  some values from: GO_0032633
definition: A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive, CXCR3-negative, CCR6-negative, and is capable of producing interleukin-4.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0001679
database_cross_reference: FMA:84385
database_cross_reference: MESH:D018418
has_exact_synonym: T helper cells type 2
has_exact_synonym: T(H)-2 cell
has_exact_synonym: Th2 T cell
has_exact_synonym: Th2 T lymphocyte
has_exact_synonym: Th2 T-cell
has_exact_synonym: Th2 T-lymphocyte
has_exact_synonym: Th2 cell
has_exact_synonym: helper T cell type 2
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: This cell type is compatible with the HIPC Lyoplate markers for 'non-Th1/Th17 CD4+ T cell' (see CL:0001051), but includes the additional necessary and sufficient conditions to allow classification as a T-helper 2 T cell.

Axiom
annotated source: T-helper 2 cell
annotated property: subClassOf
annotated target: CD4-positive helper T cell
is inferred: true

Axiom
annotated source: T-helper 2 cell
annotated property: definition
annotated target: A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive, CXCR3-negative, CCR6-negative, and is capable of producing interleukin-4.
database_cross_reference: GOC:add
database_cross_reference: GOC:pam
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: PMID:19375293
database_cross_reference: PMID:20103781
database_cross_reference: PMID:22343568

Axiom
annotated source: T-helper 2 cell
annotated property: has_exact_synonym
annotated target: T helper cells type 2
database_cross_reference: PMID:9419219

proerythroblast
type: Class
equivalent class: Class
  intersection of: erythroid lineage cell
  intersection of: Restriction
    on property: has part
    some values from: CL_0017503
  intersection of: Restriction
    on property: has part
    some values from: GO_0005730
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0002505
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0040072
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001945
subclass of: erythroid lineage cell
subclass of: CL_0002242
subclass of: Restriction
  on property: has part
  some values from: CL_0017503
subclass of: Restriction
  on property: has part
  some values from: GO_0005730
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0040072
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001945
subclass of: Restriction
  on property: develops from
  some values from: erythroid progenitor cell
definition: An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.
database_cross_reference: FMA:83518
has_exact_synonym: rubriblast
has_related_synonym: pronormoblast
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: proerythroblast
annotated property: subClassOf
annotated target: erythroid lineage cell
is inferred: true

Axiom
annotated source: proerythroblast
annotated property: definition
annotated target: An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:1638021

Axiom
annotated source: proerythroblast
annotated property: has_exact_synonym
annotated target: rubriblast
database_cross_reference: ISBN:0721601464

obsolete animal cell
type: Class
definition: OBSOLETE. A native cell that is part of some Metazoa.
term tracker item: https://github.com/obophenotype/cell-ontology/issues/2124
term replaced by: cell
has_exact_synonym: metazoan cell
in_subset: upper level
deprecated: true

basophilic erythroblast
type: Class
equivalent class: Class
  intersection of: erythroblast
  intersection of: Restriction
    on property: has part
    some values from: CL_0017503
  intersection of: Restriction
    on property: has part
    some values from: GO_0000792
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001945
subclass of: erythroblast
subclass of: Restriction
  on property: has part
  some values from: CL_0017503
subclass of: Restriction
  on property: has part
  some values from: GO_0000792
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001945
definition: A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.
database_cross_reference: FMA:83505
database_cross_reference: ZFA:0005236
has_exact_synonym: basophilic normoblast
has_exact_synonym: early erythroblast
has_exact_synonym: early normoblast
has_exact_synonym: prorubricyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: basophilic erythroblast
annotated property: subClassOf
annotated target: erythroblast
is inferred: true

Axiom
annotated source: basophilic erythroblast
annotated property: definition
annotated target: A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464

Axiom
annotated source: basophilic erythroblast
annotated property: database_cross_reference
annotated target: ZFA:0005236
mapping justification: UnspecifiedMatching

Axiom
annotated source: basophilic erythroblast
annotated property: has_exact_synonym
annotated target: basophilic normoblast
database_cross_reference: ISBN:0721601464

Axiom
annotated source: basophilic erythroblast
annotated property: has_exact_synonym
annotated target: early erythroblast
database_cross_reference: ISBN:0721601464

Axiom
annotated source: basophilic erythroblast
annotated property: has_exact_synonym
annotated target: early normoblast
database_cross_reference: ISBN:0721601464

Axiom
annotated source: basophilic erythroblast
annotated property: has_exact_synonym
annotated target: prorubricyte
database_cross_reference: ISBN:0721601464

polychromatophilic erythroblast
type: Class
equivalent class: Class
  intersection of: erythroblast
  intersection of: Restriction
    on property: has part
    some values from: CL_0017504
  intersection of: Restriction
    on property: has part
    some values from: GO_0000792
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001945
subclass of: erythroblast
subclass of: Restriction
  on property: has part
  some values from: CL_0017504
subclass of: Restriction
  on property: has part
  some values from: GO_0000792
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001945
subclass of: Restriction
  on property: develops from
  some values from: basophilic erythroblast
definition: A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.
database_cross_reference: FMA:83506
database_cross_reference: ZFA:0005241
has_exact_synonym: intermediate erythroblast
has_exact_synonym: intermediate normoblast
has_exact_synonym: polychromatic erythroblast
has_exact_synonym: polychromatic normoblast
has_exact_synonym: polychromatophilic normoblast
has_exact_synonym: rubricyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: polychromatophilic erythroblast
annotated property: subClassOf
annotated target: erythroblast
is inferred: true

Axiom
annotated source: polychromatophilic erythroblast
annotated property: definition
annotated target: A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.
database_cross_reference: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: database_cross_reference
annotated target: ZFA:0005241
mapping justification: UnspecifiedMatching

Axiom
annotated source: polychromatophilic erythroblast
annotated property: has_exact_synonym
annotated target: intermediate erythroblast
database_cross_reference: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: has_exact_synonym
annotated target: intermediate normoblast
database_cross_reference: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: has_exact_synonym
annotated target: polychromatic erythroblast
database_cross_reference: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: has_exact_synonym
annotated target: polychromatic normoblast
database_cross_reference: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: has_exact_synonym
annotated target: polychromatophilic normoblast
database_cross_reference: ISBN:0721601464

Axiom
annotated source: polychromatophilic erythroblast
annotated property: has_exact_synonym
annotated target: rubricyte
database_cross_reference: ISBN:0721601464

unimodal nocireceptor
type: Class
subclass of: pain receptor cell
in_subset: human subset
in_subset: mouse subset

orthochromatic erythroblast
type: Class
equivalent class: Class
  intersection of: erythroblast
  intersection of: Restriction
    on property: has part
    some values from: CL_0017502
  intersection of: Restriction
    on property: participates in
    some values from: GO_0030263
subclass of: erythroblast
subclass of: Restriction
  on property: has part
  some values from: CL_0017502
subclass of: Restriction
  on property: participates in
  some values from: GO_0030263
subclass of: Restriction
  on property: develops from
  some values from: polychromatophilic erythroblast
definition: The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.
database_cross_reference: FMA:84646
has_exact_synonym: acidophilic erythroblast
has_exact_synonym: eosinophilic erythroblast
has_exact_synonym: late erythoblast
has_exact_synonym: orthochromatic normoblast
has_exact_synonym: pyknotic eto enrythroblast
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: orthochromatic erythroblast
annotated property: subClassOf
annotated target: erythroblast
is inferred: true

Axiom
annotated source: orthochromatic erythroblast
annotated property: definition
annotated target: The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.
database_cross_reference: ISBN:0721601464

Axiom
annotated source: orthochromatic erythroblast
annotated property: has_exact_synonym
annotated target: acidophilic erythroblast
database_cross_reference: ISBN:0721601464

Axiom
annotated source: orthochromatic erythroblast
annotated property: has_exact_synonym
annotated target: eosinophilic erythroblast
database_cross_reference: ISBN:0721601464

Axiom
annotated source: orthochromatic erythroblast
annotated property: has_exact_synonym
annotated target: orthochromatic normoblast
database_cross_reference: ISBN:0721601464

Axiom
annotated source: orthochromatic erythroblast
annotated property: has_exact_synonym
annotated target: pyknotic eto enrythroblast
database_cross_reference: ISBN:0721601464

megakaryocyte progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0000839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: capable of
    some values from: GO_0007113
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030219
subclass of: myeloid cell
subclass of: CL_0000839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002981
subclass of: Restriction
  on property: develops from
  some values from: megakaryocyte-erythroid progenitor cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0007113
subclass of: Restriction
  on property: capable of
  some values from: GO_0030219
definition: The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0001164
database_cross_reference: CALOHA:TS-0610
database_cross_reference: FMA:84235
database_cross_reference: MESH:D055016
has_exact_synonym: CFU-Meg
has_exact_synonym: Meg-CFC
has_exact_synonym: MkP
has_exact_synonym: colony-forming unit-megakaryocyte
has_exact_synonym: megacaryoblast
has_exact_synonym: megacaryocyte progenitor cell
has_exact_synonym: megakaryoblast
has_exact_synonym: megakaryocytic progenitor cell
has_related_synonym: promegacaryocyte
has_related_synonym: promegakaryocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative.

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: subClassOf
annotated target: CL_0000839
is inferred: true

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: definition
annotated target: The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: has_exact_synonym
annotated target: CFU-Meg
database_cross_reference: PMID:11722431
database_cross_reference: PMID:12482498

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: has_exact_synonym
annotated target: Meg-CFC
database_cross_reference: PMCID:PMC1794060

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: has_exact_synonym
annotated target: MkP
database_cross_reference: PMID:21116988

Axiom
annotated source: megakaryocyte progenitor cell
annotated property: has_exact_synonym
annotated target: megakaryocytic progenitor cell
database_cross_reference: PMID:12482498

gastrin stimulating hormone secreting cell
type: Class
subclass of: peptide hormone secreting cell
definition: A peptide hormone secreting cell that secretes gastrin stimulating hormone.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: gastrin stimulating hormone secreting cell
annotated property: definition
annotated target: A peptide hormone secreting cell that secretes gastrin stimulating hormone.
database_cross_reference: GOC:tfm

obsolete neuronal brush cell
type: Class
term replaced by: CL_4023161
in_subset: cellxgene subset
deprecated: true

megakaryocyte
type: Class
subclass of: myeloid cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001393
subclass of: Restriction
  on property: develops from
  some values from: megakaryocyte progenitor cell
disjoint with: erythroid lineage cell
definition: A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000843
database_cross_reference: CALOHA:TS-0611
database_cross_reference: FMA:83555
has_exact_synonym: megacaryocyte
has_exact_synonym: megalocaryocyte
has_exact_synonym: megalokaryocyte
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Megakaryocytes are reportedly CD181-positive and CD182-positive.

Axiom
annotated source: megakaryocyte
annotated property: subClassOf
annotated target: myeloid cell
is inferred: true

Axiom
annotated source: megakaryocyte
annotated property: definition
annotated target: A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release.
database_cross_reference: ISBN:0721601464
database_cross_reference: MESH:D008533
database_cross_reference: PMID:31043076
database_cross_reference: http://en.wikipedia.org/wiki/Megakaryocyte

granulocyte monocyte progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0002032
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002371
  intersection of: Restriction
    on property: has part
    some values from: PR_000001944
  intersection of: Restriction
    on property: has part
    some values from: PR_000005307
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000007857
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000007858
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001865
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030225
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030851
subclass of: myeloid cell
subclass of: CL_0001012
subclass of: CL_1001610
subclass of: Restriction
  on property: has part
  some values from: PR_000001944
subclass of: Restriction
  on property: has part
  some values from: PR_000005307
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000007857
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000007858
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001865
subclass of: Restriction
  on property: capable of
  some values from: GO_0030225
subclass of: Restriction
  on property: capable of
  some values from: GO_0030851
definition: A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1.
present in taxon: NCBITaxon 9606
description: Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has_broad_synonym: CFU-C , Colony forming unit in culture
database_cross_reference: ZFA:0009251
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000557
has_exact_synonym: colony forming unit granulocyte macrophage
has_exact_synonym: granulocyte-macrophage progenitor
has_exact_synonym: granulocyte/monocyte precursor
has_exact_synonym: granulocyte/monocyte progenitor
has_related_synonym: CFU-GM
has_related_synonym: GMP
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative.

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: definition
annotated target: A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1.
database_cross_reference: GOC:amm
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0721601464
database_cross_reference: MESH:D055014
database_cross_reference: PMCID:PMC2213186
database_cross_reference: PMCID:PMC548021
database_cross_reference: PMID:16551251
database_cross_reference: PMID:16647566
database_cross_reference: http://en.wikipedia.org/wiki/CFU-GM
database_cross_reference: http://www.copewithcytokines.de

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: description
annotated target: Granulocyte monocyte progenitor cells (GMP cells), originating from hematopoietic stem cells in the bone marrow, are a critical intermediate in myeloid cell development. Positioned at a key differentiation juncture, these cells exhibit bidirectional potential, giving rise to both granulocyte and monocyte lineages. Their primary role is to generate mature granulocytes and monocytes, essential components of the body's innate immunity and inflammatory responses. Granulocytes, such as neutrophils, eosinophils, and basophils, contribute to the first line of defense against infections by migrating to the infection site and phagocytosing pathogens. Monocytes can differentiate into macrophages or dendritic cells, playing diverse roles in immune responses. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1016/j.immuni.2017.10.021
database_cross_reference: DOI:10.1146/annurev-immunol-081022113627
database_cross_reference: DOI:10.1186/2050-7771-2-1

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: has_broad_synonym
annotated target: CFU-C , Colony forming unit in culture
database_cross_reference: http://www.copewithcytokines.de

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: database_cross_reference
annotated target: ZFA:0009251
mapping justification: UnspecifiedMatching

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: has_exact_synonym
annotated target: colony forming unit granulocyte macrophage
database_cross_reference: ISBN:0721601464
database_cross_reference: PMCID:PMC2213186
database_cross_reference: PMCID:PMC548021

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: has_exact_synonym
annotated target: granulocyte-macrophage progenitor
database_cross_reference: ISBN:0721601464
database_cross_reference: PMCID:PMC2213186
database_cross_reference: PMCID:PMC548021

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: has_related_synonym
annotated target: CFU-GM
database_cross_reference: ISBN:0721601464
database_cross_reference: PMCID:PMC2213186
database_cross_reference: PMCID:PMC548021
has_synonym_type: abbreviation

Axiom
annotated source: granulocyte monocyte progenitor cell
annotated property: has_related_synonym
annotated target: GMP
database_cross_reference: ISBN:0721601464
database_cross_reference: PMCID:PMC2213186
database_cross_reference: PMCID:PMC548021
has_synonym_type: abbreviation

reticulocyte
type: Class
equivalent class: Class
  intersection of: erythroid lineage cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001945
  intersection of: Restriction
    on property: capable of
    some values from: GO_0071971
subclass of: erythroid lineage cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001945
subclass of: Restriction
  on property: develops from
  some values from: orthochromatic erythroblast
subclass of: Restriction
  on property: capable of
  some values from: GO_0071971
definition: An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
database_cross_reference: BTO:0001173
database_cross_reference: CALOHA:TS-0864
database_cross_reference: MESH:D012156
database_cross_reference: ZFA:0009252
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: reticulocyte
annotated property: subClassOf
annotated target: erythroid lineage cell
is inferred: true

Axiom
annotated source: reticulocyte
annotated property: definition
annotated target: An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: PMID:15946868
database_cross_reference: PMID:2037622

Axiom
annotated source: reticulocyte
annotated property: database_cross_reference
annotated target: ZFA:0009252
mapping justification: UnspecifiedMatching

promonocyte
type: Class
equivalent class: Class
  intersection of: CL_0002194
  intersection of: Restriction
    on property: has part
    some values from: GO_0042582
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001012
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030224
subclass of: myeloid cell
subclass of: CL_0002194
subclass of: Restriction
  on property: has part
  some values from: GO_0042582
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001012
subclass of: Restriction
  on property: develops from
  some values from: monoblast
definition: A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0004657
database_cross_reference: FMA:83551
database_cross_reference: ZFA:0009253
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid.

Axiom
annotated source: promonocyte
annotated property: subClassOf
annotated target: CL_0002194
is inferred: true

Axiom
annotated source: promonocyte
annotated property: definition
annotated target: A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464

Axiom
annotated source: promonocyte
annotated property: database_cross_reference
annotated target: ZFA:0009253
mapping justification: UnspecifiedMatching

band form neutrophil
type: Class
equivalent class: Class
  intersection of: mature neutrophil
  intersection of: Restriction
    on property: has part
    some values from: CL_0017506
  intersection of: Restriction
    on property: has part
    some values from: PR_000001944
  intersection of: Restriction
    on property: has part
    some values from: PR_000005307
  intersection of: Restriction
    on property: has part
    some values from: PR_000007597
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000009978
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000010799
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000009129
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000010543
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001012
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001337
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001580
subclass of: mature neutrophil
subclass of: Restriction
  on property: has part
  some values from: CL_0017506
subclass of: Restriction
  on property: has part
  some values from: PR_000001944
subclass of: Restriction
  on property: has part
  some values from: PR_000005307
subclass of: Restriction
  on property: has part
  some values from: PR_000007597
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000009129
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000010543
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001337
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001580
subclass of: Restriction
  on property: develops from
  some values from: neutrophilic metamyelocyte
definition: A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative.
has_broad_synonym: band
has_broad_synonym: band cell
has_broad_synonym: band form
has_broad_synonym: stab cell
database_cross_reference: ZFA:0009254
has_exact_synonym: rod neutrophil
in_subset: human subset
in_subset: mouse subset
comment: Found in the Band 1 fraction.

Axiom
annotated source: band form neutrophil
annotated property: subClassOf
annotated target: mature neutrophil
is inferred: true

Axiom
annotated source: band form neutrophil
annotated property: definition
annotated target: A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:10618520
database_cross_reference: PMID:12560239
database_cross_reference: PMID:15514007
database_cross_reference: http://www.cap.org

Axiom
annotated source: band form neutrophil
annotated property: database_cross_reference
annotated target: ZFA:0009254
mapping justification: UnspecifiedMatching

amacrine cell
type: Class
subclass of: BFO_0000002
subclass of: interneuron
subclass of: CL_0009004
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000966
subclass of: Restriction
  on property: synapsed to
  some values from: retinal ganglion cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 7742
definition: Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0004044
database_cross_reference: FMA:67766
database_cross_reference: ZFA:0009255
has_exact_synonym: amacrine neuron
has_related_synonym: AC
has_related_synonym: ACs
in_subset: cellxgene subset
in_subset: eye_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: amacrine cell
annotated property: definition
annotated target: Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D025042
database_cross_reference: WikipediaVersioned:Amacrine_cell&oldid=1023572246

Axiom
annotated source: amacrine cell
annotated property: database_cross_reference
annotated target: ZFA:0009255
mapping justification: UnspecifiedMatching

Axiom
annotated source: amacrine cell
annotated property: has_related_synonym
annotated target: AC
database_cross_reference: doi:10.1038/s41598-020-66092-9
has_synonym_type: abbreviation

Axiom
annotated source: amacrine cell
annotated property: has_related_synonym
annotated target: ACs
database_cross_reference: doi:10.1038/s41598-020-66092-9
has_synonym_type: abbreviation
has_synonym_type: plural form

nucleate erythrocyte
type: Class
equivalent class: Class
  intersection of: erythrocyte
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0002505
subclass of: erythrocyte
subclass of: CL_0002242
subclass of: Restriction
  on property: develops from
  some values from: CL_0002421
definition: An erythrocyte having a nucleus.
has_broad_synonym: RBC
has_broad_synonym: red blood cell
database_cross_reference: ZFA:0009256
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: nucleate erythrocyte
annotated property: subClassOf
annotated target: erythrocyte
is inferred: true

Axiom
annotated source: nucleate erythrocyte
annotated property: definition
annotated target: An erythrocyte having a nucleus.
database_cross_reference: GOC:add
database_cross_reference: GOc:tfm

Axiom
annotated source: nucleate erythrocyte
annotated property: database_cross_reference
annotated target: ZFA:0009256
mapping justification: UnspecifiedMatching

endospore
type: Class
subclass of: prokaryotic cell
definition: A rounded, inactive form that certain bacteria assume under conditions of extreme temperature, dryness, or lack of food. The bacterium develops a waterproof cell wall that protects it from being dried out or damaged.
database_cross_reference: BTO:0002779
has_exact_synonym: bacterial spore

Axiom
annotated source: endospore
annotated property: definition
annotated target: A rounded, inactive form that certain bacteria assume under conditions of extreme temperature, dryness, or lack of food. The bacterium develops a waterproof cell wall that protects it from being dried out or damaged.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0618947256

neutrophilic promyelocyte
type: Class
equivalent class: Class
  intersection of: CL_0000836
  intersection of: Restriction
    on property: has part
    some values from: PR_000001944
  intersection of: Restriction
    on property: has part
    some values from: PR_000005307
  intersection of: Restriction
    on property: has part
    some values from: PR_000007857
  intersection of: Restriction
    on property: has part
    some values from: PR_000010543
  intersection of: Restriction
    on property: has part
    some values from: PR_000014362
  intersection of: Restriction
    on property: lacks_part
    some values from: PR_000009978
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030223
subclass of: CL_0000834
subclass of: CL_0000836
subclass of: Restriction
  on property: has part
  some values from: PR_000001944
subclass of: Restriction
  on property: has part
  some values from: PR_000005307
subclass of: Restriction
  on property: has part
  some values from: PR_000007857
subclass of: Restriction
  on property: has part
  some values from: PR_000010543
subclass of: Restriction
  on property: has part
  some values from: PR_000014362
subclass of: Restriction
  on property: lacks_part
  some values from: PR_000009978
subclass of: Restriction
  on property: develops from
  some values from: neutrophilic myeloblast
definition: A promyelocyte committed to the neutrophil lineage. This cell type is GATA-1-positive, C/EBPa-positive, AML-1-positive, MPO-positive, has low expression of PU.1 transcription factor and lacks lactotransferrin expression.
database_cross_reference: FMA:84196
database_cross_reference: ZFA:0009257
has_exact_synonym: neutrophilic premyelocyte
has_exact_synonym: neutrophilic progranulocyte
in_subset: human subset
in_subset: mouse subset
comment: These cells are CD11b-negative, CD15-positive, CD16-negative, CD49d-positive, CD68-positive, CD35-negative, and fMLP receptor-negative. They are found in the Band 3 fraction.

Axiom
annotated source: neutrophilic promyelocyte
annotated property: subClassOf
annotated target: CL_0000836
is inferred: true

Axiom
annotated source: neutrophilic promyelocyte
annotated property: definition
annotated target: A promyelocyte committed to the neutrophil lineage. This cell type is GATA-1-positive, C/EBPa-positive, AML-1-positive, MPO-positive, has low expression of PU.1 transcription factor and lacks lactotransferrin expression.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:12560239
database_cross_reference: PMID:15514007

Axiom
annotated source: neutrophilic promyelocyte
annotated property: database_cross_reference
annotated target: ZFA:0009257
mapping justification: UnspecifiedMatching

fat body cell
type: Class
subclass of: stuff accumulating cell
definition: A cell found in fat bodies whose primary function is intermediary metabolism.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: fat body cell
annotated property: definition
annotated target: A cell found in fat bodies whose primary function is intermediary metabolism.
database_cross_reference: FB:ma

angioblastic mesenchymal cell
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001444
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002112
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000016043
subclass of: mesenchymal stem cell
subclass of: CL_0011026
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001444
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002112
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000016043
subclass of: Restriction
  on property: develops from
  some values from: mesenchymal stem cell
definition: A mesenchymal stem cell capable of developing into blood vessel endothelium.
database_cross_reference: ZFA:0009258
has_exact_synonym: angioblast
has_exact_synonym: chondroplast
in_subset: human subset
in_subset: mouse subset
comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.

Axiom
annotated source: angioblastic mesenchymal cell
annotated property: subClassOf
annotated target: mesenchymal stem cell
is inferred: true

Axiom
annotated source: angioblastic mesenchymal cell
annotated property: definition
annotated target: A mesenchymal stem cell capable of developing into blood vessel endothelium.
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: PMID:12768659

Axiom
annotated source: angioblastic mesenchymal cell
annotated property: database_cross_reference
annotated target: ZFA:0009258
mapping justification: UnspecifiedMatching

polymodal nocireceptor
type: Class
subclass of: pain receptor cell
in_subset: human subset
in_subset: mouse subset

amine precursor uptake and decarboxylation cell
type: Class
subclass of: neuroendocrine cell
definition: A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell.
database_cross_reference: BTO:0003866
database_cross_reference: FMA:83114
database_cross_reference: MESH:D001078
has_exact_synonym: APUD cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: amine precursor uptake and decarboxylation cell
annotated property: definition
annotated target: A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

cardiac mesenchymal cell
type: Class
equivalent class: Class
  intersection of: CL_0008019
  intersection of: Restriction
    on property: develops into
    some values from: CL_0002494
subclass of: CL_0008019
subclass of: CL_2000073
subclass of: Restriction
  on property: develops into
  some values from: CL_0002494
definition: A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field.
database_cross_reference: ZFA:0009259
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cardiac mesenchymal cell
annotated property: definition
annotated target: A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field.
database_cross_reference: PMID:18816864

Axiom
annotated source: cardiac mesenchymal cell
annotated property: database_cross_reference
annotated target: ZFA:0009259
mapping justification: UnspecifiedMatching

parafollicular cell
type: Class
equivalent class: Class
  intersection of: neurecto-epithelial cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001024
  intersection of: Restriction
    on property: capable of
    some values from: GO_0001820
  intersection of: Restriction
    on property: capable of
    some values from: GO_0014046
  intersection of: Restriction
    on property: capable of
    some values from: GO_0036161
subclass of: glandular secretory epithelial cell
subclass of: calcitonin secreting cell
subclass of: serotonin secreting cell
subclass of: neurecto-epithelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001747
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001024
subclass of: Restriction
  on property: develops from
  some values from: migratory neural crest cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0014046
definition: A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secretes calcitonin, 5-hydroxytryptamine and dopamine.
database_cross_reference: FMA:68653
database_cross_reference: SCTID:176770005
database_cross_reference: ZFA:0009260
has_exact_synonym: C cell
has_exact_synonym: C cell of thyroid gland
has_exact_synonym: clear cell of thyroid gland
has_exact_synonym: parafollicular cell of thyroid gland
has_exact_synonym: thyroid parafollicular cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: parafollicular cell
annotated property: subClassOf
annotated target: calcitonin secreting cell
is inferred: true

Axiom
annotated source: parafollicular cell
annotated property: subClassOf
annotated target: neurecto-epithelial cell
is inferred: true

Axiom
annotated source: parafollicular cell
annotated property: definition
annotated target: A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secretes calcitonin, 5-hydroxytryptamine and dopamine.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651

Axiom
annotated source: parafollicular cell
annotated property: database_cross_reference
annotated target: ZFA:0009260
mapping justification: UnspecifiedMatching

Axiom
annotated source: parafollicular cell
annotated property: has_exact_synonym
annotated target: C cell of thyroid gland
database_cross_reference: FMA:68653

Axiom
annotated source: parafollicular cell
annotated property: has_exact_synonym
annotated target: clear cell of thyroid gland
database_cross_reference: FMA:68653

Axiom
annotated source: parafollicular cell
annotated property: has_exact_synonym
annotated target: parafollicular cell of thyroid gland
database_cross_reference: FMA:68653

Axiom
annotated source: parafollicular cell
annotated property: has_exact_synonym
annotated target: thyroid parafollicular cell
database_cross_reference: FMA:68653

leucophore
type: Class
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: develops from
  some values from: CL_0005003
definition: A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light.
database_cross_reference: ZFA:0009261
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: leucophore
annotated property: definition
annotated target: A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light.
database_cross_reference: SANBI:mhl

Axiom
annotated source: leucophore
annotated property: database_cross_reference
annotated target: ZFA:0009261
mapping justification: UnspecifiedMatching

CL_0000572
type: Class
has obsolescence reason: IAO_0000227
term replaced by: melanocyte
deprecated: true

retinal cone cell
type: Class
subclass of: CL_0010009
subclass of: Restriction
  on property: develops from
  some values from: CL_0002672
definition: One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0001036
database_cross_reference: CALOHA:TS-0866
database_cross_reference: FMA:67748
database_cross_reference: ZFA:0009262
has_related_synonym: cone
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: retinal cone cell
annotated property: definition
annotated target: One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision.
database_cross_reference: MESH:D017949

Axiom
annotated source: retinal cone cell
annotated property: database_cross_reference
annotated target: ZFA:0009262
mapping justification: UnspecifiedMatching

Axiom
annotated source: retinal cone cell
annotated property: has_related_synonym
annotated target: cone
database_cross_reference: doi:10.1038/s41598-020-66092-9

erythrophore
type: Class
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: develops from
  some values from: CL_0005004
definition: A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance.
database_cross_reference: ZFA:0009263
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: erythrophore
annotated property: definition
annotated target: A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance.
database_cross_reference: SANBI:mhl

Axiom
annotated source: erythrophore
annotated property: database_cross_reference
annotated target: ZFA:0009263
mapping justification: UnspecifiedMatching

corneal epithelial cell
type: Class
equivalent class: Class
  intersection of: squamous epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0001772
subclass of: squamous epithelial cell
subclass of: CL_0002159
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001772
definition: An epithelial cell of the cornea.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0004298
database_cross_reference: CALOHA:TS-0173
database_cross_reference: FMA:70551
database_cross_reference: ZFA:0009264
has_exact_synonym: epithelial cell of cornea
in_subset: cellxgene subset
in_subset: eye_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: corneal epithelial cell
annotated property: definition
annotated target: An epithelial cell of the cornea.
database_cross_reference: GOC:tfm

Axiom
annotated source: corneal epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009264
mapping justification: UnspecifiedMatching

Axiom
annotated source: corneal epithelial cell
annotated property: has_exact_synonym
annotated target: epithelial cell of cornea
database_cross_reference: FMA:70551

monocyte
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001407
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030225
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030316
  intersection of: Restriction
    on property: capable of
    some values from: GO_0043011
subclass of: mononuclear phagocyte
subclass of: myeloid leukocyte
subclass of: CL_0011026
subclass of: Restriction
  on property: develops from
  some values from: promonocyte
subclass of: Restriction
  on property: capable of
  some values from: GO_0030225
subclass of: Restriction
  on property: capable of
  some values from: GO_0030316
subclass of: Restriction
  on property: capable of
  some values from: GO_0043011
definition: Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000876
database_cross_reference: CALOHA:TS-0638
database_cross_reference: FMA:62864
database_cross_reference: ZFA:0009265
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid.

Axiom
annotated source: monocyte
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: monocyte
annotated property: definition
annotated target: Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
database_cross_reference: GO_REF:0000031
database_cross_reference: MESH:D009000

Axiom
annotated source: monocyte
annotated property: database_cross_reference
annotated target: ZFA:0009265
mapping justification: UnspecifiedMatching

type EC enteroendocrine cell
type: Class
subclass of: enteroendocrine cell
subclass of: chromaffin cell
subclass of: serotonin secreting cell
subclass of: enkephalin secreting cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0004786
definition: A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain).
present in taxon: NCBITaxon 9606
description: Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. Via specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: FMA:62934
database_cross_reference: FMA:83132
database_cross_reference: MESH:D004759
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000577
has_exact_synonym: Kulchitsky cell
has_exact_synonym: argentaffin cell
has_exact_synonym: enterochromaffin cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: type EC enteroendocrine cell
annotated property: definition
annotated target: A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain).
database_cross_reference: PMID:9505449

Axiom
annotated source: type EC enteroendocrine cell
annotated property: description
annotated target: Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. Via specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1016/0166-4328(96)00075-7
database_cross_reference: DOI:10.1016/j.cell.2017.05.034
database_cross_reference: DOI:10.1038/s41574-019-0168-8
database_cross_reference: DOI:10.1073/pnas.1804938115

experimentally modified cell in vitro
type: Class
subclass of: CL_0001034
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
in_subset: human subset
in_subset: mouse subset
comment: This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12

Axiom
annotated source: experimentally modified cell in vitro
annotated property: definition
annotated target: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
database_cross_reference: FB:ma
database_cross_reference: ReO:mhb

border follicle cell
type: Class
subclass of: follicle cell of egg chamber
definition: A follicle cell that migrates from the anterior pole of the insect egg chamber to the anterior of the oocyte where they participate in the formation of the micropyle.
database_cross_reference: FBbt:00004905

Axiom
annotated source: border follicle cell
annotated property: definition
annotated target: A follicle cell that migrates from the anterior pole of the insect egg chamber to the anterior of the oocyte where they participate in the formation of the micropyle.
database_cross_reference: FBbt:00004905

Axiom
annotated source: border follicle cell
annotated property: database_cross_reference
annotated target: FBbt:00004905
mapping justification: ManualMappingCuration

neutrophilic myelocyte
type: Class
equivalent class: Class
  intersection of: immature neutrophil
  intersection of: Restriction
    on property: has part
    some values from: CL_0017502
  intersection of: Restriction
    on property: has part
    some values from: GO_0042582
  intersection of: Restriction
    on property: has part
    some values from: PR_000001944
  intersection of: Restriction
    on property: has part
    some values from: PR_000005307
  intersection of: Restriction
    on property: has part
    some values from: PR_000005310
  intersection of: Restriction
    on property: has part
    some values from: PR_000009725
  intersection of: Restriction
    on property: has part
    some values from: PR_000009978
  intersection of: Restriction
    on property: has part
    some values from: PR_000010543
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0070820
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001483
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001012
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001456
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001892
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001932
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002031
subclass of: immature neutrophil
subclass of: CL_0002087
subclass of: CL_0002193
subclass of: Restriction
  on property: has part
  some values from: CL_0017502
subclass of: Restriction
  on property: has part
  some values from: GO_0042582
subclass of: Restriction
  on property: has part
  some values from: PR_000001944
subclass of: Restriction
  on property: has part
  some values from: PR_000005307
subclass of: Restriction
  on property: has part
  some values from: PR_000005310
subclass of: Restriction
  on property: has part
  some values from: PR_000009725
subclass of: Restriction
  on property: has part
  some values from: PR_000009978
subclass of: Restriction
  on property: has part
  some values from: PR_000010543
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0070820
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001483
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001456
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001892
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001932
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002031
definition: A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and neutrophil-specific granules has started. No nucleolus is present. This cell type is CD13-positive, CD16-negative, integrin alpha-M-positive, CD15-positive, CD33-positive, CD24-positive, C/EBP-a-positive, C/EBPe-positive, PU.1-positive, lactotransferrin-positive, myeloperoxidase-positive and NGAL-positive.
database_cross_reference: BTO:0003455
database_cross_reference: FMA:83540
database_cross_reference: ZFA:0009266
in_subset: human subset
in_subset: mouse subset
comment: These cells are also CD15-positive, CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction.

Axiom
annotated source: neutrophilic myelocyte
annotated property: subClassOf
annotated target: immature neutrophil
is inferred: true

Axiom
annotated source: neutrophilic myelocyte
annotated property: definition
annotated target: A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and neutrophil-specific granules has started. No nucleolus is present. This cell type is CD13-positive, CD16-negative, integrin alpha-M-positive, CD15-positive, CD33-positive, CD24-positive, C/EBP-a-positive, C/EBPe-positive, PU.1-positive, lactotransferrin-positive, myeloperoxidase-positive and NGAL-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:10618520
database_cross_reference: PMID:12560239
database_cross_reference: PMID:15514007
database_cross_reference: http://www.cap.org

Axiom
annotated source: neutrophilic myelocyte
annotated property: database_cross_reference
annotated target: ZFA:0009266
mapping justification: UnspecifiedMatching

peritoneal macrophage
type: Class
equivalent class: Class
  intersection of: CL_0000864
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0042613
  intersection of: Restriction
    on property: located in
    some values from: UBERON_0001179
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001807
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002064
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000006172
  intersection of: Restriction
    on property: capable of
    some values from: GO_0042742
  intersection of: Restriction
    on property: has high plasma membrane amount
    some values from: PR_000001012
  intersection of: Restriction
    on property: has high plasma membrane amount
    some values from: PR_000001813
  intersection of: Restriction
    on property: has high plasma membrane amount
    some values from: PR_000002062
subclass of: CL_0000864
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0042613
subclass of: Restriction
  on property: located in
  some values from: UBERON_0001179
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001807
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002064
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000006172
subclass of: Restriction
  on property: capable of
  some values from: GO_0042742
subclass of: Restriction
  on property: has high plasma membrane amount
  some values from: PR_000001012
subclass of: Restriction
  on property: has high plasma membrane amount
  some values from: PR_000001813
subclass of: Restriction
  on property: has high plasma membrane amount
  some values from: PR_000002062
definition: A macrophage resident in the peritoneum under non-inflammatory conditions. Markers include F4/80-high, CD11b-high, CD68-positive, SIGNR1-positive, CD115-high, MHC-II-negative, and Dectin-1-positive.
database_cross_reference: BTO:0001034
database_cross_reference: FMA:83025
database_cross_reference: ZFA:0009267
in_subset: human subset
in_subset: mouse subset
comment: Markers: Mouse: F4/80-high, CD11b-high, CD68+, SIGNR1+, Dectin-1+.

Axiom
annotated source: peritoneal macrophage
annotated property: subClassOf
annotated target: CL_0000864
is inferred: true

Axiom
annotated source: peritoneal macrophage
annotated property: definition
annotated target: A macrophage resident in the peritoneum under non-inflammatory conditions. Markers include F4/80-high, CD11b-high, CD68-positive, SIGNR1-positive, CD115-high, MHC-II-negative, and Dectin-1-positive.
database_cross_reference: MESH:D017737
database_cross_reference: PMID:15771589
database_cross_reference: PMID:19201820

Axiom
annotated source: peritoneal macrophage
annotated property: database_cross_reference
annotated target: ZFA:0009267
mapping justification: UnspecifiedMatching

neutrophilic metamyelocyte
type: Class
equivalent class: Class
  intersection of: immature neutrophil
  intersection of: Restriction
    on property: has part
    some values from: CL_0017502
  intersection of: Restriction
    on property: has part
    some values from: CL_0017507
  intersection of: Restriction
    on property: has part
    some values from: GO_0000792
  intersection of: Restriction
    on property: has part
    some values from: GO_0042582
  intersection of: Restriction
    on property: has part
    some values from: GO_0070820
  intersection of: Restriction
    on property: has part
    some values from: PR_000001944
  intersection of: Restriction
    on property: has part
    some values from: PR_000005307
  intersection of: Restriction
    on property: has part
    some values from: PR_000005310
  intersection of: Restriction
    on property: has part
    some values from: PR_000009725
  intersection of: Restriction
    on property: has part
    some values from: PR_000009978
  intersection of: Restriction
    on property: has part
    some values from: PR_000010543
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001580
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001012
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001456
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001483
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001892
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001932
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002031
subclass of: immature neutrophil
subclass of: CL_0002192
subclass of: Restriction
  on property: has part
  some values from: CL_0017502
subclass of: Restriction
  on property: has part
  some values from: CL_0017507
subclass of: Restriction
  on property: has part
  some values from: GO_0000792
subclass of: Restriction
  on property: has part
  some values from: GO_0042582
subclass of: Restriction
  on property: has part
  some values from: GO_0070820
subclass of: Restriction
  on property: has part
  some values from: PR_000001944
subclass of: Restriction
  on property: has part
  some values from: PR_000005307
subclass of: Restriction
  on property: has part
  some values from: PR_000005310
subclass of: Restriction
  on property: has part
  some values from: PR_000009725
subclass of: Restriction
  on property: has part
  some values from: PR_000009978
subclass of: Restriction
  on property: has part
  some values from: PR_000010543
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001580
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001456
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001483
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001892
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001932
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002031
subclass of: Restriction
  on property: develops from
  some values from: neutrophilic myelocyte
definition: A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and the band form neutrophil. The protein synthesis seen in earlier stages decreases or stops; the nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare; and the cytoplasm becomes amphophilic like that of a mature granulocyte. This cell type is integrin alpha-M-positive, CD13-negative, CD15-positive, CD16-positive, CD33-positive, CD24-positive, fMLP receptor-negative and has expression of C/EBP-a, C/EBP-e, PU.1 transcription factor, lactotransferrin, myeloperoxidase and neutrophil gelatinase associated lipocalin.
database_cross_reference: FMA:84197
database_cross_reference: ZFA:0009268
has_exact_synonym: juvenile neutrophil
in_subset: human subset
in_subset: mouse subset
comment: These cells are also CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction.

Axiom
annotated source: neutrophilic metamyelocyte
annotated property: subClassOf
annotated target: immature neutrophil
is inferred: true

Axiom
annotated source: neutrophilic metamyelocyte
annotated property: definition
annotated target: A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and the band form neutrophil. The protein synthesis seen in earlier stages decreases or stops; the nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare; and the cytoplasm becomes amphophilic like that of a mature granulocyte. This cell type is integrin alpha-M-positive, CD13-negative, CD15-positive, CD16-positive, CD33-positive, CD24-positive, fMLP receptor-negative and has expression of C/EBP-a, C/EBP-e, PU.1 transcription factor, lactotransferrin, myeloperoxidase and neutrophil gelatinase associated lipocalin.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:10618520
database_cross_reference: PMID:12560239
database_cross_reference: PMID:15514007
database_cross_reference: http://www.cap.org

Axiom
annotated source: neutrophilic metamyelocyte
annotated property: database_cross_reference
annotated target: ZFA:0009268
mapping justification: UnspecifiedMatching

alveolar macrophage
type: Class
equivalent class: Class
  intersection of: CL_0000864
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001206
  intersection of: Restriction
    on property: located in
    some values from: UBERON_8850000
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001013
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001807
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001813
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001931
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002064
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002972
  intersection of: Restriction
    on property: capable of
    some values from: GO_0019882
  intersection of: Restriction
    on property: has low plasma membrane amount
    some values from: PR_000001012
subclass of: CL_0000864
subclass of: CL_1001603
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001206
subclass of: Restriction
  on property: located in
  some values from: UBERON_8850000
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001013
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001807
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001813
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001931
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002064
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002972
subclass of: Restriction
  on property: has characterizing marker set
  some values from: NS forest marker set of alveolar macrophage (Human Lung).
subclass of: Restriction
  on property: has low plasma membrane amount
  some values from: PR_000001012
definition: A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative.
present in taxon: NCBITaxon 9606
description: Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. Beyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: BTO:0000802
database_cross_reference: CALOHA:TS-0030
database_cross_reference: FMA:83023
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000583
has_exact_synonym: dust cell
has_related_synonym: MF.Lu
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Markers: Mouse: F4/80mid, CD11b-/low, CD11c+, CD68+, sialoadhesin+, dectin-1+, MR+, CX3CR1-.
comment: The marker set MSR1, FABP4 can identify the Human cell type alveolar macrophage in the Lung with a confidence of 0.80 (NS-Forest FBeta value).

Axiom
annotated source: alveolar macrophage
annotated property: subClassOf
annotated target: CL_0000864
is inferred: true

Axiom
annotated source: alveolar macrophage
annotated property: definition
annotated target: A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative.
database_cross_reference: GOC:ana
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: MESH:D016676

Axiom
annotated source: alveolar macrophage
annotated property: description
annotated target: Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. Beyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1007/s00424-017-1965-3
database_cross_reference: DOI:10.1016/j.cellimm.2018.01.005
database_cross_reference: DOI:10.1038/nri3600
database_cross_reference: DOI:10.14348/molcells.2021.0058

Axiom
annotated source: alveolar macrophage
annotated property: comment
annotated target: The marker set MSR1, FABP4 can identify the Human cell type alveolar macrophage in the Lung with a confidence of 0.80 (NS-Forest FBeta value).
database_cross_reference: https://doi.org/10.5281/zenodo.11165918

enterocyte
type: Class
subclass of: brush border epithelial cell
subclass of: gut absorptive cell
subclass of: CL_0002563
definition: An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000398
database_cross_reference: FMA:62122
database_cross_reference: MESH:D020895
database_cross_reference: ZFA:0009269
has_narrow_synonym: differentiated enterocyte
has_narrow_synonym: mature enterocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: enterocyte
annotated property: definition
annotated target: An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen.
database_cross_reference: SANBI:mhl

Axiom
annotated source: enterocyte
annotated property: database_cross_reference
annotated target: ZFA:0009269
mapping justification: UnspecifiedMatching

Axiom
annotated source: enterocyte
annotated property: has_narrow_synonym
annotated target: differentiated enterocyte
database_cross_reference: PMID:33290721
database_cross_reference: https://orcid.org/0000-0001-9610-7627

Axiom
annotated source: enterocyte
annotated property: has_narrow_synonym
annotated target: mature enterocyte
database_cross_reference: PMID:33290721
database_cross_reference: https://orcid.org/0000-0001-9610-7627

obsolete null cell
type: Class
definition: OBSOLETE: A class of lymphocytes characterized by the lack of surface markers specific for either T or B cells.
comment: This term is rather archaic; consider using 'natural killer cell ; CL:0000623', 'pro-B cell ; CL:0000826', 'pro-T cell ; CL:0000827', or other appropriate lymphocyte-related term depending on the context.
deprecated: true

germ cell
type: Class
subclass of: germ line cell
subclass of: Restriction
  on property: capable of part of
  some values from: GO_0009566
definition: The reproductive cell in multicellular organisms.
database_cross_reference: BTO:0000535
database_cross_reference: NCIT:C12597
database_cross_reference: VHOG:0001534
database_cross_reference: WBbt:0006796
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: germ cell
annotated property: subClassOf
annotated target: germ line cell
is inferred: true

Axiom
annotated source: germ cell
annotated property: definition
annotated target: The reproductive cell in multicellular organisms.
database_cross_reference: MESH:D005854

cold sensing thermoreceptor cell
type: Class
subclass of: thermoreceptor cell
definition: A thermoreceptor cell that detects reduced temperatures.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cold sensing thermoreceptor cell
annotated property: definition
annotated target: A thermoreceptor cell that detects reduced temperatures.
database_cross_reference: GOC:tfm

odontoclast
type: Class
equivalent class: Class
  intersection of: osteoclast
  intersection of: Restriction
    on property: capable of
    some values from: GO_0042483
subclass of: osteoclast
subclass of: Restriction
  on property: capable of
  some values from: GO_0042483
definition: A specialized osteoclast associated with the absorption and removal of cementum.
database_cross_reference: BTO:0002516
database_cross_reference: FMA:83027
database_cross_reference: ZFA:0009270
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: odontoclast
annotated property: subClassOf
annotated target: osteoclast
is inferred: true

Axiom
annotated source: odontoclast
annotated property: definition
annotated target: A specialized osteoclast associated with the absorption and removal of cementum.
database_cross_reference: GOC:add

Axiom
annotated source: odontoclast
annotated property: database_cross_reference
annotated target: ZFA:0009270
mapping justification: UnspecifiedMatching

cochlear inner hair cell
type: Class
subclass of: CL_4023120
definition: A bulbous cell that is medially placed in one row in the organ of Corti. In contrast to the outer hair cells, the inner hair cells are fewer in number, have fewer sensory hairs, and are less differentiated.
has_broad_synonym: inner hair cell
database_cross_reference: BTO:0003667
database_cross_reference: FMA:62365
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cochlear inner hair cell
annotated property: definition
annotated target: A bulbous cell that is medially placed in one row in the organ of Corti. In contrast to the outer hair cells, the inner hair cells are fewer in number, have fewer sensory hairs, and are less differentiated.
database_cross_reference: MESH:D006199

small luteal cell
type: Class
subclass of: BFO_0000002
subclass of: luteal cell
subclass of: Restriction
  on property: develops from
  some values from: theca cell
definition: A progesterone secreting cell in the corpus luteum that develops from theca cells.
database_cross_reference: BTO:0002850
database_cross_reference: FMA:18690
has_exact_synonym: small lutein cell
has_exact_synonym: theca lutein cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: small luteal cell
annotated property: definition
annotated target: A progesterone secreting cell in the corpus luteum that develops from theca cells.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D008184

warmth sensing thermoreceptor cell
type: Class
subclass of: thermoreceptor cell
definition: A thermoreceptor cell that detects increased temperatures.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: warmth sensing thermoreceptor cell
annotated property: definition
annotated target: A thermoreceptor cell that detects increased temperatures.
database_cross_reference: GOC:tfm
database_cross_reference: https://orcid.org/0000-0001-5208-3432

large luteal cell
type: Class
subclass of: BFO_0000002
subclass of: luteal cell
subclass of: testosterone secreting cell
subclass of: Restriction
  on property: develops from
  some values from: granulosa cell
definition: A large, progesterone secreting cell in the corpus luteum that develops from the granulosa cells.
database_cross_reference: FMA:18689
has_exact_synonym: granulosa lutein cell
has_related_synonym: granulosoluteocytus
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: large luteal cell
annotated property: definition
annotated target: A large, progesterone secreting cell in the corpus luteum that develops from the granulosa cells.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D008184

androgen secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0035935
subclass of: steroid hormone secreting cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0035935
definition: A steroid hormone secreting cell that secretes androgen.
database_cross_reference: ZFA:0009271
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: androgen secreting cell
annotated property: definition
annotated target: A steroid hormone secreting cell that secretes androgen.
database_cross_reference: GOC:tfm

Axiom
annotated source: androgen secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009271
mapping justification: UnspecifiedMatching

skeletal muscle satellite cell
type: Class
subclass of: cell of skeletal muscle
subclass of: muscle precursor cell
definition: An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers.
description: Skeletal muscle satellite cells (SMSCs) are a type of adult stem cell that nestles on the outer surface of the myofiber, positioned between the sarcolemma (plasma membrane of the muscle cell) and peripheral basement membrane. The primary function of SMSCs lies in their capacity to facilitate the growth and repair of damaged skeletal muscle. Upon muscle injury or trauma, these normally quiescent cells activate, proliferate, and differentiate into myoblasts. These myoblasts subsequently mature and fuse to form myotubes, which ultimately help in the repair and rebuilding of muscle fibers. This response is an integral part of the skeletal muscle's ability to recover from injury and adapt to enhanced or changing physical demands, thereby maintaining and improving muscle function. Furthermore, SMSCs also contribute to hypertrophic muscle growth due to resistance exercise and endurance training, with the notable feature of their multi-nucleated nature resulting from the fusion of differentiated myoblasts. The additional nuclei support enhanced protein synthesis, thus allowing the muscle fibers to grow and strengthen in response to exercise. In aging and in diseases, the number or functionality of these cells can decrease, leading to impaired muscle regeneration and progressive muscle weakness. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: ZFA:0009272
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000594
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Skeletal muscle satellite cells are not traditionally referred to as myoblasts. They are a heterogeneous population whose division, following activiation, contributes to the formation of skeletal muscle fibers and to maintenance of the skeletal muscle statelite cell population.

Axiom
annotated source: skeletal muscle satellite cell
annotated property: definition
annotated target: An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D032496
database_cross_reference: PMID:21849021
database_cross_reference: PMID:23303905

Axiom
annotated source: skeletal muscle satellite cell
annotated property: description
annotated target: Skeletal muscle satellite cells (SMSCs) are a type of adult stem cell that nestles on the outer surface of the myofiber, positioned between the sarcolemma (plasma membrane of the muscle cell) and peripheral basement membrane. The primary function of SMSCs lies in their capacity to facilitate the growth and repair of damaged skeletal muscle. Upon muscle injury or trauma, these normally quiescent cells activate, proliferate, and differentiate into myoblasts. These myoblasts subsequently mature and fuse to form myotubes, which ultimately help in the repair and rebuilding of muscle fibers. This response is an integral part of the skeletal muscle's ability to recover from injury and adapt to enhanced or changing physical demands, thereby maintaining and improving muscle function. Furthermore, SMSCs also contribute to hypertrophic muscle growth due to resistance exercise and endurance training, with the notable feature of their multi-nucleated nature resulting from the fusion of differentiated myoblasts. The additional nuclei support enhanced protein synthesis, thus allowing the muscle fibers to grow and strengthen in response to exercise. In aging and in diseases, the number or functionality of these cells can decrease, leading to impaired muscle regeneration and progressive muscle weakness. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1016/s1357-2725(03)00042-6
database_cross_reference: DOI:10.1152/physrev.00061.2017
database_cross_reference: DOI:10.1186/s13287-022-02706-5
database_cross_reference: DOI:10.1369/0022155411426780
database_cross_reference: DOI:10.22074/cellj.2016.4714

Axiom
annotated source: skeletal muscle satellite cell
annotated property: database_cross_reference
annotated target: ZFA:0009272
mapping justification: UnspecifiedMatching

enucleate erythrocyte
type: Class
equivalent class: Class
  intersection of: erythrocyte
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001405
subclass of: anucleate cell
subclass of: erythrocyte
subclass of: Restriction
  on property: develops from
  some values from: CL_0002422
definition: An erythrocyte lacking a nucleus.
has_broad_synonym: red blood cell
has_related_synonym: RBC
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: enucleate erythrocyte
annotated property: subClassOf
annotated target: erythrocyte
is inferred: true

Axiom
annotated source: enucleate erythrocyte
annotated property: definition
annotated target: An erythrocyte lacking a nucleus.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm

Axiom
annotated source: enucleate erythrocyte
annotated property: has_related_synonym
annotated target: RBC
has_synonym_type: abbreviation

sexual spore
type: Class
subclass of: CL_0002369
definition: A spore formed following meiosis. Sometimes following meiosis, prospores may undergo one or more rounds of mitosis before they are fully mature.
database_cross_reference: FAO:0000017
has_exact_synonym: meiotically-derived spore

Axiom
annotated source: sexual spore
annotated property: definition
annotated target: A spore formed following meiosis. Sometimes following meiosis, prospores may undergo one or more rounds of mitosis before they are fully mature.
database_cross_reference: FAO:0000017
database_cross_reference: GOC:tfm
database_cross_reference: SGD:clt

microconidium
type: Class
subclass of: CL_0002381
definition: The smaller of two types of asexual spores formed by some fungi. An ovoid to pear-shaped asexual spore that contains very little cytoplasm and organelles, is uninucleate, and forms in vegetative hypae within a mycelium. Micronidia are extruded from the hyphal cell wall.
database_cross_reference: FAO:0000028

Axiom
annotated source: microconidium
annotated property: definition
annotated target: The smaller of two types of asexual spores formed by some fungi. An ovoid to pear-shaped asexual spore that contains very little cytoplasm and organelles, is uninucleate, and forms in vegetative hypae within a mycelium. Micronidia are extruded from the hyphal cell wall.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0471940526
database_cross_reference: PMID:8357339
database_cross_reference: SGD:clt

pyramidal neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0070015
subclass of: CL_2000029
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0070015
definition: Pyramidal neurons have a pyramid-shaped soma with a single axon, a large apical dendrite and multiple basal dendrites. The apex and an apical dendrite typically point toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their region. Pyramidal neurons are found in the cerebral cortex, the hippocampus, and the amygdala.
database_cross_reference: BTO:0003102
database_cross_reference: FMA:67310
database_cross_reference: FMA:86775
database_cross_reference: NIFSTD:sao862606388
database_cross_reference: ZFA:0009273
has_exact_synonym: projection neuron
has_exact_synonym: pyramidal cell
in_subset: BDS subset
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pyramidal neuron
annotated property: definition
annotated target: Pyramidal neurons have a pyramid-shaped soma with a single axon, a large apical dendrite and multiple basal dendrites. The apex and an apical dendrite typically point toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their region. Pyramidal neurons are found in the cerebral cortex, the hippocampus, and the amygdala.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D017966

Axiom
annotated source: pyramidal neuron
annotated property: database_cross_reference
annotated target: ZFA:0009273
mapping justification: UnspecifiedMatching

conidium
type: Class
subclass of: fungal asexual spore
definition: An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm.
database_cross_reference: BTO:0000283
database_cross_reference: FAO:0000024

Axiom
annotated source: conidium
annotated property: definition
annotated target: An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm.
database_cross_reference: ISBN:08199377X
database_cross_reference: PMID:2524423
database_cross_reference: PMID:9529886
database_cross_reference: SGD:clt

heterokaryon
type: Class
subclass of: multinucleate cell
subclass of: fungal cell
definition: A fungal cell with two or more genetically distinct nuclei.

Axiom
annotated source: heterokaryon
annotated property: definition
annotated target: A fungal cell with two or more genetically distinct nuclei.
database_cross_reference: ISBN:08199377X

cochlear outer hair cell
type: Class
subclass of: CL_4023120
definition: A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea.
database_cross_reference: BTO:0003666
database_cross_reference: FMA:62366
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cochlear outer hair cell
annotated property: definition
annotated target: A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea.
database_cross_reference: MESH:D018072

pressoreceptor cell
type: Class
subclass of: CL_1000082
definition: A receptor in the vascular system, particularly the aorta and carotid sinus, which is sensitive to stretch of the vessel walls.
database_cross_reference: ZFA:0009274
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pressoreceptor cell
annotated property: definition
annotated target: A receptor in the vascular system, particularly the aorta and carotid sinus, which is sensitive to stretch of the vessel walls.
database_cross_reference: MESH:D011311

Axiom
annotated source: pressoreceptor cell
annotated property: database_cross_reference
annotated target: ZFA:0009274
mapping justification: UnspecifiedMatching

dikaryon
type: Class
subclass of: binucleate cell
subclass of: heterokaryon
definition: A fungal cell with two genetically distinct haploid nuclei.

Axiom
annotated source: dikaryon
annotated property: definition
annotated target: A fungal cell with two genetically distinct haploid nuclei.
database_cross_reference: ISBN:08199377X

retinal rod cell
type: Class
subclass of: CL_0010009
subclass of: Restriction
  on property: develops from
  some values from: CL_0002672
definition: One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0001024
database_cross_reference: CALOHA:TS-0870
database_cross_reference: FMA:67747
database_cross_reference: ZFA:0009275
has_related_synonym: rod
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: retinal rod cell
annotated property: definition
annotated target: One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision.
database_cross_reference: MESH:D017948

Axiom
annotated source: retinal rod cell
annotated property: database_cross_reference
annotated target: ZFA:0009275
mapping justification: UnspecifiedMatching

Axiom
annotated source: retinal rod cell
annotated property: has_related_synonym
annotated target: rod
database_cross_reference: doi:10.1038/s41598-020-66092-9

fungal asexual spore
type: Class
subclass of: CL_0002369
definition: A spore formed following mitosis or mitoses.
database_cross_reference: FAO:0000023

Axiom
annotated source: fungal asexual spore
annotated property: definition
annotated target: A spore formed following mitosis or mitoses.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:2524423
database_cross_reference: PMID:9529886
database_cross_reference: SGD:clt

macroconidium
type: Class
subclass of: conidium
definition: The larger of two types of asexual spores formed by some fungi; usually round or oblong.
database_cross_reference: FAO:0000038

Axiom
annotated source: macroconidium
annotated property: definition
annotated target: The larger of two types of asexual spores formed by some fungi; usually round or oblong.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0471940526
database_cross_reference: SGD:clt

ascospore
type: Class
subclass of: sexual spore
definition: A thick walled spore that stores and protects one or more nuclei following sexual reproduction in an Ascomycete.
database_cross_reference: BTO:0000097
database_cross_reference: FAO:0000020

Axiom
annotated source: ascospore
annotated property: definition
annotated target: A thick walled spore that stores and protects one or more nuclei following sexual reproduction in an Ascomycete.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:08199377X
database_cross_reference: SGD:clt

zygospore
type: Class
subclass of: sexual spore
definition: A thick walled, sexual, resting spore formed by Zygomycetes; sometimes refers to the spore and the multi-layered cell wall that encloses the spore, the zygosporangium.
database_cross_reference: FAO:0000040

Axiom
annotated source: zygospore
annotated property: definition
annotated target: A thick walled, sexual, resting spore formed by Zygomycetes; sometimes refers to the spore and the multi-layered cell wall that encloses the spore, the zygosporangium.
database_cross_reference: ISBN:0471940526
database_cross_reference: ISBN:08199377X
database_cross_reference: SGD:clt

vestibular hair cell
type: Class
subclass of: CL_0002374
definition: A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem.
database_cross_reference: FMA:62351
has_exact_synonym: vestibular receptor cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: vestibular hair cell
annotated property: definition
annotated target: A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem.
database_cross_reference: GOC:tfm
database_cross_reference: MESH:D018069

obsolete plant cell
type: Class
consider: PO:0009002
comment: This term was obsoleted as it is redundant with PO:0009002 in the cell ontology (PO)
deprecated: true

eosinophil progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0002191
  intersection of: Restriction
    on property: has part
    some values from: PR_000001944
  intersection of: Restriction
    on property: has part
    some values from: PR_000005307
  intersection of: Restriction
    on property: has part
    some values from: PR_000007857
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001003
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001408
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001865
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001867
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002065
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030222
subclass of: myeloid cell
subclass of: CL_0002191
subclass of: Restriction
  on property: has part
  some values from: PR_000001944
subclass of: Restriction
  on property: has part
  some values from: PR_000005307
subclass of: Restriction
  on property: has part
  some values from: PR_000007857
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002981
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001003
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001408
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001865
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001867
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002065
subclass of: Restriction
  on property: develops from
  some values from: granulocyte monocyte progenitor cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0030222
definition: Any granulocytopoietic cell that has part some transcription factor PU.1 and has part some CCAAT/enhancer-binding protein alpha and has part some erythroid transcription factor and lacks plasma membrane part some CD19 molecule and lacks plasma membrane part some CD4 molecule and lacks plasma membrane part some integrin alpha-M and lacks plasma membrane part some CD3 epsilon and lacks plasma membrane part some neural cell adhesion molecule 1 and lacks plasma membrane part some CD2 molecule and lacks plasma membrane part some T-cell surface glycoprotein CD8 alpha chain and lacks plasma membrane part some membrane-spanning 4-domains subfamily A member 1 and lacks plasma membrane part some T-cell surface glycoprotein CD5 and lacks plasma membrane part some CD14 molecule and lacks plasma membrane part some lymphocyte antigen 6G and lacks plasma membrane part some lymphocyte antigen 76 (mouse) and has plasma membrane part some CD34 molecule and has plasma membrane part some ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 and has plasma membrane part some interleukin-3 receptor class 2 alpha chain and has plasma membrane part some interleukin-5 receptor subunit alpha and has plasma membrane part some mast/stem cell growth factor receptor and is capable of some eosinophil differentiation.
has_related_synonym: CFU-Eo
has_related_synonym: EoP
has_related_synonym: colony forming unit eosinophil
has_related_synonym: eosinophil stem cell
in_subset: human subset
in_subset: mouse subset
comment: These cells are CD34-positive, CD45RA-negative, CD71-negative, and lineage-negative (CD2, CD3 epsilon, CD4, CD5, CD8a, CD14, CD19, CD20, integrin alpha-M, NCAM-1, SCA-1, Ly6G, Ly76).

Axiom
annotated source: eosinophil progenitor cell
annotated property: subClassOf
annotated target: CL_0002191
is inferred: true

Axiom
annotated source: eosinophil progenitor cell
annotated property: definition
annotated target: Any granulocytopoietic cell that has part some transcription factor PU.1 and has part some CCAAT/enhancer-binding protein alpha and has part some erythroid transcription factor and lacks plasma membrane part some CD19 molecule and lacks plasma membrane part some CD4 molecule and lacks plasma membrane part some integrin alpha-M and lacks plasma membrane part some CD3 epsilon and lacks plasma membrane part some neural cell adhesion molecule 1 and lacks plasma membrane part some CD2 molecule and lacks plasma membrane part some T-cell surface glycoprotein CD8 alpha chain and lacks plasma membrane part some membrane-spanning 4-domains subfamily A member 1 and lacks plasma membrane part some T-cell surface glycoprotein CD5 and lacks plasma membrane part some CD14 molecule and lacks plasma membrane part some lymphocyte antigen 6G and lacks plasma membrane part some lymphocyte antigen 76 (mouse) and has plasma membrane part some CD34 molecule and has plasma membrane part some ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 and has plasma membrane part some interleukin-3 receptor class 2 alpha chain and has plasma membrane part some interleukin-5 receptor subunit alpha and has plasma membrane part some mast/stem cell growth factor receptor and is capable of some eosinophil differentiation.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: eosinophil progenitor cell
annotated property: has_related_synonym
annotated target: CFU-Eo
has_synonym_type: abbreviation

Axiom
annotated source: eosinophil progenitor cell
annotated property: has_related_synonym
annotated target: EoP
database_cross_reference: PMCID:PMC2212039
database_cross_reference: PMCID:PMC2626675
has_synonym_type: abbreviation

eosinophilic myelocyte
type: Class
equivalent class: Class
  intersection of: immature eosinophil
  intersection of: Restriction
    on property: has part
    some values from: GO_0042582
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0070820
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001483
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001012
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001456
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001892
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001932
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002031
subclass of: immature eosinophil
subclass of: CL_0002087
subclass of: CL_0002193
subclass of: Restriction
  on property: has part
  some values from: GO_0042582
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0070820
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001483
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001456
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001892
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001932
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002031
definition: A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive.
database_cross_reference: BTO:0003454
database_cross_reference: FMA:83542
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: eosinophilic myelocyte
annotated property: subClassOf
annotated target: immature eosinophil
is inferred: true

Axiom
annotated source: eosinophilic myelocyte
annotated property: definition
annotated target: A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:19622087
database_cross_reference: http://www.cap.org

basophil progenitor cell
type: Class
equivalent class: Class
  intersection of: CL_0002191
  intersection of: Restriction
    on property: has part
    some values from: PR_000005307
  intersection of: Restriction
    on property: has part
    some values from: PR_000007857
  intersection of: Restriction
    on property: has part
    some values from: PR_000007858
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002065
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002981
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030221
  intersection of: Restriction
    on property: has high plasma membrane amount
    some values from: PR_000007431
  intersection of: Restriction
    on property: has low plasma membrane amount
    some values from: PR_000016401
subclass of: myeloid cell
subclass of: CL_0002191
subclass of: Restriction
  on property: has part
  some values from: PR_000005307
subclass of: Restriction
  on property: has part
  some values from: PR_000007857
subclass of: Restriction
  on property: has part
  some values from: PR_000007858
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002065
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002981
subclass of: Restriction
  on property: develops from
  some values from: CL_0002028
subclass of: Restriction
  on property: capable of
  some values from: GO_0030221
subclass of: Restriction
  on property: has high plasma membrane amount
  some values from: PR_000007431
subclass of: Restriction
  on property: has low plasma membrane amount
  some values from: PR_000016401
definition: A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa.
has_exact_synonym: BaP
has_related_synonym: CFU-Bas
has_related_synonym: basophilic stem cell
has_related_synonym: colony forming unit basophil
in_subset: human subset
in_subset: mouse subset
comment: BaP are also CD13-low and integrin beta-7-low. They are lin-negative (CD2, CD3e, CD4, CD5, CD8, CD11b, CD14, CD19, CD20, ly6g, ly76, and NCAM-1). They also lack expression of mast cell protease 1 (MCP-1) and microphthalmia-associated transcription factor (mitf).

Axiom
annotated source: basophil progenitor cell
annotated property: subClassOf
annotated target: CL_0002191
is inferred: true

Axiom
annotated source: basophil progenitor cell
annotated property: definition
annotated target: A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: PMCID:PMC1312421
database_cross_reference: http://www.copewithcytokines.de

basophilic myelocyte
type: Class
equivalent class: Class
  intersection of: immature basophil
  intersection of: Restriction
    on property: has part
    some values from: GO_0042582
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0005730
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0070820
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001483
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001012
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001456
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001892
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001932
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002031
subclass of: immature basophil
subclass of: CL_0002087
subclass of: Restriction
  on property: has part
  some values from: GO_0042582
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0005730
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0070820
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001483
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001456
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001892
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001932
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002031
definition: A basophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and basophil-specific granules has started. No nucleolus is present. Markers are being integrin alpha-M-positive, fucosyltransferase FUT4-positive, CD33-positive, CD24-positive, aminopeptidase N-positive.
database_cross_reference: BTO:0003456
database_cross_reference: FMA:83543
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: basophilic myelocyte
annotated property: subClassOf
annotated target: immature basophil
is inferred: true

Axiom
annotated source: basophilic myelocyte
annotated property: definition
annotated target: A basophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and basophil-specific granules has started. No nucleolus is present. Markers are being integrin alpha-M-positive, fucosyltransferase FUT4-positive, CD33-positive, CD24-positive, aminopeptidase N-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:18466030
database_cross_reference: http://www.cap.org

basidiospore
type: Class
subclass of: sexual spore
definition: A thick walled spore containing one or more haploid nuclei produced by sexual reproduction in an Basidiomycete; formed externally on extrusions of the basidium.
database_cross_reference: BTO:0002166
database_cross_reference: FAO:0000021

Axiom
annotated source: basidiospore
annotated property: definition
annotated target: A thick walled spore containing one or more haploid nuclei produced by sexual reproduction in an Basidiomycete; formed externally on extrusions of the basidium.
database_cross_reference: GOC:clt
database_cross_reference: ISBN:0471940526
database_cross_reference: ISBN:08199377X

obsolete sporangiospore
type: Class
definition: OBSOLETE: A walled spore produced in a sporangium.
deprecated: true

Axiom
annotated source: obsolete sporangiospore
annotated property: definition
annotated target: OBSOLETE: A walled spore produced in a sporangium.
database_cross_reference: ISBN:08199377X

GABAergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0061534
subclass of: secretory cell
subclass of: neuron
subclass of: Restriction
  on property: capable of
  some values from: GO_0061534
definition: A neuron that uses GABA as a vesicular neurotransmitter
database_cross_reference: FBbt:00007228
database_cross_reference: FMA:84788
database_cross_reference: MESH:D059330
database_cross_reference: WBbt:0005190
database_cross_reference: ZFA:0009276
has_exact_synonym: GABA-ergic neuron
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: GABAergic neuron
annotated property: definition
annotated target: A neuron that uses GABA as a vesicular neurotransmitter
database_cross_reference: GOC:tfm

Axiom
annotated source: GABAergic neuron
annotated property: database_cross_reference
annotated target: FBbt:00007228
mapping justification: ManualMappingCuration

Axiom
annotated source: GABAergic neuron
annotated property: database_cross_reference
annotated target: ZFA:0009276
mapping justification: UnspecifiedMatching

sheath cell
type: Class
subclass of: columnar/cuboidal epithelial cell
in_subset: human subset
in_subset: mouse subset

supporting cell (sensu Nematoda)
type: Class
subclass of: supporting cell (sensu Nematoda and Protostomia)
has_exact_synonym: support cell (sensu Nematoda)
in_subset: human subset
in_subset: mouse subset

obsolete zoospore
type: Class
definition: OBSOLETE: A sporangiospore that is motile, having flagella.
database_cross_reference: FAO:0000039
deprecated: true

Axiom
annotated source: obsolete zoospore
annotated property: definition
annotated target: OBSOLETE: A sporangiospore that is motile, having flagella.
database_cross_reference: ISBN:08199377X

fusion competent myoblast
type: Class
subclass of: CL_0008018
definition: A myoblast that is committed to a myotube-specific program of differentiation but not yet fused. It undergoes very limited additional proliferation. After fusion, it will take on a muscle identity specified by a `muscle founder cell` (CL:0008006).
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: fusion competent myoblast
annotated property: definition
annotated target: A myoblast that is committed to a myotube-specific program of differentiation but not yet fused. It undergoes very limited additional proliferation. After fusion, it will take on a muscle identity specified by a `muscle founder cell` (CL:0008006).
database_cross_reference: PMID:22274696

acinar cell
type: Class
equivalent class: Class
  intersection of: glandular secretory epithelial cell
  intersection of: protein secreting cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0009842
subclass of: glandular secretory epithelial cell
subclass of: protein secreting cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0009842
definition: A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus).
description: Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: FMA:83625
database_cross_reference: MESH:D061354
database_cross_reference: ZFA:0009277
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000622
has_exact_synonym: acinic cell
has_exact_synonym: acinous cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: acinar cell
annotated property: definition
annotated target: A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus).
database_cross_reference: GOC:tfm
database_cross_reference: http://www.copewithcytokines.de

Axiom
annotated source: acinar cell
annotated property: description
annotated target: Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1007/BF00710764
database_cross_reference: DOI:10.1038/nrgastro.2013.36
database_cross_reference: DOI:10.1097/MOG.0b013e32832ebfac
database_cross_reference: DOI:10.1111/prd.12116
database_cross_reference: DOI:10.1152/physrev.00011.2011

Axiom
annotated source: acinar cell
annotated property: database_cross_reference
annotated target: ZFA:0009277
mapping justification: UnspecifiedMatching

natural killer cell
type: Class
equivalent class: Class
  intersection of: CL_0001067
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002228
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050776
subclass of: CL_0001067
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: develops from
  some values from: CL_0000825
subclass of: Restriction
  on property: capable of
  some values from: GO_0002228
subclass of: Restriction
  on property: capable of
  some values from: GO_0050776
definition: A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells.
present in taxon: NCBITaxon 9606
has_broad_synonym: large granular lymphocyte
has_broad_synonym: null cell
database_cross_reference: BTO:0000914
database_cross_reference: BTO:0004716
database_cross_reference: CALOHA:TS-0664
database_cross_reference: FMA:63147
database_cross_reference: FMA:83601
database_cross_reference: MESH:D007694
database_cross_reference: VHOG:0001697
database_cross_reference: ZFA:0009278
has_exact_synonym: NK cell
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: natural killer cell
annotated property: definition
annotated target: A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0781735149
database_cross_reference: PMID:15771571

Axiom
annotated source: natural killer cell
annotated property: database_cross_reference
annotated target: ZFA:0009278
mapping justification: UnspecifiedMatching

CD4-positive, alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: mature alpha-beta T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000025402
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001004
subclass of: mature alpha-beta T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000025402
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001004
disjoint with: CD8-positive, alpha-beta T cell
definition: A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor.
present in taxon: NCBITaxon 9606
has_exact_synonym: CD4-positive, alpha-beta T lymphocyte
has_exact_synonym: CD4-positive, alpha-beta T-cell
has_exact_synonym: CD4-positive, alpha-beta T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: CD4-positive, alpha-beta T cell
annotated property: subClassOf
annotated target: mature alpha-beta T cell
is inferred: true

Axiom
annotated source: CD4-positive, alpha-beta T cell
annotated property: definition
annotated target: A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0781735149

CD8-positive, alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: mature alpha-beta T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000025402
subclass of: mature alpha-beta T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000025402
definition: A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor.
present in taxon: NCBITaxon 9606
has_exact_synonym: CD8-positive, alpha-beta T lymphocyte
has_exact_synonym: CD8-positive, alpha-beta T-cell
has_exact_synonym: CD8-positive, alpha-beta T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: CD8-positive, alpha-beta T cell
annotated property: subClassOf
annotated target: mature alpha-beta T cell
is inferred: true

Axiom
annotated source: CD8-positive, alpha-beta T cell
annotated property: definition
annotated target: A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

olfactory granule cell
type: Class
equivalent class: Class
  intersection of: granule cell
  intersection of: Restriction
    on property: has soma location
    some values from: UBERON_0005378
subclass of: granule cell
subclass of: CL_1001434
subclass of: Restriction
  on property: has soma location
  some values from: UBERON_0005378
subclass of: Restriction
  on property: synapsed by
  some values from: CL_1001502
subclass of: Restriction
  on property: synapsed by
  some values from: CL_1001503
subclass of: Restriction
  on property: synapsed to
  some values from: CL_1001502
subclass of: Restriction
  on property: synapsed to
  some values from: CL_1001503
subclass of: Restriction
  on property: involved in regulation of
  some values from: GO_0007608
definition: A granule cell that has a soma located in an olfactory bulb granule cell layer. An olfactory granule cell is an interneuron that lacks an axon, makes reciprocal dendro-dendritic synapses with mitral cells and tufted cells and is involved in the fine spatio-temporal tuning of the responses of these principal olfactory bulb neurons to odors.
database_cross_reference: ZFA:0001694
has_exact_synonym: olfactory bulb granule cell
in_subset: human subset
in_subset: mouse subset
comment: Granule cells are the most abundant neuronal population in the olfactory bulb and are continuously renewed throughout life.

Axiom
annotated source: olfactory granule cell
annotated property: definition
annotated target: A granule cell that has a soma located in an olfactory bulb granule cell layer. An olfactory granule cell is an interneuron that lacks an axon, makes reciprocal dendro-dendritic synapses with mitral cells and tufted cells and is involved in the fine spatio-temporal tuning of the responses of these principal olfactory bulb neurons to odors.
database_cross_reference: GOC:mah
database_cross_reference: doi:10.1038/s41598-018-27692-8

Axiom
annotated source: olfactory granule cell
annotated property: database_cross_reference
annotated target: ZFA:0001694
mapping justification: UnspecifiedMatching

Axiom
annotated source: olfactory granule cell
annotated property: has_exact_synonym
annotated target: olfactory bulb granule cell
database_cross_reference: doi:10.1038/s41598-018-27692-8

Axiom
annotated source: olfactory granule cell
annotated property: comment
annotated target: Granule cells are the most abundant neuronal population in the olfactory bulb and are continuously renewed throughout life.
database_cross_reference: doi:10.1038/s41598-018-27692-8

transporting cell
type: Class
subclass of: cell
definition: A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: transporting cell
annotated property: definition
annotated target: A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances.
database_cross_reference: TAIR:sr

photosynthetic cell
type: Class
subclass of: cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0015979
definition: A cell that can perform photosynthesis, in which carbohydrates are synthesized from carbon dioxide and water, using light as the energy source.
comment: see PMID:21177950, The making of a photosynthetic animal.

Axiom
annotated source: photosynthetic cell
annotated property: definition
annotated target: A cell that can perform photosynthesis, in which carbohydrates are synthesized from carbon dioxide and water, using light as the energy source.
database_cross_reference: TAIR:sr

storage cell
type: Class
subclass of: stuff accumulating cell
definition: A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: storage cell
annotated property: definition
annotated target: A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose.
database_cross_reference: FB:ma

supporting cell
type: Class
subclass of: cell
definition: A cell whose primary function is to support other cell types.
database_cross_reference: BTO:0002315
database_cross_reference: ZFA:0009387
has_exact_synonym: supportive cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: supporting cell
annotated property: definition
annotated target: A cell whose primary function is to support other cell types.
database_cross_reference: FB:ma
database_cross_reference: GOC:tfm

Axiom
annotated source: supporting cell
annotated property: database_cross_reference
annotated target: ZFA:0009387
mapping justification: UnspecifiedMatching

labyrinth supporting cell
type: Class
subclass of: supporting cell
definition: Cells forming a framework supporting the organ of Corti. Specific cells are those of Claudius, Deiters and Hensen.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: labyrinth supporting cell
annotated property: definition
annotated target: Cells forming a framework supporting the organ of Corti. Specific cells are those of Claudius, Deiters and Hensen.
database_cross_reference: MESH:D007760

hepatic stellate cell
type: Class
equivalent class: Class
  intersection of: CL_0002320
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002107
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000007939
subclass of: fibroblast
subclass of: extracellular matrix secreting cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002107
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000007939
definition: A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0002741
database_cross_reference: CALOHA:TS-0452
database_cross_reference: FMA:67763
database_cross_reference: ZFA:0009279
has_exact_synonym: Ito cell
has_exact_synonym: hepatic perisinusoidal cell
has_exact_synonym: perisinusoidal cell
has_related_synonym: fat-storing cell
has_related_synonym: lipocyte
has_related_synonym: vitamin A-storing cells
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Hepatic stellate cells are CD271-positive, desmin-positive, DDR-2-positive, GFAP-positive, synamin-positive, synaptophysin-positive, vimentin-positive, They are capable of producing angiotensin II, fibronectin, laminin, MMP-1, MMP-2, MMP-3, MMP-9, MMP-11, TGF-beta1, TIMP-1, TIMP-2, type I collagen, type III collagen, type IV collagen, and type VI collagen.

Axiom
annotated source: hepatic stellate cell
annotated property: definition
annotated target: A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver.
database_cross_reference: GOC:dsd
database_cross_reference: MESH:D055166
database_cross_reference: PMID:12808230
database_cross_reference: PMID:17239632
database_cross_reference: PMID:18222966
database_cross_reference: PMID:9302568
database_cross_reference: http://en.wikipedia.org/wiki/Hepatic_stellate_cell

Axiom
annotated source: hepatic stellate cell
annotated property: database_cross_reference
annotated target: ZFA:0009279
mapping justification: UnspecifiedMatching

Axiom
annotated source: hepatic stellate cell
annotated property: has_related_synonym
annotated target: vitamin A-storing cells
database_cross_reference: PMID:12808230

Hensen cell
type: Class
subclass of: CL_0002490
definition: A tall supporting cell that is arranged in rows adjacent to the last row of outer phalangeal cells. This cell type constitutes the outer border of the organ of Corti.
database_cross_reference: FMA:79799
has_exact_synonym: Hensen's cell
has_exact_synonym: cell of Hensen
has_exact_synonym: external limiting cell of organ of Corti
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: Hensen cell
annotated property: definition
annotated target: A tall supporting cell that is arranged in rows adjacent to the last row of outer phalangeal cells. This cell type constitutes the outer border of the organ of Corti.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Claudius cell
type: Class
subclass of: CL_0002315
definition: A cuboidal cell which along with Boettcher's cells form the floor of the external spiral sulcus, external to the organ of Corti.
database_cross_reference: FMA:79802
has_exact_synonym: cell of Claudius
has_related_synonym: external supporting cell of Claudius
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: Claudius cell
annotated property: definition
annotated target: A cuboidal cell which along with Boettcher's cells form the floor of the external spiral sulcus, external to the organ of Corti.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Deiter's cell
type: Class
subclass of: CL_0002165
definition: The outer phalangeal cells of the organ of Corti. This cell holds the base of the hair cell in a cup-shaped depression.
database_cross_reference: FMA:75725
has_exact_synonym: Deiters cell
has_exact_synonym: outer phalangeal cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: Deiter's cell
annotated property: definition
annotated target: The outer phalangeal cells of the organ of Corti. This cell holds the base of the hair cell in a cup-shaped depression.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544
database_cross_reference: http://www.britannica.com/EBchecked/topic/156177/Deiters-cell

Mueller cell
type: Class
subclass of: radial glial cell
subclass of: CL_0009004
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000966
definition: Astrocyte-like radial glial cell that extends vertically throughout the retina, with the nucleus are usually in the middle of the inner nuclear layer.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0003064
database_cross_reference: ZFA:0009280
has_exact_synonym: Muller cell
has_exact_synonym: Muller glia
has_exact_synonym: Müller cell
in_subset: cellxgene subset
in_subset: eye_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: Mueller cell
annotated property: definition
annotated target: Astrocyte-like radial glial cell that extends vertically throughout the retina, with the nucleus are usually in the middle of the inner nuclear layer.
database_cross_reference: GOC:NV
database_cross_reference: PMID:21911394

Axiom
annotated source: Mueller cell
annotated property: database_cross_reference
annotated target: ZFA:0009280
mapping justification: UnspecifiedMatching

Axiom
annotated source: Mueller cell
annotated property: has_exact_synonym
annotated target: Muller cell
database_cross_reference: doi:10.21769/BioProtoc.4179
has_synonym_type: a mis-spelling that is in common use and thus recorded

chromophil cell of anterior pituitary gland
type: Class
equivalent class: Class
  intersection of: chromaffin cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002196
subclass of: glandular secretory epithelial cell
subclass of: chromaffin cell
subclass of: peptide hormone secreting cell
subclass of: CL_2000004
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002196
definition: A cell that stains readily in the anterior pituitary gland.
database_cross_reference: FMA:83089
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: chromophil cell of anterior pituitary gland
annotated property: definition
annotated target: A cell that stains readily in the anterior pituitary gland.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0618947256

acidophil cell of pars distalis of adenohypophysis
type: Class
subclass of: chromophil cell of anterior pituitary gland
subclass of: Restriction
  on property: part of
  some values from: UBERON_0006964
definition: An acidophilic chromophil cell that of the anterior pituitary gland.
database_cross_reference: FMA:83093
has_exact_synonym: acidophil cell of pars anterior of adenohypophysis
has_exact_synonym: acidophil of pars anterior of adenohypophysis
has_exact_synonym: acidophil of pars distalis of adenohypophysis
has_exact_synonym: pituitary alpha cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: acidophil cell of pars distalis of adenohypophysis
annotated property: definition
annotated target: An acidophilic chromophil cell that of the anterior pituitary gland.
database_cross_reference: GOC:tfm

basophil cell of pars distalis of adenohypophysis
type: Class
subclass of: chromophil cell of anterior pituitary gland
definition: A basophilic chromophil cell that of the anterior pituitary gland.
database_cross_reference: FMA:83094
has_exact_synonym: basophil cell of anterior lobe of hypophysis
has_related_synonym: beta cell
has_related_synonym: pituitary beta cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: basophil cell of pars distalis of adenohypophysis
annotated property: definition
annotated target: A basophilic chromophil cell that of the anterior pituitary gland.
database_cross_reference: GOC:tfm

CL_0000640
type: Class
has obsolescence reason: IAO_0000227
term replaced by: adrenocorticotropic hormone secreting cell
deprecated: true

chromophobe cell
type: Class
subclass of: endocrine cell
definition: A cell that is resistant to stains.
database_cross_reference: FMA:83626
has_exact_synonym: chromophobic cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: chromophobe cell
annotated property: definition
annotated target: A cell that is resistant to stains.
database_cross_reference: GOC:tfm

folliculostellate cell
type: Class
subclass of: supporting cell
subclass of: CL_2000004
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002196
definition: An agranular supporting cell of the anterior pituitary (adenohypophysis) that is characterized by a star-like morphology and ability to form follicles. Folliculostellate cells communicate with each other and with endocrine cells via gap junctions.
database_cross_reference: ZFA:0009281
has_exact_synonym: folliculo-stellate cell
has_exact_synonym: pituitary folliculostellate cell
has_related_synonym: FS cell
has_related_synonym: FSC
has_related_synonym: Sox2-positive stem cell
in_subset: human subset
in_subset: mouse subset
comment: Folliculostellate cells are a heterogeneous group of cells rather than a single cell type, with different morphology and gene expression profiles. Due to this heterogeneity, it is unclear if different properties that have been attributed to folliculostellate cells (pluripotent, proliferative, phagocytic) are common in all folliculostellate cells or limited to particular subsets.

Axiom
annotated source: folliculostellate cell
annotated property: definition
annotated target: An agranular supporting cell of the anterior pituitary (adenohypophysis) that is characterized by a star-like morphology and ability to form follicles. Folliculostellate cells communicate with each other and with endocrine cells via gap junctions.
database_cross_reference: JB:jb
database_cross_reference: PMID:10495875
database_cross_reference: PMID:15961560
database_cross_reference: doi:10.23937/2572-407X.1510006

Axiom
annotated source: folliculostellate cell
annotated property: database_cross_reference
annotated target: ZFA:0009281
mapping justification: UnspecifiedMatching

Axiom
annotated source: folliculostellate cell
annotated property: has_exact_synonym
annotated target: folliculo-stellate cell
database_cross_reference: doi:10.23937/2572-407X.1510006

Axiom
annotated source: folliculostellate cell
annotated property: has_exact_synonym
annotated target: pituitary folliculostellate cell
database_cross_reference: PMID:34734454

Axiom
annotated source: folliculostellate cell
annotated property: has_related_synonym
annotated target: FS cell
database_cross_reference: PMID:34734454
has_synonym_type: abbreviation

Axiom
annotated source: folliculostellate cell
annotated property: has_related_synonym
annotated target: FSC
database_cross_reference: doi:10.23937/2572-407X.1510006
has_synonym_type: abbreviation

Axiom
annotated source: folliculostellate cell
annotated property: has_related_synonym
annotated target: Sox2-positive stem cell
database_cross_reference: PMID:34734454

Axiom
annotated source: folliculostellate cell
annotated property: comment
annotated target: Folliculostellate cells are a heterogeneous group of cells rather than a single cell type, with different morphology and gene expression profiles. Due to this heterogeneity, it is unclear if different properties that have been attributed to folliculostellate cells (pluripotent, proliferative, phagocytic) are common in all folliculostellate cells or limited to particular subsets.
database_cross_reference: PMID:18287078
database_cross_reference: PMID:31620083
database_cross_reference: PMID:34734454
database_cross_reference: doi:10.23937/2572-407X.1510006

CL_0000643
type: Class
has obsolescence reason: IAO_0000227
term replaced by: CL_0002085
deprecated: true

Bergmann glial cell
type: Class
subclass of: astrocyte
definition: Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses.
present in taxon: NCBITaxon 9606
database_cross_reference: FMA:54559
database_cross_reference: ZFA:0009282
has_exact_synonym: Bergmann astrocyte
has_exact_synonym: Bergmann glial cell of cerebellum
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: Bergmann glial cell
annotated property: definition
annotated target: Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses.
database_cross_reference: GOC:tfm
database_cross_reference: http://www.neurolex.org/wiki/Category:Bergmann_Glial_Cell

Axiom
annotated source: Bergmann glial cell
annotated property: database_cross_reference
annotated target: ZFA:0009282
mapping justification: UnspecifiedMatching

pituicyte
type: Class
subclass of: CL_0012000
subclass of: CL_2000004
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002198
definition: A glial cell of astrocytic lineage with long processes running parallel to adjacent axons in the proximal infundibulum of the neurohypophysis. These processes form a three-dimensional network among the axons of the hypothalamic neurosecretory cells and are connected by gap junctions which provide for their metabolic coupling. This cell type constitutes most of the nonexcitable tissue in the neurohypophsis; function may include possibly acting as an intermediate in the modulation of oxytocin and vasopressin release. This cell type is highly variable in size and shape and commonly contain lipid droplets and deposits of lipochrome pigment.
database_cross_reference: BTO:0003793
database_cross_reference: FMA:83503
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pituicyte
annotated property: definition
annotated target: A glial cell of astrocytic lineage with long processes running parallel to adjacent axons in the proximal infundibulum of the neurohypophysis. These processes form a three-dimensional network among the axons of the hypothalamic neurosecretory cells and are connected by gap junctions which provide for their metabolic coupling. This cell type constitutes most of the nonexcitable tissue in the neurohypophsis; function may include possibly acting as an intermediate in the modulation of oxytocin and vasopressin release. This cell type is highly variable in size and shape and commonly contain lipid droplets and deposits of lipochrome pigment.
database_cross_reference: ISBN:0412046911
database_cross_reference: ISBN:0517223651
database_cross_reference: PMID:31915267
database_cross_reference: http://en.wikipedia.org/wiki/Pituicyte

basal cell
type: Class
subclass of: epithelial fate stem cell
definition: Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000939
database_cross_reference: FMA:62516
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: basal cell
annotated property: definition
annotated target: Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651

multinucleated giant cell
type: Class
equivalent class: Class
  intersection of: myeloid leukocyte
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001908
  intersection of: Restriction
    on property: participates in
    some values from: GO_0002432
  intersection of: Restriction
    on property: participates in
    some values from: GO_0002544
subclass of: myeloid leukocyte
subclass of: CL_4052002
subclass of: Restriction
  on property: participates in
  some values from: GO_0002432
subclass of: Restriction
  on property: participates in
  some values from: GO_0002544
subclass of: Restriction
  on property: develops from
  some values from: macrophage
definition: A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes.
database_cross_reference: BTO:0003107
database_cross_reference: FMA:83035
database_cross_reference: MESH:D015726
has_exact_synonym: Langerhans giant cell
has_exact_synonym: foreign body giant cell
has_exact_synonym: macrophage polykaryon
has_exact_synonym: multinucleate giant cell
has_exact_synonym: syncytial giant cell
has_related_synonym: MGC
in_subset: blood_and_immune_upper_slim
in_subset: human subset
in_subset: mouse subset
comment: Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this.

Axiom
annotated source: multinucleated giant cell
annotated property: subClassOf
annotated target: myeloid leukocyte
is inferred: true

Axiom
annotated source: multinucleated giant cell
annotated property: definition
annotated target: A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0702022918
database_cross_reference: ISBN:0702024783
database_cross_reference: PMID:33348900
database_cross_reference: Wikipedia:Giant_cell

Axiom
annotated source: multinucleated giant cell
annotated property: has_exact_synonym
annotated target: Langerhans giant cell
database_cross_reference: ISBN:0702022918
database_cross_reference: ISBN:0702024783

Axiom
annotated source: multinucleated giant cell
annotated property: has_exact_synonym
annotated target: foreign body giant cell
database_cross_reference: ISBN:0702022918
database_cross_reference: ISBN:0702024783

Axiom
annotated source: multinucleated giant cell
annotated property: has_exact_synonym
annotated target: macrophage polykaryon
database_cross_reference: ISBN:0702022918
database_cross_reference: ISBN:0702024783

Axiom
annotated source: multinucleated giant cell
annotated property: has_exact_synonym
annotated target: multinucleate giant cell
database_cross_reference: ISBN:0702022918
database_cross_reference: ISBN:0702024783

Axiom
annotated source: multinucleated giant cell
annotated property: has_exact_synonym
annotated target: syncytial giant cell
database_cross_reference: ISBN:0702022918
database_cross_reference: ISBN:0702024783

Axiom
annotated source: multinucleated giant cell
annotated property: has_related_synonym
annotated target: MGC
database_cross_reference: PMID:33348900
has_synonym_type: abbreviation

kidney granular cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002113
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002001
subclass of: protein secreting cell
subclass of: smooth muscle cell
subclass of: CL_1000618
subclass of: Restriction
  on property: capable of
  some values from: GO_0002001
definition: A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation.
present in taxon: NCBITaxon 9606
has_broad_synonym: juxtaglomerular cell
database_cross_reference: FMA:84138
database_cross_reference: ZFA:0005238
has_exact_synonym: JG cell
has_exact_synonym: renin secreting cell
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: kidney granular cell
annotated property: definition
annotated target: A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation.
database_cross_reference: GOC:cvs
database_cross_reference: GOC:tfm
database_cross_reference: PMID:11457727

Axiom
annotated source: kidney granular cell
annotated property: database_cross_reference
annotated target: ZFA:0005238
mapping justification: UnspecifiedMatching

prickle cell
type: Class
subclass of: keratinocyte
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002026
definition: A cell with delicate radiating processes known as desmosomes that form intercellular bridges between other cells of this type. This cell type forms the stratum spinosum (prickle cell layer). A function of this cell is to generate keratin.
present in taxon: NCBITaxon 9606
database_cross_reference: FMA:69059
has_exact_synonym: prickle cell of epidermis
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: prickle cell
annotated property: definition
annotated target: A cell with delicate radiating processes known as desmosomes that form intercellular bridges between other cells of this type. This cell type forms the stratum spinosum (prickle cell layer). A function of this cell is to generate keratin.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544
database_cross_reference: ISBN:0815332181

mesangial cell
type: Class
subclass of: BFO_0000002
subclass of: pericyte
subclass of: Restriction
  on property: develops from
  some values from: mesenchymal stem cell
definition: A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries.
database_cross_reference: BTO:0000853
database_cross_reference: CALOHA:TS-0617
database_cross_reference: FMA:70972
database_cross_reference: MESH:D050527
database_cross_reference: ZFA:0009283
has_exact_synonym: kidney mesangial cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Do all of these cells really develop from some mesenchymal stem cell?

Axiom
annotated source: mesangial cell
annotated property: definition
annotated target: A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries.
database_cross_reference: GOC:tfm
database_cross_reference: http://www.copewithcytokines.de/cope.cgi

Axiom
annotated source: mesangial cell
annotated property: database_cross_reference
annotated target: ZFA:0009283
mapping justification: UnspecifiedMatching

obsolete mucous neck cell
type: Class
definition: OBSOLETE. A mucus-secreting cell, with numerous apical secretory vesicles containing mucins; nucleus are basally displaced; numerous at the neck of mucus secreting glands
term replaced by: CL_0002181
has_broad_synonym: neck cell
in_subset: cellxgene subset
comment: duplicate term
deprecated: true

Axiom
annotated source: obsolete mucous neck cell
annotated property: definition
annotated target: OBSOLETE. A mucus-secreting cell, with numerous apical secretory vesicles containing mucins; nucleus are basally displaced; numerous at the neck of mucus secreting glands
database_cross_reference: GOC:tfm

pinealocyte
type: Class
subclass of: glandular secretory epithelial cell
subclass of: endocrine cell
subclass of: neurecto-epithelial cell
subclass of: CL_0002319
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001905
subclass of: Restriction
  on property: capable of
  some values from: GO_0030187
definition: This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation.
database_cross_reference: BTO:0001068
database_cross_reference: FMA:83417
database_cross_reference: ZFA:0009284
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: pinealocyte
annotated property: definition
annotated target: This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0517223651
database_cross_reference: PMID:16687276
database_cross_reference: http://en.wikipedia.org/wiki/Pinealocyte

Axiom
annotated source: pinealocyte
annotated property: database_cross_reference
annotated target: ZFA:0009284
mapping justification: UnspecifiedMatching

podocyte
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0005751
subclass of: CL_0002522
subclass of: CL_1000450
subclass of: Restriction
  on property: part of
  some values from: UBERON_0005751
definition: A specialized kidney epithelial cell, contained within a glomerulus, that contains "feet" that interdigitate with the "feet" of other podocytes.
present in taxon: NCBITaxon 9606
description: Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in "effacement" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approve…
has_broad_synonym: epithelial cell of visceral layer of glomerular capsule
database_cross_reference: BTO:0002295
database_cross_reference: FMA:70967
database_cross_reference: ZFA:0009285
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000653
has_exact_synonym: glomerular podocyte
has_exact_synonym: glomerular visceral epithelial cell
has_exact_synonym: kidney podocyte
has_exact_synonym: renal podocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: podocyte
annotated property: definition
annotated target: A specialized kidney epithelial cell, contained within a glomerulus, that contains "feet" that interdigitate with the "feet" of other podocytes.
database_cross_reference: GOC:tfm
database_cross_reference: https://doi.org/10.1101/2021.10.10.463829

Axiom
annotated source: podocyte
annotated property: description
annotated target: Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in "effacement" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approve…
database_cross_reference: DOI:10.1038/s41467-022-33748-1
database_cross_reference: DOI:10.1038/s41572-020-0196-7
database_cross_reference: DOI:10.1146/annurev-physiol-020911-153238
database_cross_reference: DOI:10.1159/000481633
database_cross_reference: DOI:10.3389/fcell.2021.771931

Axiom
annotated source: podocyte
annotated property: has_broad_synonym
annotated target: epithelial cell of visceral layer of glomerular capsule
database_cross_reference: FMA:70967

Axiom
annotated source: podocyte
annotated property: database_cross_reference
annotated target: ZFA:0009285
mapping justification: UnspecifiedMatching

Axiom
annotated source: podocyte
annotated property: has_exact_synonym
annotated target: glomerular podocyte
database_cross_reference: FMA:70967

primary oocyte
type: Class
equivalent class: Class
  intersection of: oocyte
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0051321
subclass of: oocyte
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0051321
subclass of: Restriction
  on property: develops from
  some values from: oogonial cell
definition: A primary oocyte is an oocyte that has not completed female meosis I.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000512
database_cross_reference: FMA:18645
has_related_synonym: primary oogonium
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: primary oocyte
annotated property: subClassOf
annotated target: oocyte
is inferred: true

Axiom
annotated source: primary oocyte
annotated property: definition
annotated target: A primary oocyte is an oocyte that has not completed female meosis I.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

secondary oocyte
type: Class
equivalent class: Class
  intersection of: oocyte
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0007147
subclass of: oocyte
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0007147
subclass of: Restriction
  on property: develops from
  some values from: primary oocyte
definition: A secondary oocyte is an oocyte that has not completed meiosis II.
database_cross_reference: BTO:0003094
database_cross_reference: FMA:18646
has_related_synonym: primary oogonium
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: secondary oocyte
annotated property: subClassOf
annotated target: oocyte
is inferred: true

Axiom
annotated source: secondary oocyte
annotated property: definition
annotated target: A secondary oocyte is an oocyte that has not completed meiosis II.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

primary spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001394
  intersection of: Restriction
    on property: capable of
    some values from: GO_0007140
subclass of: spermatocyte
subclass of: eukaryotic cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001394
subclass of: Restriction
  on property: capable of
  some values from: GO_0007140
definition: A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes.
database_cross_reference: BTO:0001115
database_cross_reference: CALOHA:TS-2194
database_cross_reference: FMA:72292
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: primary spermatocyte
annotated property: definition
annotated target: A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

secondary spermatocyte
type: Class
equivalent class: Class
  intersection of: spermatocyte
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001375
  intersection of: Restriction
    on property: capable of
    some values from: GO_0007142
subclass of: spermatocyte
subclass of: eukaryotic cell
subclass of: haploid cell
subclass of: Restriction
  on property: develops from
  some values from: primary spermatocyte
subclass of: Restriction
  on property: capable of
  some values from: GO_0007142
definition: One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids.
database_cross_reference: BTO:0000709
database_cross_reference: CALOHA:TS-2195
database_cross_reference: FBbt:00004941
database_cross_reference: FMA:72293
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: secondary spermatocyte
annotated property: definition
annotated target: One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: secondary spermatocyte
annotated property: database_cross_reference
annotated target: FBbt:00004941
mapping justification: ManualMappingCuration

cuticle secreting cell
type: Class
subclass of: epithelial cell
subclass of: extracellular matrix secreting cell
definition: An epithelial cell that secretes cuticle.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cuticle secreting cell
annotated property: definition
annotated target: An epithelial cell that secretes cuticle.
database_cross_reference: GOC:tfm

eggshell secreting cell
type: Class
subclass of: extracellular matrix secreting cell
subclass of: follicular epithelial cell
definition: An extracellular matrix secreting cell that secretes eggshell.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: eggshell secreting cell
annotated property: definition
annotated target: An extracellular matrix secreting cell that secretes eggshell.
database_cross_reference: GOC:tfm

glycocalyx secreting cell
type: Class
subclass of: extracellular matrix secreting cell
definition: An extracellular matrix secreting cell that secretes glycocalyx.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: glycocalyx secreting cell
annotated property: definition
annotated target: An extracellular matrix secreting cell that secretes glycocalyx.
database_cross_reference: GOC:tfm

distal tip cell (sensu Nematoda)
type: Class
subclass of: mitogenic signaling cell
in_subset: human subset
in_subset: mouse subset

neuroglioblast (sensu Nematoda)
type: Class
subclass of: neuroglioblast (sensu Nematoda and Protostomia)

obsolete valve cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/726
term replaced by: CL_1000147
deprecated: true

obsolete closable valve cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/726
term replaced by: CL_1000147
deprecated: true

obsolete permanently open valve cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/726
term replaced by: CL_1000147
deprecated: true

fenestrated endothelial cell
type: Class
equivalent class: Class
  intersection of: endothelial cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0002064
subclass of: endothelial cell
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0002064
definition: An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues.
description: Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. Overa…
database_cross_reference: ZFA:0009286
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000666
has_exact_synonym: window cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: fenestrated endothelial cell
annotated property: definition
annotated target: An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues.
database_cross_reference: DOI:10.1007/978-3-211-99390-3_133

Axiom
annotated source: fenestrated endothelial cell
annotated property: description
annotated target: Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. Overa…
database_cross_reference: DOI:10.1002/ar.1092200109
database_cross_reference: DOI:10.1016/0306-4522(86)90162-4
database_cross_reference: DOI:10.1016/j.devcel.2012.11.003
database_cross_reference: DOI:10.1038/s41467-022-31571-2
database_cross_reference: DOI:10.1152/ajprenal.90601.2008

Axiom
annotated source: fenestrated endothelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009286
mapping justification: UnspecifiedMatching

collagen secreting cell
type: Class
subclass of: extracellular matrix secreting cell
definition: An extracellular matrix secreting cell that secretes collagen.
database_cross_reference: ZFA:0009287
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: collagen secreting cell
annotated property: definition
annotated target: An extracellular matrix secreting cell that secretes collagen.
database_cross_reference: GOC:tfm

Axiom
annotated source: collagen secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009287
mapping justification: UnspecifiedMatching

obsolete parenchymal cell
type: Class
definition: OBSOLETE: The cell characteristic of an organ, as distinguished from associated connective or supporting tissues.
database_cross_reference: BTO:0002174
database_cross_reference: FMA:84638
comment: OBSOLETE: Term was made obsolete to avoid confusion with plant parenchymal cell. Cell type has a similar but slightly different meaning in botany (plants): see PO:0000074.
deprecated: true

Axiom
annotated source: obsolete parenchymal cell
annotated property: definition
annotated target: OBSOLETE: The cell characteristic of an organ, as distinguished from associated connective or supporting tissues.
database_cross_reference: ISBN:0471245208

pericyte
type: Class
subclass of: contractile cell
subclass of: supporting cell
subclass of: CL_0002320
subclass of: CL_0008034
definition: An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0002441
database_cross_reference: FMA:63174
database_cross_reference: ZFA:0009112
has_exact_synonym: ARC
has_exact_synonym: adventitial reticular cell
has_exact_synonym: cell of Rouget
has_exact_synonym: pericyte cell
has_exact_synonym: pericyte of Rouget
has_related_synonym: adventitial cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A.

Axiom
annotated source: pericyte
annotated property: definition
annotated target: An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells.
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544
database_cross_reference: MESH:D020286
database_cross_reference: PMID:16807374
database_cross_reference: PMID:17986482
database_cross_reference: PMID:20024907

Axiom
annotated source: pericyte
annotated property: database_cross_reference
annotated target: ZFA:0009112
mapping justification: UnspecifiedMatching

Axiom
annotated source: pericyte
annotated property: has_exact_synonym
annotated target: ARC
database_cross_reference: PMID:17986482

primordial germ cell
type: Class
equivalent class: Class
  intersection of: germ line cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000922
  intersection of: Restriction
    on property: capable of
    some values from: GO_0048870
subclass of: germ line cell
subclass of: motile cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000922
definition: A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells.
database_cross_reference: FMA:70567
database_cross_reference: ZFA:0009288
has_exact_synonym: gonocyte
has_exact_synonym: primitive germ cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: primordial germ cell
annotated property: subClassOf
annotated target: germ line cell
is inferred: true

Axiom
annotated source: primordial germ cell
annotated property: subClassOf
annotated target: motile cell
is inferred: true

Axiom
annotated source: primordial germ cell
annotated property: definition
annotated target: A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:1381289

Axiom
annotated source: primordial germ cell
annotated property: database_cross_reference
annotated target: ZFA:0009288
mapping justification: UnspecifiedMatching

centripetally migrating follicle cell
type: Class
subclass of: follicle cell of egg chamber
definition: A follicle cell that migrates from the dorso-anterior part of the oocyte associated follicular epithelium, in between the nurse cells and the oocyte, and participates in the formation of the operculum.
database_cross_reference: FBbt:00004906
has_exact_synonym: centripetal follicle cell

Axiom
annotated source: centripetally migrating follicle cell
annotated property: definition
annotated target: A follicle cell that migrates from the dorso-anterior part of the oocyte associated follicular epithelium, in between the nurse cells and the oocyte, and participates in the formation of the operculum.
database_cross_reference: PMID:36807509

Axiom
annotated source: centripetally migrating follicle cell
annotated property: database_cross_reference
annotated target: FBbt:00004906
mapping justification: ManualMappingCuration

obsolete tracheary element
type: Class
definition: Obsolete. Use PO:0000290 from Plant Ontology instead. A water conducting cell, tracheid or vessel member.
term replaced by: PO_0000290
deprecated: true

Axiom
annotated source: obsolete tracheary element
annotated property: definition
annotated target: Obsolete. Use PO:0000290 from Plant Ontology instead. A water conducting cell, tracheid or vessel member.
database_cross_reference: ISBN:0471245208

Kenyon cell
type: Class
subclass of: CNS neuron (sensu Nematoda and Protostomia)
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001058
definition: An intrinsic neuron of the mushroom body of arthropods and annelids. They have tightly packed, cytoplasm-poor cell bodies.
has_broad_synonym: mushroom body intrinsic neuron
database_cross_reference: FBbt:00003686
has_related_synonym: globuli cell

Axiom
annotated source: Kenyon cell
annotated property: definition
annotated target: An intrinsic neuron of the mushroom body of arthropods and annelids. They have tightly packed, cytoplasm-poor cell bodies.
database_cross_reference: doi:10.1016/S1467-8039(03)00009-4

Axiom
annotated source: Kenyon cell
annotated property: database_cross_reference
annotated target: FBbt:00003686
mapping justification: ManualMappingCuration

interfollicle cell
type: Class
subclass of: follicle cell of egg chamber
definition: A follicle cell that is part of the stalk connecting adjacent egg chambers.
database_cross_reference: FBbt:00004910
has_exact_synonym: stalk cell
has_exact_synonym: stalk follicle cell

Axiom
annotated source: interfollicle cell
annotated property: definition
annotated target: A follicle cell that is part of the stalk connecting adjacent egg chambers.
database_cross_reference: PMID:36531940

Axiom
annotated source: interfollicle cell
annotated property: database_cross_reference
annotated target: FBbt:00004910
mapping justification: ManualMappingCuration

female gamete
type: Class
subclass of: female germ cell
subclass of: gamete
definition: A mature sexual reproductive cell of the female germline.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: female gamete
annotated property: subClassOf
annotated target: female germ cell
is inferred: true

Axiom
annotated source: female gamete
annotated property: definition
annotated target: A mature sexual reproductive cell of the female germline.
database_cross_reference: GOC:tfm

cap cell
type: Class
subclass of: supporting cell (sensu Nematoda and Protostomia)
database_cross_reference: BTO:0001033
in_subset: human subset
in_subset: mouse subset

gut absorptive cell
type: Class
subclass of: eukaryotic cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0001277
definition: Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules.
database_cross_reference: ZFA:0009289
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: gut absorptive cell
annotated property: definition
annotated target: Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules.
database_cross_reference: JB:jb

Axiom
annotated source: gut absorptive cell
annotated property: database_cross_reference
annotated target: ZFA:0009289
mapping justification: UnspecifiedMatching

commissural neuron
type: Class
subclass of: CL_2000029
definition: A neuron with soma location in the central nervous system that project its axon to the contralateral side of a central nervous system. This neuron can have its soma in the spinal cord, in the hemisphere of the brain, in the retina or in the ventral nerve cord of invertebrates.
in_subset: human subset
in_subset: mouse subset
comment: Historically, commissural neurons, particularly in the spinal cord, have been used as a model to understand axon guidance during development.

Axiom
annotated source: commissural neuron
annotated property: definition
annotated target: A neuron with soma location in the central nervous system that project its axon to the contralateral side of a central nervous system. This neuron can have its soma in the spinal cord, in the hemisphere of the brain, in the retina or in the ventral nerve cord of invertebrates.
database_cross_reference: PMID:17560562
database_cross_reference: PMID:31693445

Axiom
annotated source: commissural neuron
annotated property: comment
annotated target: Historically, commissural neurons, particularly in the spinal cord, have been used as a model to understand axon guidance during development.
database_cross_reference: PMID:25960414
database_cross_reference: PMID:27532244
database_cross_reference: PMID:31514748
database_cross_reference: PMID:33438755

glutamatergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0061535
subclass of: secretory cell
subclass of: neuron
subclass of: Restriction
  on property: capable of
  some values from: GO_0061535
definition: A neuron that is capable of some neurotansmission by glutamate secretion.
present in taxon: NCBITaxon 9606
database_cross_reference: FBbt:00100291
database_cross_reference: WBbt:0006829
database_cross_reference: ZFA:0009290
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: glutamatergic neuron
annotated property: database_cross_reference
annotated target: FBbt:00100291
mapping justification: ManualMappingCuration

Axiom
annotated source: glutamatergic neuron
annotated property: database_cross_reference
annotated target: ZFA:0009290
mapping justification: UnspecifiedMatching

muscle precursor cell
type: Class
equivalent class: Class
  intersection of: CL_0011115
  intersection of: Restriction
    on property: develops into
    some values from: muscle cell
subclass of: BFO_0000002
subclass of: non-terminally differentiated cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: develops from
  some values from: mesodermal cell
subclass of: Restriction
  on property: develops into
  some values from: muscle cell
definition: A non-terminally differentiated cell that is capable of developing into a muscle cell.
database_cross_reference: ZFA:0009291
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: muscle precursor cell
annotated property: definition
annotated target: A non-terminally differentiated cell that is capable of developing into a muscle cell.
database_cross_reference: GOC:add

Axiom
annotated source: muscle precursor cell
annotated property: database_cross_reference
annotated target: ZFA:0009291
mapping justification: UnspecifiedMatching

radial glial cell
type: Class
subclass of: glial cell
subclass of: Restriction
  on property: develops from
  some values from: neurecto-epithelial cell
definition: A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration.
database_cross_reference: ZFA:0009292
has_narrow_synonym: forebrain radial glial cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of radial glial cells acting as neural progenitors throughout life.

Axiom
annotated source: radial glial cell
annotated property: definition
annotated target: A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration.
database_cross_reference: GOC:dph

Axiom
annotated source: radial glial cell
annotated property: database_cross_reference
annotated target: ZFA:0009292
mapping justification: UnspecifiedMatching

M cell of gut
type: Class
subclass of: transporting cell
subclass of: CL_0002563
subclass of: Restriction
  on property: part of
  some values from: UBERON_0004693
definition: An absorptive cell of the gut epithelium that endocytoses microorganisms and intact macromolecules from the gut lumen and transports them to the subepithelial space where they are presented to antigen-presenting cells and lymphocytes.
present in taxon: NCBITaxon 9606
description: M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. These morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
has_broad_synonym: M cell
database_cross_reference: BTO:0003600
database_cross_reference: FMA:62929
database_cross_reference: ZFA:0009293
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000682
has_exact_synonym: M-cell
has_exact_synonym: microfold cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Should double check and see if M cells are particular to a specific region.

Axiom
annotated source: M cell of gut
annotated property: definition
annotated target: An absorptive cell of the gut epithelium that endocytoses microorganisms and intact macromolecules from the gut lumen and transports them to the subepithelial space where they are presented to antigen-presenting cells and lymphocytes.
database_cross_reference: GOC:jb
database_cross_reference: GOC:tfm

Axiom
annotated source: M cell of gut
annotated property: description
annotated target: M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. These morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1038/nature08529
database_cross_reference: DOI:10.1093/jb/mvv121
database_cross_reference: DOI:10.1136/gut.47.5.735
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK534232/
database_cross_reference: https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell

Axiom
annotated source: M cell of gut
annotated property: database_cross_reference
annotated target: ZFA:0009293
mapping justification: UnspecifiedMatching

ependymoglial cell
type: Class
subclass of: astrocyte
definition: A cell that transports hormones from neurosecretory cells. This nerve cell is characterized by bipolar shape and endfeet that contact a basal lamina around blood vessels, and/or the pia mater or vitreous body of the eye and additionally contact the ventricular surface or sub-retinal space.
database_cross_reference: MESH:D063928
database_cross_reference: ZFA:0009294
has_exact_synonym: ependymal astrocyte
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: ependymoglial cell
annotated property: definition
annotated target: A cell that transports hormones from neurosecretory cells. This nerve cell is characterized by bipolar shape and endfeet that contact a basal lamina around blood vessels, and/or the pia mater or vitreous body of the eye and additionally contact the ventricular surface or sub-retinal space.
database_cross_reference: JB:jb
database_cross_reference: http://neurolex.org/wiki/Category:Ependymoglial_Cell

Axiom
annotated source: ependymoglial cell
annotated property: database_cross_reference
annotated target: ZFA:0009294
mapping justification: UnspecifiedMatching

littoral cell of liver
type: Class
subclass of: mesothelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002107
in_subset: human subset
in_subset: mouse subset

obsolete meristematic cell
type: Class
definition: Obsolete. Use PO:0004010 from Plant Ontology instead. A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall.
term replaced by: PO_0004010
deprecated: true

Axiom
annotated source: obsolete meristematic cell
annotated property: definition
annotated target: Obsolete. Use PO:0004010 from Plant Ontology instead. A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall.
database_cross_reference: PO:0004010

cerebrospinal fluid secreting cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0033326
subclass of: neurecto-epithelial cell
subclass of: CL_1100001
subclass of: Restriction
  on property: develops from
  some values from: migratory neural crest cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0033326
definition: A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid.
database_cross_reference: ZFA:0009295
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cerebrospinal fluid secreting cell
annotated property: definition
annotated target: A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid.
database_cross_reference: GOC:tfm

Axiom
annotated source: cerebrospinal fluid secreting cell
annotated property: database_cross_reference
annotated target: ZFA:0009295
mapping justification: UnspecifiedMatching

R1 photoreceptor cell
type: Class
subclass of: visible light photoreceptor cell
subclass of: CL_2000019
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000971
database_cross_reference: FBbt:00004213
has_exact_synonym: R1 cell

Axiom
annotated source: R1 photoreceptor cell
annotated property: database_cross_reference
annotated target: FBbt:00004213
mapping justification: ManualMappingCuration

perijunctional fibroblast
type: Class
subclass of: fibroblast
subclass of: supporting cell
definition: A fibroblast-like cell that provides support at neuromuscular junctions in vertebrates and are localized outside the synaptic basal lamina.
database_cross_reference: ZFA:0009296
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: perijunctional fibroblast
annotated property: definition
annotated target: A fibroblast-like cell that provides support at neuromuscular junctions in vertebrates and are localized outside the synaptic basal lamina.
database_cross_reference: JB:jb

Axiom
annotated source: perijunctional fibroblast
annotated property: database_cross_reference
annotated target: ZFA:0009296
mapping justification: UnspecifiedMatching

myoendocrine cell
type: Class
subclass of: endocrine cell
definition: A cell with both myofibrils and secretory granules.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: myoendocrine cell
annotated property: definition
annotated target: A cell with both myofibrils and secretory granules.
database_cross_reference: JB:jb

R2 photoreceptor cell
type: Class
subclass of: visible light photoreceptor cell
subclass of: CL_2000019
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000971
database_cross_reference: FBbt:00004215
has_exact_synonym: R2 cell

Axiom
annotated source: R2 photoreceptor cell
annotated property: database_cross_reference
annotated target: FBbt:00004215
mapping justification: ManualMappingCuration

stellate interneuron
type: Class
equivalent class: Class
  intersection of: interneuron
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0070010
subclass of: interneuron
subclass of: stellate neuron
definition: Any interneuron that has characteristic some stellate morphology.
database_cross_reference: ZFA:0009297
in_subset: BDS subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: stellate interneuron
annotated property: definition
annotated target: Any interneuron that has characteristic some stellate morphology.
database_cross_reference: FBC:Autogenerated

Axiom
annotated source: stellate interneuron
annotated property: database_cross_reference
annotated target: ZFA:0009297
mapping justification: UnspecifiedMatching

terminal Schwann cell
type: Class
subclass of: supporting cell
subclass of: CL_0002376
definition: A neuroglial cell of the peripheral nervous system inside the basal lamina of the neuromuscular junction providing chemical and physical support to the synapse.
has_broad_synonym: Schwann cell
database_cross_reference: ZFA:0009298
has_exact_synonym: perisynaptic Schwann cell
has_exact_synonym: teloglia
has_related_synonym: tSC
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: terminal Schwann cell
annotated property: definition
annotated target: A neuroglial cell of the peripheral nervous system inside the basal lamina of the neuromuscular junction providing chemical and physical support to the synapse.
database_cross_reference: JB:jb
database_cross_reference: PMID:16136171

Axiom
annotated source: terminal Schwann cell
annotated property: database_cross_reference
annotated target: ZFA:0009298
mapping justification: UnspecifiedMatching

Axiom
annotated source: terminal Schwann cell
annotated property: has_exact_synonym
annotated target: perisynaptic Schwann cell
database_cross_reference: PMID:18803315

Axiom
annotated source: terminal Schwann cell
annotated property: has_exact_synonym
annotated target: teloglia
database_cross_reference: PMID:18803315

Axiom
annotated source: terminal Schwann cell
annotated property: has_related_synonym
annotated target: tSC
database_cross_reference: PMID:18803315
has_synonym_type: abbreviation

neurogliaform cell
type: Class
equivalent class: Class
  intersection of: interneuron
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0070001
subclass of: interneuron
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0070001
definition: An interneuron that has spider-like appearance with a small round soma, a large number (7-10) of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts.
database_cross_reference: ZFA:0009299
has_exact_synonym: NGF cell
has_exact_synonym: neuroglioform cell
has_exact_synonym: spiderweb cell
in_subset: BDS subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: neurogliaform cell
annotated property: definition
annotated target: An interneuron that has spider-like appearance with a small round soma, a large number (7-10) of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts.
database_cross_reference: JB:jb
database_cross_reference: PMID:17122314

Axiom
annotated source: neurogliaform cell
annotated property: database_cross_reference
annotated target: ZFA:0009299
mapping justification: UnspecifiedMatching

Axiom
annotated source: neurogliaform cell
annotated property: has_exact_synonym
annotated target: NGF cell
database_cross_reference: PMID:18568015

Axiom
annotated source: neurogliaform cell
annotated property: has_exact_synonym
annotated target: neuroglioform cell
database_cross_reference: PMID:3235828

R3 photoreceptor cell
type: Class
subclass of: visible light photoreceptor cell
subclass of: CL_2000019
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000971
database_cross_reference: FBbt:00004217
has_exact_synonym: R3 cell

Axiom
annotated source: R3 photoreceptor cell
annotated property: database_cross_reference
annotated target: FBbt:00004217
mapping justification: ManualMappingCuration

Cajal-Retzius cell
type: Class
subclass of: CL_2000029
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0070006
subclass of: Restriction
  on property: has soma location
  some values from: UBERON_0010403
definition: A neuron of the human embryonic marginal zone which display, as a salient feature, radial ascending processes that contact the pial surface, and a horizontal axon plexus located in the deep marginal zone. One feature of these cells in mammals is that they express the Reelin gene.
contributor: https://orcid.org/0000-0001-7258-9596
database_cross_reference: ZFA:0009300
has_exact_synonym: CR cells
has_exact_synonym: Horizontal cells of Cajal
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: While previously called 'pioneer neurons' of the marginal zone, Cajal-Retzius cells are differentiated from pioneer neurons (which are Reln-negative) by their Reln-immunoreactivity.

Axiom
annotated source: Cajal-Retzius cell
annotated property: definition
annotated target: A neuron of the human embryonic marginal zone which display, as a salient feature, radial ascending processes that contact the pial surface, and a horizontal axon plexus located in the deep marginal zone. One feature of these cells in mammals is that they express the Reelin gene.
database_cross_reference: PMID:10600995
database_cross_reference: PMID:9728912

Axiom
annotated source: Cajal-Retzius cell
annotated property: database_cross_reference
annotated target: ZFA:0009300
mapping justification: UnspecifiedMatching

Axiom
annotated source: Cajal-Retzius cell
annotated property: has_exact_synonym
annotated target: CR cells
database_cross_reference: WikipediaVersioned:Cajal–Retzius_cell&oldid=1032081753

Axiom
annotated source: Cajal-Retzius cell
annotated property: has_exact_synonym
annotated target: Horizontal cells of Cajal
database_cross_reference: WikipediaVersioned:Cajal–Retzius_cell&oldid=1032081753

Axiom
annotated source: Cajal-Retzius cell
annotated property: comment
annotated target: While previously called 'pioneer neurons' of the marginal zone, Cajal-Retzius cells are differentiated from pioneer neurons (which are Reln-negative) by their Reln-immunoreactivity.
database_cross_reference: PMID:10600995

PP cell
type: Class
subclass of: enteroendocrine cell
subclass of: peptide hormone secreting cell
definition: A cell that stores and secretes pancreatic polypeptide hormone.
description: PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: FMA:62938
database_cross_reference: FMA:83409
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000696
has_exact_synonym: type F enteroendocrine cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: PP cell
annotated property: definition
annotated target: A cell that stores and secretes pancreatic polypeptide hormone.
database_cross_reference: GOC:tfm
database_cross_reference: JB:jb
database_cross_reference: PMID:15153415

Axiom
annotated source: PP cell
annotated property: description
annotated target: PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to some subtypes and species, and so should not be considered definitional.)
database_cross_reference: DOI:10.1016/j.febslet.2014.07.005
database_cross_reference: DOI:10.1016/j.mce.2015.06.028
database_cross_reference: DOI:10.1038/s41580-020-00317-7
database_cross_reference: DOI:10.1210/jc.2003-030630
database_cross_reference: DOI:10.1369/00221554155835

R4 photoreceptor cell
type: Class
subclass of: visible light photoreceptor cell
subclass of: CL_2000019
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000971
database_cross_reference: FBbt:00004219
has_exact_synonym: R4 cell

Axiom
annotated source: R4 photoreceptor cell
annotated property: database_cross_reference
annotated target: FBbt:00004219
mapping justification: ManualMappingCuration

obsolete paraganglial cell
type: Class
deprecated: true

paraganglial type 1 cell
type: Class
subclass of: neuroendocrine cell
definition: A type of glomus or chief cell, is sensitive to hypoxia and produce catecholamines.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: paraganglial type 1 cell
annotated property: definition
annotated target: A type of glomus or chief cell, is sensitive to hypoxia and produce catecholamines.
database_cross_reference: GOC:tfm

dopaminergic neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: GO_0061527
subclass of: CL_4033050
subclass of: Restriction
  on property: capable of
  some values from: GO_0061527
definition: A neuron that releases dopamine as a neurotransmitter.
database_cross_reference: BTO:0004032
database_cross_reference: FBbt:00005131
database_cross_reference: FMA:84787
database_cross_reference: MESH:D059290
database_cross_reference: WBbt:0006746
database_cross_reference: ZFA:0009301
has_exact_synonym: dopaminergic cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: dopaminergic neuron
annotated property: definition
annotated target: A neuron that releases dopamine as a neurotransmitter.
database_cross_reference: GOC:dhill

Axiom
annotated source: dopaminergic neuron
annotated property: database_cross_reference
annotated target: FBbt:00005131
mapping justification: ManualMappingCuration

Axiom
annotated source: dopaminergic neuron
annotated property: database_cross_reference
annotated target: ZFA:0009301
mapping justification: UnspecifiedMatching

paraganglia type 2 cell
type: Class
subclass of: supporting cell
definition: Supports paraganglial type 1 cell.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: paraganglia type 2 cell
annotated property: definition
annotated target: Supports paraganglial type 1 cell.
database_cross_reference: JB:jb

R5 photoreceptor cell
type: Class
subclass of: visible light photoreceptor cell
subclass of: CL_2000019
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000971
database_cross_reference: FBbt:00004221
has_exact_synonym: R5 cell

Axiom
annotated source: R5 photoreceptor cell
annotated property: database_cross_reference
annotated target: FBbt:00004221
mapping justification: ManualMappingCuration

sustentacular cell
type: Class
subclass of: supporting cell
definition: Cell that provides some or all mechanical, nutritional and phagocytic support to their neighbors.
database_cross_reference: BTO:0002315
database_cross_reference: ZFA:0009302
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: sustentacular cell
annotated property: definition
annotated target: Cell that provides some or all mechanical, nutritional and phagocytic support to their neighbors.
database_cross_reference: JB:jb

Axiom
annotated source: sustentacular cell
annotated property: database_cross_reference
annotated target: ZFA:0009302
mapping justification: UnspecifiedMatching

endothelial tip cell
type: Class
subclass of: blood vessel endothelial cell
definition: A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels.
database_cross_reference: ZFA:0009303
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: endothelial tip cell
annotated property: definition
annotated target: A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels.
database_cross_reference: PMID:15376331

Axiom
annotated source: endothelial tip cell
annotated property: database_cross_reference
annotated target: ZFA:0009303
mapping justification: UnspecifiedMatching

R6 photoreceptor cell
type: Class
subclass of: visible light photoreceptor cell
subclass of: CL_2000019
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000971
database_cross_reference: FBbt:00004223
has_exact_synonym: R6 cell

Axiom
annotated source: R6 photoreceptor cell
annotated property: database_cross_reference
annotated target: FBbt:00004223
mapping justification: ManualMappingCuration

choroid plexus epithelial cell
type: Class
equivalent class: Class
  intersection of: ependymal cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0003911
subclass of: ependymal cell
subclass of: brush border epithelial cell
subclass of: transporting cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0003911
subclass of: Restriction
  on property: capable of
  some values from: GO_0033326
definition: A specialized ependymal cell that is part of the choroid plexus epithelium, responsible for producing cerebrospinal fluid (CSF) by selectively filtering and modifying blood plasma components before secreting it into the brain and spinal cord. This cell is characterized by a brush border on its apical surface, which enhances the secretion of CSF.
present in taxon: NCBITaxon 9606
date: 2023-08-04T08:48:30Z
has_broad_synonym: choroid plexus cell
database_cross_reference: FMA:70549
database_cross_reference: ZFA:0009304
has_exact_synonym: epithelial cell of choroid plexus
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: A choroid plexus epithelial cell possesses non-motile 9+0 cilia. While these cilia can exhibit transient motility during development, they generally do not contribute significantly to the directional flow of cerebrospinal fluid (CSF). Instead, they are primarily involved in sensory functions.

Axiom
annotated source: choroid plexus epithelial cell
annotated property: definition
annotated target: A specialized ependymal cell that is part of the choroid plexus epithelium, responsible for producing cerebrospinal fluid (CSF) by selectively filtering and modifying blood plasma components before secreting it into the brain and spinal cord. This cell is characterized by a brush border on its apical surface, which enhances the secretion of CSF.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: JB:jb
database_cross_reference: PMID:15561411
database_cross_reference: PMID:9550134

Axiom
annotated source: choroid plexus epithelial cell
annotated property: has_broad_synonym
annotated target: choroid plexus cell
database_cross_reference: DOI:10.1101/2022.10.12.511898

Axiom
annotated source: choroid plexus epithelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009304
mapping justification: UnspecifiedMatching

Axiom
annotated source: choroid plexus epithelial cell
annotated property: comment
annotated target: A choroid plexus epithelial cell possesses non-motile 9+0 cilia. While these cilia can exhibit transient motility during development, they generally do not contribute significantly to the directional flow of cerebrospinal fluid (CSF). Instead, they are primarily involved in sensory functions.
database_cross_reference: PMID:25729351

R7 photoreceptor cell
type: Class
subclass of: UV sensitive photoreceptor cell
subclass of: CL_2000019
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000971
database_cross_reference: FBbt:00004225
has_exact_synonym: R7 cell

Axiom
annotated source: R7 photoreceptor cell
annotated property: database_cross_reference
annotated target: FBbt:00004225
mapping justification: ManualMappingCuration

leptomeningeal cell
type: Class
equivalent class: Class
  intersection of: extracellular matrix secreting cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0003210
subclass of: extracellular matrix secreting cell
subclass of: CL_0002319
subclass of: Restriction
  on property: part of
  some values from: UBERON_0003210
definition: Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus.
database_cross_reference: ZFA:0009305
has_related_synonym: leptomemingeal cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: leptomeningeal cell
annotated property: subClassOf
annotated target: extracellular matrix secreting cell
is inferred: true

Axiom
annotated source: leptomeningeal cell
annotated property: definition
annotated target: Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus.
database_cross_reference: JB:jb

Axiom
annotated source: leptomeningeal cell
annotated property: database_cross_reference
annotated target: ZFA:0009305
mapping justification: UnspecifiedMatching

R8 photoreceptor cell
type: Class
subclass of: visible light photoreceptor cell
subclass of: CL_2000019
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000971
database_cross_reference: FBbt:00004227
has_exact_synonym: R8 cell

Axiom
annotated source: R8 photoreceptor cell
annotated property: database_cross_reference
annotated target: FBbt:00004227
mapping justification: ManualMappingCuration

neurecto-epithelial cell
type: Class
equivalent class: Class
  intersection of: CL_0002077
  intersection of: Restriction
    on property: develops from
    some values from: neurectodermal cell
subclass of: columnar/cuboidal epithelial cell
subclass of: CL_0002077
subclass of: Restriction
  on property: develops from
  some values from: neurectodermal cell
definition: Epithelial cells derived from neural plate and neural crest.
has_broad_synonym: neuroepithelial cell
database_cross_reference: BTO:0004301
database_cross_reference: FMA:70557
in_subset: human subset
in_subset: mouse subset
comment: The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098).

Axiom
annotated source: neurecto-epithelial cell
annotated property: definition
annotated target: Epithelial cells derived from neural plate and neural crest.
database_cross_reference: GOC:tfm

cumulus granulosa cell
type: Class
subclass of: protein secreting cell
subclass of: granulosa cell
subclass of: UBERON_0004120
subclass of: Restriction
  on property: develops from
  some values from: CL_4033084
definition: Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0002236
database_cross_reference: MESH:D054885
has_exact_synonym: cumulus cell
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: cumulus granulosa cell
annotated property: definition
annotated target: Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle.
database_cross_reference: GOC:tfm
database_cross_reference: http://www.copewithcytokines.org/cope.cgi

stratum granulosum cell
type: Class
equivalent class: Class
  intersection of: epidermal cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002069
subclass of: epidermal cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002069
definition: Any epidermal cell that is part of some stratum granulosum of epidermis.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: stratum granulosum cell
annotated property: definition
annotated target: Any epidermal cell that is part of some stratum granulosum of epidermis.
database_cross_reference: FBC:Autogenerated

corona radiata cell
type: Class
subclass of: cumulus granulosa cell
in_subset: human subset
in_subset: mouse subset

CL_0000714
type: Class
has obsolescence reason: IAO_0000227
term replaced by: cardiac muscle myoblast
deprecated: true

embryonic crystal cell
type: Class
subclass of: crystal cell
subclass of: CL_0011008
definition: A crystal cell that derives from the embryonic head mesoderm.
database_cross_reference: FBbt:00001690

Axiom
annotated source: embryonic crystal cell
annotated property: database_cross_reference
annotated target: FBbt:00001690
mapping justification: ManualMappingCuration

lymph gland crystal cell
type: Class
subclass of: crystal cell
subclass of: lymph gland hemocyte
definition: A crystal cell that derives from the larval lymph gland.

obsolete fusimotor neuron
type: Class
definition: OBSOLETE. A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons.
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1364
term replaced by: CL_0008037
comment: Term merged into CL:0008037.
deprecated: true

Axiom
annotated source: obsolete fusimotor neuron
annotated property: definition
annotated target: OBSOLETE. A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons.
database_cross_reference: PMID:15582775

compound eye cone cell
type: Class
subclass of: crystallin accumulating cell
subclass of: CL_0002319
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000971
definition: A cell of an ommatidium that secretes lens materials.
database_cross_reference: FBbt:00004193
has_exact_synonym: Semper cell
has_related_synonym: cone cell (sensu Endopterygota)
comment: Not to be confused with the Semper cells of the Semper organ found in gastropods.

Axiom
annotated source: compound eye cone cell
annotated property: definition
annotated target: A cell of an ommatidium that secretes lens materials.
database_cross_reference: PMID:34343526
database_cross_reference: doi:10.1017/CBO9780511818202.023

Axiom
annotated source: compound eye cone cell
annotated property: database_cross_reference
annotated target: FBbt:00004193
mapping justification: ManualMappingCuration

Axiom
annotated source: compound eye cone cell
annotated property: comment
annotated target: Not to be confused with the Semper cells of the Semper organ found in gastropods.
database_cross_reference: doi:10.1242/jcs.s3-105.71.331

posterior cone cell (sensu Endopterygota)
type: Class
subclass of: compound eye cone cell

anterior cone cell (sensu Endopterygota)
type: Class
subclass of: compound eye cone cell

equatorial cone cell (sensu Endopterygota)
type: Class
subclass of: compound eye cone cell

cystoblast
type: Class
subclass of: eukaryotic cell
subclass of: germ cell
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 6656

somatic stem cell
type: Class
equivalent class: Class
  intersection of: stem cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0048103
subclass of: stem cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0048103
definition: A stem cell that can give rise to cell types of the body other than those of the germ-line.
database_cross_reference: CALOHA:TS-2086
database_cross_reference: MESH:D053687
database_cross_reference: ZFA:0009307
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: somatic stem cell
annotated property: definition
annotated target: A stem cell that can give rise to cell types of the body other than those of the germ-line.
database_cross_reference: GO:0048103

Axiom
annotated source: somatic stem cell
annotated property: database_cross_reference
annotated target: ZFA:0009307
mapping justification: UnspecifiedMatching

heterocyst
type: Class
subclass of: prokaryotic cell
subclass of: nitrogen fixing cell
definition: A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions.
database_cross_reference: BTO:0000600

Axiom
annotated source: heterocyst
annotated property: definition
annotated target: A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions.
database_cross_reference: MA:ma

nitrogen fixing cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0009399
subclass of: cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0009399
definition: Any cell that is capable of some nitrogen fixation.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: nitrogen fixing cell
annotated property: definition
annotated target: Any cell that is capable of some nitrogen fixation.
database_cross_reference: FBC:Autogenerated

chlamydospore
type: Class
subclass of: fungal asexual spore
definition: An asexual 1-celled spore (primarily for perennation, not dissemination). Originates endogenously and singly within part of a pre-existing cell by the contraction of the protoplast. Possesses an inner secondary and often thickened hyaline or brown wall, usually impregnated with hydrophobic material.
comment: Considering obsoleting as sometimes used to refer to protozoans too. But reference indicates term was intended for fungus.

Axiom
annotated source: chlamydospore
annotated property: definition
annotated target: An asexual 1-celled spore (primarily for perennation, not dissemination). Originates endogenously and singly within part of a pre-existing cell by the contraction of the protoplast. Possesses an inner secondary and often thickened hyaline or brown wall, usually impregnated with hydrophobic material.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:085199377X

obsolete primary pigment cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1930
comment: Obsoleted as this level of precision is deemed unnecessary for CL. Consider using either the more general CL:0001658 or, if you need to refer to primary pigment cells specifically, a term from a taxon-specific ontology such as FBbt:00004231.
deprecated: true

obsolete secondary pigment cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1930
comment: Obsoleted as this level of precision is deemed unnecessary for CL. Consider using either the more general CL:0001658 or, if you need to refer to secondary pigment cells specifically, a term from a taxon-specific ontology such as FBbt:00004232.
deprecated: true

obsolete tertiary pigment cell
type: Class
term tracker item: https://github.com/obophenotype/cell-ontology/issues/1930
comment: Obsoleted as this level of precision is deemed unnecessary for CL. Consider using either the more general CL:0001658 or, if you need to refer to tertiary pigment cells specifically, a term from a taxon-specific ontology such as FBbt:00004233.
deprecated: true

leading edge cell
type: Class
subclass of: epithelial cell
definition: A cell at the front of a migrating epithelial sheet.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: leading edge cell
annotated property: definition
annotated target: A cell at the front of a migrating epithelial sheet.
database_cross_reference: MA:ma

urothelial cell
type: Class
equivalent class: Class
  intersection of: transitional epithelial cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0000365
subclass of: transitional epithelial cell
subclass of: Restriction
  on property: part of
  some values from: UBERON_0000365
definition: A cell of a layer of transitional epithelium in the wall of the proximal urethra, bladder, ureter or renal pelvis, external to the lamina propria.
description: Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis. (This extended descripti…
database_cross_reference: FMA:84127
database_cross_reference: ZFA:0009308
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000731
has_narrow_synonym: urinary tract transitional epithelial cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: urothelial cell
annotated property: definition
annotated target: A cell of a layer of transitional epithelium in the wall of the proximal urethra, bladder, ureter or renal pelvis, external to the lamina propria.
database_cross_reference: GOC:tfm
database_cross_reference: MA:ma
database_cross_reference: doi:10.1038/s41385-022-00565-0

Axiom
annotated source: urothelial cell
annotated property: description
annotated target: Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis. (This extended descripti…
database_cross_reference: DOI:10.1002/nau.22195
database_cross_reference: DOI:10.1038/ki.2009.73
database_cross_reference: DOI:10.1038/ncpuro0672
database_cross_reference: DOI:10.1038/s41579-020-0324-0
database_cross_reference: DOI:10.1152/physrev.00041.2019

Axiom
annotated source: urothelial cell
annotated property: database_cross_reference
annotated target: ZFA:0009308
mapping justification: UnspecifiedMatching

amoeboid cell
type: Class
subclass of: motile cell
in_subset: human subset
in_subset: mouse subset

lymph gland plasmatocyte
type: Class
subclass of: plasmatocyte
subclass of: lymph gland hemocyte
definition: A plasmatocyte that derives from the larval lymph gland.

obsolete embryonic gland plasmatocyte
type: Class
term replaced by: CL_0011009
comment: Obsoleted as this is the same thing as 'embryonic plasmatocyte'.
deprecated: true

lymph gland hemocyte
type: Class
subclass of: hemocyte (sensu Arthropoda)
definition: A hemocyte that derives from the larval lymph gland.
database_cross_reference: FBbt:00005917

Axiom
annotated source: lymph gland hemocyte
annotated property: definition
annotated target: A hemocyte that derives from the larval lymph gland.
database_cross_reference: doi:10.1242/dev.00702

Axiom
annotated source: lymph gland hemocyte
annotated property: database_cross_reference
annotated target: FBbt:00005917
mapping justification: ManualMappingCuration

obsolete embryonic gland hemocyte
type: Class
term replaced by: CL_0011008
comment: Obsoleted as this term probably resulted from a confusion. Hemocytes are either derived from the embryonic head mesoderm ("embryonic hemocytes") or from the larval lymph gland ("lymph gland hemocytes"), not from an "embryonic gland".
deprecated: true

striated muscle cell
type: Class
equivalent class: Class
  intersection of: muscle cell
  intersection of: Restriction
    on property: has part
    some values from: GO_0030017
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001410
subclass of: muscle cell
subclass of: Restriction
  on property: has part
  some values from: GO_0030017
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001410
disjoint with: CL_0008000
definition: Muscle cell which has as its direct parts myofilaments organized into sarcomeres.
database_cross_reference: BTO:0002916
database_cross_reference: CALOHA:TS-2157
database_cross_reference: FMA:86936
database_cross_reference: ZFA:0005784
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: striated muscle cell
annotated property: definition
annotated target: Muscle cell which has as its direct parts myofilaments organized into sarcomeres.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721662544

Axiom
annotated source: striated muscle cell
annotated property: database_cross_reference
annotated target: ZFA:0005784
mapping justification: UnspecifiedMatching

leukocyte
type: Class
equivalent class: Class
  intersection of: CL_0000988
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0002505
  intersection of: Restriction
    on property: capable of
    some values from: GO_0001667
subclass of: BFO_0000002
subclass of: motile cell
subclass of: eukaryotic cell
subclass of: CL_0000988
subclass of: CL_0002242
subclass of: Restriction
  on property: part of
  some values from: UBERON_0002405
subclass of: Restriction
  on property: in taxon
  some values from: NCBITaxon 7742
subclass of: Restriction
  on property: develops from
  some values from: hematopoietic stem cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0001667
definition: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000751
database_cross_reference: CALOHA:TS-0549
database_cross_reference: FMA:62852
database_cross_reference: MESH:D007962
database_cross_reference: NCIT:C12529
database_cross_reference: ZFA:0009309
has_exact_synonym: leucocyte
has_exact_synonym: white blood cell
has_related_synonym: immune cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: leukocyte
annotated property: subClassOf
annotated target: CL_0000988
is inferred: true

Axiom
annotated source: leukocyte
annotated property: definition
annotated target: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:978-0-323-05290-0

Axiom
annotated source: leukocyte
annotated property: database_cross_reference
annotated target: ZFA:0009309
mapping justification: UnspecifiedMatching

CL_0000739
type: Class
has obsolescence reason: IAO_0000227
term replaced by: mature basophil
deprecated: true

retinal ganglion cell
type: Class
subclass of: neuron
subclass of: Restriction
  on property: has soma location
  some values from: UBERON_0000966
definition: The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0001800
database_cross_reference: FMA:67765
database_cross_reference: MESH:D012165
database_cross_reference: ZFA:0009310
has_exact_synonym: gangliocyte
has_exact_synonym: ganglion cell of retina
has_related_synonym: RGC
has_related_synonym: RGCs
in_subset: cellxgene subset
in_subset: eye_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: retinal ganglion cell
annotated property: definition
annotated target: The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve.
database_cross_reference: GOC:dph

Axiom
annotated source: retinal ganglion cell
annotated property: database_cross_reference
annotated target: ZFA:0009310
mapping justification: UnspecifiedMatching

Axiom
annotated source: retinal ganglion cell
annotated property: has_related_synonym
annotated target: RGC
database_cross_reference: doi:10.1038/s41598-020-66092-9
has_synonym_type: abbreviation

Axiom
annotated source: retinal ganglion cell
annotated property: has_related_synonym
annotated target: RGCs
database_cross_reference: doi:10.1038/s41598-020-66092-9
has_synonym_type: abbreviation
has_synonym_type: plural form

spinal accessory motor neuron
type: Class
subclass of: CL_0008039
definition: A motor neuron that is located in the cervical region of the spinal cord and selectively innervates the sternocleidmastoid or trapezius muscle. Unlike other motor neurons, they extend axons dorsally along lateral margins of the spinal cord.
database_cross_reference: ZFA:0009311
has_exact_synonym: SACMN
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: spinal accessory motor neuron
annotated property: definition
annotated target: A motor neuron that is located in the cervical region of the spinal cord and selectively innervates the sternocleidmastoid or trapezius muscle. Unlike other motor neurons, they extend axons dorsally along lateral margins of the spinal cord.
database_cross_reference: PMID:16267219

Axiom
annotated source: spinal accessory motor neuron
annotated property: database_cross_reference
annotated target: ZFA:0009311
mapping justification: UnspecifiedMatching

periarticular chondrocyte
type: Class
subclass of: CL_1001607
definition: A round chondrocyte that first differentiates in the late embryonic growth plate of bone.
database_cross_reference: ZFA:0009312
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: periarticular chondrocyte
annotated property: definition
annotated target: A round chondrocyte that first differentiates in the late embryonic growth plate of bone.
database_cross_reference: PMID:15951842

Axiom
annotated source: periarticular chondrocyte
annotated property: database_cross_reference
annotated target: ZFA:0009312
mapping justification: UnspecifiedMatching

hypertrophic chondrocyte
type: Class
subclass of: chondrocyte
definition: Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification).
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009313
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: is hypertrophic pathological or normal? and can it be described using a pato term?

Axiom
annotated source: hypertrophic chondrocyte
annotated property: definition
annotated target: Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification).
database_cross_reference: GO_REF:0000034
database_cross_reference: PMID:15951842

Axiom
annotated source: hypertrophic chondrocyte
annotated property: database_cross_reference
annotated target: ZFA:0009313
mapping justification: UnspecifiedMatching

columnar chondrocyte
type: Class
subclass of: chondrocyte
definition: A columnar chondrocyte that differentiates in the late embryonic growth plate of bone. Columnar chondrocytes vigorously proliferate and form columns in the growth plate.
database_cross_reference: ZFA:0009314
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: columnar chondrocyte
annotated property: definition
annotated target: A columnar chondrocyte that differentiates in the late embryonic growth plate of bone. Columnar chondrocytes vigorously proliferate and form columns in the growth plate.
database_cross_reference: PMID:15951842

Axiom
annotated source: columnar chondrocyte
annotated property: database_cross_reference
annotated target: ZFA:0009314
mapping justification: UnspecifiedMatching

retina horizontal cell
type: Class
subclass of: interneuron
subclass of: Restriction
  on property: has soma location
  some values from: UBERON_0003902
definition: A neuron that laterally connects other neurons in the inner nuclear layer of the retina.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0004120
database_cross_reference: ZFA:0009315
has_exact_synonym: horizontal cell
has_related_synonym: HC
has_related_synonym: HCs
in_subset: cellxgene subset
in_subset: eye_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: retina horizontal cell
annotated property: definition
annotated target: A neuron that laterally connects other neurons in the inner nuclear layer of the retina.
database_cross_reference: ISBN:0195088433

Axiom
annotated source: retina horizontal cell
annotated property: database_cross_reference
annotated target: ZFA:0009315
mapping justification: UnspecifiedMatching

Axiom
annotated source: retina horizontal cell
annotated property: has_related_synonym
annotated target: HC
database_cross_reference: doi:10.1038/s41598-020-66092-9
has_synonym_type: abbreviation

Axiom
annotated source: retina horizontal cell
annotated property: has_related_synonym
annotated target: HCs
database_cross_reference: doi:10.1038/s41598-020-66092-9
has_synonym_type: abbreviation
has_synonym_type: plural form

cardiac muscle cell
type: Class
equivalent class: Class
  intersection of: muscle cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0007100
  intersection of: Restriction
    on property: has part
    some values from: GO_0030017
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0002478
  intersection of: Restriction
    on property: participates in
    some values from: GO_0060047
subclass of: striated muscle cell
subclass of: CL_0002494
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0002478
subclass of: Restriction
  on property: participates in
  some values from: GO_0060047
subclass of: Restriction
  on property: develops from
  some values from: cardiac muscle myoblast
definition: Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei.
present in taxon: NCBITaxon 9606
description: Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to…
has_broad_synonym: cardiocyte
database_cross_reference: BTO:0001539
database_cross_reference: CALOHA:TS-0115
database_cross_reference: FMA:14067
database_cross_reference: MESH:D032383
database_cross_reference: ZFA:0009316
database_cross_reference: https://cellxgene.cziscience.com/cellguide/CL_0000746
has_exact_synonym: cardiac muscle fiber
has_exact_synonym: cardiac myocyte
has_exact_synonym: cardiomyocyte
has_exact_synonym: heart muscle cell
in_subset: cellxgene subset
in_subset: general_cell_types_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction.

Axiom
annotated source: cardiac muscle cell
annotated property: definition
annotated target: Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei.
database_cross_reference: GOC:mtg_cardiacconduct_nov11
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0323052908
database_cross_reference: PMID:22426062
database_cross_reference: PMID:4711263

Axiom
annotated source: cardiac muscle cell
annotated property: description
annotated target: Cardiac muscle cells, also known as cardiomyocytes or cardiac myocytes, are specialized cells that form the heart tissue. These cells are elongated, branched, and contain a single centrally located nucleus. Their anatomy is composed primarily of densely packed myofibrils, which are protein structures that consist of sarcomeres - the fundamental units of muscle contraction. Cardiac muscle cells are united at their ends through specialized junctions known as intercalated discs, which allow the heart to contract in a unified, powerful and rhythmic way. Functionally, cardiac muscle cells are responsible for the heart's consistent pumping action that circulates blood throughout the body. Unlike most cells in the body, cardiac muscle cells spontaneously depolarize and generate action potentials without external stimulation. This unique trait stems from the presence of ion channels in the cells' membrane that allow a cyclic flow of ions across the membrane, which create the electrical impulses necessary for heart contraction. The spread of these electrical signals from one cardiac muscle cell to another - facilitated by the interconnected network made by the intercalated disks - results in a synchronized contraction of the heart muscle. Unlike skeletal muscle cells which can tire and need rest, cardiac muscle cells have to work ceaselessly throughout the entire lifespan, without the opportunity for rest, to ensure continuous circulation of blood. This is made possible through the high volume of mitochondria and a constant supply of oxygen from coronary circulation. In conclusion, cardiac muscle cells, through their unique structure and vital functionality, play a pivotal role in sustaining life by providing the means for blood to reach every cell in the body. (This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies only to…
database_cross_reference: DOI:10.1016/j.ccep.2010.10.012
database_cross_reference: DOI:10.1038/nrcardio.2016.203
database_cross_reference: https://www.ncbi.nlm.nih.gov/books/NBK572070
database_cross_reference: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/cardiac-muscle

Axiom
annotated source: cardiac muscle cell
annotated property: database_cross_reference
annotated target: ZFA:0009316
mapping justification: UnspecifiedMatching

Axiom
annotated source: cardiac muscle cell
annotated property: has_exact_synonym
annotated target: cardiac muscle fiber
database_cross_reference: GO:0048739

cyanophore
type: Class
subclass of: BFO_0000002
subclass of: pigment cell
subclass of: eukaryotic cell
subclass of: Restriction
  on property: develops from
  some values from: CL_0005005
definition: A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance.
database_cross_reference: ZFA:0009317
has_related_synonym: blue chromatophore
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cyanophore
annotated property: definition
annotated target: A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance.
database_cross_reference: SANBI:mhl

Axiom
annotated source: cyanophore
annotated property: database_cross_reference
annotated target: ZFA:0009317
mapping justification: UnspecifiedMatching

retinal bipolar neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: has soma location
    some values from: UBERON_0001791
subclass of: glutamatergic neuron
subclass of: CL_0008028
subclass of: CL_0009004
subclass of: Restriction
  on property: has soma location
  some values from: UBERON_0001791
subclass of: Restriction
  on property: capable of
  some values from: Class
    intersection of: GO_0061535
    intersection of: Restriction
      on property: part of
      some values from: GO_0098976
definition: A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009318
has_related_synonym: BC
has_related_synonym: BCs
has_related_synonym: BPs
in_subset: cellxgene subset
in_subset: eye_upper_slim
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: retinal bipolar neuron
annotated property: definition
annotated target: A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer.
database_cross_reference: PMID:14689473

Axiom
annotated source: retinal bipolar neuron
annotated property: database_cross_reference
annotated target: ZFA:0009318
mapping justification: UnspecifiedMatching

Axiom
annotated source: retinal bipolar neuron
annotated property: has_related_synonym
annotated target: BC
database_cross_reference: doi:10.1038/s41598-020-66092-9
has_synonym_type: abbreviation

Axiom
annotated source: retinal bipolar neuron
annotated property: has_related_synonym
annotated target: BCs
database_cross_reference: doi:10.1038/s41598-020-66092-9
has_synonym_type: abbreviation
has_synonym_type: plural form

Axiom
annotated source: retinal bipolar neuron
annotated property: has_related_synonym
annotated target: BPs
database_cross_reference: GSE137537
has_synonym_type: abbreviation
has_synonym_type: plural form

ON-bipolar cell
type: Class
subclass of: retinal bipolar neuron
definition: A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009319
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: ON-bipolar cell
annotated property: definition
annotated target: A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors.
database_cross_reference: PMID:14689473

Axiom
annotated source: ON-bipolar cell
annotated property: database_cross_reference
annotated target: ZFA:0009319
mapping justification: UnspecifiedMatching

OFF-bipolar cell
type: Class
subclass of: retinal bipolar neuron
definition: A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the outer half of the inner plexiform layer. These cells depolarize in response to light to dark transition.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009320
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: OFF-bipolar cell
annotated property: definition
annotated target: A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the outer half of the inner plexiform layer. These cells depolarize in response to light to dark transition.
database_cross_reference: PMID:14689473

Axiom
annotated source: OFF-bipolar cell
annotated property: database_cross_reference
annotated target: ZFA:0009320
mapping justification: UnspecifiedMatching

rod bipolar cell
type: Class
subclass of: ON-bipolar cell
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008925
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008926
subclass of: Restriction
  on property: synapsed by
  some values from: retinal rod cell
definition: A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light.
present in taxon: NCBITaxon_32443
database_cross_reference: FMA:67750
database_cross_reference: ZFA:0009321
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: rod bipolar cell
annotated property: definition
annotated target: A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light.
database_cross_reference: GOC:tfm
database_cross_reference: PMID:14689473

Axiom
annotated source: rod bipolar cell
annotated property: present in taxon
annotated target: NCBITaxon_32443
database_cross_reference: PMID:38627529

Axiom
annotated source: rod bipolar cell
annotated property: database_cross_reference
annotated target: ZFA:0009321
mapping justification: UnspecifiedMatching

cone retinal bipolar cell
type: Class
equivalent class: Class
  intersection of: retinal bipolar neuron
  intersection of: Restriction
    on property: synapsed by
    some values from: retinal cone cell
subclass of: retinal bipolar neuron
subclass of: Restriction
  on property: synapsed by
  some values from: retinal cone cell
definition: A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer.
database_cross_reference: ZFA:0009322
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: cone retinal bipolar cell
annotated property: definition
annotated target: A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer.
database_cross_reference: PMID:14689473

Axiom
annotated source: cone retinal bipolar cell
annotated property: database_cross_reference
annotated target: ZFA:0009322
mapping justification: UnspecifiedMatching

type 1 cone bipolar cell (sensu Mus)
type: Class
subclass of: cone retinal bipolar cell
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008922
definition: An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell body of these cells is in the middle of the inner plexiform layer. The dendritic tree is stout and the axon terminates in sublamina 1. The axonal terminal is wide and has only a few varicosities.
has_exact_synonym: DB1 cone bipolar cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: type 1 cone bipolar cell (sensu Mus)
annotated property: definition
annotated target: An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell body of these cells is in the middle of the inner plexiform layer. The dendritic tree is stout and the axon terminates in sublamina 1. The axonal terminal is wide and has only a few varicosities.
database_cross_reference: PMID:14689473

type 2 cone bipolar cell (sensu Mus)
type: Class
equivalent class: Class
subclass of: BFO_0000002
subclass of: cone retinal bipolar cell
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008922
subclass of: Restriction
  on property: expresses
  some values from: PR P50481
subclass of: Restriction
  on property: expresses
  some values from: PR Q8R4I7
subclass of: Restriction
  on property: expresses
  some values from: PR Q9ER75
definition: An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is not well filled and the dendrites are more delicate than in type 1 cells. The axon terminal is bushier and exhibits a dense plexus of varicosities in the inner part of sublamina 1 (Ghosh et al., 2004). It can be differentiated from other retinal bipolar neurons by its expression of marker genes: Neto1, Lhx3 and Irx-6 (Shekhar, 2016).
has_exact_synonym: FMB cone bipolar cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: type 2 cone bipolar cell (sensu Mus)
annotated property: equivalentClass
annotated target: Class
database_cross_reference: PMID:27565351

Axiom
annotated source: type 2 cone bipolar cell (sensu Mus)
annotated property: definition
annotated target: An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is not well filled and the dendrites are more delicate than in type 1 cells. The axon terminal is bushier and exhibits a dense plexus of varicosities in the inner part of sublamina 1 (Ghosh et al., 2004). It can be differentiated from other retinal bipolar neurons by its expression of marker genes: Neto1, Lhx3 and Irx-6 (Shekhar, 2016).
database_cross_reference: PMID:14689473
database_cross_reference: PMID:27565351

type 3 cone bipolar cell (sensu Mus)
type: Class
subclass of: cone retinal bipolar cell
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008923
subclass of: Restriction
  on property: synapsed by
  some values from: retinal rod cell
definition: An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is delicate and the dendritic tips appear small when compared with type 1 cells. The axon terminal is stratified and restricted to sublamina 2 of the inner plexiform layer.
has_exact_synonym: DB2 cone bipolar cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: type 3 cone bipolar cell (sensu Mus)
annotated property: definition
annotated target: An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is delicate and the dendritic tips appear small when compared with type 1 cells. The axon terminal is stratified and restricted to sublamina 2 of the inner plexiform layer.
database_cross_reference: PMID:14689473

type 4 cone bipolar cell (sensu Mus)
type: Class
subclass of: cone retinal bipolar cell
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008923
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008924
subclass of: Restriction
  on property: synapsed by
  some values from: retinal rod cell
definition: An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell has a diffuse axon terminal with varicosities in sublaminae 1 and 2 of the inner plexiform layer.
has_exact_synonym: DB3 cone bipolar cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: type 4 cone bipolar cell (sensu Mus)
annotated property: definition
annotated target: An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell has a diffuse axon terminal with varicosities in sublaminae 1 and 2 of the inner plexiform layer.
database_cross_reference: PMID:14689473

type 5 cone bipolar cell (sensu Mus)
type: Class
subclass of: cone retinal bipolar cell
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008924
definition: An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is restricted to sublamina 3 of the inner plexiform layer. It is narrowly stratified and branched. The dendritic tree has many delicate branches.
has_exact_synonym: DB4 cone bipolar cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: type 5 cone bipolar cell (sensu Mus)
annotated property: definition
annotated target: An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is restricted to sublamina 3 of the inner plexiform layer. It is narrowly stratified and branched. The dendritic tree has many delicate branches.
database_cross_reference: PMID:14689473

type 6 cone bipolar cell (sensu Mus)
type: Class
subclass of: cone retinal bipolar cell
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008925
definition: An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The cell has a loose, delicate axon terminal that opens in sublamina 3 of the inner plexiform layer and descends into sublamina 4.
has_exact_synonym: DB5 cone bipolar cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: type 6 cone bipolar cell (sensu Mus)
annotated property: definition
annotated target: An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The cell has a loose, delicate axon terminal that opens in sublamina 3 of the inner plexiform layer and descends into sublamina 4.
database_cross_reference: PMID:14689473

type 7 cone bipolar cell (sensu Mus)
type: Class
subclass of: cone retinal bipolar cell
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008925
definition: An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is narrowly stratified and are found just below a calretinin-expressing band in sublamina 4 of the inner plexiform layer.
has_exact_synonym: IMB cone bipolar cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: type 7 cone bipolar cell (sensu Mus)
annotated property: definition
annotated target: An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is narrowly stratified and are found just below a calretinin-expressing band in sublamina 4 of the inner plexiform layer.
database_cross_reference: PMID:14689473

type 8 cone bipolar cell (sensu Mus)
type: Class
subclass of: cone retinal bipolar cell
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008925
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008926
definition: An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. This cell has the widest dendritic field and the widest axon terminal of all retinal bipolar cells. The axon terminal is delicate and stratified through sublaminae 4 and 5 of the inner plexiform layer.
has_exact_synonym: DB6 cone bipolar cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: type 8 cone bipolar cell (sensu Mus)
annotated property: definition
annotated target: An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. This cell has the widest dendritic field and the widest axon terminal of all retinal bipolar cells. The axon terminal is delicate and stratified through sublaminae 4 and 5 of the inner plexiform layer.
database_cross_reference: PMID:14689473

type 9 cone bipolar cell (sensu Mus)
type: Class
subclass of: cone retinal bipolar cell
subclass of: Restriction
  on property: axon synapses in
  some values from: UBERON_0008926
definition: An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The dendritic tree is wide and the dendritic convergence indicates cone selectivity. The axon terminal is sparsely branched and terminates in sublamina 5 of the inner plexiform layer.
has_exact_synonym: BB cone bipolar cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: type 9 cone bipolar cell (sensu Mus)
annotated property: definition
annotated target: An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The dendritic tree is wide and the dendritic convergence indicates cone selectivity. The axon terminal is sparsely branched and terminates in sublamina 5 of the inner plexiform layer.
database_cross_reference: PMID:14689473

nucleated thrombocyte
type: Class
equivalent class: Class
  intersection of: myeloid cell
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001407
  intersection of: Restriction
    on property: capable of
    some values from: GO_0007596
subclass of: single nucleate cell
subclass of: myeloid cell
subclass of: Restriction
  on property: develops from
  some values from: CL_0000828
subclass of: Restriction
  on property: capable of
  some values from: GO_0007596
definition: A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates.
database_cross_reference: ZFA:0009323
in_subset: blood_and_immune_upper_slim
in_subset: human subset
in_subset: mouse subset
comment: Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals.

Axiom
annotated source: nucleated thrombocyte
annotated property: subClassOf
annotated target: myeloid cell
is inferred: true

Axiom
annotated source: nucleated thrombocyte
annotated property: definition
annotated target: A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: PMID:16360205

Axiom
annotated source: nucleated thrombocyte
annotated property: database_cross_reference
annotated target: ZFA:0009323
mapping justification: UnspecifiedMatching

myeloid cell
type: Class
equivalent class: Class
  intersection of: CL_0000988
  intersection of: Restriction
    on property: develops from
    some values from: common myeloid progenitor
subclass of: BFO_0000002
subclass of: eukaryotic cell
subclass of: CL_0000988
subclass of: Restriction
  on property: develops from
  some values from: common myeloid progenitor
definition: A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
database_cross_reference: BTO:0001441
database_cross_reference: CALOHA:TS-0647
database_cross_reference: MESH:D022423
database_cross_reference: ZFA:0009324
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: myeloid cell
annotated property: subClassOf
annotated target: CL_0000988
is inferred: true

Axiom
annotated source: myeloid cell
annotated property: definition
annotated target: A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
database_cross_reference: GOC:add

Axiom
annotated source: myeloid cell
annotated property: database_cross_reference
annotated target: ZFA:0009324
mapping justification: UnspecifiedMatching

erythroid lineage cell
type: Class
subclass of: myeloid cell
definition: A immature or mature cell in the lineage leading to and including erythrocytes.
present in taxon: NCBITaxon 9606
database_cross_reference: CALOHA:TS-0290
database_cross_reference: FMA:62845
database_cross_reference: FMA:83516
database_cross_reference: ZFA:0009325
has_exact_synonym: erythropoietic cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes.

Axiom
annotated source: erythroid lineage cell
annotated property: definition
annotated target: A immature or mature cell in the lineage leading to and including erythrocytes.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm

Axiom
annotated source: erythroid lineage cell
annotated property: database_cross_reference
annotated target: ZFA:0009325
mapping justification: UnspecifiedMatching

erythroblast
type: Class
equivalent class: Class
  intersection of: erythroid lineage cell
  intersection of: Restriction
    on property: has part
    some values from: GO_0005634
  intersection of: Restriction
    on property: lacks_part
    some values from: GO_0005730
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001002
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001012
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001020
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001024
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001083
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001839
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001889
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000002978
  intersection of: Restriction
    on property: capable of
    some values from: GO_0030218
subclass of: erythroid lineage cell
subclass of: CL_0011026
subclass of: Restriction
  on property: has part
  some values from: GO_0005634
subclass of: Restriction
  on property: lacks_part
  some values from: GO_0005730
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001002
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001012
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001020
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001024
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001083
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001839
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001889
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000002978
subclass of: Restriction
  on property: develops from
  some values from: proerythroblast
subclass of: Restriction
  on property: capable of
  some values from: GO_0030218
definition: A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
database_cross_reference: BTO:0001571
database_cross_reference: CALOHA:TS-0289
database_cross_reference: FMA:83504
database_cross_reference: MESH:D004900
database_cross_reference: ZFA:0005237
has_exact_synonym: normoblast
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: erythroblast
annotated property: subClassOf
annotated target: erythroid lineage cell
is inferred: true

Axiom
annotated source: erythroblast
annotated property: definition
annotated target: A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:18174176

Axiom
annotated source: erythroblast
annotated property: database_cross_reference
annotated target: ZFA:0005237
mapping justification: UnspecifiedMatching

myeloid leukocyte
type: Class
equivalent class: Class
  intersection of: leukocyte
  intersection of: Restriction
    on property: develops from
    some values from: common myeloid progenitor
subclass of: leukocyte
subclass of: myeloid cell
definition: A cell of the monocyte, granulocyte, or mast cell lineage.
database_cross_reference: ZFA:0009326
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: myeloid leukocyte
annotated property: subClassOf
annotated target: leukocyte
is inferred: true

Axiom
annotated source: myeloid leukocyte
annotated property: definition
annotated target: A cell of the monocyte, granulocyte, or mast cell lineage.
database_cross_reference: GOC:add

Axiom
annotated source: myeloid leukocyte
annotated property: database_cross_reference
annotated target: ZFA:0009326
mapping justification: UnspecifiedMatching

basophil
type: Class
equivalent class: Class
  intersection of: granulocyte
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001344
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001950
  intersection of: Restriction
    on property: has high plasma membrane amount
    some values from: PR_000001255
  intersection of: Restriction
    on property: has high plasma membrane amount
    some values from: PR_000001865
  intersection of: Restriction
    on property: has high plasma membrane amount
    some values from: PR_000007431
subclass of: granulocyte
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001344
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001950
subclass of: Restriction
  on property: has high plasma membrane amount
  some values from: PR_000001255
subclass of: Restriction
  on property: has high plasma membrane amount
  some values from: PR_000001865
subclass of: Restriction
  on property: has high plasma membrane amount
  some values from: PR_000007431
definition: Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
present in taxon: NCBITaxon 9606
has_broad_synonym: polymorphonuclear leucocyte
has_broad_synonym: polymorphonuclear leukocyte
database_cross_reference: BTO:0000129
database_cross_reference: CALOHA:TS-0073
database_cross_reference: FMA:62862
has_exact_synonym: basophilic leucocyte
has_exact_synonym: basophilic leukocyte
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive.

Axiom
annotated source: basophil
annotated property: subClassOf
annotated target: granulocyte
is inferred: true

Axiom
annotated source: basophil
annotated property: definition
annotated target: Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:amm
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: MESH:D001491
database_cross_reference: PMCID:PMC2626675
database_cross_reference: PMID:11927641
database_cross_reference: PMID:19741522
database_cross_reference: PMID:21236338
database_cross_reference: PMID:9933081

immature basophil
type: Class
equivalent class: Class
  intersection of: basophil
  intersection of: Restriction
    on property: has part
    some values from: CL_0017509
subclass of: basophil
subclass of: Restriction
  on property: has part
  some values from: CL_0017509
subclass of: Restriction
  on property: develops from
  some values from: CL_0000830
definition: Any of the immature forms of a basophil, in which basophilic specific granules are present but other phenotypic features of the mature form may be lacking.
has_exact_synonym: immature basophilic leucocyte
has_exact_synonym: immature basophilic leukocyte
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: immature basophil
annotated property: subClassOf
annotated target: basophil
is inferred: true

Axiom
annotated source: immature basophil
annotated property: definition
annotated target: Any of the immature forms of a basophil, in which basophilic specific granules are present but other phenotypic features of the mature form may be lacking.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0721601464

basophilic metamyelocyte
type: Class
equivalent class: Class
  intersection of: immature basophil
  intersection of: Restriction
    on property: has part
    some values from: CL_0017507
  intersection of: Restriction
    on property: has part
    some values from: GO_0000792
  intersection of: Restriction
    on property: has part
    some values from: GO_0042582
  intersection of: Restriction
    on property: has part
    some values from: GO_0070820
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001012
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001456
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001483
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001892
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001932
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002031
subclass of: immature basophil
subclass of: CL_0002192
subclass of: Restriction
  on property: has part
  some values from: CL_0017507
subclass of: Restriction
  on property: has part
  some values from: GO_0000792
subclass of: Restriction
  on property: has part
  some values from: GO_0042582
subclass of: Restriction
  on property: has part
  some values from: GO_0070820
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001456
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001483
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001892
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001932
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002031
subclass of: Restriction
  on property: develops from
  some values from: basophilic myelocyte
definition: A basophil precursor in the granulocytic series, being a cell intermediate in development between a basophilic myelocyte and a band form basophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are CD11b-positive, CD15-positive, CD16-positive, CD24-positive, CD33-positive, and CD13-positive.
database_cross_reference: FMA:84198
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: basophilic metamyelocyte
annotated property: subClassOf
annotated target: immature basophil
is inferred: true

Axiom
annotated source: basophilic metamyelocyte
annotated property: definition
annotated target: A basophil precursor in the granulocytic series, being a cell intermediate in development between a basophilic myelocyte and a band form basophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are CD11b-positive, CD15-positive, CD16-positive, CD24-positive, CD33-positive, and CD13-positive.
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:18466030

band form basophil
type: Class
equivalent class: Class
  intersection of: immature basophil
  intersection of: Restriction
    on property: has part
    some values from: CL_0017506
subclass of: immature basophil
subclass of: Restriction
  on property: has part
  some values from: CL_0017506
subclass of: Restriction
  on property: develops from
  some values from: basophilic metamyelocyte
definition: A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: band form basophil
annotated property: subClassOf
annotated target: immature basophil
is inferred: true

Axiom
annotated source: band form basophil
annotated property: definition
annotated target: A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:18466030
database_cross_reference: http://www.cap.org

eosinophil
type: Class
equivalent class: Class
  intersection of: granulocyte
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001254
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001255
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001307
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001343
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000005178
subclass of: granulocyte
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001254
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001255
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001307
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001343
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000005178
definition: Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive.
present in taxon: NCBITaxon 9606
has_broad_synonym: polymorphonuclear leucocyte
has_broad_synonym: polymorphonuclear leukocyte
database_cross_reference: BTO:0000399
database_cross_reference: CALOHA:TS-0279
database_cross_reference: FMA:62861
database_cross_reference: MESH:D004804
has_exact_synonym: eosinocyte
has_exact_synonym: eosinophilic granulocyte
has_exact_synonym: eosinophilic leucocyte
has_exact_synonym: eosinophilic leukocyte
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte.

Axiom
annotated source: eosinophil
annotated property: subClassOf
annotated target: granulocyte
is inferred: true

Axiom
annotated source: eosinophil
annotated property: definition
annotated target: Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:amm
database_cross_reference: GOC:dsd
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: PMCID:PMC2626675
database_cross_reference: PMID:10914487
database_cross_reference: PMID:1662676

immature eosinophil
type: Class
equivalent class: Class
  intersection of: eosinophil
  intersection of: Restriction
    on property: has part
    some values from: CL_0017509
subclass of: eosinophil
subclass of: Restriction
  on property: has part
  some values from: CL_0017509
subclass of: Restriction
  on property: develops from
  some values from: CL_0000833
definition: Any of the immature forms of an eosinophil, in which eosinophilic specific granules are present but other phenotypic features of the mature form may be lacking.
has_exact_synonym: immature eosinocyte
has_exact_synonym: immature eosinophilic leucocyte
has_exact_synonym: immature eosinophilic leukocyte
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: immature eosinophil
annotated property: subClassOf
annotated target: eosinophil
is inferred: true

Axiom
annotated source: immature eosinophil
annotated property: definition
annotated target: Any of the immature forms of an eosinophil, in which eosinophilic specific granules are present but other phenotypic features of the mature form may be lacking.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0721601464

eosinophilic metamyelocyte
type: Class
equivalent class: Class
  intersection of: immature eosinophil
  intersection of: Restriction
    on property: has part
    some values from: CL_0017502
  intersection of: Restriction
    on property: has part
    some values from: CL_0017507
  intersection of: Restriction
    on property: has part
    some values from: GO_0000792
  intersection of: Restriction
    on property: has part
    some values from: GO_0042582
  intersection of: Restriction
    on property: has part
    some values from: GO_0070820
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001012
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001456
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001483
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001892
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001932
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000002031
subclass of: immature eosinophil
subclass of: CL_0002192
subclass of: Restriction
  on property: has part
  some values from: CL_0017502
subclass of: Restriction
  on property: has part
  some values from: CL_0017507
subclass of: Restriction
  on property: has part
  some values from: GO_0000792
subclass of: Restriction
  on property: has part
  some values from: GO_0042582
subclass of: Restriction
  on property: has part
  some values from: GO_0070820
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001456
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001483
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001892
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001932
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000002031
subclass of: Restriction
  on property: develops from
  some values from: eosinophilic myelocyte
definition: A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a eosinophilic myelocyte and a band form eosinophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are integrin alpha-M-positive, fucosyltransferase FUT4-positive, low affinity immunoglobulin gamma Fc region receptor III-positive, CD33-positive, CD24-positive and aminopeptidase N-negative.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: eosinophilic metamyelocyte
annotated property: subClassOf
annotated target: immature eosinophil
is inferred: true

Axiom
annotated source: eosinophilic metamyelocyte
annotated property: definition
annotated target: A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a eosinophilic myelocyte and a band form eosinophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are integrin alpha-M-positive, fucosyltransferase FUT4-positive, low affinity immunoglobulin gamma Fc region receptor III-positive, CD33-positive, CD24-positive and aminopeptidase N-negative.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:19622087

band form eosinophil
type: Class
equivalent class: Class
  intersection of: immature eosinophil
  intersection of: Restriction
    on property: has part
    some values from: CL_0017506
subclass of: immature eosinophil
subclass of: Restriction
  on property: has part
  some values from: CL_0017506
subclass of: Restriction
  on property: develops from
  some values from: eosinophilic metamyelocyte
definition: A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature eosinophil.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: band form eosinophil
annotated property: subClassOf
annotated target: immature eosinophil
is inferred: true

Axiom
annotated source: band form eosinophil
annotated property: definition
annotated target: A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature eosinophil.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464
database_cross_reference: PMID:19622087
database_cross_reference: http://www.cap.org

neutrophil
type: Class
equivalent class: Class
  intersection of: granulocyte
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001479
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001879
subclass of: granulocyte
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001479
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001879
definition: Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
present in taxon: NCBITaxon 9606
has_broad_synonym: PMN
has_broad_synonym: poly
has_broad_synonym: polymorphonuclear leucocyte
has_broad_synonym: polymorphonuclear leukocyte
has_broad_synonym: polymorphonuclear neutrophil
has_broad_synonym: polynuclear neutrophilic leucocyte
has_broad_synonym: polynuclear neutrophilic leukocyte
database_cross_reference: BTO:0000130
database_cross_reference: CALOHA:TS-0688
database_cross_reference: FMA:62860
database_cross_reference: MESH:D009504
database_cross_reference: ZFA:0009327
has_exact_synonym: neutrocyte
has_exact_synonym: neutrophil leucocyte
has_exact_synonym: neutrophil leukocyte
has_exact_synonym: neutrophilic leucocyte
has_exact_synonym: neutrophilic leukocyte
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: neutrophil
annotated property: subClassOf
annotated target: granulocyte
is inferred: true

Axiom
annotated source: neutrophil
annotated property: definition
annotated target: Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
database_cross_reference: GOC:add
database_cross_reference: GOC:amm
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0721601464

Axiom
annotated source: neutrophil
annotated property: database_cross_reference
annotated target: ZFA:0009327
mapping justification: UnspecifiedMatching

immature neutrophil
type: Class
equivalent class: Class
  intersection of: neutrophil
  intersection of: Restriction
    on property: has part
    some values from: CL_0017509
subclass of: neutrophil
subclass of: Restriction
  on property: has part
  some values from: CL_0017509
subclass of: Restriction
  on property: develops from
  some values from: neutrophilic promyelocyte
definition: Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking.
database_cross_reference: ZFA:0009328
has_exact_synonym: immatuer neutrophilic leukocyte
has_exact_synonym: immature neutrocyte
has_exact_synonym: immature neutrophil leucocyte
has_exact_synonym: immature neutrophil leukocyte
has_exact_synonym: immature neutrophilic leucocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: immature neutrophil
annotated property: subClassOf
annotated target: neutrophil
is inferred: true

Axiom
annotated source: immature neutrophil
annotated property: definition
annotated target: Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0721601464

Axiom
annotated source: immature neutrophil
annotated property: database_cross_reference
annotated target: ZFA:0009328
mapping justification: UnspecifiedMatching

mesangial phagocyte
type: Class
equivalent class: Class
  intersection of: CL_0000864
  intersection of: Restriction
    on property: located in
    some values from: UBERON_0002320
  intersection of: Restriction
    on property: capable of
    some values from: GO_0019882
  intersection of: Restriction
    on property: capable of
    some values from: GO_0048771
subclass of: CL_0000864
subclass of: Restriction
  on property: located in
  some values from: UBERON_0002320
subclass of: Restriction
  on property: capable of
  some values from: GO_0048771
definition: A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling.
has_broad_synonym: mesangial cell
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: mesangial phagocyte
annotated property: subClassOf
annotated target: CL_0000864
is inferred: true

Axiom
annotated source: mesangial phagocyte
annotated property: definition
annotated target: A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0702022918
database_cross_reference: ISBN:3540536663
database_cross_reference: PMID:1600140
database_cross_reference: PMID:16146841

mononuclear osteoclast
type: Class
equivalent class: Class
  intersection of: osteoclast
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001407
subclass of: osteoclast
subclass of: mononuclear phagocyte
definition: A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts.
database_cross_reference: ZFA:0009329
in_subset: human subset
in_subset: mouse subset
comment: Morphology: mononuclear, highly vesicular.

Axiom
annotated source: mononuclear osteoclast
annotated property: subClassOf
annotated target: osteoclast
is inferred: true

Axiom
annotated source: mononuclear osteoclast
annotated property: definition
annotated target: A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: PMID:12713016
database_cross_reference: PMID:15055519
database_cross_reference: PMID:17380158
database_cross_reference: PMID:9415452

Axiom
annotated source: mononuclear osteoclast
annotated property: database_cross_reference
annotated target: ZFA:0009329
mapping justification: UnspecifiedMatching

multinuclear osteoclast
type: Class
equivalent class: Class
  intersection of: osteoclast
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001908
subclass of: osteoclast
subclass of: multinucleated phagocyte
subclass of: CL_4052002
subclass of: Restriction
  on property: develops from
  some values from: mononuclear osteoclast
definition: A specialized multinuclear osteoclast, forming a syncytium through the fusion of mononuclear precursor cells, associated with the absorption and removal of bone.
has_exact_synonym: multinucleated osteoclast
in_subset: human subset
in_subset: mouse subset
comment: Morphology: multinucleated, highly vesicular.

Axiom
annotated source: multinuclear osteoclast
annotated property: subClassOf
annotated target: osteoclast
is inferred: true

Axiom
annotated source: multinuclear osteoclast
annotated property: definition
annotated target: A specialized multinuclear osteoclast, forming a syncytium through the fusion of mononuclear precursor cells, associated with the absorption and removal of bone.
database_cross_reference: GOC:add
database_cross_reference: PMID:12713016
database_cross_reference: PMID:29379067
database_cross_reference: PMID:38903088
database_cross_reference: PMID:9415452

multinuclear odontoclast
type: Class
equivalent class: Class
  intersection of: odontoclast
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001908
subclass of: odontoclast
subclass of: multinuclear osteoclast
subclass of: Restriction
  on property: develops from
  some values from: mononuclear odontoclast
definition: A specialized multinuclear osteoclast associated with the absorption and removal of cementum.
has_exact_synonym: multinucleated odontoclast
in_subset: human subset
in_subset: mouse subset
comment: Morphology: multinucleated, highly vesicular; location: roots of deciduous (milk) teeth.

Axiom
annotated source: multinuclear odontoclast
annotated property: subClassOf
annotated target: odontoclast
is inferred: true

Axiom
annotated source: multinuclear odontoclast
annotated property: definition
annotated target: A specialized multinuclear osteoclast associated with the absorption and removal of cementum.
database_cross_reference: GOC:add
database_cross_reference: PMID:9415452

mononuclear odontoclast
type: Class
equivalent class: Class
  intersection of: odontoclast
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001407
subclass of: odontoclast
subclass of: mononuclear osteoclast
definition: A specialized mononuclear osteoclast associated with the absorption and removal of cementum.
database_cross_reference: ZFA:0009330
in_subset: human subset
in_subset: mouse subset
comment: Morphology: Mononuclear, highly vesicular; location: roots of deciduous (milk) teeth.

Axiom
annotated source: mononuclear odontoclast
annotated property: subClassOf
annotated target: odontoclast
is inferred: true

Axiom
annotated source: mononuclear odontoclast
annotated property: subClassOf
annotated target: mononuclear osteoclast
is inferred: true

Axiom
annotated source: mononuclear odontoclast
annotated property: definition
annotated target: A specialized mononuclear osteoclast associated with the absorption and removal of cementum.
database_cross_reference: GOC:add
database_cross_reference: PMID:9415452

Axiom
annotated source: mononuclear odontoclast
annotated property: database_cross_reference
annotated target: ZFA:0009330
mapping justification: UnspecifiedMatching

myeloid dendritic cell
type: Class
equivalent class: Class
  intersection of: CL_0000990
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001865
  intersection of: Restriction
    on property: develops from
    some values from: myeloid cell
subclass of: myeloid leukocyte
subclass of: CL_0000990
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001865
subclass of: Restriction
  on property: develops from
  some values from: myeloid cell
definition: A dendritic cell of the myeloid lineage.
has_broad_synonym: interdigitating cell
has_broad_synonym: veiled cell
database_cross_reference: BTO:0004721
has_exact_synonym: CD11c+CD123- DC
has_exact_synonym: mDC
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8).

Axiom
annotated source: myeloid dendritic cell
annotated property: subClassOf
annotated target: CL_0000990
is inferred: true

Axiom
annotated source: myeloid dendritic cell
annotated property: definition
annotated target: A dendritic cell of the myeloid lineage.
database_cross_reference: GOC:add
database_cross_reference: PMID:10449155
database_cross_reference: PMID:17332250
database_cross_reference: PMID:9521319

multinucleated phagocyte
type: Class
equivalent class: Class
  intersection of: phagocyte (sensu Vertebrata)
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001908
subclass of: multinucleate cell
subclass of: phagocyte (sensu Vertebrata)
definition: A phagocyte formed by the fusion of mononuclear phagocytes.
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: multinucleated phagocyte
annotated property: subClassOf
annotated target: phagocyte (sensu Vertebrata)
is inferred: true

Axiom
annotated source: multinucleated phagocyte
annotated property: definition
annotated target: A phagocyte formed by the fusion of mononuclear phagocytes.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm

plasmacytoid dendritic cell
type: Class
equivalent class: Class
  intersection of: dendritic cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0032606
subclass of: dendritic cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0032606
definition: A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0004625
has_exact_synonym: DC2
has_exact_synonym: IPC
has_exact_synonym: T-associated plasma cell
has_exact_synonym: interferon-producing cell
has_exact_synonym: lymphoid dendritic cell
has_exact_synonym: pDC
has_exact_synonym: plasmacytoid T cell
has_exact_synonym: plasmacytoid monocyte
has_exact_synonym: type 2 DC
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: plasmacytoid dendritic cell
annotated property: subClassOf
annotated target: dendritic cell
is inferred: true

Axiom
annotated source: plasmacytoid dendritic cell
annotated property: definition
annotated target: A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: PMCID:PMC2118448
database_cross_reference: PMCID:PMC538703
database_cross_reference: PMID:15549123
database_cross_reference: PMID:17332250
database_cross_reference: PMID:17850486
database_cross_reference: PMID:20304825

mature B cell
type: Class
equivalent class: Class
  intersection of: CL_0001201
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002504
  intersection of: Restriction
    on property: capable of
    some values from: GO_0042113
  intersection of: Restriction
    on property: output of
    some values from: GO_0002335
subclass of: professional antigen presenting cell
subclass of: CL_0001201
subclass of: Restriction
  on property: develops from
  some values from: transitional stage B cell
subclass of: Restriction
  on property: capable of
  some values from: GO_0042113
subclass of: Restriction
  on property: output of
  some values from: GO_0002335
disjoint with: immature B cell
disjoint with: precursor B cell
disjoint with: transitional stage B cell
definition: A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen.
database_cross_reference: ZFA:0009331
has_exact_synonym: mature B lymphocyte
has_exact_synonym: mature B-cell
has_exact_synonym: mature B-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive.

Axiom
annotated source: mature B cell
annotated property: subClassOf
annotated target: CL_0001201
is inferred: true

Axiom
annotated source: mature B cell
annotated property: definition
annotated target: A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: ISBN:0781735149

Axiom
annotated source: mature B cell
annotated property: database_cross_reference
annotated target: ZFA:0009331
mapping justification: UnspecifiedMatching

plasma cell
type: Class
equivalent class: Class
  intersection of: CL_0000946
  intersection of: Restriction
    on property: has part
    some values from: CL_0017508
  intersection of: Restriction
    on property: has part
    some values from: GO_0005794
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0019814
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0042613
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001289
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001935
subclass of: CL_0000946
subclass of: Restriction
  on property: has part
  some values from: CL_0017508
subclass of: Restriction
  on property: has part
  some values from: GO_0005794
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0019814
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0042613
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001289
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001935
subclass of: Restriction
  on property: develops from
  some values from: CL_0000980
definition: A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0000392
database_cross_reference: FMA:70574
database_cross_reference: MESH:D010950
database_cross_reference: ZFA:0009332
has_exact_synonym: plasma B cell
has_exact_synonym: plasma B-cell
has_exact_synonym: plasmacyte
has_exact_synonym: plasmocyte
has_related_synonym: effector B cell
has_related_synonym: effector B-cell
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Plasma cells develop in the spleen and migrate to the bone marrow. Plasma cells are also reportedly CD5-negative, CD10-negative, CD19-positive, CD20-negative, CD21-negative, CD22-negative, CD23-negative, CD24-negative, CD25-negative, CD27-positive, CD34-negative, CD38-positive, CD40-positive, CD43-positive, CD45-positive, CD48-positive, CD53-low, CD80-negative, CD81-positive, CD86-positive, CD95-positive, CD196-negative, CD229-positive, CD270-positive, CD352-positive, CD361-positive, and IgD-negative. Transcription factors: BLIMP1-positive, IRF4-positive, PAX5-negative, SpiB-negative, Ets1-negative, and XBP1-positive.

Axiom
annotated source: plasma cell
annotated property: subClassOf
annotated target: CL_0000946
is inferred: true

Axiom
annotated source: plasma cell
annotated property: definition
annotated target: A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0721601464
database_cross_reference: ISBN:0781735149
database_cross_reference: PMID:19447676
database_cross_reference: PMID:20081059
database_cross_reference: PMID:20839338
database_cross_reference: PMID:20951740
database_cross_reference: http://en.wikipedia.org/wiki/Plasma_cell

Axiom
annotated source: plasma cell
annotated property: database_cross_reference
annotated target: ZFA:0009332
mapping justification: UnspecifiedMatching

memory B cell
type: Class
equivalent class: Class
  intersection of: mature B cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001935
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: GO_0042613
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001289
  intersection of: Restriction
    on property: output of
    some values from: GO_0002344
subclass of: mature B cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001935
subclass of: Restriction
  on property: has plasma membrane part
  some values from: GO_0042613
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001289
subclass of: Restriction
  on property: output of
  some values from: GO_0002344
definition: A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009333
has_exact_synonym: memory B lymphocyte
has_exact_synonym: memory B-cell
has_exact_synonym: memory B-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Memory B-cells are also reportedly CD5-negative, CD10-negative, CD21-positive, CD22-positive, CD23-negative, CD24-positive, CD25-positive, CD27-positive, CD34-negative, CD38-negative, CD40-positive, CD43-negative, CD44-positive, CD45-positive, CD53-positive, CD80-negative, CD81-negative, CD86-positive, and CD196/CCR6-positive.

Axiom
annotated source: memory B cell
annotated property: subClassOf
annotated target: mature B cell
is inferred: true

Axiom
annotated source: memory B cell
annotated property: definition
annotated target: A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:rhs
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149
database_cross_reference: PMID:20081059
database_cross_reference: PMID:20839338
database_cross_reference: http://en.wikipedia.org/wiki/Memory_B_cell

Axiom
annotated source: memory B cell
annotated property: database_cross_reference
annotated target: ZFA:0009333
mapping justification: UnspecifiedMatching

naive B cell
type: Class
equivalent class: Class
  intersection of: mature B cell
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0002344
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001963
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: GO_0071738
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: GO_0071753
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001289
subclass of: mature B cell
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0002344
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001963
subclass of: Restriction
  on property: has plasma membrane part
  some values from: GO_0071738
subclass of: Restriction
  on property: has plasma membrane part
  some values from: GO_0071753
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001289
definition: A naive B cell is a mature B cell that has the phenotype surface IgD-positive, surface IgM-positive, CD20-positive, CD27-negative and that has not yet been activated by antigen in the periphery.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009334
has_exact_synonym: naive B lymphocyte
has_exact_synonym: naive B-cell
has_exact_synonym: naive B-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: This cell type is compatible with the HIPC Lyoplate markers for 'naive B cell'. Per DSD: Naive B cells are also reportedly CD10-negative, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD25-negative, CD27-negative, CD34-negative, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD80-negative, CD81-positive, CD84-positive, CD86-negative, CD95-negative, CD138-negative, CD150-positive, CD184/CXCR4-positive, CD185/CXCR5-positive, CD196/CCR6-positive, CD200-positive, CD229-positive, CD243-positive, CD289-positive, CD290-positive, CD352-positive, MHCII/HLA-DR-positive, cadherin 9-positive, and sIgH-positive, Transcription factors: Pax5-positive, ETS1-positive, FOXO1A-positive, KLF4-positive, KLF9-positive, MiTF-positive, OBF1-positive, PLZF-positive, and SpiB-positive.

Axiom
annotated source: naive B cell
annotated property: subClassOf
annotated target: mature B cell
is inferred: true

Axiom
annotated source: naive B cell
annotated property: definition
annotated target: A naive B cell is a mature B cell that has the phenotype surface IgD-positive, surface IgM-positive, CD20-positive, CD27-negative and that has not yet been activated by antigen in the periphery.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:rhs
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781765196
database_cross_reference: PMID:19447676
database_cross_reference: PMID:20081059
database_cross_reference: PMID:20839338
database_cross_reference: PMID:20933013
database_cross_reference: PMID:22343568

Axiom
annotated source: naive B cell
annotated property: database_cross_reference
annotated target: ZFA:0009334
mapping justification: UnspecifiedMatching

alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: T cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: GO_0042105
subclass of: T cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: GO_0042105
disjoint with: gamma-delta T cell
definition: A T cell that expresses an alpha-beta T cell receptor complex.
database_cross_reference: ZFA:0009335
has_exact_synonym: alpha-beta T lymphocyte
has_exact_synonym: alpha-beta T-cell
has_exact_synonym: alpha-beta T-lymphocyte
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: alpha-beta T cell
annotated property: subClassOf
annotated target: T cell
is inferred: true

Axiom
annotated source: alpha-beta T cell
annotated property: definition
annotated target: A T cell that expresses an alpha-beta T cell receptor complex.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

Axiom
annotated source: alpha-beta T cell
annotated property: database_cross_reference
annotated target: ZFA:0009335
mapping justification: UnspecifiedMatching

immature alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: alpha-beta T cell
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0045058
subclass of: alpha-beta T cell
subclass of: CL_0002420
definition: An alpha-beta T cell that has an immature phenotype and has not completed T cell selection.
has_exact_synonym: immature alpha-beta T lymphocyte
has_exact_synonym: immature alpha-beta T-cell
has_exact_synonym: immature alpha-beta T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: immature alpha-beta T cell
annotated property: subClassOf
annotated target: alpha-beta T cell
is inferred: true

Axiom
annotated source: immature alpha-beta T cell
annotated property: definition
annotated target: An alpha-beta T cell that has an immature phenotype and has not completed T cell selection.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

mature alpha-beta T cell
type: Class
equivalent class: Class
  intersection of: alpha-beta T cell
  intersection of: Restriction
    on property: output of
    some values from: GO_0045058
subclass of: alpha-beta T cell
subclass of: CL_0002419
subclass of: Restriction
  on property: develops from
  some values from: immature alpha-beta T cell
definition: A alpha-beta T cell that has a mature phenotype.
has_exact_synonym: mature alpha-beta T lymphocyte
has_exact_synonym: mature alpha-beta T-cell
has_exact_synonym: mature alpha-beta T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: mature alpha-beta T cell
annotated property: subClassOf
annotated target: alpha-beta T cell
is inferred: true

Axiom
annotated source: mature alpha-beta T cell
annotated property: definition
annotated target: A alpha-beta T cell that has a mature phenotype.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

CD4-positive, CD25-positive, alpha-beta regulatory T cell
type: Class
equivalent class: Class
  intersection of: CD4-positive, alpha-beta T cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001380
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050777
  intersection of: Restriction
    on property: has low plasma membrane amount
    some values from: PR_000001869
subclass of: CD4-positive, alpha-beta T cell
subclass of: regulatory T cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001380
subclass of: Restriction
  on property: has low plasma membrane amount
  some values from: PR_000001869
definition: A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
has_broad_synonym: Treg
has_broad_synonym: suppressor T cell
has_broad_synonym: suppressor T lymphocyte
has_broad_synonym: suppressor T-cell
has_broad_synonym: suppressor T-lymphocyte
has_exact_synonym: CD4-positive, CD25-positive, alpha-beta regulatory T lymphocyte
has_exact_synonym: CD4-positive, CD25-positive, alpha-beta regulatory T-cell
has_exact_synonym: CD4-positive, CD25-positive, alpha-beta regulatory T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: This cell type is compatible with the HIPC Lyoplate markers for 'Treg'. The inclusion of CD127lo in the logical definition is compatible with both human and mouse T cells of this subtype.

Axiom
annotated source: CD4-positive, CD25-positive, alpha-beta regulatory T cell
annotated property: subClassOf
annotated target: CD4-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD4-positive, CD25-positive, alpha-beta regulatory T cell
annotated property: definition
annotated target: A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149
database_cross_reference: PMID:19464985
database_cross_reference: PMID:22343568

Axiom
annotated source: CD4-positive, CD25-positive, alpha-beta regulatory T cell
annotated property: has_broad_synonym
annotated target: Treg
database_cross_reference: PMID:22343568

CD4-positive, alpha-beta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: CD4-positive, alpha-beta T cell
  intersection of: Restriction
    on property: located in
    some values from: UBERON_0001277
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002385
subclass of: CD4-positive, alpha-beta T cell
subclass of: alpha-beta intraepithelial T cell
subclass of: Restriction
  on property: develops from
  some values from: CD4-positive, alpha-beta thymocyte
definition: A CD4-positive, alpha-beta T cell that is found in the columnar epithelium of the gastrointestinal tract.
present in taxon: NCBITaxon 9606
has_broad_synonym: IEL
has_broad_synonym: intraepithelial lymphocyte
has_exact_synonym: CD4-positive, alpha-beta intraepithelial T lymphocyte
has_exact_synonym: CD4-positive, alpha-beta intraepithelial T-cell
has_exact_synonym: CD4-positive, alpha-beta intraepithelial T-lymphocyte
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: CD4-positive, alpha-beta intraepithelial T cell
annotated property: subClassOf
annotated target: CD4-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD4-positive, alpha-beta intraepithelial T cell
annotated property: definition
annotated target: A CD4-positive, alpha-beta T cell that is found in the columnar epithelium of the gastrointestinal tract.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

CD8-positive, alpha-beta cytotoxic T cell
type: Class
equivalent class: Class
  intersection of: CD8-positive, alpha-beta T cell
  intersection of: Restriction
    on property: has part
    some values from: PR_000003466
  intersection of: Restriction
    on property: has part
    some values from: PR_000003499
  intersection of: Restriction
    on property: capable of
    some values from: GO_0001913
  intersection of: Restriction
    on property: capable of
    some values from: GO_0033380
  intersection of: Restriction
    on property: output of
    some values from: GO_0030217
subclass of: CD8-positive, alpha-beta T cell
subclass of: Restriction
  on property: has part
  some values from: PR_000003466
subclass of: Restriction
  on property: has part
  some values from: PR_000003499
subclass of: Restriction
  on property: develops from
  some values from: CL_0000906
subclass of: Restriction
  on property: capable of
  some values from: GO_0001913
subclass of: Restriction
  on property: capable of
  some values from: GO_0033380
subclass of: Restriction
  on property: output of
  some values from: GO_0030217
definition: A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive.
present in taxon: NCBITaxon 9606
has_broad_synonym: cytotoxic T cell
has_broad_synonym: cytotoxic T lymphocyte
has_broad_synonym: cytotoxic T-cell
has_broad_synonym: cytotoxic T-lymphocyte
has_broad_synonym: killer T cell
has_broad_synonym: killer T lymphocyte
has_broad_synonym: killer T-cell
has_broad_synonym: killer T-lymphocyte
database_cross_reference: CALOHA:TS-0190
has_exact_synonym: CD8-positive, alpha-beta cytotoxic T lymphocyte
has_exact_synonym: CD8-positive, alpha-beta cytotoxic T-cell
has_exact_synonym: CD8-positive, alpha-beta cytotoxic T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Note that while T cells of this subset are loosely referred to 'cytotoxic T cells,' as many other T cell types, including CD4-positive, alpha-beta T cells and gamma-delta T cells exhibit cytotoxicity in vitro and in vivo.

Axiom
annotated source: CD8-positive, alpha-beta cytotoxic T cell
annotated property: subClassOf
annotated target: CD8-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD8-positive, alpha-beta cytotoxic T cell
annotated property: definition
annotated target: A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:pam
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149

CD8-positive, alpha-beta regulatory T cell
type: Class
equivalent class: Class
  intersection of: CD8-positive, alpha-beta T cell
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050777
subclass of: CD8-positive, alpha-beta T cell
subclass of: regulatory T cell
definition: A CD8-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
has_broad_synonym: suppressor T cell
has_broad_synonym: suppressor T lymphocyte
has_broad_synonym: suppressor T-cell
has_broad_synonym: suppressor T-lymphocyte
has_exact_synonym: CD8+ T(reg)
has_exact_synonym: CD8+ Treg
has_exact_synonym: CD8+ regulatory T cell
has_exact_synonym: CD8-positive T(reg)
has_exact_synonym: CD8-positive Treg
has_exact_synonym: CD8-positive, alpha-beta Treg
has_exact_synonym: CD8-positive, alpha-beta regulatory T lymphocyte
has_exact_synonym: CD8-positive, alpha-beta regulatory T-cell
has_exact_synonym: CD8-positive, alpha-beta regulatory T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: CD8-positive, alpha-beta regulatory T cell
annotated property: subClassOf
annotated target: CD8-positive, alpha-beta T cell
is inferred: true

Axiom
annotated source: CD8-positive, alpha-beta regulatory T cell
annotated property: definition
annotated target: A CD8-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

CD8-alpha-beta-positive, alpha-beta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: alpha-beta intraepithelial T cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000025402
subclass of: alpha-beta intraepithelial T cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000025402
definition: A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements.
present in taxon: NCBITaxon 9606
has_broad_synonym: IEL
has_broad_synonym: intraepithelial lymphocyte
has_exact_synonym: CD8-positive, alpha-beta intraepithelial T lymphocyte
has_exact_synonym: CD8-positive, alpha-beta intraepithelial T-cell
has_exact_synonym: CD8-positive, alpha-beta intraepithelial T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell
annotated property: subClassOf
annotated target: alpha-beta intraepithelial T cell
is inferred: true

Axiom
annotated source: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell
annotated property: definition
annotated target: A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0781735149

alpha-beta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: mature alpha-beta T cell
  intersection of: Restriction
    on property: located in
    some values from: UBERON_0001277
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002385
subclass of: mature alpha-beta T cell
subclass of: CL_0002496
definition: A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements.
has_broad_synonym: IEL
has_broad_synonym: intraepithelial lymphocyte
has_exact_synonym: alpha-beta intraepithelial T lymphocyte
has_exact_synonym: alpha-beta intraepithelial T-cell
has_exact_synonym: alpha-beta intraepithelial T-lymphocyte
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: alpha-beta intraepithelial T cell
annotated property: subClassOf
annotated target: mature alpha-beta T cell
is inferred: true

Axiom
annotated source: alpha-beta intraepithelial T cell
annotated property: definition
annotated target: A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

gamma-delta T cell
type: Class
equivalent class: Class
  intersection of: T cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: GO_0042106
subclass of: T cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: GO_0042106
definition: A T cell that expresses a gamma-delta T cell receptor complex.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009336
has_exact_synonym: gamma-delta T lymphocyte
has_exact_synonym: gamma-delta T-cell
has_exact_synonym: gamma-delta T-lymphocyte
has_exact_synonym: gammadelta T cell
has_related_synonym: gd T cell
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways.

Axiom
annotated source: gamma-delta T cell
annotated property: subClassOf
annotated target: T cell
is inferred: true

Axiom
annotated source: gamma-delta T cell
annotated property: definition
annotated target: A T cell that expresses a gamma-delta T cell receptor complex.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

Axiom
annotated source: gamma-delta T cell
annotated property: database_cross_reference
annotated target: ZFA:0009336
mapping justification: UnspecifiedMatching

Axiom
annotated source: gamma-delta T cell
annotated property: has_related_synonym
annotated target: gd T cell
has_synonym_type: abbreviation

immature gamma-delta T cell
type: Class
equivalent class: Class
  intersection of: gamma-delta T cell
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0042492
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0045058
subclass of: gamma-delta T cell
subclass of: CL_0002420
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0042492
subclass of: Restriction
  on property: develops from
  some values from: DN3 thymocyte
definition: A gamma-delta T cell that has an immature phenotype.
database_cross_reference: ZFA:0009337
has_exact_synonym: immature gamma-delta T lymphocyte
has_exact_synonym: immature gamma-delta T-cell
has_exact_synonym: immature gamma-delta T-lymphocyte
in_subset: human subset
in_subset: mouse subset
comment: Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways.

Axiom
annotated source: immature gamma-delta T cell
annotated property: subClassOf
annotated target: gamma-delta T cell
is inferred: true

Axiom
annotated source: immature gamma-delta T cell
annotated property: definition
annotated target: A gamma-delta T cell that has an immature phenotype.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0781735149

Axiom
annotated source: immature gamma-delta T cell
annotated property: database_cross_reference
annotated target: ZFA:0009337
mapping justification: UnspecifiedMatching

mature gamma-delta T cell
type: Class
equivalent class: Class
  intersection of: gamma-delta T cell
  intersection of: Restriction
    on property: output of
    some values from: GO_0045058
subclass of: gamma-delta T cell
subclass of: CL_0002419
subclass of: Restriction
  on property: develops from
  some values from: immature gamma-delta T cell
definition: A gamma-delta T cell that has a mature phenotype. These cells can be found in tissues and circulation where they express unique TCR repertoire depending on their location.
database_cross_reference: ZFA:0009338
has_exact_synonym: mature gamma-delta T lymphocyte
has_exact_synonym: mature gamma-delta T-cell
has_exact_synonym: mature gamma-delta T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: mature gamma-delta T cell
annotated property: subClassOf
annotated target: gamma-delta T cell
is inferred: true

Axiom
annotated source: mature gamma-delta T cell
annotated property: definition
annotated target: A gamma-delta T cell that has a mature phenotype. These cells can be found in tissues and circulation where they express unique TCR repertoire depending on their location.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

Axiom
annotated source: mature gamma-delta T cell
annotated property: database_cross_reference
annotated target: ZFA:0009338
mapping justification: UnspecifiedMatching

gamma-delta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: mature gamma-delta T cell
  intersection of: Restriction
    on property: located in
    some values from: UBERON_0001277
  intersection of: Restriction
    on property: capable of
    some values from: GO_0002385
subclass of: mature gamma-delta T cell
subclass of: CL_0002496
definition: A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses.
has_broad_synonym: IEL
has_broad_synonym: intraepithelial lymphocyte
database_cross_reference: ZFA:0009339
has_exact_synonym: gamma-delta intraepithelial T lymphocyte
has_exact_synonym: gamma-delta intraepithelial T-cell
has_exact_synonym: gamma-delta intraepithelial T-lymphocyte
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: gamma-delta intraepithelial T cell
annotated property: subClassOf
annotated target: mature gamma-delta T cell
is inferred: true

Axiom
annotated source: gamma-delta intraepithelial T cell
annotated property: definition
annotated target: A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

Axiom
annotated source: gamma-delta intraepithelial T cell
annotated property: database_cross_reference
annotated target: ZFA:0009339
mapping justification: UnspecifiedMatching

CD8-alpha alpha positive, gamma-delta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: gamma-delta intraepithelial T cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001084
subclass of: gamma-delta intraepithelial T cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001084
definition: A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive.
present in taxon: NCBITaxon 9606
has_broad_synonym: IEL
has_broad_synonym: intraepithelial lymphocyte
has_exact_synonym: CD8-positive, gamma-delta intraepithelial T lymphocyte
has_exact_synonym: CD8-positive, gamma-delta intraepithelial T-cell
has_exact_synonym: CD8-positive, gamma-delta intraepithelial T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: CD8-alpha alpha positive, gamma-delta intraepithelial T cell
annotated property: subClassOf
annotated target: gamma-delta intraepithelial T cell
is inferred: true

Axiom
annotated source: CD8-alpha alpha positive, gamma-delta intraepithelial T cell
annotated property: definition
annotated target: A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

CD4-negative CD8-negative gamma-delta intraepithelial T cell
type: Class
equivalent class: Class
  intersection of: gamma-delta intraepithelial T cell
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
subclass of: gamma-delta intraepithelial T cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
definition: A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative.
has_broad_synonym: IEL
has_broad_synonym: intraepithelial lymphocyte
has_exact_synonym: CD4-positive, gamma-delta intraepithelial T lymphocyte
has_exact_synonym: CD4-positive, gamma-delta intraepithelial T-cell
has_exact_synonym: CD4-positive, gamma-delta intraepithelial T-lymphocyte
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: CD4-negative CD8-negative gamma-delta intraepithelial T cell
annotated property: subClassOf
annotated target: gamma-delta intraepithelial T cell
is inferred: true

Axiom
annotated source: CD4-negative CD8-negative gamma-delta intraepithelial T cell
annotated property: definition
annotated target: A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: ISBN:0781735149

CL_0000804
type: Class
has obsolescence reason: IAO_0000227
term replaced by: T cell
deprecated: true

immature single positive thymocyte
type: Class
equivalent class: Class
  intersection of: CL_0000893
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001307
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001380
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: GO_0043384
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000025402
  intersection of: Restriction
    on property: has high plasma membrane amount
    some values from: PR_000001932
subclass of: CL_0000893
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001307
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001380
subclass of: Restriction
  on property: has plasma membrane part
  some values from: GO_0043384
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000025402
subclass of: Restriction
  on property: develops from
  some values from: DN4 thymocyte
subclass of: Restriction
  on property: has high plasma membrane amount
  some values from: PR_000001932
definition: A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive.
has_exact_synonym: ISP
has_exact_synonym: T.ISP.th
has_exact_synonym: immature single positive T cell
has_exact_synonym: immature single positive T lymphocyte
has_exact_synonym: immature single positive T-lymphocyte
in_subset: human subset
in_subset: mouse subset
comment: Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and rearranging the T cell receptor alpha chain and expressing the CD8 coreceptor. This stage comes between the DN4 and DP stages.

Axiom
annotated source: immature single positive thymocyte
annotated property: subClassOf
annotated target: CL_0000893
is inferred: true

Axiom
annotated source: immature single positive thymocyte
annotated property: definition
annotated target: A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149
database_cross_reference: http://www.immgen.org/index_content.html

DN2 thymocyte
type: Class
equivalent class: Class
  intersection of: CL_0000893
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000025402
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001307
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001380
subclass of: CL_0002489
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001307
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001380
subclass of: Restriction
  on property: develops from
  some values from: CL_0000894
definition: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive.
has_exact_synonym: DN2 alpha-beta immature T lymphocyte
has_exact_synonym: DN2 alpha-beta immature T-cell
has_exact_synonym: DN2 alpha-beta immature T-lymphocyte
has_exact_synonym: DN2 cell
has_exact_synonym: DN2 immature T cell
has_exact_synonym: TN2 cell
has_exact_synonym: TN2 thymocyte
has_exact_synonym: double negative 2
has_exact_synonym: preT.DN2.Th
in_subset: human subset
in_subset: mouse subset
comment: Note that this type of thymocyte is at the earliest stage of T cell receptor rearrangement of the beta, gamma, and delta T cell receptor chains. Also, there is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'.

Axiom
annotated source: DN2 thymocyte
annotated property: definition
annotated target: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149

DN3 thymocyte
type: Class
equivalent class: Class
  intersection of: CL_0000893
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001307
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000025402
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: GO_0043384
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001380
subclass of: CL_0002489
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001307
subclass of: Restriction
  on property: has plasma membrane part
  some values from: GO_0043384
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001380
subclass of: Restriction
  on property: develops from
  some values from: DN2 thymocyte
definition: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain.
has_broad_synonym: early cortical thymocyte
has_exact_synonym: DN3 alpha-beta immature T lymphocyte
has_exact_synonym: DN3 alpha-beta immature T-cell
has_exact_synonym: DN3 alpha-beta immature T-lymphocyte
has_exact_synonym: DN3 cell
has_exact_synonym: DN3 immature T cell
has_exact_synonym: TN3 cell
has_exact_synonym: TN3 thymocyte
has_exact_synonym: double negative 3
has_exact_synonym: preT.DN3.Th
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'.

Axiom
annotated source: DN3 thymocyte
annotated property: definition
annotated target: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149

DN4 thymocyte
type: Class
equivalent class: Class
  intersection of: CL_0000893
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001307
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001380
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000025402
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: GO_0043384
subclass of: CL_0002489
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001307
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001380
subclass of: Restriction
  on property: has plasma membrane part
  some values from: GO_0043384
subclass of: Restriction
  on property: develops from
  some values from: DN3 thymocyte
definition: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, CD25-negative, and pre-TCR-positive.
has_broad_synonym: early cortical thymocyte
has_exact_synonym: DN4 alpha-beta immature T lymphocyte
has_exact_synonym: DN4 alpha-beta immature T-lymphocyte
has_exact_synonym: DN4 cell
has_exact_synonym: DN4 immature T cell
has_exact_synonym: DN4 immature T-cell
has_exact_synonym: T.DN4.th
has_exact_synonym: double negative 4
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
comment: Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and beginning to rearrange the T cell receptor alpha chain. There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'.

Axiom
annotated source: DN4 thymocyte
annotated property: definition
annotated target: A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, CD25-negative, and pre-TCR-positive.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149

double-positive, alpha-beta thymocyte
type: Class
equivalent class: Class
  intersection of: immature alpha-beta T cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002370
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001004
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000025402
subclass of: immature alpha-beta T cell
subclass of: CL_0000893
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001004
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000025402
subclass of: Restriction
  on property: develops from
  some values from: immature single positive thymocyte
definition: A thymocyte expressing the alpha-beta T cell receptor complex as well as both the CD4 and CD8 coreceptors.
present in taxon: NCBITaxon 9606
has_broad_synonym: late cortical thymocyte
has_exact_synonym: DP cell
has_exact_synonym: DP thymocyte
has_exact_synonym: double-positive, alpha-beta immature T lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Thymocytes of this stage are undergoing positive and negative selection.

Axiom
annotated source: double-positive, alpha-beta thymocyte
annotated property: subClassOf
annotated target: immature alpha-beta T cell
is inferred: true

Axiom
annotated source: double-positive, alpha-beta thymocyte
annotated property: definition
annotated target: A thymocyte expressing the alpha-beta T cell receptor complex as well as both the CD4 and CD8 coreceptors.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149

CD4-positive, alpha-beta thymocyte
type: Class
equivalent class: Class
  intersection of: immature alpha-beta T cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002370
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001084
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001004
subclass of: immature alpha-beta T cell
subclass of: CL_0000893
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001084
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001004
subclass of: Restriction
  on property: develops from
  some values from: double-positive, alpha-beta thymocyte
definition: An immature alpha-beta T cell that is located in the thymus and is CD4-positive and CD8-negative.
has_exact_synonym: CD4-positive, alpha-beta immature T lymphocyte
has_exact_synonym: CD4-positive, alpha-beta immature T-cell
has_exact_synonym: CD4-positive, alpha-beta immature T-lymphocyte
has_exact_synonym: SP CD4 cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: CD4-positive, alpha-beta thymocyte
annotated property: subClassOf
annotated target: immature alpha-beta T cell
is inferred: true

Axiom
annotated source: CD4-positive, alpha-beta thymocyte
annotated property: definition
annotated target: An immature alpha-beta T cell that is located in the thymus and is CD4-positive and CD8-negative.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149

CD8-positive, alpha-beta thymocyte
type: Class
equivalent class: Class
  intersection of: immature alpha-beta T cell
  intersection of: Restriction
    on property: part of
    some values from: UBERON_0002370
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: PR_000001004
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000025402
subclass of: immature alpha-beta T cell
subclass of: CL_0000893
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: PR_000001004
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000025402
subclass of: Restriction
  on property: develops from
  some values from: double-positive, alpha-beta thymocyte
definition: An immature alpha-beta T cell that is located in the thymus and is CD8-positive and CD4-negative.
has_exact_synonym: CD8-positive, alpha-beta immature T lymphocyte
has_exact_synonym: CD8-positive, alpha-beta immature T-cell
has_exact_synonym: CD8-positive, alpha-beta immature T-lymphocyte
has_exact_synonym: SP CD8 cell
has_related_synonym: CD8-positive, alpha-beta immature T cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: CD8-positive, alpha-beta thymocyte
annotated property: subClassOf
annotated target: immature alpha-beta T cell
is inferred: true

Axiom
annotated source: CD8-positive, alpha-beta thymocyte
annotated property: definition
annotated target: An immature alpha-beta T cell that is located in the thymus and is CD8-positive and CD4-negative.
database_cross_reference: GOC:add
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149

CL_0000812
type: Class
has obsolescence reason: IAO_0000227
term replaced by: T cell
deprecated: true

memory T cell
type: Class
equivalent class: Class
  intersection of: CL_0002419
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001603
  intersection of: Restriction
    on property: output of
    some values from: GO_0002286
  intersection of: Restriction
    on property: output of
    some values from: GO_0043379
subclass of: CL_0002419
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0001603
subclass of: Restriction
  on property: output of
  some values from: GO_0043379
disjoint with: CL_0000898
definition: A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure.
database_cross_reference: BTO:0003435
database_cross_reference: ZFA:0009342
has_exact_synonym: memory T lymphocyte
has_exact_synonym: memory T-cell
has_exact_synonym: memory T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset

Axiom
annotated source: memory T cell
annotated property: subClassOf
annotated target: CL_0002419
is inferred: true

Axiom
annotated source: memory T cell
annotated property: definition
annotated target: A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure.
database_cross_reference: GOC:add
database_cross_reference: GOC:pam
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149

Axiom
annotated source: memory T cell
annotated property: database_cross_reference
annotated target: ZFA:0009342
mapping justification: UnspecifiedMatching

mature NK T cell
type: Class
equivalent class: Class
  intersection of: mature alpha-beta T cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001874
  intersection of: Restriction
    on property: capable of
    some values from: GO_0032394
  intersection of: Restriction
    on property: capable of
    some values from: GO_0045087
  intersection of: Restriction
    on property: output of
    some values from: GO_0030217
subclass of: mature alpha-beta T cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001874
subclass of: Restriction
  on property: develops from
  some values from: CL_0002042
subclass of: Restriction
  on property: capable of
  some values from: GO_0032394
subclass of: Restriction
  on property: capable of
  some values from: GO_0045087
subclass of: Restriction
  on property: output of
  some values from: GO_0030217
definition: A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response.
present in taxon: NCBITaxon 9606
has_exact_synonym: mature NK T lymphocyte
has_exact_synonym: mature NK T-cell
has_exact_synonym: mature NK T-lymphocyte
has_exact_synonym: mature NKT cell
has_exact_synonym: mature natural killer T cell
has_exact_synonym: mature natural killer T lymphocyte
has_exact_synonym: mature natural killer T-cell
has_exact_synonym: mature natural killer T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: mature NK T cell
annotated property: subClassOf
annotated target: mature alpha-beta T cell
is inferred: true

Axiom
annotated source: mature NK T cell
annotated property: definition
annotated target: A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response.
database_cross_reference: GOC:add
database_cross_reference: ISBN:0781735149

regulatory T cell
type: Class
equivalent class: Class
  intersection of: CL_0002419
  intersection of: Restriction
    on property: capable of
    some values from: GO_0050777
subclass of: CL_0002419
subclass of: Restriction
  on property: capable of
  some values from: GO_0050777
definition: A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
present in taxon: NCBITaxon 9606
has_broad_synonym: suppressor T cell
has_broad_synonym: suppressor T lymphocyte
has_broad_synonym: suppressor T-cell
has_broad_synonym: suppressor T-lymphocyte
database_cross_reference: BTO:0004520
database_cross_reference: FMA:84070
database_cross_reference: MESH:D050378
has_exact_synonym: Treg
has_exact_synonym: regulatory T lymphocyte
has_exact_synonym: regulatory T-cell
has_exact_synonym: regulatory T-lymphocyte
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: This cell type may express FoxP3 and CD25 and secretes IL-10 and TGF-beta.

Axiom
annotated source: regulatory T cell
annotated property: subClassOf
annotated target: CL_0002419
is inferred: true

Axiom
annotated source: regulatory T cell
annotated property: definition
annotated target: A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release.
database_cross_reference: GOC:add
database_cross_reference: GO_REF:0000031

immature B cell
type: Class
equivalent class: Class
  intersection of: CL_0001201
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0045190
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071738
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: GO_0071753
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001289
subclass of: CL_0001201
subclass of: Restriction
  on property: has_not_completed
  some values from: GO_0045190
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071738
subclass of: Restriction
  on property: has plasma membrane part
  some values from: GO_0071753
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001289
subclass of: Restriction
  on property: develops from
  some values from: CL_0000954
definition: An immature B cell is a B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009343
has_exact_synonym: immature B lymphocyte
has_exact_synonym: immature B-cell
has_exact_synonym: immature B-lymphocyte
has_exact_synonym: newly formed B cell
in_subset: blood_and_immune_upper_slim
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: Immature B cells are also reportedly CD5-positive, CD10-positive, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD24-positive, CD25-negative, CD27-negative, CD34-negative, CD38-positive, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD79a-positive, CD80-negative, CD81-positive, CD86-negative, CD95-negative, CD127-negative, CD138-negative, CD185-positive, CD196-positive, MHCII/HLA-DR-positive, RAG-positive, TdT-negative, Vpre-B-negative, and preBCR-negative. Transcription factors expressed: Pax5-positive.

Axiom
annotated source: immature B cell
annotated property: definition
annotated target: An immature B cell is a B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation.
database_cross_reference: GOC:add
database_cross_reference: GOC:dsd
database_cross_reference: GOC:rhs
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031
database_cross_reference: ISBN:0781735149
database_cross_reference: PMID:20081059
database_cross_reference: PMID:20839338

Axiom
annotated source: immature B cell
annotated property: database_cross_reference
annotated target: ZFA:0009343
mapping justification: UnspecifiedMatching

Axiom
annotated source: immature B cell
annotated property: has_exact_synonym
annotated target: newly formed B cell
database_cross_reference: ISBN:781735149

precursor B cell
type: Class
equivalent class: Class
  intersection of: CL_0001201
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: GO_0071753
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: PR_000001898
subclass of: CL_0001201
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: GO_0071753
subclass of: Restriction
  on property: has plasma membrane part
  some values from: PR_000001898
disjoint with: CL_0000826
definition: A precursor B cell is a B cell with the phenotype CD10-positive.
present in taxon: NCBITaxon 9606
database_cross_reference: BTO:0001133
database_cross_reference: CALOHA:TS-0819
database_cross_reference: ZFA:0009344
has_related_synonym: pre-B cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas

Axiom
annotated source: precursor B cell
annotated property: subClassOf
annotated target: CL_0001201
is inferred: true

Axiom
annotated source: precursor B cell
annotated property: definition
annotated target: A precursor B cell is a B cell with the phenotype CD10-positive.
database_cross_reference: GOC:rhs
database_cross_reference: GOC:tfm
database_cross_reference: GO_REF:0000031

Axiom
annotated source: precursor B cell
annotated property: database_cross_reference
annotated target: ZFA:0009344
mapping justification: UnspecifiedMatching

transitional stage B cell
type: Class
equivalent class: Class
  intersection of: CL_0001201
  intersection of: Restriction
    on property: has_not_completed
    some values from: GO_0002335
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: GO_0071753
subclass of: CL_0001201
definition: An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen.
present in taxon: NCBITaxon 9606
database_cross_reference: ZFA:0009345
has_exact_synonym: transitional B cell
has_exact_synonym: transitional stage B lymphocyte
has_exact_synonym: transitional stage B-cell
has_exact_synonym: transitional stage B-lymphocyte
has_narrow_synonym: T1 B cell
has_narrow_synonym: T2 B cell
has_narrow_synonym: T3 B cell
in_subset: cellxgene subset
in_subset: human subset
in_subset: mouse subset
in_subset: human reference atlas
comment: This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'.