OSCI: Ontology of Stem Cell Investigation
type: Ontology
version IRI: osci.owl
version info: Vision Release: 1.0.02
creator: Jens Hansen
creator: Yongqun Oliver He
date: 05-25-2018
creator: Alexander Diehl
description: OSCI is a biomedical ontology in the area of stem cell investigation. OSCI imports existing ontologies such as CL, CLO, and OBI, and aims to support standardized stem cell representation, integration, and analysis.
subject: A biomedical ontology to support stem cell investigation
Format: OWL-DL
creator: William Duncan

BFO OWL specification label
type: AnnotationProperty
editor preferred label: BFO OWL specification label
definition: Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
curator note: Really of interest to developers only
sub property of: label

BFO CLIF specification label
type: AnnotationProperty
editor preferred label: BFO CLIF specification label
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only
sub property of: label

LINCS ID
type: AnnotationProperty
definition: An annotation property that represents an ID used in the NIH LINCS project.
definition editor: Oliver He, Jiangan Xie, Jie Zheng

PubChem AID
type: AnnotationProperty
definition source: https://pubchem.ncbi.nlm.nih.gov/help.html
definition: An annotation property that represents a PubMed BioAssay Identifier accession number.
definition editor: Oliver He

Known mutation annotation
type: AnnotationProperty
definition editor: Oliver He
definition: An annotation property that describes known mutation(s) about a cell.

Cell culture condition
type: AnnotationProperty

editor preferred label
type: AnnotationProperty
editor preferred label: editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
has curation status: IAO_0000122
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: editor preferred term
label: editor preferred term~editor preferred label

example of usage
type: AnnotationProperty
editor preferred label: example
editor preferred label: example of usage
has curation status: IAO_0000122
definition: A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has curation status
type: AnnotationProperty
editor preferred label: has curation status
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bill Bug
definition editor: PERSON:Melanie Courtot
definition source: OBI_0000281

definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
has curation status: IAO_0000122
definition: English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
has exact synonym: DEFINITION
label: textual definition

editor note
type: AnnotationProperty
editor preferred label: editor note
has curation status: IAO_0000122
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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
has db xref: IAO:0000116
has OBO namespace: uberon
id: editor_note
is metadata tag: true
shorthand: editor_note

definition editor
type: AnnotationProperty
editor preferred label: term editor
has curation status: IAO_0000122
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: term editor

alternative term
type: AnnotationProperty
editor preferred label: alternative term
has curation status: IAO_0000125
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
editor preferred label: definition source
has curation status: IAO_0000122
definition: formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
definition editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

curator note
type: AnnotationProperty
editor preferred label: curator note
has curation status: IAO_0000122
definition: An administrative note of use for a curator but of no use for a user
definition editor: PERSON:Alan Ruttenberg
has db xref: IAO:0000232
has OBO namespace: uberon
id: curator_notes
is metadata tag: true
shorthand: curator_notes
label: curator notes

term tracker item
type: AnnotationProperty
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: IAO_0000125
definition: An IRI or similar locator for a request or discussion of an ontology term.
definition editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

ontology term requester
type: AnnotationProperty
has curation status: IAO_0000125
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
definition editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

imported from
type: AnnotationProperty
editor preferred label: imported from
has curation status: IAO_0000125
definition: For external terms/classes, the ontology from which the term was imported
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

expand expression to
type: AnnotationProperty

OBO foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
has curation status: IAO_0000125
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
definition editor: PERSON:Chris Mungall
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

elucidation
type: AnnotationProperty
editor preferred label: elucidation
definition editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms

has associated axiom(nl)
type: AnnotationProperty
editor preferred label: has associated axiom(nl)
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
type: AnnotationProperty
editor preferred label: has associated axiom(fol)
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

code
type: AnnotationProperty
read only: true
code: NHC0
Preferred_Name: code
has exact synonym: code

Semantic_Type
type: AnnotationProperty
definition: The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
code: P106
Semantic_Type: Conceptual Entity
Display_Name: Semantic Type
Preferred_Name: Semantic_Type
DesignNote: In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS.
has exact synonym: Semantic_Type

Display_Name
type: AnnotationProperty
definition: Provides an alternative Preferred Name for use in some NCI systems.
code: P107
Semantic_Type: Conceptual Entity
Display_Name: Display Name
Preferred_Name: Display_Name
has exact synonym: Display Name
has exact synonym: Display_Name

Preferred_Name
type: AnnotationProperty
definition: The word or phrase that NCI uses by preference to refer to the concept.
code: P108
Semantic_Type: Conceptual Entity
Display_Name: Preferred Name
Preferred_Name: Preferred_Name
has exact synonym: Preferred Name
has exact synonym: Preferred Term
has exact synonym: Preferred_Name

UMLS_CUI
type: AnnotationProperty
definition: Concept Unique Identifiers, or CUIs, are concept numbers assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept.
code: P207
Semantic_Type: Conceptual Entity
Display_Name: UMLS CUI
Preferred_Name: UMLS_CUI
has exact synonym: UMLS_CUI

Contributing_Source
type: AnnotationProperty
definition: This property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake.
code: P322
Semantic_Type: Conceptual Entity
Display_Name: Contributing Source
Preferred_Name: Contributing_Source
has exact synonym: Contributing_Source

ALT_DEFINITION
type: AnnotationProperty
definition: English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software.
code: P325
Semantic_Type: Conceptual Entity
Display_Name: [source] Definition
Preferred_Name: ALT_DEFINITION
has exact synonym: ALT_DEFINITION

Legacy_Concept_Name
type: AnnotationProperty
read only: true
definition: A retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding.
code: P366
Semantic_Type: Conceptual Entity
Preferred_Name: Legacy Concept Name
has exact synonym: Legacy Concept Name

DesignNote
type: AnnotationProperty
definition: Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
code: P98
Semantic_Type: Conceptual Entity
Display_Name: DesignNote
Preferred_Name: DesignNote
has exact synonym: DesignNote

ISA alternative term
type: AnnotationProperty
editor preferred label: ISA alternative term
has curation status: IAO_0000122
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
definition editor: Person: Alejandra Gonzalez-Beltran
definition editor: Person: Philippe Rocca-Serra
definition source: ISA tools project (http://isa-tools.org)
sub property of: alternative term

NIAID GSCID-BRC alternative term
type: AnnotationProperty
editor preferred label: NIAID GSCID-BRC alternative term
has curation status: IAO_0000122
definition: An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
sub property of: alternative term

IEDB alternative term
type: AnnotationProperty
editor preferred label: IEDB alternative term
has curation status: IAO_0000122
definition: An alternative term used by the IEDB.
definition editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
sub property of: alternative term

symbol from nomenclature authority
type: AnnotationProperty
definition: the symbol assigned by the nomenclature authority
definition editor: Oliver He, Yue Liu

full name from nomenclature authority
type: AnnotationProperty
definition: the full name assigned by the nomenclature authority
definition editor: Oliver He, Yue Liu

NCBI GeneID
type: AnnotationProperty
definition: A GeneID in the NCBI Gene database
definition editor: Oliver He, Yue Liu

NCBI LocusTag
type: AnnotationProperty
definition: the NCBI LocusTag name of a gene
definition editor: Oliver He, Yue Liu

gene map location
type: AnnotationProperty
definition: the map location of a gene
definition editor: Oliver He, Yue Liu

modification date
type: AnnotationProperty
definition: a date of content modification
definition editor: Oliver He, Yue Liu

organism NCBITaxon ID
type: AnnotationProperty
definition: The NCBITaxon ontology ID of an organism.
definition editor: Oliver He, Yue Liu

chromosome ID of gene
type: AnnotationProperty
definition: A chromosome ID where a gene is located.
definition editor: Oliver He

type of gene
type: AnnotationProperty
definition: an annotation property that specifies the type of a gene
definition editor: Oliver He

nomenclature status
type: AnnotationProperty
definition: an annotation property that specifies a nomenclature status
definition editor: Oliver He

has GO association
type: AnnotationProperty
definition: an annotation property that shows the GO information associated with a specific gene.
definition editor: Yongqun He
comment: YH: use the convention: GO_ID (EC: xx; Qualifier: xx; PMID: xxxxx;) where GO_ID is a GO ID, EC is the Evidence Code, Qualifier is a specific association type, and PMID is a PubMed ID of a paper that supports the gene-GO association.
domain: gene

has PubMed association
type: AnnotationProperty
definition: An annotation property that represents a gene's association with PubMed publication(s).
definition editor: Yongqun He
comment: YH: use the format: PMID: pmid1, pmid2, ... where pmid1 and pmid2 are specfic PubMed IDs (PMIDs).

stem cell ID
type: AnnotationProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T21:59:53Z

lot number
type: AnnotationProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:00:25Z

cell grade
type: AnnotationProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:00:39Z

contact information
type: AnnotationProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:02:49Z

reference publication
type: AnnotationProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:08:30Z

donor ID
type: AnnotationProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:31:59Z

donor testing method
type: AnnotationProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:56:10Z

donor screening method
type: AnnotationProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:56:31Z

source cell ID
type: AnnotationProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:56:59Z

temporal interpretation
type: AnnotationProperty
editor preferred label: temporal interpretation
definition: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
sub property of: RO_0002422

external_definition
type: AnnotationProperty
has db xref: UBPROP:0000001
has OBO namespace: uberon
id: external_definition
is metadata tag: true
shorthand: external_definition
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO
IAO_0000115: An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.

has_relational_adjective
type: AnnotationProperty
has db xref: UBPROP:0000007
has OBO namespace: uberon
id: has_relational_adjective
is metadata tag: true
shorthand: has_relational_adjective
IAO_0000232: Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.

external_ontology_notes
type: AnnotationProperty
has db xref: UBPROP:0000012
has OBO namespace: uberon
id: external_ontology_notes
is metadata tag: true
shorthand: external_ontology_notes
IAO_0000115: Notes on how similar or equivalent classes are represented in other ontologies.
IAO_0000116: This annotation property may be replaced with an annotation property from an external ontology such as IAO

has_rank
type: AnnotationProperty
definition: A metadata relation between a class and its taxonomic rank (eg species, family)
has_obo_namespace: ncbi_taxonomy

Contributor
type: AnnotationProperty
has OBO namespace: uberon
id: dc-contributor
is metadata tag: true
shorthand: dc-contributor
description: Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
comment: An entity responsible for making contributions to the content of the resource.
label: contributor

Creator
type: AnnotationProperty
description: Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
comment: An entity primarily responsible for making the content of the resource.

Date
type: AnnotationProperty
description: Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
comment: A date associated with an event in the life cycle of the resource.

Description
type: AnnotationProperty
description: Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
comment: An account of the content of the resource.

Format
type: AnnotationProperty
description: Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
comment: The physical or digital manifestation of the resource.

Source
type: AnnotationProperty
description: The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
comment: A reference to a resource from which the present resource is derived.

Subject and Keywords
type: AnnotationProperty
description: Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
comment: The topic of the content of the resource.

Title
type: AnnotationProperty
description: Typically, a Title will be a name by which the resource is formally known.
comment: A name given to the resource.

license
type: AnnotationProperty
definition editor: Mark Miller
date: 2018-05-11T13:47:29Z

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has exact synonym
type: AnnotationProperty
definition: Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
has exact synonym: FULL_SYN
has exact synonym: Synonym with Source Data
label: has_exact_synonym

has_narrow_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in subset
type: AnnotationProperty
definition: Used to associate the concept defining a particular terminology subset with concepts that belong to this subset.
has exact synonym: Concept_In_Subset
label: in_subset

label
type: AnnotationProperty
editor preferred label: label

part_of
type: ObjectProperty
equivalent property:
  inverse of: has part
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
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'.
alternative term: part_of
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
imported from: omrse.owl
imported from: ro.owl
temporal interpretation: RO_0001901
label: part of

has part
type: ObjectProperty
equivalent property:
  inverse of: part_of
sub property of: overlaps
type: TransitiveProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
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'.
alternative term: has_part
imported from: BFO
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
imported from: ro.owl
imported from: uberon.owl
temporal interpretation: RO_0001901

inheres in at all times
type: ObjectProperty
sub property of: specifically depends on at all times
domain: specifically dependent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
BFO OWL specification label: inheres-in_at
BFO CLIF specification label: inheresInAt
definition: b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in@en(x,y,t)'.
editor note: BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.)
editor note: BFO2 Reference: independent continuant that is not a spatial region
editor note: BFO2 Reference: specifically dependent continuant
imported from: ogg.owl
has associated axiom(fol): (iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002]

realized in
type: ObjectProperty
equivalent property:
  inverse of: realizes
inverse of: realizes
domain: realizable entity
range: process
editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
imported from: obi.owl
imported from: omrse.owl
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
equivalent property:
  inverse of: realized in
domain: process
range: realizable entity
editor preferred label: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
imported from: clo.owl
imported from: obi.owl
imported from: omrse.owl
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

concretized by at some time
type: ObjectProperty
inverse of: concretizes at some time
domain: generically dependent continuant
range: specifically dependent continuant
BFO OWL specification label: concretized-by_st
example of usage: [copied from inverse property 'concretizes at some time'] You may concretize a piece of software by installing it in your computer
example of usage: [copied from inverse property 'concretizes at some time'] You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
example of usage: [copied from inverse property 'concretizes at some time'] you may concretize a poem as a pattern of memory traces in your head
editor note: [copied from inverse property 'concretizes at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
imported from: ogg.owl
elucidation: [copied from inverse property 'concretizes at some time'] b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])

concretizes at some time
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
BFO OWL specification label: concretizes_st
BFO CLIF specification label: concretizesAt
example of usage: You may concretize a piece of software by installing it in your computer
example of usage: You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
example of usage: you may concretize a poem as a pattern of memory traces in your head
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
imported from: ogg.owl
elucidation: b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
has associated axiom(nl): if b g-depends on c at some time t, then there is some d, such that d concretizes b at t and d s-depends_on c at t. (axiom label in BFO2 Reference: [076-001])
has associated axiom(fol): (forall (x y t) (if (concretizesAt x y t) (and (SpecificallyDependentContinuant x) (GenericallyDependentContinuant y) (exists (z) (and (IndependentContinuant z) (specificallyDependsOnAt x z t) (genericallyDependsOnAt y z t)))))) // axiom label in BFO2 CLIF: [075-002]
has associated axiom(fol): (forall (x y t) (if (genericallyDependsOnAt x y t) (exists (z) (and (concretizesAt z x t) (specificallyDependsOnAt z y t))))) // axiom label in BFO2 CLIF: [076-001]

specifically depends on at all times
type: ObjectProperty
sub property of: specifically depends on at some time
BFO OWL specification label: s-depends-on_at
BFO CLIF specification label: specificallyDependsOn
example of usage: A pain s-depends_on the organism that is experiencing the pain
example of usage: a gait s-depends_on the walking object. (All at some specific time.)
example of usage: a shape s-depends_on the shaped object
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
example of usage: one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
example of usage: one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
example of usage: one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
example of usage: one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
example of usage: reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
example of usage: reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
example of usage: reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
example of usage: the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
example of usage: the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
example of usage: the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
example of usage: the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
example of usage: the two-sided reciprocal s-dependence of the roles of husband and wife [20
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'.
editor note: BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
editor note: BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
editor note: BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
editor note: BFO2 Reference: specifically dependent continuant\; process; process boundary
imported from: ogg.owl
elucidation: To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
has associated axiom(nl): If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
has associated axiom(nl): If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
has associated axiom(nl): If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
has associated axiom(nl): an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
has associated axiom(nl): if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
has associated axiom(fol): (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
has associated axiom(fol): (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
has associated axiom(fol): (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
has associated axiom(fol): (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
has associated axiom(fol): (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]

occupies spatial region at some time
type: ObjectProperty
inverse of: has spatial occupant at some time
domain: independent continuant
range: spatial region
BFO OWL specification label: located-at-r_st
BFO CLIF specification label: occupiesSpatialRegionAt
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
editor note: BFO2 Reference: independent continuant
editor note: BFO2 Reference: spatial region
imported from: ogg.owl
elucidation: b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
has associated axiom(nl): every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])
has associated axiom(nl): if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])
has associated axiom(fol): (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002]
has associated axiom(fol): (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002]
has associated axiom(fol): (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001]

has_quality
type: ObjectProperty
imported from: clo.owl
EFO URI: http://www.ebi.ac.uk/efo/has_quality

exists at
type: ObjectProperty
inverse of: during which exists
domain: entity
range: temporal region
BFO OWL specification label: exists-at
BFO CLIF specification label: existsAt
editor note: BFO2 Reference: entity
editor note: BFO2 Reference: temporal region
imported from: ogg.owl
elucidation: b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])

has occurrent part
type: ObjectProperty
inverse of: part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-has-part
BFO CLIF specification label: hasOccurrentPart
example of usage: [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
example of usage: [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
example of usage: [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
definition: b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
editor note: [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
imported from: ogg.owl
elucidation: [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
has associated axiom(fol): (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]

has proper occurrent part
type: ObjectProperty
sub property of: has occurrent part
inverse of: proper part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-has-ppart
BFO CLIF specification label: hasProperOccurrentPart
definition: [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
definition: b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
imported from: ogg.owl

has spatial occupant at some time
type: ObjectProperty
domain: spatial region
range: independent continuant
BFO OWL specification label: r-location-of_st
editor note: [copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
editor note: [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant
editor note: [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region
imported from: ogg.owl
elucidation: [copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])

has specific dependent at some time
type: ObjectProperty
inverse of: specifically depends on at some time
domain: Class
  union of: process
  union of: specifically dependent continuant
  union of: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region
range: Class
  union of: process
  union of: specifically dependent continuant
BFO OWL specification label: has-s-dep_st
example of usage: [copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain
example of usage: [copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.)
example of usage: [copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
example of usage: [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
example of usage: [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
example of usage: [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
example of usage: [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
example of usage: [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
example of usage: [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
example of usage: [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
example of usage: [copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20
editor note: [copied from inverse property 'specifically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
editor note: [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
editor note: [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
editor note: [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
editor note: [copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary
imported from: ogg.owl
elucidation: [copied from inverse property 'specifically depends on at some time'] To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64

has spatiotemporal occupant
type: ObjectProperty
inverse of: occupies spatiotemporal region
domain: spatiotemporal region
range: occurrent
BFO OWL specification label: occupied-by
editor note: [copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
imported from: ogg.owl
elucidation: [copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])

occupies spatiotemporal region
type: ObjectProperty
domain: occurrent
range: spatiotemporal region
BFO OWL specification label: occupies
BFO CLIF specification label: occupiesSpatiotemporalRegion
editor note: BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
imported from: ogg.owl
elucidation: p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])

part of occurrent
type: ObjectProperty
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-part-of
BFO CLIF specification label: occurrentPartOf
example of usage: Mary’s 5th birthday occurrent_part_of Mary’s life
example of usage: The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
example of usage: the first set of the tennis match occurrent_part_of the tennis match.
definition: [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
editor note: BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: BFO2 Reference: occurrent
imported from: ogg.owl
elucidation: b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
has associated axiom(nl): occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
has associated axiom(nl): occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
has associated axiom(nl): occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
has associated axiom(nl): occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
has associated axiom(nl): occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
has associated axiom(fol): (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
has associated axiom(fol): (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
has associated axiom(fol): (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
has associated axiom(fol): (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
has associated axiom(fol): (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]

proper part of occurrent
type: ObjectProperty
sub property of: part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-ppart-of
BFO CLIF specification label: properOccurrentPartOf
definition: [copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
definition: b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
imported from: ogg.owl
has associated axiom(fol): (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001]

temporal part of
type: ObjectProperty
sub property of: part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: t-part-of
BFO CLIF specification label: temporalPartOf
example of usage: the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
example of usage: the process boundary which separates the 3rd and 4th years of your life.
example of usage: your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
definition: b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
definition: b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
imported from: ogg.owl
has associated axiom(nl): if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])
has associated axiom(fol): (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
has associated axiom(fol): (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
has associated axiom(fol): (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]

projects onto spatial region at some time
type: ObjectProperty
inverse of: spatial projection of spatiotemporal at some time
domain: spatiotemporal region
range: spatial region
BFO OWL specification label: st-projects-onto-s_st
imported from: ogg.owl

spatial projection of spatiotemporal at some time
type: ObjectProperty
domain: spatial region
range: spatiotemporal region
BFO OWL specification label: s-projection-of-st_st
imported from: ogg.owl

projects onto temporal region
type: ObjectProperty
sub property of: exists at
inverse of: temporal projection of spatiotemporal
domain: spatiotemporal region
range: temporal region
BFO OWL specification label: st-projects-onto-t
imported from: ogg.owl

temporal projection of spatiotemporal
type: ObjectProperty
sub property of: during which exists
domain: temporal region
range: spatiotemporal region
BFO OWL specification label: t-projection-of-st
imported from: ogg.owl

occupies temporal region
type: ObjectProperty
sub property of: exists at
inverse of: has temporal occupant
domain: occurrent
range: temporal region
BFO OWL specification label: spans
BFO CLIF specification label: occupiesTemporalRegion
imported from: ogg.owl
elucidation: p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])

has temporal occupant
type: ObjectProperty
sub property of: during which exists
domain: temporal region
range: occurrent
BFO OWL specification label: span-of
BFO CLIF specification label: spanOf
imported from: ogg.owl
elucidation: [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])

during which exists
type: ObjectProperty
domain: temporal region
range: entity
BFO OWL specification label: during-which-exists
editor note: [copied from inverse property 'exists at'] BFO2 Reference: entity
editor note: [copied from inverse property 'exists at'] BFO2 Reference: temporal region
imported from: ogg.owl
elucidation: [copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])

bearer of at all times
type: ObjectProperty
sub property of: has specific dependent at all times
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: specifically dependent continuant
BFO OWL specification label: bearer-of_at
BFO CLIF specification label: bearerOfAt
definition: b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'bearer of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'.
editor note: BFO2 Reference: independent continuant that is not a spatial region
editor note: BFO2 Reference: specifically dependent continuant
imported from: ogg.owl
has associated axiom(fol): (iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004]

has disposition at all times
type: ObjectProperty
sub property of: bearer of at all times
range: disposition
BFO OWL specification label: has-d_at
BFO CLIF specification label: hasDispositionAt
definition: a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has disposition at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has disposition@en(x,y,t)'.
imported from: ogg.owl
has associated axiom(fol): (iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001]

has specific dependent at all times
type: ObjectProperty
sub property of: has specific dependent at some time
BFO OWL specification label: has-s-dep_at
imported from: ogg.owl

specifically depends on at some time
type: ObjectProperty
domain: Class
  union of: process
  union of: specifically dependent continuant
range: Class
  union of: process
  union of: specifically dependent continuant
  union of: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region
BFO OWL specification label: s-depends-on_st
BFO CLIF specification label: specificallyDependsOn
example of usage: A pain s-depends_on the organism that is experiencing the pain
example of usage: a gait s-depends_on the walking object. (All at some specific time.)
example of usage: a shape s-depends_on the shaped object
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
example of usage: one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
example of usage: one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
example of usage: one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
example of usage: one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
example of usage: reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
example of usage: reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
example of usage: reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
example of usage: the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
example of usage: the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
example of usage: the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
example of usage: the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
example of usage: the two-sided reciprocal s-dependence of the roles of husband and wife [20
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
editor note: BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
editor note: BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
editor note: BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
editor note: BFO2 Reference: specifically dependent continuant\; process; process boundary
imported from: ogg.owl
elucidation: To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
has associated axiom(nl): If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
has associated axiom(nl): If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
has associated axiom(nl): If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
has associated axiom(nl): an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
has associated axiom(nl): if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
has associated axiom(fol): (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
has associated axiom(fol): (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
has associated axiom(fol): (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
has associated axiom(fol): (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
has associated axiom(fol): (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]

part of continuant at some time
type: ObjectProperty
inverse of: has continuant part at some time
domain: continuant
range: continuant
BFO OWL specification label: c-part-of_st
BFO CLIF specification label: continuantPartOfAt
example of usage: Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
example of usage: the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
definition: [copied from inverse property 'has continuant part at some time'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
editor note: BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
editor note: BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: BFO2 Reference: continuant
editor note: BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
editor note: [copied from inverse property 'has continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
imported from: ogg.owl
elucidation: b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
has associated axiom(nl): continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])
has associated axiom(nl): continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])
has associated axiom(nl): continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])
has associated axiom(nl): continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])
has associated axiom(nl): continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])
has associated axiom(nl): if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])
has associated axiom(fol): (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002]
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002]
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001]
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001]
has associated axiom(fol): (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001]
has associated axiom(fol): (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001]
has associated axiom(fol): (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001]

has continuant part at some time
type: ObjectProperty
domain: continuant
range: continuant
BFO OWL specification label: c-has-part_st
BFO CLIF specification label: hasContinuantPartAt
example of usage: [copied from inverse property 'part of continuant at some time'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
example of usage: [copied from inverse property 'part of continuant at some time'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
definition: b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
editor note: [copied from inverse property 'part of continuant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
editor note: [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
editor note: [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuant
editor note: [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
imported from: ogg.owl
elucidation: [copied from inverse property 'part of continuant at some time'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
has associated axiom(fol): (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001]

part of continuant at all times that whole exists
type: ObjectProperty
sub property of: part of continuant at some time
type: TransitiveProperty
domain: continuant
range: continuant
BFO OWL specification label: c-part-of-object_at
definition: [copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
definition: forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)
editor note: This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'
editor note: [copied from inverse property 'has continuant part at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.
imported from: ogg.owl

has continuant part at all times that part exists
type: ObjectProperty
sub property of: has continuant part at some time
type: TransitiveProperty
domain: continuant
range: continuant
BFO OWL specification label: c-has-part-object_at
example of usage: [copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
example of usage: [copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
definition: forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
editor note: This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
editor note: [copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
editor note: [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
editor note: [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant
editor note: [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
imported from: ogg.owl
elucidation: [copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])

derives from patient having disease
type: ObjectProperty
sub property of: topObjectProperty
imported from: clo.owl
definition: a 'derives from' object property between an entity (in CLO case, cell line) and a disease in a patient where the entity is derived from some cell in the patient who has the disease. This is a short cut relation that represents: 'derived from' some (cell and ('part of' some 'organism' and ('has disease' some disease)))
definition editor: Yongqun He
comment: In most cases, the patient in the relation is used to refer human patient. However, an animal patient (or veterinary patient) can also be referred.

is in cell line repository
type: ObjectProperty
domain: cell line cell
range: cell line repository
definition: an object property that specifies a cell line repository for a specifc cell line.
definition editor: SS, YH, UV, SS
imported from: clo.owl

is disease model for
type: ObjectProperty
sub property of: topObjectProperty
imported from: clo.owl
definition: an object property that represents a relation between a cell line cell and a disease.
definition editor: Asiyah Yu Lin, Yongqun He
comment: This object property is largely equivalent to the previous term 'is model for' (http://www.ebi.ac.uk/cellline#is_model_for).

derived from organism
type: ObjectProperty
sub property of: derives_from
definition: a 'cell line cell derives from' object property between an entity (e.g., cell line cell in CLO) and an organism where the cell line cell is derived from some cell from the organism. In CLO, this is a short cut relation that represents: 'derived from' some (cell and ('part of' some organism))
imported from: clo.owl

derived from cell
type: ObjectProperty
sub property of: derives_from
imported from: clo.owl

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
range: measurement unit label
imported from: obi.owl

is about
type: ObjectProperty
domain: information content entity
editor preferred label: is about
example of usage: This document is about information artifacts and their representations
has curation status: IAO_0000125
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
definition editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: clo.owl
imported from: iao.owl
imported from: obi.owl
imported from: omrse.owl

denotes
type: ObjectProperty
sub property of: is about
example of usage: A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
definition: denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
editor note: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
definition editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
imported from: obi.owl

is quality measurement of
type: ObjectProperty
equivalent property:
  inverse of: is quality measured as
sub property of: is about
inverse of: is quality measured as
domain: measurement datum
range: quality
definition: m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q
editor note: 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
editor note: From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
editor note: From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
editor note: From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
editor note: This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
definition editor: Alan Ruttenberg
imported from: obi.owl

is duration of
type: ObjectProperty
sub property of: is about
domain: time measurement datum
range: process
has curation status: IAO_0000120
definition: relates a process to a time-measurement-datum that represents the duration of the process
definition editor: Person:Alan Ruttenberg
imported from: obi.owl

is quality measured as
type: ObjectProperty
equivalent property:
  inverse of: is quality measurement of
has curation status: IAO_0000120
definition: inverse of the relation of is quality measurement of
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
definition editor: Person:Alan Ruttenberg
imported from: obi.owl

has time stamp
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
domain: time stamped measurement datum
range: time measurement datum
has curation status: IAO_0000123
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
definition editor: Alan Ruttenberg
imported from: obi.owl

has measurement datum
type: ObjectProperty
sub property of: has part
domain: time stamped measurement datum
range: Class
  intersection of: measurement datum
  intersection of: Class
    complement of: time measurement datum
has curation status: IAO_0000123
definition: relates a time stamped measurement datum to the measurement datum that was measured
definition editor: Alan Ruttenberg
imported from: obi.owl

is_supported_by_data
type: ObjectProperty
domain: conclusion based on data
range: data item
editor preferred label: is_supported_by_data
example of usage: The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
has curation status: IAO_0000122
definition: The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
definition editor: OBI
definition source: OBI
definition source: Philly 2011 workshop
imported from: obi.owl

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has_participant
inverse of: is_specified_input_of
domain: planned process
editor preferred label: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: IAO_0000122
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot
imported from: clo.owl
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_input
sub property of: participates in
range: planned process
editor preferred label: is_specified_input_of
example of usage: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has curation status: IAO_0000122
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: clo.owl
imported from: obi.owl

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has_participant
sub property of: topObjectProperty
inverse of: is_specified_output_of
domain: planned process
editor preferred label: has_specified_output
has curation status: IAO_0000122
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Courtot
imported from: clo.owl
imported from: obi.owl
imported from: omrse.owl

is_specified_output_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_output
sub property of: participates in
range: planned process
editor preferred label: is_specified_output_of
has curation status: IAO_0000122
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: clo.owl
imported from: obi.owl
imported from: omrse.owl

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred label: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
has curation status: IAO_0000120
definition: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
definition editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
imported from: clo.owl
imported from: obi.owl

has grain
type: ObjectProperty
sub property of: has part
editor preferred label: has grain
has curation status: IAO_0000120
definition: the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
editor note: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
definition editor: PERSON: Alan Ruttenberg
definition source: PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
imported from: clo.owl
imported from: obi.owl

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred label: objective_achieved_by
has curation status: IAO_0000122
definition: This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
definition editor: OBI
definition source: OBI
imported from: clo.owl
imported from: obi.owl

has category label
type: ObjectProperty
sub property of: has part
domain: categorical measurement datum
range: categorical label
editor preferred label: has category label
has curation status: IAO_0000123
definition: A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale.
imported from: obi.owl

specifies value of
type: ObjectProperty
sub property of: is about
domain: value specification
editor preferred label: specifies value of
has curation status: IAO_0000123
definition: A relation between a value specification and an entity which the specification is about.
imported from: obi.owl

has value specification
type: ObjectProperty
sub property of: has part
domain: information content entity
range: value specification
editor preferred label: has value specification
has curation status: IAO_0000120
definition: A relation between an information content entity and a value specification that specifies its value.
definition editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

is genome of organism
type: ObjectProperty
sub property of: part of continuant at some time
definition: a 'part of continuant at some time' relation that incides a genome belongs to a organism.
definition editor: Yongqun He, Bin Zhao
imported from: ogg.owl

is gene of organism
type: ObjectProperty
sub property of: part of continuant at some time
domain: gene
range: organism
definition: a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method.
definition editor: Oliver He, Yue Liu
imported from: ogg.owl

produced by
type: ObjectProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:02:00Z

provided by
type: ObjectProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:07:22Z

inheres in
type: ObjectProperty
equivalent property:
  inverse of: bearer of
inverse of: bearer of
type: FunctionalProperty
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: 'inheres in at all times'
alternative term: inheres_in
imported from: obi.owl
imported from: omrse.owl
temporal interpretation: RO_0001901

bearer of
type: ObjectProperty
equivalent property:
  inverse of: inheres in
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
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.
alternative term: bearer of
alternative term: bearer_of
alternative term: is bearer of
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
imported from: omrse.owl
imported from: ro.owl
temporal interpretation: RO_0001901
label: bearer_of
label: is bearer of

participates in
type: ObjectProperty
equivalent property:
  inverse of: has_participant
inverse of: has_participant
domain: continuant
range: occurrent
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
imported from: omrse.owl

has_participant
type: ObjectProperty
equivalent property:
  inverse of: participates in
domain: occurrent
range: continuant
property chain axiom: has part
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
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.
alternative term: has_participant
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
imported from: omrse.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
label: has participant

is concretized as
type: ObjectProperty
equivalent property:
  inverse of: concretizes
sub property of: topObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
editor preferred label: is concretized as
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
alternative term: concretized by at some time
imported from: obi.owl
imported from: omrse.owl

concretizes
type: ObjectProperty
equivalent property:
  inverse of: is concretized as
sub property of: topObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
editor preferred label: concretizes
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
imported from: clo.owl
imported from: obi.owl
imported from: omrse.owl
comment: It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation.

function of
type: ObjectProperty
equivalent property:
  inverse of: has function
sub property of: inheres in
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative term: function_of
alternative term: is function of
imported from: obi.owl

role of
type: ObjectProperty
equivalent property:
  inverse of: has role
sub property of: inheres in
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative term: is role of
alternative term: role_of
imported from: obi.owl

has function
type: ObjectProperty
equivalent property:
  inverse of: function of
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative term: has_function
imported from: obi.owl

has role
type: ObjectProperty
equivalent property:
  inverse of: role of
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative term: has_role
imported from: obi.owl

derives_from
type: ObjectProperty
sub property of: topObjectProperty
inverse of: derives into
type: SymmetricProperty
domain: independent continuant
range: independent continuant
editor preferred label: derives from
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: IAO_0000125
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'.
alternative term: derives_from
imported from: clo.owl
imported from: obi.owl
imported from: ro.owl
label: derives from

derives into
type: ObjectProperty
editor preferred label: derives into
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: IAO_0000125
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'.
alternative term: derives_into
imported from: clo.owl
imported from: obi.owl

located in
type: ObjectProperty
type: TransitiveProperty
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
imported from: cl.owl

has plasma membrane part
type: ObjectProperty
sub property of: has part
has curation status: IAO_0000125
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.
imported from: cl.owl
imported from: clo.owl

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
property chain axiom: part_of
property chain axiom: has part
has curation status: IAO_0000125
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
imported from: cl.owl
imported from: clo.owl
imported from: ro.owl
imported from: uberon.owl
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
temporal interpretation: RO_0001901
in subset: ro-eco

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
imported from: cl.owl

develops from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: independent continuant
range: independent continuant
property chain axiom: part_of
has curation status: IAO_0000125
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
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl

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
has curation status: IAO_0000125
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
has curation status: IAO_0000125
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.
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in
property chain axiom: capable of
property chain axiom: part_of
has curation status: IAO_0000125
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.
imported from: cl.owl
imported from: clo.owl

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: independent continuant
range: independent continuant
definition: x adjacent to y if and only if x and y share a boundary
imported from: cl.owl

temporal relation
type: ObjectProperty
range: occurrent
has curation status: IAO_0000125
editor note: move to BFO?
definition source: Allen
imported from: obi.owl
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: temporal relation
has curation status: IAO_0000125
definition: inverse of starts with
definition editor: Chris Mungall
definition source: Allen
imported from: obi.owl

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
has curation status: IAO_0000125
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
imported from: cl.owl
imported from: clo.owl

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: IAO_0000125
definition: Inverse of developmentally preceded by
imported from: cl.owl
imported from: clo.owl

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
imported from: cl.owl
imported from: clo.owl
imported from: ro.owl
temporal interpretation: RO_0001901

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)
imported from: cl.owl
imported from: clo.owl

functionally related to
type: ObjectProperty
imported from: cl.owl
imported from: clo.owl

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
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).
imported from: cl.owl
imported from: clo.owl

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
imported from: cl.owl
imported from: clo.owl

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
imported from: cl.owl
imported from: clo.owl

causally related to
type: ObjectProperty
sub property of: related via dependence to
definition: This relation groups causal relations between material entities and causal relations between processes
imported from: cl.owl
imported from: clo.owl

causal agent in
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: 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
imported from: cl.owl
imported from: clo.owl

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
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.
imported from: cl.owl
imported from: clo.owl

has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in'
imported from: cl.owl
imported from: clo.owl

related via dependence to
type: ObjectProperty
definition: A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
imported from: cl.owl
imported from: clo.owl

has_low_plasma_membrane_amount
type: ObjectProperty
sub property of: has plasma membrane part
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. For the formal definition, see Masci et al (PMID:19243617).
imported from: cl.owl

lacks_plasma_membrane_part
type: ObjectProperty
imported from: cl.owl
imported from: clo.owl
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)

has_disease_location
type: ObjectProperty
imported from: clo.owl

has measurement value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: scalar measurement datum
range: double
imported from: obi.owl

has specified numeric value
type: DatatypeProperty
sub property of: has specified value
domain: value specification
range: real
editor preferred label: has specified numeric value
has curation status: IAO_0000120
definition: A relation between a value specification and a number that quantifies it.
editor note: A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
definition editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

has specified value
type: DatatypeProperty
domain: value specification
editor preferred label: has specified value
has curation status: IAO_0000123
definition: A relation between a value specification and a literal.
editor note: This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
definition source: OBI
imported from: obi.owl

date placed in storage
type: DatatypeProperty
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:01:30Z

entity
type: Class
subclass of: Thing
BFO OWL specification label: entity
BFO CLIF specification label: Entity
editor preferred label: entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
imported from: BFO
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: subClassOf
annotated target: Thing
is inferred: true

continuant
type: Class
subclass of: entity
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
editor preferred label: continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: subClassOf
annotated target: entity
is inferred: true

occurrent
type: Class
subclass of: entity
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
editor preferred label: occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: subClassOf
annotated target: entity
is inferred: true

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: occupies spatial region at some time
  some values from: spatial region
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: Class
      union of: specifically dependent continuant
      union of: generically dependent continuant
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: Class
      union of: specifically dependent continuant
      union of: generically dependent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
editor preferred label: independent continuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: subClassOf
annotated target: continuant
is inferred: true

spatial region
type: Class
subclass of: immaterial entity
subclass of: Restriction
  on property: part of continuant at some time
  all values from: spatial region
subclass of: Restriction
  on property: has continuant part at some time
  all values from: spatial region
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: spatial region
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: spatial region
subclass of: Restriction
  on property: occupies spatial region at some time
  has self: true
subclass of: Restriction
  on property: has spatial occupant at some time
  has self: true
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
imported from: ogg.owl
elucidation: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

Axiom
annotated source: spatial region
annotated property: subClassOf
annotated target: immaterial entity
is inferred: true

temporal region
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: has occurrent part
  all values from: temporal region
subclass of: Restriction
  on property: part of occurrent
  all values from: temporal region
subclass of: Restriction
  on property: occupies temporal region
  has self: true
subclass of: Restriction
  on property: has temporal occupant
  has self: true
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
imported from: ogg.owl
elucidation: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
annotated source: temporal region
annotated property: subClassOf
annotated target: occurrent
is inferred: true

spatiotemporal region
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: projects onto spatial region at some time
  some values from: spatial region
subclass of: Restriction
  on property: projects onto temporal region
  some values from: temporal region
subclass of: Restriction
  on property: has occurrent part
  all values from: spatiotemporal region
subclass of: Restriction
  on property: part of occurrent
  all values from: spatiotemporal region
subclass of: Restriction
  on property: has spatiotemporal occupant
  has self: true
subclass of: Restriction
  on property: occupies spatiotemporal region
  has self: true
BFO OWL specification label: st-region
BFO CLIF specification label: SpatiotemporalRegion
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
imported from: ogg.owl
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]

Axiom
annotated source: spatiotemporal region
annotated property: subClassOf
annotated target: occurrent
is inferred: true

process
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: specifically depends on at some time
  some values from: material entity
subclass of: Restriction
  on property: has occurrent part
  all values from: Class
    union of: process
    union of: process boundary
subclass of: Restriction
  on property: part of occurrent
  all values from: process
BFO OWL specification label: process
BFO CLIF specification label: Process
editor preferred label: process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
editor note: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
has associated axiom(fol): (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]

Axiom
annotated source: process
annotated property: subClassOf
annotated target: occurrent
is inferred: true

disposition
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: role
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: role
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
editor preferred label: disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocitosis and exocitosis
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: subClassOf
annotated target: realizable entity
is inferred: true

realizable entity
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: quality
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: quality
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
editor preferred label: realizable entity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

Axiom
annotated source: realizable entity
annotated property: subClassOf
annotated target: specifically dependent continuant
is inferred: true

quality
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: realizable entity
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: realizable entity
BFO OWL specification label: quality
BFO CLIF specification label: Quality
editor preferred label: quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

Axiom
annotated source: quality
annotated property: subClassOf
annotated target: specifically dependent continuant
is inferred: true

specifically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: inheres in at all times
  some values from: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: generically dependent continuant
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: generically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
editor preferred label: specifically dependent continuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
definition: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

Axiom
annotated source: specifically dependent continuant
annotated property: subClassOf
annotated target: continuant
is inferred: true

role
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: disposition
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: disposition
BFO OWL specification label: role
BFO CLIF specification label: Role
editor preferred label: role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: subClassOf
annotated target: realizable entity
is inferred: true

three-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
imported from: ogg.owl
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

Axiom
annotated source: three-dimensional spatial region
annotated property: subClassOf
annotated target: spatial region
is inferred: true

generically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: concretized by at some time
  some values from: specifically dependent continuant
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: specifically dependent continuant
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: specifically dependent continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
editor preferred label: generically dependent continuant
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: generically dependent continuant
annotated property: subClassOf
annotated target: continuant
is inferred: true

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
imported from: obi.owl
elucidation: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: subClassOf
annotated target: disposition
is inferred: true

process boundary
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: exists at
  all values from: zero-dimensional temporal region
subclass of: Restriction
  on property: has occurrent part
  all values from: process boundary
subclass of: Restriction
  on property: occupies spatiotemporal region
  all values from: Class
    intersection of: spatiotemporal region
    intersection of: Restriction
      on property: temporal part of
      some values from: spatiotemporal region
subclass of: Restriction
  on property: part of occurrent
  all values from: Class
    union of: process
    union of: process boundary
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
imported from: obi.owl
imported from: ogg.owl
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]

Axiom
annotated source: process boundary
annotated property: subClassOf
annotated target: occurrent
is inferred: true

material entity
type: Class
subclass of: independent continuant
subclass of: Restriction
  on property: occupies spatial region at some time
  all values from: three-dimensional spatial region
subclass of: Restriction
  on property: part of continuant at some time
  all values from: material entity
subclass of: Restriction
  on property: has continuant part at some time
  all values from: Class
    union of: material entity
    union of: immaterial entity
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: material entity
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: Class
    union of: material entity
    union of: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
editor preferred label: material entity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

Axiom
annotated source: material entity
annotated property: subClassOf
annotated target: independent continuant
is inferred: true

immaterial entity
type: Class
subclass of: independent continuant
subclass of: Restriction
  on property: has continuant part at some time
  all values from: immaterial entity
subclass of: Restriction
  on property: has continuant part at some time
  all values from: Class
    complement of: material entity
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: immaterial entity
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: Class
    complement of: material entity
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
imported from: ogg.owl

Axiom
annotated source: immaterial entity
annotated property: subClassOf
annotated target: independent continuant
is inferred: true

zero-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative term: temporal instant.
imported from: ogg.owl
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

Axiom
annotated source: zero-dimensional temporal region
annotated property: subClassOf
annotated target: temporal region
is inferred: true

anatomical structure
type: Class
subclass of: material anatomical entity
imported from: caro.owl
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: anatomical structure
annotated property: subClassOf
annotated target: material anatomical entity
is inferred: true

material anatomical entity
type: Class
subclass of: material entity
imported from: caro.owl
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: material anatomical entity
annotated property: subClassOf
annotated target: material entity
is inferred: true

cell part
type: Class
subclass of: anatomical structure
imported from: caro.owl
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: cell part
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: deoxyribonucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
imported from: chebi.owl
imported from: obi.owl

Axiom
annotated source: deoxyribonucleic acid
annotated property: subClassOf
annotated target: nucleic acid
is inferred: true

molecular entity
type: Class
subclass of: material entity
editor preferred label: molecular entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
imported from: chebi.owl
imported from: obi.owl

Axiom
annotated source: molecular entity
annotated property: subClassOf
annotated target: material entity
is inferred: true

atom
type: Class
subclass of: material entity
editor preferred label: atom
definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.
imported from: chebi.owl
imported from: obi.owl

Axiom
annotated source: atom
annotated property: subClassOf
annotated target: material entity
is inferred: true

nucleic acid
type: Class
subclass of: macromolecule
editor preferred label: nucleic acid
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
imported from: chebi.owl
imported from: obi.owl

Axiom
annotated source: nucleic acid
annotated property: subClassOf
annotated target: macromolecule
is inferred: true

macromolecule
type: Class
subclass of: molecular entity
editor preferred label: macromolecule
definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
alternative term: polymer
imported from: chebi.owl
imported from: obi.owl

Axiom
annotated source: macromolecule
annotated property: subClassOf
annotated target: molecular entity
is inferred: true

cell line cell
type: Class
subclass of: secondary cultured cell
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: establishing cell line
  union of: Restriction
    on property: derives_from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: establishing cell line
subclass of: Restriction
  on property: derives_from
  some values from: primary cultured cell
editor preferred label: cell line cell
definition: A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
definition editor: Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters
imported from: clo.owl
imported from: obi.owl
comment: A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures.

Axiom
annotated source: cell line cell
annotated property: subClassOf
annotated target: secondary cultured cell
is inferred: true

cell line repository role
type: Class
subclass of: role
definition: a role that inheres in a cell line repository organization.
definition editor: SS, YH
imported from: clo.owl

Axiom
annotated source: cell line repository role
annotated property: subClassOf
annotated target: role
is inferred: true

cell line repository
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: has role
    some values from: cell line repository role
subclass of: organization
definition: an organization that serves as a repository of cell lines.
definition editor: SS, YH
imported from: clo.owl

Axiom
annotated source: cell line repository
annotated property: subClassOf
annotated target: organization
is inferred: true

cell line
type: Class
subclass of: secondary cultured cell population
subclass of: Restriction
  on property: has grain
  some values from: cell line cell
subclass of: Restriction
  on property: has grain
  all values from: cell line cell
editor preferred label: cell line
example of usage: He, Tong-Chuan, et al., Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512.: "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene". Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'.
definition: A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
editor note: In the spring of 2013, a working group comprised of domain experts and representatives from CLO, OBI, CL, and ReO worked to establish a consensus model and definitions of cultured cells across these efforts. This included a careful characterization of how the term 'cell line' should be defined and applied. Notes about this work and its outcomes can be found on the CLO wiki here: http://code.google.com/p/clo-ontology/wiki/Cell_Lines
definition editor: MB, SS, JZ, MAH, BP, CS, YH
imported from: clo.owl
imported from: obi.owl
comment: The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history. As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use.

Axiom
annotated source: cell line
annotated property: subClassOf
annotated target: secondary cultured cell population
is inferred: true

GM00232 cell
type: Class
subclass of: primary cultured human fibroblast cell
subclass of: Restriction
  on property: is disease model for
  some values from: hereditary motor neuropathy proximal type I
subclass of: Restriction
  on property: derives_from
  some values from: Class
    intersection of: fibroblast
    intersection of: Restriction
      on property: part_of
      some values from: Class
        intersection of: EFO_0000635
        intersection of: Restriction
LINCS ID: LPC-1021
Known mutation annotation: only one copy of the SMN2 gene; homozygous for deletion of exons 7 and 8 of the SMN1 gene
definition editor: Chao Pang, Oliver He, Daniel Cooper
alternative term: GM00232
definition source: http://lincsportal.ccs.miami.edu/cells/#/view/LPC-1021
definition source: http://web.expasy.org/cellosaurus/CVCL_Y965
imported from: clo.owl
alternative term: GM-232
comment: SPINAL MUSCULAR ATROPHY I; SMA1
comment: Cell center: NeuroLINCS
comment: Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository
see also: OMIM: 253300

Axiom
annotated source: GM00232 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

stem cell line cell
type: Class
equivalent class: Class
  intersection of: cell line cell
  intersection of: Restriction
    on property: capable of
    some values from: stem cell division
  intersection of: Restriction
    on property: capable of
    some values from: cell differentiation
subclass of: cell line cell
subclass of: Restriction
  on property: capable of
  some values from: stem cell division
subclass of: Restriction
  on property: capable of
  some values from: cell differentiation
definition: A cell line cell that is cultured in vitro and possesses two capabilities: (1) it can self-renew, which means that it can divide indefinitely while remaining in an undifferentiated state; and (2) it is pluripotent or multipotent, which means that it can differentiate to form a specialized cell type.
definition editor: Yongqun He, Sirarat Sarntivijai, Alexander Diehl
definition source: WEB: https://en.wikipedia.org/wiki/Stem-cell_line
imported from: clo.owl
comment: While stem cells hold great promise for biomedical research, the in vitro propagation and maintenance of these cells in an undifferentiated state is essential. Reference: https://www.atcc.org/~/media/7E031EF950594BC3B85A411AE1DC9684.ashx

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

mouse stem cell line cell
type: Class
subclass of: stem cell line cell
imported from: clo.owl
definition: A stem cell line cell that is derived from mouse.
definition editor: YH

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

mouse neural progenitor cell line cell
type: Class
subclass of: mouse stem cell line cell
imported from: clo.owl
definition: A mouse stem cell line cell that is derived from a mouse neural progenitor cell and capable of differentiation in vitro.
definition editor: YH
alternative term: immortalized mouse neural progenitor cell

Axiom
annotated source: mouse neural progenitor cell line cell
annotated property: subClassOf
annotated target: mouse stem cell line cell
is inferred: true

C17.2 cell
type: Class
subclass of: mouse neural progenitor cell line cell
PubChem AID: 1353
definition source: http://web.expasy.org/cellosaurus/CVCL_4511
definition source: http://www.sigmaaldrich.com/catalog/product/sigma/07062902
imported from: clo.owl
definition: An immortalised mouse neural progenitor cell line cell that is capable of differentiation in vitro and is established by retorviral-mediated transduction of the avian myc oncogene into mitotic progenitor cells of neonatal mouse cerrebellum. Mouse strain CD1 x C57BL/6.
definition editor: BAO, YH
see also: BAO: BAO_0030046

Axiom
annotated source: C17.2 cell
annotated property: subClassOf
annotated target: mouse neural progenitor cell line cell
is inferred: true

embryonic stem cell line cell
type: Class
subclass of: stem cell line cell
subclass of: Restriction
  on property: has_quality
  some values from: pluripotent
definition editor: YH, AD
definition source: https://en.wikipedia.org/wiki/Embryonic_stem_cell
imported from: clo.owl
definition: A stem cell line cell that is dervied from an embryotic stem cell, a pluripotent stem cell derived from the inner cell mass of a blastocyst, an early-stage perimplantation embryo.
alternative term: ES cell line cell

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

human embryonic stem cell line cell
type: Class
subclass of: embryonic stem cell line cell
subclass of: Restriction
  on property: derived from organism
  some values from: Homo sapiens
definition editor: YH, AD
alternative term: hES cell line cell
definition source: https://en.wikipedia.org/wiki/Embryonic_stem_cell
imported from: clo.owl
definition: An embryonic stem cell line cell that is dervied from a cell in human embryo.
alternative term: hESC line cell

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

Line H1 cell
type: Class
subclass of: human embryonic stem cell line cell
definition editor: YH, AD
definition source: https://discovery.lifemapsc.com/stem-cell-differentiation/in-vitro-cells/inner-cell-mass-homo-sapiens-line-h1-wa01-wicell-research-institute-inc
imported from: clo.owl
alternative term: H1-hESC
definition: A human ES cell line cell that expresses cell surface markers specific to undifferentiated nonhuman primate ES and human EC cells: : stage-specific embryonic antigen (SSEA)–3, SSEA-4, TRA-l-60, TRA-1- 81, and alkaline phosphatase. It has a normal 46, XY karyotype, O+ blood type. Teratomas are formed upon cell injection into SCID mice. These teratomas include cells from all three germ layers.

Axiom
annotated source: Line H1 cell
annotated property: subClassOf
annotated target: human embryonic stem cell line cell
is inferred: true

primary cultured fibroblast cell
type: Class
subclass of: primary cultured connective tissue cell
subclass of: Restriction
  on property: derived from cell
  some values from: fibroblast
definition editor: Oliver He
imported from: clo.owl
definition: A primary cultured cell that is derived from fibroblast cell in vivo

Axiom
annotated source: primary cultured fibroblast cell
annotated property: subClassOf
annotated target: primary cultured connective tissue cell
is inferred: true

primary cultured human fibroblast cell
type: Class
subclass of: primary cultured fibroblast cell
definition editor: Oliver He
imported from: clo.owl
definition: A primary cultured fibroblast cell that is from human

Axiom
annotated source: primary cultured human fibroblast cell
annotated property: subClassOf
annotated target: primary cultured fibroblast cell
is inferred: true

adult stem cell line cell
type: Class
subclass of: stem cell line cell
subclass of: Restriction
  on property: has_quality
  some values from: multipotent
definition editor: YH, AD
definition source: https://en.wikipedia.org/wiki/Stem-cell_line
imported from: clo.owl
definition: A stem cell line cell that is multipotent and is isolated and prepared from an juvenile or adult tissue.

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

hematopoetic stem cell line cell
type: Class
subclass of: adult stem cell line cell
definition editor: YH, AD
definition source: https://en.wikipedia.org/wiki/Stem-cell_line
imported from: clo.owl
definition: An adult stem cell line cell that is isolated and prepared using bone marrow tissue and is able to generate all cells of the immune system and all blood cell types.
comment: Of the types of adult stem cells have successfully been isolated and identified, only mesenchymal stem cells can successfully be grown in culture for long periods of time. Hematopoietic stem cells are difficult to grow and propagate in vitro.[4] Identifying methods for maintaining hematopoietic stem cells in vitro is an active area of research. Reference: https://en.wikipedia.org/wiki/Stem-cell_line

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

mesenchymal stem cell line cell
type: Class
subclass of: adult stem cell line cell
definition editor: YH
definition source: https://en.wikipedia.org/wiki/Stem-cell_line
imported from: clo.owl
definition: An adult stem cell line cell that is isolated and prepared using umbilical cord blood, amniotic fluid, and adipose tissue and can generate a number of cell types, including osteoblasts, chondrocytes, and adipocytes.
alternative term: MSC line cell

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

umbilical cord mesenchymal stem cell line cell
type: Class
subclass of: mesenchymal stem cell line cell
definition editor: YH, AD
definition source: https://en.wikipedia.org/wiki/Stem-cell_line
imported from: clo.owl
definition: A mesenchymal stem cell line cell that is isolated and prepared using umbilical cord blood.

Axiom
annotated source: umbilical cord mesenchymal stem cell line cell
annotated property: subClassOf
annotated target: mesenchymal stem cell line cell
is inferred: true

induced pluripotent stem cell line cell
type: Class
subclass of: stem cell line cell
subclass of: Restriction
  on property: has_quality
  some values from: pluripotent
subclass of: Restriction
  on property: derived from cell
  some values from: cell in vitro
definition editor: YH, AD
definition source: https://en.wikipedia.org/wiki/Embryonic_stem_cell
definition source: https://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell
definition source: https://www.ncbi.nlm.nih.gov/pubmed/16904174
imported from: clo.owl
definition: A stem cell line cell that is pluripotent and is generated from an adult somatic cell.
alternative term: iPS cell
alternative term: iPSC

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

human induced pluripotent stem cell line cell
type: Class
subclass of: induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from organism
  some values from: Homo sapiens
definition editor: YH, AD
imported from: clo.owl
definition: An induced pluripotent stem cell line cell that is derived from a human cell.
alternative term: human iPS cell line cell

Axiom
annotated source: human induced pluripotent stem cell line cell
annotated property: subClassOf
annotated target: induced pluripotent stem cell line cell
is inferred: true

H9 ES cell
type: Class
subclass of: human embryonic stem cell line cell
subclass of: Restriction
  on property: is in cell line repository
  has value: CLO_0037314
LINCS ID: LES-1001
definition editor: LINCS team, YH
definition source: http://lincsportal.ccs.miami.edu/cells/#/view/LES-1001
definition source: https://discovery.lifemapsc.com/stem-cell-differentiation/in-vitro-cells/inner-cell-mass-homo-sapiens-line-h9-wa09-wicell-research-institute-inc
imported from: clo.owl
comment: This human ES cell line expresses cell surface markers specific to undifferentiated nonhuman primate ES and human EC cells: stage-specific embryonic antigen (SSEA)–3, SSEA-4, TRA-l-60, TRA-1- 81, and alkaline phosphatase. It has a normal 46, XX karyotype. Teratomas are formed upon cell injection into SCID mice. These teratomas include cells from all three germ layers.

Axiom
annotated source: H9 ES cell
annotated property: subClassOf
annotated target: human embryonic stem cell line cell
is inferred: true

HUES3 ES cell
type: Class
subclass of: human embryonic stem cell line cell
subclass of: Restriction
  on property: is in cell line repository
  has value: CLO_0037315
LINCS ID: LES-1002
definition editor: LINCS team, YH
definition source: http://lincsportal.ccs.miami.edu/cells/#/view/LES-1002
definition source: https://grants.nih.gov/stem_cells/registry/current.htm
imported from: clo.owl
alternative term: HUES 3

Axiom
annotated source: HUES3 ES cell
annotated property: subClassOf
annotated target: human embryonic stem cell line cell
is inferred: true

mouse embryonic stem cell line cell
type: Class
subclass of: embryonic stem cell line cell
subclass of: Restriction
  on property: derived from organism
  some values from: Mus musculus
definition editor: YH
alternative term: mES cell line cell
definition source: https://en.wikipedia.org/wiki/Embryonic_stem_cell
imported from: clo.owl
definition: A embryotic stem cell line cell that is dervied from a cell in mouse embryo.
alternative term: mESC line cell

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

somatic cell nuclear transfer-derived stem cell line cell
type: Class
subclass of: stem cell line cell
subclass of: Restriction
  on property: has_quality
  some values from: pluripotent
definition editor: YH, AD
definition source: https://en.wikipedia.org/wiki/Somatic_cell_nuclear_transfer#Stem_cell_research
imported from: clo.owl
definition: A stem cell line cell that is dervied from using the somatic cell nuclear transfer method.
alternative term: SCNT-derived stem cell line cell

Axiom
annotated source: somatic cell nuclear transfer-derived stem cell line cell
annotated property: subClassOf
annotated target: stem cell line cell
is inferred: true

human embryonic stem cell line cell derived by somatic cell nuclear transfer
type: Class
subclass of: human embryonic stem cell line cell
subclass of: somatic cell nuclear transfer-derived stem cell line cell
subclass of: Restriction
  on property: has_quality
  some values from: pluripotent
definition editor: YH
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772789/
imported from: clo.owl
definition: a human embryonic stem cell line cell that is derived by somatic cell nuclear transfer
alternative term: human embryonic stem cell line cell derived by SCNT

Axiom
annotated source: human embryonic stem cell line cell derived by somatic cell nuclear transfer
annotated property: subClassOf
annotated target: human embryonic stem cell line cell
is inferred: true

Axiom
annotated source: human embryonic stem cell line cell derived by somatic cell nuclear transfer
annotated property: subClassOf
annotated target: somatic cell nuclear transfer-derived stem cell line cell
is inferred: true

human fibroblast-induced pluripotent stem cell line cell
type: Class
subclass of: human induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: primary cultured human fibroblast cell
imported from: clo.owl
alternative term: human fibroblast-iPS cell line cell

Axiom
annotated source: human fibroblast-induced pluripotent stem cell line cell
annotated property: subClassOf
annotated target: human induced pluripotent stem cell line cell
is inferred: true

primary cultured connective tissue cell
type: Class
subclass of: primary cultured cell
subclass of: Restriction
  on property: derived from cell
  some values from: connective tissue cell
definition editor: Oliver He
imported from: clo.owl
definition: A primary cultured cell that is derived from in vivo connective tissue cell

Axiom
annotated source: primary cultured connective tissue cell
annotated property: subClassOf
annotated target: primary cultured cell
is inferred: true

GM03814 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1014
Known mutation annotation: Donor subject has two copies of the SMN2 and is heterozygous for deletion of exons 7 and 8 in the SMN1 gene
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository

Axiom
annotated source: GM03814 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

GM02183 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1015
Known mutation annotation: Unclassified
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository

Axiom
annotated source: GM02183 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

ND30625 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1016
Known mutation annotation: CAG length Allele 1 = 18; Allele 2 = 17
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository

Axiom
annotated source: ND30625 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

F09128 cell
type: Class
subclass of: primary cultured human fibroblast cell
subclass of: Restriction
  on property: derives from patient having disease
  some values from: EFO_0000253
LINCS ID: LPC-1017
Known mutation annotation: C9orf72; repeat number not indicated
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Wasington University; Cell provider catalog number: Wasington University

Axiom
annotated source: F09128 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

F09229 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1018
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: F09229 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

F10-330 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1019
Known mutation annotation: C9orf72; repeat number not indicated
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Wasington University; Cell provider catalog number: Wasington University

Axiom
annotated source: F10-330 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

F09152 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1020
Known mutation annotation: C9orf72; repeat number not indicated
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Wasington University; Cell provider catalog number: Wasington University

Axiom
annotated source: F09152 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

83 Fibroblast cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1022
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository

Axiom
annotated source: 83 Fibroblast cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

GM09677 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1023
Known mutation annotation: donor subject has 2 copies of the SMN2 gene and is homozygous for deletion of exons 7 and 8 of the SMN1 gene
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository

Axiom
annotated source: GM09677 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

MSF01 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1024
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS
comment: Cell provider: ISMMS; Cell provider catalog number: ISMMS

Axiom
annotated source: MSF01 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

MSF02 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1025
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS
comment: Cell provider: ISMMS; Cell provider catalog number: ISMMS

Axiom
annotated source: MSF02 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

MSF03 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1026
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS
comment: Cell provider: ISMMS; Cell provider catalog number: ISMMS

Axiom
annotated source: MSF03 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

MSF05 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1028
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS
comment: Cell provider: ISMMS; Cell provider catalog number: ISMMS

Axiom
annotated source: MSF05 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

MSF06 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1029
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS
comment: Cell provider: ISMMS; Cell provider catalog number: ISMMS

Axiom
annotated source: MSF06 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

MSF08 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1031
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS
comment: Cell provider: ISMMS; Cell provider catalog number: ISMMS

Axiom
annotated source: MSF08 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

MSF09 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1032
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS
comment: Cell provider: ISMMS; Cell provider catalog number: ISMMS

Axiom
annotated source: MSF09 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

MSF10 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1033
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS
comment: Cell provider: ISMMS; Cell provider catalog number: ISMMS

Axiom
annotated source: MSF10 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

GM05400 cell
type: Class
subclass of: primary cultured human fibroblast cell
LINCS ID: LPC-1044
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Coriell Cell Repository; Cell provider catalog number: Coriell Cell Repository

Axiom
annotated source: GM05400 cell
annotated property: subClassOf
annotated target: primary cultured human fibroblast cell
is inferred: true

W14-C146 cell
type: Class
subclass of: primary cultured cell
LINCS ID: LPC-1054
Known mutation annotation: ALS-Sporadic
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: W14-C146 cell
annotated property: subClassOf
annotated target: primary cultured cell
is inferred: true

F13-C004 cell
type: Class
subclass of: primary cultured cell
LINCS ID: LPC-1055
Known mutation annotation: ALS-SOD1
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: F13-C004 cell
annotated property: subClassOf
annotated target: primary cultured cell
is inferred: true

W15-C166 cell
type: Class
subclass of: primary cultured cell
LINCS ID: LPC-1056
Known mutation annotation: ALS-Sporadic
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: W15-C166 cell
annotated property: subClassOf
annotated target: primary cultured cell
is inferred: true

SAB-701-022 cell
type: Class
subclass of: primary cultured cell
LINCS ID: LPC-1057
Known mutation annotation: ALS-SOD1
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: SAB-701-022 cell
annotated property: subClassOf
annotated target: primary cultured cell
is inferred: true

W14-C138 cell
type: Class
subclass of: primary cultured cell
LINCS ID: LPC-1058
Known mutation annotation: ALS-Sporadic
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: W14-C138 cell
annotated property: subClassOf
annotated target: primary cultured cell
is inferred: true

W14-C152 cell
type: Class
subclass of: primary cultured cell
LINCS ID: LPC-1059
Known mutation annotation: ALS-Sporadic
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: W14-C152 cell
annotated property: subClassOf
annotated target: primary cultured cell
is inferred: true

CS14iCTR-n6 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: GM03814 cell
LINCS ID: LSC-1002
Known mutation annotation: Donor subject has two copies of the SMN2 and is heterozygous for deletion of exons 7 and 8 in the SMN1 gene
Cell culture condition: mTeSR1, Growth Factor Reduced Matrigel
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS14iCTR-n6

Axiom
annotated source: CS14iCTR-n6 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS83iCTR-33n1 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: GM02183 cell
LINCS ID: LSC-1003
Known mutation annotation: Unclassified
Cell culture condition: mTeSR1, Growth Factor Reduced Matrigel
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS83iCTR-33n1

Axiom
annotated source: CS83iCTR-33n1 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS25iCTR-18n2 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: ND30625 cell
LINCS ID: LSC-1004
Known mutation annotation: CAG length Allele 1 = 18; Allele 2 = 17
Cell culture condition: mTeSR1, Growth Factor Reduced Matrigel
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS25iCTR-18n2

Axiom
annotated source: CS25iCTR-18n2 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS28iALS-n2A cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: F09128 cell
LINCS ID: LSC-1005
Known mutation annotation: C9orf72; repeat number not indicated
Cell culture condition: mTeSR1, Growth Factor Reduced Matrigel
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS28iALS-n2A

Axiom
annotated source: CS28iALS-n2A cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS29iALS-n1N cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: F09229 cell
LINCS ID: LSC-1006
Known mutation annotation: C9orf72; repeat number not indicated
Cell culture condition: mTeSR1, Growth Factor Reduced Matrigel
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS29iALS-n1N

Axiom
annotated source: CS29iALS-n1N cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS30iALS-n1N cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: F10-330 cell
LINCS ID: LSC-1007
Known mutation annotation: C9orf72; repeat number not indicated
Cell culture condition: mTeSR1, Growth Factor Reduced Matrigel
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS30iALS-n1N

Axiom
annotated source: CS30iALS-n1N cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS52iALS-n6A cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: F09152 cell
LINCS ID: LSC-1008
Known mutation annotation: C9orf72; repeat number not indicated
Cell culture condition: mTeSR1, Growth Factor Reduced Matrigel
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS52iALS-n6A

Axiom
annotated source: CS52iALS-n6A cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS32iSMA-n3 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: GM00232 cell
LINCS ID: LSC-1009
Known mutation annotation: only one copy of the SMN2 gene; homozygous for deletion of exons 7 and 8 of the SMN1 gene
Cell culture condition: mTeSR1, Growth Factor Reduced Matrigel
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS32iSMA-n3

Axiom
annotated source: CS32iSMA-n3 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS83iSMA-n5 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: 83 Fibroblast cell
LINCS ID: LSC-1011
Known mutation annotation: Unknown
Cell culture condition: mTeSR1, Growth Factor Reduced Matrigel
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS83iSMA-n5

Axiom
annotated source: CS83iSMA-n5 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS77iSMA-n5 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: GM09677 cell
LINCS ID: LSC-1012
Known mutation annotation: donor subject has 2 copies of the SMN2 gene and is homozygous for deletion of exons 7 and 8 of the SMN1 gene
Cell culture condition: mTeSR1, Growth Factor Reduced Matrigel
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS
comment: Cell provider: Cedars-Sinai Stem Cell Core Laboratory; Cell provider catalog number: CS77iSMA-n5

Axiom
annotated source: CS77iSMA-n5 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

MSN01-3 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: MSF01 cell
LINCS ID: LSC-1013
Known mutation annotation: none/healthy
Cell culture condition: human pluripotent stem cell medium, includign mTeSR
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS

Axiom
annotated source: MSN01-3 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

MSN03-7 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: MSF03 cell
LINCS ID: LSC-1014
Known mutation annotation: none/healthy
Cell culture condition: human pluripotent stem cell medium, includign mTeSR
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS

Axiom
annotated source: MSN03-7 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

MSN05-1 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: MSF05 cell
LINCS ID: LSC-1015
Known mutation annotation: none/healthy
Cell culture condition: human pluripotent stem cell medium, includign mTeSR
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS

Axiom
annotated source: MSN05-1 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

MSN06-7 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: MSF06 cell
LINCS ID: LSC-1016
Known mutation annotation: none/healthy
Cell culture condition: human pluripotent stem cell medium, includign mTeSR
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS

Axiom
annotated source: MSN06-7 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

MSN02-4 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: MSF02 cell
LINCS ID: LSC-1017
Known mutation annotation: none/healthy
Cell culture condition: human pluripotent stem cell medium, includign mTeSR
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS

Axiom
annotated source: MSN02-4 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

MSN08-13 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: MSF08 cell
LINCS ID: LSC-1018
Known mutation annotation: none/healthy
Cell culture condition: human pluripotent stem cell medium, includign mTeSR
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS

Axiom
annotated source: MSN08-13 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

MSN09-4 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: MSF09 cell
LINCS ID: LSC-1019
Known mutation annotation: none/healthy
Cell culture condition: human pluripotent stem cell medium, includign mTeSR
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS

Axiom
annotated source: MSN09-4 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

MSN10-1 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: MSF10 cell
LINCS ID: LSC-1020
Known mutation annotation: none/healthy
Cell culture condition: human pluripotent stem cell medium, includign mTeSR
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: DToxS

Axiom
annotated source: MSN10-1 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

FIBRNPC cell
type: Class
subclass of: stem cell line cell
LINCS ID: LSC-1021
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: BROAD_T

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

CS14isALS-Tn16 cell
type: Class
subclass of: stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: W14-C146 cell
LINCS ID: LSC-1022
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS14isALS-Tn16 cell
annotated property: subClassOf
annotated target: stem cell line cell
is inferred: true

CS04iALS-SOD1H44Rn3 cell
type: Class
subclass of: stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: F13-C004 cell
LINCS ID: LSC-1023
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS04iALS-SOD1H44Rn3 cell
annotated property: subClassOf
annotated target: stem cell line cell
is inferred: true

CS00iCTR-n2 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: GM05400 cell
LINCS ID: LSC-1024
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS00iCTR-n2 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS29iALS-C9n1 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: F09229 cell
LINCS ID: LSC-1025
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS29iALS-C9n1 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS30iALS-C9n1 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: F10-330 cell
LINCS ID: LSC-1026
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS30iALS-C9n1 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS166isALS-Tn2 cell
type: Class
subclass of: stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: W15-C166 cell
LINCS ID: LSC-1027
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS166isALS-Tn2 cell
annotated property: subClassOf
annotated target: stem cell line cell
is inferred: true

CS22iALS-SOD1I113Tn2 cell
type: Class
subclass of: stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: SAB-701-022 cell
LINCS ID: LSC-1028
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS22iALS-SOD1I113Tn2 cell
annotated property: subClassOf
annotated target: stem cell line cell
is inferred: true

CS138isALS-Tn1 cell
type: Class
subclass of: stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: W14-C138 cell
LINCS ID: LSC-1029
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS138isALS-Tn1 cell
annotated property: subClassOf
annotated target: stem cell line cell
is inferred: true

CS152isALS-Tn2 cell
type: Class
subclass of: stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: W14-C152 cell
LINCS ID: LSC-1030
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS152isALS-Tn2 cell
annotated property: subClassOf
annotated target: stem cell line cell
is inferred: true

CS28iALS-C9n2 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: F09128 cell
LINCS ID: LSC-1031
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS28iALS-C9n2 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS52iALS-C9n6 cell
type: Class
subclass of: human fibroblast-induced pluripotent stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: F09152 cell
LINCS ID: LSC-1032
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS52iALS-C9n6 cell
annotated property: subClassOf
annotated target: human fibroblast-induced pluripotent stem cell line cell
is inferred: true

CS11iALS-SOD1I113Tn10 cell
type: Class
subclass of: stem cell line cell
subclass of: Restriction
  on property: derived from cell
  some values from: F13-C004 cell
LINCS ID: LSC-1033
definition editor: Daniel Cooper, Oliver He
imported from: clo.owl
comment: Cell center: NeuroLINCS

Axiom
annotated source: CS11iALS-SOD1I113Tn10 cell
annotated property: subClassOf
annotated target: stem cell line cell
is inferred: true

cell type
type: Class
equivalent class: cell
subclass of: anatomical structure
subclass of: cellular_component
editor preferred label: cell
example of usage: PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
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.
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
database_cross_reference: CALOHA:TS-2035
database_cross_reference: FMA:68646
database_cross_reference: GO:0005623
database_cross_reference: KUPO:0000002
database_cross_reference: VHOG:0001533
database_cross_reference: WBbt:0004017
database_cross_reference: XAO:0003012
has_obo_namespace: cell
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).
label: cell
see also: EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000324

Axiom
annotated source: cell type
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: cell type
annotated property: subClassOf
annotated target: cellular_component
is inferred: true

primary cultured cell
type: Class
subclass of: cultured cell
subclass of: Class
  complement of: Restriction
    on property: is_specified_output_of
    some values from: cell culture splitting
subclass of: Class
  complement of: Restriction
    on property: derives_from
    some values from: Class
      intersection of: cultured cell
      intersection of: Restriction
        on property: is_specified_output_of
        some values from: cell culture splitting
editor preferred label: primary 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.
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: primary cultured cell
annotated property: subClassOf
annotated target: cultured cell
is inferred: true

native cell
type: Class
subclass of: cell type
subclass of: cell
definition: 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).
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
database_cross_reference: CARO:0000013
has_narrow_synonym: cell in vivo
has_obo_namespace: cell
in subset: upper level
comment: To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).

Axiom
annotated source: native cell
annotated property: subClassOf
annotated target: cell type
is inferred: true

Axiom
annotated source: native cell
annotated property: subClassOf
annotated target: cell
is inferred: true

neuronal receptor cell
type: Class
equivalent class: Class
  intersection of: receptor cell
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: detection of stimulus involved in sensory perception
subclass of: sensory neuron
subclass of: receptor cell
subclass of: Restriction
  on property: capable of
  some values from: detection of stimulus involved in sensory perception
imported from: cl.owl
has exact synonym: neuronal receptor cell (sensu Animalia)
has_obo_namespace: cell

Axiom
annotated source: neuronal receptor cell
annotated property: subClassOf
annotated target: sensory neuron
is inferred: true

Axiom
annotated source: neuronal receptor cell
annotated property: subClassOf
annotated target: receptor cell
is inferred: true

migratory cranial neural crest cell
type: Class
subclass of: migratory neural crest cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: migratory cranial neural crest cell
annotated property: subClassOf
annotated target: migratory neural crest cell
is inferred: true

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: establishing cell culture
  union of: Restriction
    on property: derives_from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: establishing cell culture
editor preferred label: cultured cell
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
has_obo_namespace: cell
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: subClassOf
annotated target: experimentally modified cell in vitro
is inferred: true

migratory trunk neural crest cell
type: Class
subclass of: migratory neural crest cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: migratory trunk neural crest cell
annotated property: subClassOf
annotated target: migratory neural crest cell
is inferred: 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: stem cell division
subclass of: stem cell
subclass of: germ line cell
subclass of: Restriction
  on property: capable of
  some values from: stem cell division
imported from: cl.owl
has exact synonym: germline stem cell
has_obo_namespace: cell

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: subClassOf
annotated target: germ line cell
is inferred: true

male germ cell
type: Class
equivalent class: Class
  intersection of: germ cell
  intersection of: Restriction
    on property: capable of
    some values from: spermatogenesis
subclass of: germ cell
subclass of: Restriction
  on property: capable of
  some values from: spermatogenesis
imported from: cl.owl
database_cross_reference: FMA:72290
database_cross_reference: MA:0002765
database_cross_reference: VHOG:0001531
database_cross_reference: ncithesaurus:Spermatogenic_Cell
has_obo_namespace: cell

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

male germ line stem cell
type: Class
subclass of: germ line stem cell
subclass of: male germ cell
imported from: cl.owl
has_obo_namespace: cell

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

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

female germ cell
type: Class
equivalent class: Class
  intersection of: germ cell
  intersection of: Restriction
    on property: capable of
    some values from: oogenesis
subclass of: germ cell
subclass of: Restriction
  on property: capable of
  some values from: oogenesis
definition: Female germ cell is a germ cell that supports female gamete production.
imported from: cl.owl
database_cross_reference: MA:0000388
database_cross_reference: VHOG:0001530
database_cross_reference: ncithesaurus:Egg
has_obo_namespace: cell

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

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: stem cell division
subclass of: germ line stem cell
subclass of: female germ cell
subclass of: Restriction
  on property: capable of
  some values from: stem cell division
imported from: cl.owl
has_obo_namespace: cell

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

neuroblast
type: Class
subclass of: neuronal stem cell
subclass of: non-terminally differentiated cell
definition: A cell that will develop into a neuron often after a migration phase.
imported from: cl.owl
database_cross_reference: BTO:0000930
database_cross_reference: FBbt:00005146
database_cross_reference: FMA:70563
has_obo_namespace: cell

Axiom
annotated source: neuroblast
annotated property: subClassOf
annotated target: neuronal stem cell
is inferred: true

Axiom
annotated source: neuroblast
annotated property: subClassOf
annotated target: non-terminally differentiated cell
is inferred: true

stem cell
type: Class
equivalent class: Class
  intersection of: native cell
  intersection of: Restriction
    on property: capable of
    some values from: stem cell division
subclass of: precursor cell
subclass of: Restriction
  on property: capable of
  some values from: stem cell division
subclass of: Restriction
  on property: capable of
  some values from: cell differentiation
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.
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
database_cross_reference: CALOHA:TS-2086
database_cross_reference: FMA:63368
has_obo_namespace: cell

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

single fate stem cell
type: Class
equivalent class: Class
  intersection of: native cell
  intersection of: Restriction
    on property: bearer of
    some values from: unipotent
  intersection of: Restriction
    on property: capable of
    some values from: stem cell division
subclass of: somatic stem cell
subclass of: Restriction
  on property: bearer of
  some values from: unipotent
subclass of: Restriction
  on property: capable of
  some values from: stem cell division
definition: A stem cell that self-renews as well as give rise to a single mature cell type.
imported from: cl.owl
database_cross_reference: FMA:70569
has exact synonym: unipotent stem cell
has exact synonym: unipotential stem cell
has_obo_namespace: cell

Axiom
annotated source: single fate stem cell
annotated property: subClassOf
annotated target: somatic stem cell
is inferred: true

epithelial fate stem cell
type: Class
subclass of: single fate stem cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: epithelial fate stem cell
annotated property: subClassOf
annotated target: single fate stem cell
is inferred: true

hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: hematopoietic cell
  intersection of: Restriction
    on property: capable of
    some values from: hematopoietic progenitor cell differentiation
  intersection of: Restriction
    on property: capable of
    some values from: somatic stem cell division
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: CD19 molecule
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: CD4 molecule
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: integrin alpha-M
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: CD3 epsilon
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: neural cell adhesion molecule 1
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: CD2 molecule
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: T-cell surface glycoprotein CD8 alpha chain
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: membrane-spanning 4-domains subfamily A member 1
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: T-cell surface glycoprotein CD5
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: CD14 molecule
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: lymphocyte antigen 6G
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: lymphocyte antigen 76
subclass of: somatic stem cell
subclass of: hematopoietic precursor cell
subclass of: Restriction
  on property: develops from
  some values from: angioblastic mesenchymal cell
subclass of: Restriction
  on property: capable of
  some values from: hematopoietic progenitor cell differentiation
subclass of: Restriction
  on property: capable of
  some values from: somatic stem cell division
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: CD19 molecule
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: CD4 molecule
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: integrin alpha-M
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: CD3 epsilon
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: neural cell adhesion molecule 1
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: CD2 molecule
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: T-cell surface glycoprotein CD8 alpha chain
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: membrane-spanning 4-domains subfamily A member 1
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: T-cell surface glycoprotein CD5
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: CD14 molecule
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: lymphocyte antigen 6G
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: lymphocyte antigen 76
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.
imported from: cl.owl
database_cross_reference: BTO:0000725
database_cross_reference: CALOHA:TS-0448
database_cross_reference: FMA:70337
database_cross_reference: FMA:86475
database_cross_reference: VHOG:0001485
has exact synonym: HSC
has exact synonym: blood forming stem cell
has exact synonym: hemopoietic stem cell
has_obo_namespace: cell
has_related_synonym: colony forming unit hematopoietic
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: subClassOf
annotated target: somatic stem cell
is inferred: true

Axiom
annotated source: hematopoietic stem cell
annotated property: subClassOf
annotated target: hematopoietic precursor cell
is inferred: true

germ line cell
type: Class
subclass of: animal cell
subclass of: Restriction
  on property: capable of
  some values from: reproductive process
definition: A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
imported from: cl.owl
has_obo_namespace: cell
in subset: upper level
comment: Originally this term had some plant germ line cell children.

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

neuronal stem cell
type: Class
equivalent class: Class
  intersection of: multi fate stem cell
  intersection of: Restriction
    on property: part_of
    some values from: central nervous system
subclass of: multi fate stem cell
subclass of: neural cell
subclass of: Restriction
  on property: part_of
  some values from: central nervous system
subclass of: Restriction
  on property: develops from
  some values from: neurectodermal cell
definition: Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors.
imported from: cl.owl
database_cross_reference: BTO:0002881
database_cross_reference: CALOHA:TS-2360
database_cross_reference: FMA:86684
has exact synonym: NSC
has exact synonym: neural stem cell
has_obo_namespace: cell

Axiom
annotated source: neuronal stem cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

Axiom
annotated source: neuronal stem cell
annotated property: subClassOf
annotated target: neural cell
is inferred: true

multi fate stem cell
type: Class
equivalent class: Class
  intersection of: somatic cell
  intersection of: Restriction
    on property: bearer of
    some values from: multipotent
  intersection of: Restriction
    on property: capable of
    some values from: stem cell division
subclass of: stem cell
subclass of: somatic cell
subclass of: Restriction
  on property: bearer of
  some values from: multipotent
subclass of: Restriction
  on property: capable of
  some values from: stem cell division
definition: A stem cell that can give rise to multiple lineages of cells.
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
database_cross_reference: FMA:84789
has exact synonym: multi-fate stem cell
has exact synonym: multifate stem cell
has exact synonym: multipotent cell
has exact synonym: multipotent stem cell
has_obo_namespace: cell

Axiom
annotated source: multi fate stem cell
annotated property: subClassOf
annotated target: stem cell
is inferred: true

Axiom
annotated source: multi fate stem cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

totipotent stem cell
type: Class
subclass of: somatic stem cell
definition: A stem cell from which all cells of the body can form.
imported from: cl.owl
database_cross_reference: FMA:84790
has exact synonym: totipotential stem cell
has_obo_namespace: cell

Axiom
annotated source: totipotent stem cell
annotated property: subClassOf
annotated target: somatic stem cell
is inferred: true

non-terminally differentiated cell
type: Class
subclass of: precursor cell
subclass of: Restriction
  on property: capable of
  some values from: cell differentiation
definition: A precursor cell with a limited number of potential fates.
imported from: cl.owl
database_cross_reference: BTO:0000125
database_cross_reference: FMA:84782
has exact synonym: blast cell
has_obo_namespace: cell
comment: define using PATO mulit-potent or oligopotent?

Axiom
annotated source: non-terminally differentiated cell
annotated property: subClassOf
annotated target: precursor cell
is inferred: true

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.
imported from: cl.owl
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
has_obo_namespace: cell

Axiom
annotated source: myoblast
annotated property: subClassOf
annotated target: muscle precursor cell
is inferred: true

fibroblast
type: Class
subclass of: connective tissue cell
subclass of: Restriction
  on property: develops from
  some values from: mesenchymal stem 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.
definition editor: James Malone
definition editor: Tomasz Adamusiak
alternative term: mouse embryonic fibroblast
alternative term: primary dermal fibroblast
definition source: BTO:0000452
definition source: CL:0000057
definition source: NIFSTD:nlx_cell_20090201
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
database_cross_reference: BTO:0000452
database_cross_reference: CALOHA:TS-0362
database_cross_reference: FMA:63877
database_cross_reference: VHOG:0001482
has_obo_namespace: cell
comment: A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules.
comment: A connective-tissue cell of mesenchymal origin that secretes proteins and especially molecular collagen from which the extracellular fibrillar matrix of connective tissue forms.
comment: A large, flat, oval cell found in connective tissue and responsible for the formation of fibers.
comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.
see also: EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000496
see also: URI: http://www.ebi.ac.uk/cellline#fibroblast

Axiom
annotated source: fibroblast
annotated property: subClassOf
annotated target: connective tissue cell
is inferred: true

epithelial cell
type: Class
equivalent class: Class
  intersection of: animal cell
  intersection of: Restriction
    on property: part_of
    some values from: epithelium
subclass of: animal cell
subclass of: Restriction
  on property: part_of
  some values from: epithelium
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.
imported from: cl.owl
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
has exact synonym: epitheliocyte
has_obo_namespace: cell

Axiom
annotated source: epithelial cell
annotated property: subClassOf
annotated target: animal cell
is inferred: true

duct epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: duct
subclass of: epithelial cell
subclass of: somatic cell
subclass of: Restriction
  on property: part_of
  some values from: duct
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: duct epithelial cell
annotated property: subClassOf
annotated target: epithelial cell
is inferred: true

Axiom
annotated source: duct epithelial cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

branched duct epithelial cell
type: Class
subclass of: duct epithelial cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: branched duct epithelial cell
annotated property: subClassOf
annotated target: duct epithelial cell
is inferred: true

columnar/cuboidal epithelial cell
type: Class
subclass of: epithelial cell
subclass of: somatic cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: columnar/cuboidal epithelial cell
annotated property: subClassOf
annotated target: epithelial cell
is inferred: true

Axiom
annotated source: columnar/cuboidal epithelial cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

squamous epithelial cell
type: Class
subclass of: epithelial cell
imported from: cl.owl
database_cross_reference: CALOHA:TS-1249
has_obo_namespace: cell

Axiom
annotated source: squamous epithelial cell
annotated property: subClassOf
annotated target: epithelial cell
is inferred: true

stratified epithelial cell
type: Class
subclass of: epithelial cell
subclass of: somatic cell
subclass of: Restriction
  on property: develops from
  some values from: stratified epithelial stem cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: stratified epithelial cell
annotated property: subClassOf
annotated target: epithelial cell
is inferred: true

Axiom
annotated source: stratified epithelial cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

circulating cell
type: Class
equivalent class: Class
  intersection of: native cell
  intersection of: Restriction
    on property: part_of
    some values from: haemolymphatic fluid
subclass of: native cell
subclass of: Restriction
  on property: part_of
  some values from: haemolymphatic fluid
definition: A cell which moves among different tissues of the body, via blood, lymph, or other medium.
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: circulating cell
annotated property: subClassOf
annotated target: native cell
is inferred: true

epithelial cell of lung
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: lung
subclass of: epithelial cell
subclass of: Restriction
  on property: part_of
  some values from: lung epithelium
subclass of: Restriction
  on property: part_of
  some values from: lung
imported from: cl.owl
database_cross_reference: BTO:0004299
has exact synonym: lung epithelial cell
has_obo_namespace: cell

Axiom
annotated source: epithelial cell of lung
annotated property: subClassOf
annotated target: epithelial cell
is inferred: true

germ line stem cell (sensu Vertebrata)
type: Class
subclass of: germ line stem cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: germ line stem cell (sensu Vertebrata)
annotated property: subClassOf
annotated target: germ line stem cell
is inferred: true

germ line stem cell (sensu Nematoda and Protostomia)
type: Class
subclass of: germ line stem cell
imported from: cl.owl
database_cross_reference: FBbt:00004861
has_obo_namespace: cell

Axiom
annotated source: germ line stem cell (sensu Nematoda and Protostomia)
annotated property: subClassOf
annotated target: germ line stem cell
is inferred: true

male germ line stem cell (sensu Nematoda and Protostomia)
type: Class
subclass of: male germ line stem cell
subclass of: germ line stem cell (sensu Nematoda and Protostomia)
imported from: cl.owl
database_cross_reference: FBbt:00004929
has_obo_namespace: cell

Axiom
annotated source: male germ line stem cell (sensu Nematoda and Protostomia)
annotated property: subClassOf
annotated target: male germ line stem cell
is inferred: true

Axiom
annotated source: male germ line stem cell (sensu Nematoda and Protostomia)
annotated property: subClassOf
annotated target: germ line stem cell (sensu Nematoda and Protostomia)
is inferred: true

female germ line stem cell (sensu Nematoda and Protostomia)
type: Class
subclass of: female germ line stem cell
subclass of: germ line stem cell (sensu Nematoda and Protostomia)
imported from: cl.owl
database_cross_reference: FBbt:00004873
has_obo_namespace: cell

Axiom
annotated source: female germ line stem cell (sensu Nematoda and Protostomia)
annotated property: subClassOf
annotated target: female germ line stem cell
is inferred: true

Axiom
annotated source: female germ line stem cell (sensu Nematoda and Protostomia)
annotated property: subClassOf
annotated target: germ line stem cell (sensu Nematoda and Protostomia)
is inferred: true

male germ line stem cell (sensu Vertebrata)
type: Class
subclass of: male germ line stem cell
subclass of: germ line stem cell (sensu Vertebrata)
imported from: cl.owl
has exact synonym: spermatogonial stem cell
has_obo_namespace: cell

Axiom
annotated source: male germ line stem cell (sensu Vertebrata)
annotated property: subClassOf
annotated target: male germ line stem cell
is inferred: true

Axiom
annotated source: male germ line stem cell (sensu Vertebrata)
annotated property: subClassOf
annotated target: germ line stem cell (sensu Vertebrata)
is inferred: true

female germ line stem cell (sensu Vertebrata)
type: Class
subclass of: female germ line stem cell
subclass of: germ line stem cell (sensu Vertebrata)
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: female germ line stem cell (sensu Vertebrata)
annotated property: subClassOf
annotated target: female germ line stem cell
is inferred: true

Axiom
annotated source: female germ line stem cell (sensu Vertebrata)
annotated property: subClassOf
annotated target: germ line stem cell (sensu Vertebrata)
is inferred: true

sensory epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: capable of
    some values from: detection of stimulus involved in sensory perception
subclass of: epithelial cell
subclass of: receptor cell
subclass of: somatic cell
subclass of: Restriction
  on property: capable of
  some values from: detection of stimulus involved in sensory perception
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.
imported from: cl.owl
has_broad_synonym: neuroepithelial cell
database_cross_reference: BTO:0004301
has_obo_namespace: cell
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: subClassOf
annotated target: epithelial cell
is inferred: true

Axiom
annotated source: sensory epithelial cell
annotated property: subClassOf
annotated target: receptor cell
is inferred: true

Axiom
annotated source: sensory epithelial cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

sensory neuron
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: detection of stimulus involved in sensory perception
subclass of: afferent neuron
subclass of: Restriction
  on property: capable of
  some values from: detection of stimulus involved in sensory perception
definition: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
imported from: cl.owl
database_cross_reference: BTO:0001037
database_cross_reference: FBbt:00005124
database_cross_reference: FMA:84649
database_cross_reference: WBbt:0005759
has_obo_namespace: cell

Axiom
annotated source: sensory neuron
annotated property: subClassOf
annotated target: afferent neuron
is inferred: true

surface ectodermal cell
type: Class
subclass of: ectodermal cell
imported from: cl.owl
database_cross_reference: FMA:72552
has exact synonym: cell of surface ectoderm
has exact synonym: surface ectoderm cell
has_obo_namespace: cell

Axiom
annotated source: surface ectodermal cell
annotated property: subClassOf
annotated target: ectodermal cell
is inferred: true

neurectodermal cell
type: Class
subclass of: ectodermal cell
definition: Ectoderm destined to be nervous tissue.
imported from: cl.owl
has exact synonym: neurectoderm cell
has_obo_namespace: cell

Axiom
annotated source: neurectodermal cell
annotated property: subClassOf
annotated target: ectodermal cell
is inferred: true

mesenchymal stem cell
type: Class
equivalent class: Class
  intersection of: connective tissue cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: endoglin
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: 5'-nucleotidase
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: Thy-1 membrane glycoprotein
  intersection of: Restriction
    on property: capable of
    some values from: osteoblast differentiation
  intersection of: Restriction
    on property: capable of
    some values from: cell migration
  intersection of: Restriction
    on property: capable of
    some values from: neuron differentiation
  intersection of: Restriction
    on property: capable of
    some values from: epithelial cell differentiation
  intersection of: Restriction
    on property: capable of
    some values from: fat cell differentiation
  intersection of: Restriction
    on property: capable of
    some values from: cardiac muscle cell differentiation
  intersection of: Restriction
    on property: capable of
    some values from: chondroblast differentiation
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: MHC class II protein complex
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: CD34 molecule
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: receptor-type tyrosine-protein phosphatase C
subclass of: multi fate stem cell
subclass of: motile cell
subclass of: connective tissue cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: endoglin
subclass of: Restriction
  on property: has plasma membrane part
  some values from: 5'-nucleotidase
subclass of: Restriction
  on property: has plasma membrane part
  some values from: Thy-1 membrane glycoprotein
subclass of: Restriction
  on property: capable of
  some values from: osteoblast differentiation
subclass of: Restriction
  on property: capable of
  some values from: cell migration
subclass of: Restriction
  on property: capable of
  some values from: neuron differentiation
subclass of: Restriction
  on property: capable of
  some values from: epithelial cell differentiation
subclass of: Restriction
  on property: capable of
  some values from: fat cell differentiation
subclass of: Restriction
  on property: capable of
  some values from: cardiac muscle cell differentiation
subclass of: Restriction
  on property: capable of
  some values from: chondroblast differentiation
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: MHC class II protein complex
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: CD34 molecule
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: receptor-type tyrosine-protein phosphatase C
definition: A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. 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.
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
has_alternative_id: CL:0002452
database_cross_reference: BTO:0002625
database_cross_reference: BTO:0003298
database_cross_reference: FMA:70546
has_narrow_synonym: BMSC
has_narrow_synonym: bone marrow stromal cells
has_narrow_synonym: colony-forming unit-fibroblast
has_narrow_synonym: marrow stromal cells
has_obo_namespace: cell
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
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: multi fate stem cell
is inferred: true

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

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

glandular epithelial cell
type: Class
subclass of: epithelial cell
subclass of: secretory cell
subclass of: somatic cell
subclass of: Restriction
  on property: part_of
  some values from: glandular epithelium
definition: A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules.
imported from: cl.owl
database_cross_reference: CALOHA:TS-2085
database_cross_reference: FMA:86494
has_obo_namespace: cell

Axiom
annotated source: glandular epithelial cell
annotated property: subClassOf
annotated target: epithelial cell
is inferred: true

Axiom
annotated source: glandular epithelial cell
annotated property: subClassOf
annotated target: secretory cell
is inferred: true

Axiom
annotated source: glandular epithelial cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

secretory cell
type: Class
equivalent class: Class
  intersection of: native cell
  intersection of: Restriction
    on property: capable of
    some values from: secretion by cell
subclass of: native cell
subclass of: Restriction
  on property: capable of
  some values from: secretion by cell
definition: A cell that specializes in controlled release of one or more substances.
imported from: cl.owl
database_cross_reference: BTO:0003659
database_cross_reference: FMA:86916
has_obo_namespace: cell

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

exocrine cell
type: Class
equivalent class: Class
  intersection of: secretory cell
  intersection of: Restriction
    on property: part_of
    some values from: exocrine gland
subclass of: secretory cell
subclass of: Restriction
  on property: part_of
  some values from: exocrine gland
definition: A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.
imported from: cl.owl
database_cross_reference: FMA:16014
has_obo_namespace: cell

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

contractile cell
type: Class
subclass of: native cell
definition: A cell whose primary function is to shorten.
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: contractile cell
annotated property: subClassOf
annotated target: native cell
is inferred: true

muscle cell
type: Class
subclass of: contractile cell
subclass of: electrically responsive cell
subclass of: animal cell
subclass of: somatic 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.
imported from: cl.owl
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
has exact synonym: muscle fiber
has exact synonym: myocyte
has_obo_namespace: cell

Axiom
annotated source: muscle cell
annotated property: subClassOf
annotated target: contractile cell
is inferred: true

Axiom
annotated source: muscle cell
annotated property: subClassOf
annotated target: electrically responsive cell
is inferred: true

Axiom
annotated source: muscle cell
annotated property: subClassOf
annotated target: animal cell
is inferred: true

Axiom
annotated source: muscle cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

cell of skeletal muscle
type: Class
equivalent class: Class
  intersection of: somatic cell
  intersection of: Restriction
    on property: part_of
    some values from: skeletal muscle tissue
subclass of: somatic cell
subclass of: Restriction
  on property: part_of
  some values from: skeletal muscle tissue
definition: A somatic cell located in skeletal muscle.
imported from: cl.owl
database_cross_reference: BTO:0004392
database_cross_reference: CALOHA:TS-2158
database_cross_reference: FMA:9727
has exact synonym: skeletal muscle cell
has_obo_namespace: cell

Axiom
annotated source: cell of skeletal muscle
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

receptor cell
type: Class
subclass of: native cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: receptor cell
annotated property: subClassOf
annotated target: native cell
is inferred: true

chemoreceptor cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: detection of chemical stimulus involved in sensory perception
subclass of: sensory neuron
subclass of: Restriction
  on property: capable of
  some values from: detection of chemical stimulus involved in sensory perception
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.
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: chemoreceptor cell
annotated property: subClassOf
annotated target: sensory neuron
is inferred: true

taste receptor cell
type: Class
equivalent class: Class
  intersection of: neuron
  intersection of: Restriction
    on property: capable of
    some values from: detection of chemical stimulus involved in sensory perception of taste
subclass of: neuronal receptor cell
subclass of: sensory epithelial cell
subclass of: chemoreceptor cell
subclass of: epidermal cell
subclass of: neurecto-epithelial cell
subclass of: endo-epithelial cell
subclass of: Restriction
  on property: part_of
  some values from: stratum basale of epidermis
subclass of: Restriction
  on property: capable of
  some values from: detection of chemical stimulus involved in sensory perception of taste
definition: A cell type found in the spherical or ovoid clusters of receptor cells found mainly in the epithelium of the tongue and constituting the end organs of the sense of taste.
imported from: cl.owl
database_cross_reference: FMA:67910
has exact synonym: taste bud cell
has_obo_namespace: cell

Axiom
annotated source: taste receptor cell
annotated property: subClassOf
annotated target: neuronal receptor cell
is inferred: true

Axiom
annotated source: taste receptor cell
annotated property: subClassOf
annotated target: sensory epithelial cell
is inferred: true

Axiom
annotated source: taste receptor cell
annotated property: subClassOf
annotated target: chemoreceptor cell
is inferred: true

Axiom
annotated source: taste receptor cell
annotated property: subClassOf
annotated target: epidermal cell
is inferred: true

Axiom
annotated source: taste receptor cell
annotated property: subClassOf
annotated target: neurecto-epithelial cell
is inferred: true

Axiom
annotated source: taste receptor cell
annotated property: subClassOf
annotated target: endo-epithelial cell
is inferred: true

electrically active cell
type: Class
subclass of: native cell
definition: A cell whose function is determined by the generation or the reception of an electric signal.
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: electrically active cell
annotated property: subClassOf
annotated target: native cell
is inferred: true

motile cell
type: Class
equivalent class: Class
  intersection of: native cell
  intersection of: Restriction
    on property: capable of
    some values from: cell motility
subclass of: native cell
subclass of: Restriction
  on property: capable of
  some values from: cell motility
definition: A cell that moves by its own activities.
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
has_obo_namespace: cell

Axiom
annotated source: motile cell
annotated property: subClassOf
annotated target: native cell
is inferred: true

ectodermal cell
type: Class
subclass of: embryonic cell
subclass of: Restriction
  on property: part_of
  some values from: ectoderm
definition: A cell of the outer of the three germ layers of the embryo.
imported from: cl.owl
database_cross_reference: FMA:72549
has exact synonym: ectoderm cell
has_obo_namespace: cell

Axiom
annotated source: ectodermal cell
annotated property: subClassOf
annotated target: embryonic cell
is inferred: true

mesodermal cell
type: Class
subclass of: embryonic cell
subclass of: Restriction
  on property: part_of
  some values from: mesoderm
definition: A cell of the middle germ layer of the embryo.
imported from: cl.owl
database_cross_reference: FMA:72554
has exact synonym: mesoblast
has exact synonym: mesoderm cell
has_obo_namespace: cell

Axiom
annotated source: mesodermal cell
annotated property: subClassOf
annotated target: embryonic cell
is inferred: true

endodermal cell
type: Class
subclass of: embryonic cell
subclass of: Restriction
  on property: part_of
  some values from: endoderm
definition: A cell of the inner of the three germ layers of the embryo.
imported from: cl.owl
database_cross_reference: FMA:72555
has exact synonym: endoderm cell
has_obo_namespace: cell

Axiom
annotated source: endodermal cell
annotated property: subClassOf
annotated target: embryonic cell
is inferred: true

keratinizing barrier epithelial cell
type: Class
subclass of: stratified squamous epithelial cell
subclass of: keratin accumulating cell
subclass of: ecto-epithelial cell
subclass of: Restriction
  on property: develops from
  some values from: surface ectodermal cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: keratinizing barrier epithelial cell
annotated property: subClassOf
annotated target: stratified squamous epithelial cell
is inferred: true

Axiom
annotated source: keratinizing barrier epithelial cell
annotated property: subClassOf
annotated target: keratin accumulating cell
is inferred: true

Axiom
annotated source: keratinizing barrier epithelial cell
annotated property: subClassOf
annotated target: ecto-epithelial cell
is inferred: true

stratified squamous epithelial cell
type: Class
subclass of: squamous epithelial cell
subclass of: stratified epithelial cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: stratified squamous epithelial cell
annotated property: subClassOf
annotated target: squamous epithelial cell
is inferred: true

Axiom
annotated source: stratified squamous epithelial cell
annotated property: subClassOf
annotated target: stratified epithelial cell
is inferred: true

eukaryotic cell
type: Class
subclass of: native cell
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
has_obo_namespace: cell

Axiom
annotated source: eukaryotic cell
annotated property: subClassOf
annotated target: native cell
is inferred: true

tracheal epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: trachea
subclass of: epithelial cell of tracheobronchial tree
subclass of: Restriction
  on property: part_of
  some values from: trachea
subclass of: Restriction
  on property: develops from
  some values from: tracheoblast
definition: An epithelial cell found in the trachea.
imported from: cl.owl
has_alternative_id: CL:1000474
database_cross_reference: FMA:74793
has exact synonym: tracheocyte
has_obo_namespace: cell
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: epithelial cell of tracheobronchial tree
is inferred: true

keratin accumulating cell
type: Class
subclass of: stuff accumulating cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: keratin accumulating cell
annotated property: subClassOf
annotated target: stuff accumulating cell
is inferred: true

keratinocyte
type: Class
equivalent class: Class
  intersection of: keratinizing barrier epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: skin epidermis
subclass of: keratinizing barrier epithelial cell
subclass of: epidermal cell
subclass of: Restriction
  on property: part_of
  some values from: skin epidermis
subclass of: Restriction
  on property: capable of
  some values from: antimicrobial peptide production
subclass of: Restriction
  on property: capable of
  some values from: antimicrobial peptide secretion
subclass of: Restriction
  on property: capable of
  some values from: positive regulation of neutrophil chemotaxis
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.
imported from: cl.owl
has_alternative_id: CL:0002185
database_cross_reference: BTO:0000667
database_cross_reference: CALOHA:TS-0500
database_cross_reference: FMA:62879
has exact synonym: keratinized cell of epidermis
has exact synonym: malpighian cell
has_obo_namespace: cell
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

metanephric mesenchyme stem cell
type: Class
subclass of: mesenchymal stem cell
subclass of: Restriction
  on property: develops from
  some values from: mesodermal cell
imported from: cl.owl
has_obo_namespace: cell

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

stuff accumulating cell
type: Class
subclass of: native cell
definition: A cell that is specialised to accumulate a particular substance(s).
imported from: cl.owl
has_obo_namespace: cell
in subset: upper level

Axiom
annotated source: stuff accumulating cell
annotated property: subClassOf
annotated target: native cell
is inferred: true

migratory neural crest cell
type: Class
subclass of: motile cell
subclass of: neural crest cell
subclass of: Restriction
  on property: develops from
  some values from: premigratory neural crest cell
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.
imported from: cl.owl
database_cross_reference: FMA:86667
has_obo_namespace: cell

Axiom
annotated source: migratory neural crest cell
annotated property: subClassOf
annotated target: motile cell
is inferred: true

Axiom
annotated source: migratory neural crest cell
annotated property: subClassOf
annotated target: neural crest cell
is inferred: true

neuroblast (sensu Vertebrata)
type: Class
subclass of: neuroblast
definition: An embryonic cell that develops into a nerve cell or neuron.
imported from: cl.owl
has_obo_namespace: cell

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

neuroblast (sensu Nematoda and Protostomia)
type: Class
subclass of: neuroblast
imported from: cl.owl
has_broad_synonym: neuroblast
has_obo_namespace: cell

Axiom
annotated source: neuroblast (sensu Nematoda and Protostomia)
annotated property: subClassOf
annotated target: neuroblast
is inferred: true

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: dermal papilla
subclass of: mesenchymal stem cell
subclass of: Restriction
  on property: part_of
  some values from: dermal papilla
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.
imported from: cl.owl
has_obo_namespace: cell
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

extraembryonic cell
type: Class
equivalent class: Class
  intersection of: animal cell
  intersection of: Restriction
    on property: part_of
    some values from: extraembryonic structure
subclass of: animal cell
subclass of: somatic cell
subclass of: Restriction
  on property: part_of
  some values from: extraembryonic structure
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: extraembryonic cell
annotated property: subClassOf
annotated target: animal cell
is inferred: true

Axiom
annotated source: extraembryonic cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

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.
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: epiblast cell
annotated property: subClassOf
annotated target: totipotent stem cell
is inferred: true

blastemal cell
type: Class
subclass of: multi fate stem cell
imported from: cl.owl
database_cross_reference: ncithesaurus:Blastemal_Cell
has exact synonym: blastema cell
has_obo_namespace: cell

Axiom
annotated source: blastemal cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

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: skeletal muscle tissue
subclass of: multi fate stem cell
subclass of: cell of skeletal muscle
subclass of: Restriction
  on property: part_of
  some values from: skeletal muscle tissue
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.
imported from: cl.owl
database_cross_reference: FMA:86767
has_obo_namespace: cell
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: subClassOf
annotated target: cell of skeletal muscle
is inferred: true

hair matrix stem cell
type: Class
subclass of: single fate stem cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: hair matrix stem cell
annotated property: subClassOf
annotated target: single fate stem cell
is inferred: true

stratified epithelial stem cell
type: Class
subclass of: epithelial fate stem cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: stratified epithelial stem cell
annotated property: subClassOf
annotated target: epithelial fate stem cell
is inferred: true

epidermal cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: outer epithelium
subclass of: general ecto-epithelial cell
subclass of: Restriction
  on property: part_of
  some values from: outer epithelium
definition: An epithelial cell of the integument (the outer layer of an organism).
imported from: cl.owl
has_alternative_id: CL:1000396
database_cross_reference: BTO:0001470
database_cross_reference: CALOHA:TS-0283
database_cross_reference: FMA:62411
has exact synonym: cell of epidermis
has_narrow_synonym: epithelial cell of skin
has_obo_namespace: cell

Axiom
annotated source: epidermal cell
annotated property: subClassOf
annotated target: general ecto-epithelial cell
is inferred: true

tracheoblast
type: Class
subclass of: branched duct epithelial cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: tracheoblast
annotated property: subClassOf
annotated target: branched duct epithelial cell
is inferred: true

nephrogenic mesenchyme stem cell
type: Class
subclass of: mesenchymal stem cell
subclass of: Restriction
  on property: develops from
  some values from: mesenchymal stem cell
imported from: cl.owl
has_obo_namespace: cell

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

electrically responsive cell
type: Class
subclass of: electrically active cell
definition: A cell whose function is determined by its response to an electric signal.
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: electrically responsive cell
annotated property: subClassOf
annotated target: electrically active cell
is inferred: 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.
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: electrically signaling cell
annotated property: subClassOf
annotated target: electrically active cell
is inferred: true

neuroepidermoblast
type: Class
subclass of: neuroblast (sensu Nematoda and Protostomia)
imported from: cl.owl
database_cross_reference: FBbt:00005148
has_obo_namespace: cell

Axiom
annotated source: neuroepidermoblast
annotated property: subClassOf
annotated target: neuroblast (sensu Nematoda and Protostomia)
is inferred: true

seam cell
type: Class
subclass of: epithelial fate stem cell
definition: An epithelial fate stem cell found in flatworms.
imported from: cl.owl
database_cross_reference: BTO:0003039
has_obo_namespace: cell

Axiom
annotated source: seam cell
annotated property: subClassOf
annotated target: epithelial fate stem cell
is inferred: true

follicle stem cell
type: Class
subclass of: epithelial fate stem cell
imported from: cl.owl
database_cross_reference: FBbt:00004903
has_obo_namespace: cell

Axiom
annotated source: follicle stem cell
annotated property: subClassOf
annotated target: epithelial fate stem cell
is inferred: true

neuroglioblast
type: Class
subclass of: neuronal stem cell
subclass of: non-terminally differentiated cell
imported from: cl.owl
database_cross_reference: FBbt:00005147
has_obo_namespace: cell

Axiom
annotated source: neuroglioblast
annotated property: subClassOf
annotated target: neuronal stem cell
is inferred: true

Axiom
annotated source: neuroglioblast
annotated property: subClassOf
annotated target: non-terminally differentiated cell
is inferred: true

ganglion mother cell
type: Class
subclass of: neuroglioblast
imported from: cl.owl
database_cross_reference: FBbt:00005149
has_obo_namespace: cell

Axiom
annotated source: ganglion mother cell
annotated property: subClassOf
annotated target: neuroglioblast
is inferred: true

afferent neuron
type: Class
subclass of: neuron
definition: A neuron which conveys sensory information centrally from the periphery.
imported from: cl.owl
database_cross_reference: FMA:87653
has exact synonym: input neuron
has_obo_namespace: cell

Axiom
annotated source: afferent neuron
annotated property: subClassOf
annotated target: neuron
is inferred: true

neuron
type: Class
subclass of: electrically responsive cell
subclass of: electrically signaling cell
subclass of: neural cell
subclass of: Restriction
  on property: develops from
  some values from: neuroblast
subclass of: Restriction
  on property: capable of
  some values from: transmission of nerve impulse
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.
imported from: cl.owl
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
has exact synonym: nerve cell
has_obo_namespace: cell
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: subClassOf
annotated target: electrically responsive cell
is inferred: true

Axiom
annotated source: neuron
annotated property: subClassOf
annotated target: electrically signaling cell
is inferred: true

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

animal cell
type: Class
subclass of: eukaryotic cell
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
has_obo_namespace: cell
in subset: upper level

Axiom
annotated source: animal cell
annotated property: subClassOf
annotated target: eukaryotic cell
is inferred: true

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: cadherin-5
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: vascular endothelial growth factor receptor 2
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: T-cell acute lymphocytic leukemia protein 1
subclass of: mesenchymal stem cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: cadherin-5
subclass of: Restriction
  on property: has plasma membrane part
  some values from: vascular endothelial growth factor receptor 2
subclass of: Restriction
  on property: has plasma membrane part
  some values from: T-cell acute lymphocytic leukemia protein 1
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.
imported from: cl.owl
has exact synonym: angioblast
has exact synonym: chondroplast
has_obo_namespace: cell
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

experimentally modified cell in vitro
type: Class
subclass of: cell in vitro
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred label: experimentally modified cell in vitro
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
imported from: cl.owl
imported from: clo.owl
imported from: obi.owl
has_obo_namespace: cell
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: subClassOf
annotated target: cell in vitro
is inferred: true

Axiom
annotated source: experimentally modified cell in vitro
annotated property: subClassOf
annotated target: processed material
is inferred: true

germ cell
type: Class
subclass of: germ line cell
subclass of: Restriction
  on property: capable of
  some values from: multicellular organismal reproductive process
definition: The reproductive cell in multicellular organisms.
imported from: cl.owl
database_cross_reference: BTO:0000535
database_cross_reference: VHOG:0001534
database_cross_reference: WBbt:0006796
has_obo_namespace: cell

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

skeletal muscle satellite cell
type: Class
subclass of: cell of skeletal muscle
subclass of: muscle precursor cell
subclass of: Restriction
  on property: part_of
  some values from: skeletal muscle tissue
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.
imported from: cl.owl
has_obo_namespace: cell
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: subClassOf
annotated target: cell of skeletal muscle
is inferred: true

Axiom
annotated source: skeletal muscle satellite cell
annotated property: subClassOf
annotated target: muscle precursor cell
is inferred: true

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.
imported from: cl.owl
database_cross_reference: BTO:0000939
database_cross_reference: FMA:62516
has_obo_namespace: cell

Axiom
annotated source: basal cell
annotated property: subClassOf
annotated target: epithelial fate stem cell
is inferred: true

neuroglioblast (sensu Nematoda)
type: Class
subclass of: neuroglioblast
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: neuroglioblast (sensu Nematoda)
annotated property: subClassOf
annotated target: neuroglioblast
is inferred: true

muscle precursor cell
type: Class
equivalent class: Class
  intersection of: precursor cell
  intersection of: Restriction
    on property: develops into
    some values from: muscle cell
subclass of: non-terminally differentiated cell
subclass of: somatic 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.
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: muscle precursor cell
annotated property: subClassOf
annotated target: non-terminally differentiated cell
is inferred: true

Axiom
annotated source: muscle precursor cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

neurecto-epithelial cell
type: Class
equivalent class: Class
  intersection of: ecto-epithelial cell
  intersection of: Restriction
    on property: develops from
    some values from: neurectodermal cell
subclass of: columnar/cuboidal epithelial cell
subclass of: ecto-epithelial cell
subclass of: Restriction
  on property: develops from
  some values from: neurectodermal cell
definition: Epithelial cells derived from neural plate and neural crest.
imported from: cl.owl
has_broad_synonym: neuroepithelial cell
database_cross_reference: BTO:0004301
database_cross_reference: FMA:70557
has_obo_namespace: cell
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: subClassOf
annotated target: columnar/cuboidal epithelial cell
is inferred: true

Axiom
annotated source: neurecto-epithelial cell
annotated property: subClassOf
annotated target: ecto-epithelial cell
is inferred: true

somatic stem cell
type: Class
equivalent class: Class
  intersection of: stem cell
  intersection of: Restriction
    on property: capable of
    some values from: somatic stem cell division
subclass of: stem cell
subclass of: somatic cell
subclass of: Restriction
  on property: capable of
  some values from: somatic stem cell division
definition: A stem cell that can give rise to cell types of the body other than those of the germ-line.
imported from: cl.owl
database_cross_reference: CALOHA:TS-2086
database_cross_reference: FMA:63368
has_obo_namespace: cell

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

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

hematopoietic cell
type: Class
subclass of: animal cell
subclass of: somatic cell
definition: A cell of a hematopoietic lineage.
imported from: cl.owl
database_cross_reference: BTO:0000574
database_cross_reference: CALOHA:TS-2017
database_cross_reference: FMA:70366
database_cross_reference: FMA:83598
has exact synonym: haematopoietic cell
has exact synonym: haemopoietic cell
has exact synonym: hemopoietic cell
has_obo_namespace: cell

Axiom
annotated source: hematopoietic cell
annotated property: subClassOf
annotated target: animal cell
is inferred: true

Axiom
annotated source: hematopoietic cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

Kit and Sca1-positive hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: hematopoietic stem cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: SLAM family member 1
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: mast/stem cell growth factor receptor
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: lymphocyte antigen 6A-2/6E-1
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: receptor-type tyrosine-protein phosphatase C isoform CD45R
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: T-cell surface glycoprotein CD8 alpha chain
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: CD48 molecule
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: T-cell surface glycoprotein CD5
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: interleukin-7 receptor subunit alpha
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: natural killer cell receptor 2B4
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: killer cell lectin-like receptor subfamily B member 1C
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: lymphocyte antigen 76
subclass of: hematopoietic stem cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: SLAM family member 1
subclass of: Restriction
  on property: has plasma membrane part
  some values from: mast/stem cell growth factor receptor
subclass of: Restriction
  on property: has plasma membrane part
  some values from: lymphocyte antigen 6A-2/6E-1
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: receptor-type tyrosine-protein phosphatase C isoform CD45R
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: T-cell surface glycoprotein CD8 alpha chain
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: CD48 molecule
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: T-cell surface glycoprotein CD5
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: interleukin-7 receptor subunit alpha
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: natural killer cell receptor 2B4
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: killer cell lectin-like receptor subfamily B member 1C
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: lymphocyte antigen 76
definition: A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative.
imported from: cl.owl
has exact synonym: LSK stem cell
has exact synonym: Sca1-positive hematopoietic stem cell
has_obo_namespace: cell
comment: Cell markers are associated with mouse hematopoietic stem cell. Originally described in the dendritic cell ontology (DC_CL:0000043)(PMID:19243617).

Axiom
annotated source: Kit and Sca1-positive hematopoietic stem cell
annotated property: subClassOf
annotated target: hematopoietic stem cell
is inferred: true

CD34-positive, CD38-negative hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: hematopoietic stem cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: CD34 molecule
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: prominin-1
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: CD59-like glycoprotein
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: Thy-1 membrane glycoprotein
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: neural cell adhesion molecule 1
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: ADP-ribosyl cyclase 1
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: low affinity immunoglobulin gamma Fc region receptor III
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: CD33 molecule
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: transferrin receptor protein 1
subclass of: hematopoietic stem cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: CD34 molecule
subclass of: Restriction
  on property: has plasma membrane part
  some values from: prominin-1
subclass of: Restriction
  on property: has plasma membrane part
  some values from: CD59-like glycoprotein
subclass of: Restriction
  on property: has plasma membrane part
  some values from: Thy-1 membrane glycoprotein
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: neural cell adhesion molecule 1
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: ADP-ribosyl cyclase 1
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: low affinity immunoglobulin gamma Fc region receptor III
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: CD33 molecule
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: transferrin receptor protein 1
definition: CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive.
imported from: cl.owl
database_cross_reference: CALOHA:TS-0448
database_cross_reference: FMA:86475
has exact synonym: CD133-positive hematopoietic stem cell
has_obo_namespace: cell
comment: Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617).

Axiom
annotated source: CD34-positive, CD38-negative hematopoietic stem cell
annotated property: subClassOf
annotated target: hematopoietic stem cell
is inferred: true

cell in vitro
type: Class
subclass of: cell type
subclass of: cell
definition: A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.
imported from: cl.owl
imported from: clo.owl
created by: haendel
creation date: 2012-01-12T09:58:38Z
has_obo_namespace: cell
comment: 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells.

Axiom
annotated source: cell in vitro
annotated property: subClassOf
annotated target: cell type
is inferred: true

Axiom
annotated source: cell in vitro
annotated property: subClassOf
annotated target: cell
is inferred: true

bone cell
type: Class
equivalent class: Class
  intersection of: animal cell
  intersection of: Restriction
    on property: part_of
    some values from: bone element
subclass of: animal cell
subclass of: Restriction
  on property: part_of
  some values from: bone element
definition: A connective tissue cell found in bone.
imported from: cl.owl
created by: adiehl
creation date: 2011-11-16T04:28:16Z
has_obo_namespace: cell

Axiom
annotated source: bone cell
annotated property: subClassOf
annotated target: animal cell
is inferred: true

short term hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: Kit and Sca1-positive hematopoietic stem cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: CD34 molecule
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: SLAM family member 1
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: receptor-type tyrosine-protein kinase FLT3
subclass of: Kit and Sca1-positive hematopoietic stem cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: CD34 molecule
subclass of: Restriction
  on property: has plasma membrane part
  some values from: SLAM family member 1
subclass of: Restriction
  on property: develops from
  some values from: long term hematopoietic stem cell
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: receptor-type tyrosine-protein kinase FLT3
definition: A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative.
imported from: cl.owl
created by: tmeehan
creation date: 2010-01-08T09:19:25Z
has exact synonym: ST stem cell
has exact synonym: ST-HSC
has_obo_namespace: cell
comment: Markers are associated with mouse cells. These cells are also reportedly CD11b-low and CD90-low.

Axiom
annotated source: short term hematopoietic stem cell
annotated property: subClassOf
annotated target: Kit and Sca1-positive hematopoietic stem cell
is inferred: true

long term hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: Kit and Sca1-positive hematopoietic stem cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: SLAM family member 1
  intersection of: Restriction
    on property: has_low_plasma_membrane_amount
    some values from: Thy-1 membrane glycoprotein
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: CD34 molecule
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: receptor-type tyrosine-protein kinase FLT3
subclass of: Kit and Sca1-positive hematopoietic stem cell
subclass of: Restriction
  on property: has plasma membrane part
  some values from: SLAM family member 1
subclass of: Restriction
  on property: has_low_plasma_membrane_amount
  some values from: Thy-1 membrane glycoprotein
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: CD34 molecule
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: receptor-type tyrosine-protein kinase FLT3
definition: A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative.
imported from: cl.owl
created by: tmeehan
creation date: 2010-01-08T09:19:28Z
has exact synonym: LT stem cell
has exact synonym: LT-HSC
has_obo_namespace: cell
comment: Markers are associated with mouse cells.

Axiom
annotated source: long term hematopoietic stem cell
annotated property: subClassOf
annotated target: Kit and Sca1-positive hematopoietic stem cell
is inferred: true

endo-epithelial cell
type: Class
subclass of: epithelial cell
subclass of: somatic cell
subclass of: Restriction
  on property: develops from
  some values from: endodermal cell
definition: An epithelial cell derived from endoderm.
imported from: cl.owl
created by: tmeehan
creation date: 2010-06-29T03:38:14Z
database_cross_reference: FMA:69075
has_obo_namespace: cell

Axiom
annotated source: endo-epithelial cell
annotated property: subClassOf
annotated target: epithelial cell
is inferred: true

Axiom
annotated source: endo-epithelial cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

ecto-epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: develops from
    some values from: ectodermal cell
subclass of: epithelial cell
subclass of: somatic cell
subclass of: Restriction
  on property: develops from
  some values from: ectodermal cell
definition: An epithelial cell derived from ectoderm.
imported from: cl.owl
created by: tmeehan
creation date: 2010-06-29T03:38:22Z
database_cross_reference: FMA:69074
has_obo_namespace: cell

Axiom
annotated source: ecto-epithelial cell
annotated property: subClassOf
annotated target: epithelial cell
is inferred: true

Axiom
annotated source: ecto-epithelial cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

meso-epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: develops from
    some values from: mesodermal cell
subclass of: epithelial cell
subclass of: somatic cell
subclass of: Restriction
  on property: develops from
  some values from: mesodermal cell
definition: Epithelial cell derived from mesoderm or mesenchyme.
imported from: cl.owl
created by: tmeehan
creation date: 2010-06-29T03:49:14Z
database_cross_reference: FMA:69076
has exact synonym: epithelial mesenchymal cell
has_obo_namespace: cell

Axiom
annotated source: meso-epithelial cell
annotated property: subClassOf
annotated target: epithelial cell
is inferred: true

Axiom
annotated source: meso-epithelial cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

bone marrow cell
type: Class
equivalent class: Class
  intersection of: bone cell
  intersection of: Restriction
    on property: part_of
    some values from: bone marrow
subclass of: bone cell
subclass of: Restriction
  on property: part_of
  some values from: bone marrow
definition: A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells.
imported from: cl.owl
created by: tmeehan
creation date: 2010-07-22T04:48:15Z
database_cross_reference: BTO:0004850
database_cross_reference: FMA:83621
has_obo_namespace: cell
comment: MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense.

Axiom
annotated source: bone marrow cell
annotated property: subClassOf
annotated target: bone cell
is inferred: true

general ecto-epithelial cell
type: Class
subclass of: ecto-epithelial cell
definition: Epithelial cells derived from general body ectoderm and ectoderm placodes.
imported from: cl.owl
created by: tmeehan
creation date: 2010-08-26T08:31:08Z
database_cross_reference: FMA:70556
has_obo_namespace: cell

Axiom
annotated source: general ecto-epithelial cell
annotated property: subClassOf
annotated target: ecto-epithelial cell
is inferred: true

epithelial cell of stomach
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: stomach
subclass of: epithelial cell of alimentary canal
subclass of: Restriction
  on property: part_of
  some values from: stomach
definition: An epithelial cell found in the lining of the stomach.
imported from: cl.owl
created by: tmeehan
creation date: 2010-08-25T03:22:08Z
has_alternative_id: CL:1000399
database_cross_reference: FMA:62948
has_obo_namespace: cell

Axiom
annotated source: epithelial cell of stomach
annotated property: subClassOf
annotated target: epithelial cell of alimentary canal
is inferred: true

mucous cell of stomach
type: Class
equivalent class: Class
  intersection of: epithelial cell of stomach
  intersection of: Restriction
    on property: part_of
    some values from: mucosa of stomach
subclass of: glandular cell of stomach
subclass of: Restriction
  on property: part_of
  some values from: mucosa of stomach
definition: A mucous cell in the epithelium of the stomach.
imported from: cl.owl
created by: tmeehan
creation date: 2010-08-25T03:38:51Z
has_alternative_id: CL:1000404
database_cross_reference: FMA:63464
has_obo_namespace: cell

Axiom
annotated source: mucous cell of stomach
annotated property: subClassOf
annotated target: glandular cell of stomach
is inferred: true

stem cell of gastric gland
type: Class
equivalent class: Class
  intersection of: multi fate stem cell
  intersection of: Restriction
    on property: part_of
    some values from: gastric gland
subclass of: multi fate stem cell
subclass of: exocrine cell
subclass of: mucous cell of stomach
subclass of: Restriction
  on property: part_of
  some values from: gastric gland
definition: A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit.
imported from: cl.owl
created by: tmeehan
creation date: 2010-08-25T03:57:08Z
has_alternative_id: CL:1000400
database_cross_reference: FMA:62953
has_obo_namespace: cell

Axiom
annotated source: stem cell of gastric gland
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

Axiom
annotated source: stem cell of gastric gland
annotated property: subClassOf
annotated target: exocrine cell
is inferred: true

Axiom
annotated source: stem cell of gastric gland
annotated property: subClassOf
annotated target: mucous cell of stomach
is inferred: true

basal cell of epidermis
type: Class
equivalent class: Class
  intersection of: basal cell
  intersection of: Restriction
    on property: part_of
    some values from: skin epidermis
subclass of: keratinocyte
subclass of: basal cell
subclass of: stem cell of epidermis
subclass of: Restriction
  on property: part_of
  some values from: skin epidermis
definition: A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane.
imported from: cl.owl
created by: tmeehan
creation date: 2010-08-26T03:12:49Z
has_alternative_id: CL:1000439
database_cross_reference: FMA:70571
has_obo_namespace: cell

Axiom
annotated source: basal cell of epidermis
annotated property: subClassOf
annotated target: keratinocyte
is inferred: true

Axiom
annotated source: basal cell of epidermis
annotated property: subClassOf
annotated target: basal cell
is inferred: true

Axiom
annotated source: basal cell of epidermis
annotated property: subClassOf
annotated target: stem cell of epidermis
is inferred: true

hepatic stem cell
type: Class
equivalent class: Class
  intersection of: multi fate stem cell
  intersection of: Restriction
    on property: part_of
    some values from: liver
subclass of: multi fate stem cell
subclass of: Restriction
  on property: part_of
  some values from: liver
definition: A stem cell that can give rise to the cells of the liver.
imported from: cl.owl
created by: tmeehan
creation date: 2010-08-30T02:00:42Z
database_cross_reference: FMA:86577
has_obo_namespace: cell

Axiom
annotated source: hepatic stem cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

hepatic oval stem cell
type: Class
subclass of: hepatic stem cell
definition: A transient hepatic stem cell observed after liver injury with a high nuclear to cytoplasm ratio that can differentiate into mature hepatocytes and bile duct cells. Arises from more than one tissue.
imported from: cl.owl
created by: tmeehan
creation date: 2010-08-30T02:01:49Z
has_alternative_id: CL:1000036
database_cross_reference: BTO:0004270
database_cross_reference: FMA:86576
has exact synonym: hepatic oval cell
has_obo_namespace: cell

Axiom
annotated source: hepatic oval stem cell
annotated property: subClassOf
annotated target: hepatic stem cell
is inferred: true

epithelial cell of tracheobronchial tree
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: tracheobronchial tree
subclass of: epithelial cell of lower respiratory tract
subclass of: Restriction
  on property: part_of
  some values from: tracheobronchial tree
definition: An epithelial cell of the tracheobronchial tree.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-02T02:09:14Z
has_alternative_id: CL:1000407
database_cross_reference: FMA:66816
has_obo_namespace: cell

Axiom
annotated source: epithelial cell of tracheobronchial tree
annotated property: subClassOf
annotated target: epithelial cell of lower respiratory tract
is inferred: true

epithelial cell of prostate
type: Class
equivalent class: Class
  intersection of: endo-epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: prostate gland
subclass of: endo-epithelial cell
subclass of: Restriction
  on property: part_of
  some values from: prostate gland
definition: An epithelial cell of the prostate.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-07T01:49:29Z
has_alternative_id: CL:1000295
has_alternative_id: CL:1000408
database_cross_reference: FMA:256163
database_cross_reference: FMA:66817
has exact synonym: prostate epithelial cell
has_obo_namespace: cell

Axiom
annotated source: epithelial cell of prostate
annotated property: subClassOf
annotated target: endo-epithelial cell
is inferred: true

peripheral blood stem cell
type: Class
equivalent class: Class
  intersection of: hematopoietic stem cell
  intersection of: Restriction
    on property: part_of
    some values from: blood
subclass of: hematopoietic stem cell
subclass of: circulating cell
subclass of: Restriction
  on property: part_of
  some values from: blood
definition: A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells).
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-07T03:57:09Z
database_cross_reference: BTO:0002669
database_cross_reference: FMA:86711
has exact synonym: PBSC
has_obo_namespace: cell

Axiom
annotated source: peripheral blood stem cell
annotated property: subClassOf
annotated target: hematopoietic stem cell
is inferred: true

Axiom
annotated source: peripheral blood stem cell
annotated property: subClassOf
annotated target: circulating cell
is inferred: true

pluripotent stem cell
type: Class
subclass of: somatic stem cell
definition: A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-07T04:26:06Z
database_cross_reference: FMA:70570
has_obo_namespace: cell

Axiom
annotated source: pluripotent stem cell
annotated property: subClassOf
annotated target: somatic stem cell
is inferred: true

primitive cardiac myocyte
type: Class
subclass of: single fate stem cell
subclass of: meso-epithelial cell
definition: A stem cell that can differentiate into a cardiac myocyte.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-07T04:40:32Z
database_cross_reference: FMA:75620
has_obo_namespace: cell

Axiom
annotated source: primitive cardiac myocyte
annotated property: subClassOf
annotated target: single fate stem cell
is inferred: true

Axiom
annotated source: primitive cardiac myocyte
annotated property: subClassOf
annotated target: meso-epithelial cell
is inferred: true

intestinal crypt stem cell
type: Class
equivalent class: Class
  intersection of: stem cell
  intersection of: Restriction
    on property: part_of
    some values from: crypt of Lieberkuhn
subclass of: multi fate stem cell
subclass of: intestinal epithelial cell
subclass of: Restriction
  on property: part_of
  some values from: crypt of Lieberkuhn
definition: A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-08T09:21:22Z
database_cross_reference: FMA:63379
has exact synonym: stem cell of intestinal crypt of Lieberkuhn
has_obo_namespace: cell

Axiom
annotated source: intestinal crypt stem cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

Axiom
annotated source: intestinal crypt stem cell
annotated property: subClassOf
annotated target: intestinal epithelial cell
is inferred: true

epithelial cell of alimentary canal
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: digestive tract
subclass of: endo-epithelial cell
subclass of: Restriction
  on property: part_of
  some values from: digestive tract
definition: An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-08T09:26:53Z
has_obo_namespace: cell

Axiom
annotated source: epithelial cell of alimentary canal
annotated property: subClassOf
annotated target: endo-epithelial cell
is inferred: true

neuroepithelial stem cell
type: Class
subclass of: somatic stem cell
definition: The stem cell from which glial precursor cell arises from.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-08T02:14:14Z
database_cross_reference: FMA:87171
has_narrow_synonym: totipotent neuroepithelial stem cell
has_obo_namespace: cell

Axiom
annotated source: neuroepithelial stem cell
annotated property: subClassOf
annotated target: somatic stem cell
is inferred: true

type III taste bud cell
type: Class
subclass of: multi fate stem cell
subclass of: taste receptor cell
definition: A taste receptor cell that is characterized by morphologically identifiable synaptic contacts with the gustatory nerve fibers and expression of the synaptic membrane protein-25 (SNAP-25) and NCAM.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-13T10:57:21Z
has_broad_synonym: taste bud basal cell
database_cross_reference: FMA:67940
has exact synonym: type 3 taste cell
has_obo_namespace: cell

Axiom
annotated source: type III taste bud cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

Axiom
annotated source: type III taste bud cell
annotated property: subClassOf
annotated target: taste receptor cell
is inferred: true

type IV taste receptor cell
type: Class
subclass of: stem cell
subclass of: taste receptor cell
definition: A rounded, mitotically active stem cell which is the source of new cells of the taste bud; located basally.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-13T10:57:29Z
has_broad_synonym: taste bud basal cell
database_cross_reference: FMA:62380
has exact synonym: type 4 taste cell
has_obo_namespace: cell
comment: There is debate about the exact lineage of these cell types from this progenitor. See PMID:15738192.

Axiom
annotated source: type IV taste receptor cell
annotated property: subClassOf
annotated target: stem cell
is inferred: true

Axiom
annotated source: type IV taste receptor cell
annotated property: subClassOf
annotated target: taste receptor cell
is inferred: true

neural cell
type: Class
equivalent class: Class
  intersection of: cell type
  intersection of: Restriction
    on property: part_of
    some values from: nervous system
subclass of: animal cell
subclass of: somatic cell
subclass of: Restriction
  on property: part_of
  some values from: nervous system
definition: A cell that is part of the nervous system.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-15T01:34:57Z
database_cross_reference: CALOHA:TS-2040
database_cross_reference: FMA:70333
has_obo_namespace: cell

Axiom
annotated source: neural cell
annotated property: subClassOf
annotated target: animal cell
is inferred: true

Axiom
annotated source: neural cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

connective tissue cell
type: Class
equivalent class: Class
  intersection of: somatic cell
  intersection of: Restriction
    on property: part_of
    some values from: connective tissue
subclass of: animal cell
subclass of: somatic cell
subclass of: Restriction
  on property: part_of
  some values from: connective tissue
definition: A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
created by: tmeehan
creation date: 2010-09-15T03:01:54Z
has_alternative_id: CL:1000406
database_cross_reference: CALOHA:TS-2096
database_cross_reference: FMA:63875
has_obo_namespace: cell

Axiom
annotated source: connective tissue cell
annotated property: subClassOf
annotated target: animal cell
is inferred: true

Axiom
annotated source: connective tissue cell
annotated property: subClassOf
annotated target: somatic cell
is inferred: true

embryonic cell
type: Class
subclass of: animal cell
definition: A cell of the embryo.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-15T03:39:21Z
database_cross_reference: CALOHA:TS-0263
database_cross_reference: FMA:82840
database_cross_reference: FMA:82841
database_cross_reference: WBbt:0007028
has_obo_namespace: cell

Axiom
annotated source: embryonic cell
annotated property: subClassOf
annotated target: animal cell
is inferred: true

embryonic stem cell
type: Class
subclass of: stem cell
subclass of: embryonic cell
definition: A stem cell of embryonic origin.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-15T03:44:35Z
database_cross_reference: BTO:0001086
database_cross_reference: CALOHA:TS-0263
database_cross_reference: FMA:82841
has exact synonym: ESC
has_obo_namespace: cell
comment: This is an in vitro cell type and may be removed in future releases. These cells are reportedly SSEA-4-positive, CD73-negative, and CD324-positive.

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

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

amniocyte
type: Class
equivalent class: Class
  intersection of: extraembryonic cell
  intersection of: Restriction
    on property: located in
    some values from: amniotic fluid
subclass of: extraembryonic cell
subclass of: Restriction
  on property: located in
  some values from: amniotic fluid
definition: A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-20T10:13:37Z
database_cross_reference: BTO:0000066
has_obo_namespace: cell

Axiom
annotated source: amniocyte
annotated property: subClassOf
annotated target: extraembryonic cell
is inferred: true

bronchial epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: bronchus
subclass of: epithelial cell of tracheobronchial tree
subclass of: Restriction
  on property: part_of
  some values from: epithelium of bronchus
subclass of: Restriction
  on property: part_of
  some values from: bronchus
definition: An epithelial cell of the bronchus.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-20T02:00:00Z
database_cross_reference: BTO:0002922
has_obo_namespace: cell

Axiom
annotated source: bronchial epithelial cell
annotated property: subClassOf
annotated target: epithelial cell of tracheobronchial tree
is inferred: true

basal epithelial cell of tracheobronchial tree
type: Class
subclass of: epithelial cell of tracheobronchial tree
definition: An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-20T02:10:36Z
has_obo_namespace: cell

Axiom
annotated source: basal epithelial cell of tracheobronchial tree
annotated property: subClassOf
annotated target: epithelial cell of tracheobronchial tree
is inferred: true

keratinocyte stem cell
type: Class
subclass of: multi fate stem cell
subclass of: keratinocyte
definition: A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-20T03:07:03Z
has exact synonym: bulge keratinocyte
has_obo_namespace: cell

Axiom
annotated source: keratinocyte stem cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

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

prostate stem cell
type: Class
equivalent class: Class
  intersection of: stem cell
  intersection of: Restriction
    on property: part_of
    some values from: prostate gland
subclass of: multi fate stem cell
subclass of: basal cell of prostate epithelium
subclass of: Restriction
  on property: part_of
  some values from: prostate gland
definition: A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-20T03:21:06Z
has exact synonym: CD133-positive prostate epithelial cell
has_obo_namespace: cell

Axiom
annotated source: prostate stem cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

Axiom
annotated source: prostate stem cell
annotated property: subClassOf
annotated target: basal cell of prostate epithelium
is inferred: true

basal cell of prostate epithelium
type: Class
subclass of: epithelial cell of prostate
definition: An undifferentiated cell of the prostate epithelium that lacks secretory activity.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-20T03:34:10Z
has_obo_namespace: cell

Axiom
annotated source: basal cell of prostate epithelium
annotated property: subClassOf
annotated target: epithelial cell of prostate
is inferred: true

progenitor cell of endocrine pancreas
type: Class
subclass of: multi fate stem cell
definition: A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-21T04:41:06Z
has exact synonym: pancreatic endocrine progenitor
has exact synonym: pancreatic islet progenitor cell
has_obo_namespace: cell

Axiom
annotated source: progenitor cell of endocrine pancreas
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

gestational hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: hematopoietic stem cell
  intersection of: Restriction
    on property: part_of
    some values from: embryo
subclass of: hematopoietic stem cell
subclass of: Restriction
  on property: part_of
  some values from: embryo
definition: A hematopoietic stem cell that exists during embryogenesis.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-22T09:05:13Z
has_obo_namespace: cell

Axiom
annotated source: gestational hematopoietic stem cell
annotated property: subClassOf
annotated target: hematopoietic stem cell
is inferred: true

fetal liver hematopoietic progenitor cell
type: Class
equivalent class: Class
  intersection of: gestational hematopoietic stem cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: MHC protein complex
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: receptor-type tyrosine-protein phosphatase C
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: SLAM family member 1
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: signal transducer CD24
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: complement component C1q receptor
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: lymphocyte antigen 6A-2/6E-1
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: CD48 molecule
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: natural killer cell receptor 2B4
subclass of: gestational hematopoietic stem cell
subclass of: Restriction
  on property: part_of
  some values from: liver
subclass of: Restriction
  on property: has plasma membrane part
  some values from: MHC protein complex
subclass of: Restriction
  on property: has plasma membrane part
  some values from: receptor-type tyrosine-protein phosphatase C
subclass of: Restriction
  on property: has plasma membrane part
  some values from: SLAM family member 1
subclass of: Restriction
  on property: has plasma membrane part
  some values from: signal transducer CD24
subclass of: Restriction
  on property: has plasma membrane part
  some values from: complement component C1q receptor
subclass of: Restriction
  on property: has plasma membrane part
  some values from: lymphocyte antigen 6A-2/6E-1
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: CD48 molecule
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: natural killer cell receptor 2B4
definition: A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-22T09:08:32Z
has_obo_namespace: cell

Axiom
annotated source: fetal liver hematopoietic progenitor cell
annotated property: subClassOf
annotated target: gestational hematopoietic stem cell
is inferred: true

yolk sac hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: gestational hematopoietic stem cell
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: CD44 molecule
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: signal transducer CD24
  intersection of: Restriction
    on property: has plasma membrane part
    some values from: complement component C1q receptor
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: MHC protein complex
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: receptor-type tyrosine-protein phosphatase C
  intersection of: Restriction
    on property: lacks_plasma_membrane_part
    some values from: lymphocyte antigen 6A-2/6E-1
subclass of: epithelial cell
subclass of: gestational hematopoietic stem cell
subclass of: Restriction
  on property: part_of
  some values from: yolk sac
subclass of: Restriction
  on property: has plasma membrane part
  some values from: CD44 molecule
subclass of: Restriction
  on property: has plasma membrane part
  some values from: signal transducer CD24
subclass of: Restriction
  on property: has plasma membrane part
  some values from: complement component C1q receptor
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: MHC protein complex
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: receptor-type tyrosine-protein phosphatase C
subclass of: Restriction
  on property: lacks_plasma_membrane_part
  some values from: lymphocyte antigen 6A-2/6E-1
definition: A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-22T09:08:34Z
has exact synonym: hemangioblast precursor
has_obo_namespace: cell

Axiom
annotated source: yolk sac hematopoietic stem cell
annotated property: subClassOf
annotated target: epithelial cell
is inferred: true

Axiom
annotated source: yolk sac hematopoietic stem cell
annotated property: subClassOf
annotated target: gestational hematopoietic stem cell
is inferred: true

placental hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: hematopoietic stem cell
  intersection of: Restriction
    on property: part_of
    some values from: placenta
subclass of: gestational hematopoietic stem cell
subclass of: Restriction
  on property: part_of
  some values from: placenta
definition: A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-22T10:30:02Z
has_obo_namespace: cell

Axiom
annotated source: placental hematopoietic stem cell
annotated property: subClassOf
annotated target: gestational hematopoietic stem cell
is inferred: true

AGM hematopoietic stem cell
type: Class
subclass of: gestational hematopoietic stem cell
definition: A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-22T10:31:49Z
has_obo_namespace: cell

Axiom
annotated source: AGM hematopoietic stem cell
annotated property: subClassOf
annotated target: gestational hematopoietic stem cell
is inferred: true

granule cell precursor
type: Class
subclass of: neuroblast (sensu Vertebrata)
definition: A cell located in the outermost proliferative zone of the external germinal layer that can differentiate into astroglial cells and granule cells. This cell type is glial fibrillary acidic protein-positive and NK1-positive.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-22T01:40:44Z
has_obo_namespace: cell

Axiom
annotated source: granule cell precursor
annotated property: subClassOf
annotated target: neuroblast (sensu Vertebrata)
is inferred: true

respiratory epithelial cell
type: Class
equivalent class: Class
  intersection of: endo-epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: respiratory tract
subclass of: endo-epithelial cell
subclass of: Restriction
  on property: part_of
  some values from: respiratory tract
definition: An endo-epithelial cell of the respiratory tract.
imported from: cl.owl
created by: tmeehan
creation date: 2010-09-23T04:38:49Z
database_cross_reference: BTO:0004533
has exact synonym: airway epithelial cell
has_obo_namespace: cell

Axiom
annotated source: respiratory epithelial cell
annotated property: subClassOf
annotated target: endo-epithelial cell
is inferred: true

somatic cell
type: Class
subclass of: native cell
definition: A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
created by: tmeehan
creation date: 2010-09-24T09:44:42Z
database_cross_reference: BTO:0001268
database_cross_reference: FMA:72300
database_cross_reference: WBbt:0008378
has_obo_namespace: cell
in subset: upper level

Axiom
annotated source: somatic cell
annotated property: subClassOf
annotated target: native cell
is inferred: true

mammary stem cell
type: Class
subclass of: multi fate stem cell
definition: A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi.
imported from: cl.owl
created by: tmeehan
creation date: 2010-11-10T01:46:51Z
has_obo_namespace: cell

Axiom
annotated source: mammary stem cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

amnion mesenchymal stem cell
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell
  intersection of: Restriction
    on property: part_of
    some values from: amnion
subclass of: mesenchymal stem cell
subclass of: Restriction
  on property: part_of
  some values from: amnion
definition: A mesenchymal stem cell of the amnion membrane.
imported from: cl.owl
created by: tmeehan
creation date: 2011-02-28T12:44:24Z
has exact synonym: amniotic membrane stem cell
has_obo_namespace: cell

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

mesenchymal stem cell of the bone marrow
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell
  intersection of: Restriction
    on property: part_of
    some values from: bone marrow
subclass of: mesenchymal stem cell
subclass of: bone marrow cell
subclass of: Restriction
  on property: part_of
  some values from: bone marrow
definition: A mesenchymal stem cell that is part of the bone marrow.
imported from: cl.owl
created by: tmeehan
creation date: 2011-02-28T01:47:47Z
has_obo_namespace: cell

Axiom
annotated source: mesenchymal stem cell of the bone marrow
annotated property: subClassOf
annotated target: mesenchymal stem cell
is inferred: true

Axiom
annotated source: mesenchymal stem cell of the bone marrow
annotated property: subClassOf
annotated target: bone marrow cell
is inferred: true

chorionic membrane mesenchymal stem cell
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell
  intersection of: Restriction
    on property: part_of
    some values from: chorion
subclass of: mesenchymal stem cell
subclass of: Restriction
  on property: part_of
  some values from: chorion
definition: A mesenchymal stem cell of the chorionic membrane.
imported from: cl.owl
created by: tmeehan
creation date: 2011-02-28T03:04:35Z
has_obo_namespace: cell

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

intestinal epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: intestine
subclass of: epithelial cell of alimentary canal
subclass of: Restriction
  on property: part_of
  some values from: intestine
subclass of: Restriction
  on property: part_of
  some values from: intestinal epithelium
definition: An epithelial cell of the intestine.
imported from: cl.owl
created by: tmeehan
creation date: 2011-03-01T05:18:31Z
has_obo_namespace: cell

Axiom
annotated source: intestinal epithelial cell
annotated property: subClassOf
annotated target: epithelial cell of alimentary canal
is inferred: true

mesenchymal stem cell of Wharton's jelly
type: Class
subclass of: mesenchymal stem cell of umbilical cord
definition: A mesenchymal stem cell that is part of Wharton's jelly.
imported from: cl.owl
created by: tmeehan
creation date: 2011-03-01T09:51:18Z
has_obo_namespace: cell

Axiom
annotated source: mesenchymal stem cell of Wharton's jelly
annotated property: subClassOf
annotated target: mesenchymal stem cell of umbilical cord
is inferred: true

mesenchymal stem cell of umbilical cord
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell
  intersection of: Restriction
    on property: part_of
    some values from: mesenchyme of umbilical cord
subclass of: mesenchymal stem cell
subclass of: extraembryonic cell
subclass of: Restriction
  on property: part_of
  some values from: mesenchyme of umbilical cord
definition: A mesenchymal stem cell of the umbilical cord.
imported from: cl.owl
created by: tmeehan
creation date: 2011-03-01T09:55:12Z
has_obo_namespace: cell

Axiom
annotated source: mesenchymal stem cell of umbilical cord
annotated property: subClassOf
annotated target: mesenchymal stem cell
is inferred: true

Axiom
annotated source: mesenchymal stem cell of umbilical cord
annotated property: subClassOf
annotated target: extraembryonic cell
is inferred: true

mesenchymal stem cell of adipose
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell
  intersection of: Restriction
    on property: part_of
    some values from: adipose tissue
subclass of: mesenchymal stem cell
subclass of: Restriction
  on property: part_of
  some values from: adipose tissue
definition: A mesenchymal stem cell of adipose tissue.
imported from: cl.owl
created by: tmeehan
creation date: 2011-03-01T09:57:17Z
has_obo_namespace: cell

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

hepatic mesenchymal stem cell
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell
  intersection of: Restriction
    on property: part_of
    some values from: liver
subclass of: mesenchymal stem cell
subclass of: hepatic stem cell
subclass of: Restriction
  on property: part_of
  some values from: liver
definition: A mesenchymal stem cell of liver.
imported from: cl.owl
created by: tmeehan
creation date: 2011-03-01T09:58:51Z
has_obo_namespace: cell

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

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

vertebral mesenchymal stem cell
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell
  intersection of: Restriction
    on property: part_of
    some values from: vertebra
subclass of: mesenchymal stem cell
subclass of: bone cell
subclass of: Restriction
  on property: part_of
  some values from: vertebra
definition: A mesenchymal stem cell of the vertebrae.
imported from: cl.owl
created by: tmeehan
creation date: 2011-03-01T10:40:27Z
has_obo_namespace: cell

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

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

migratory enteric neural crest cell
type: Class
subclass of: migratory neural crest cell
definition: A neural crest cell that gives rise to cells of the enteric nervous system.
imported from: cl.owl
created by: tmeehan
creation date: 2011-03-06T07:24:35Z
has_obo_namespace: cell

Axiom
annotated source: migratory enteric neural crest cell
annotated property: subClassOf
annotated target: migratory neural crest cell
is inferred: true

adult endothelial progenitor cell
type: Class
subclass of: angioblastic mesenchymal cell
definition: An adult angioblastic cell released from the bone marrow, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells. Their existence is controversial.
imported from: cl.owl
created by: tmeehan
creation date: 2011-03-14T12:11:18Z
has exact synonym: EPC
has_obo_namespace: cell

Axiom
annotated source: adult endothelial progenitor cell
annotated property: subClassOf
annotated target: angioblastic mesenchymal cell
is inferred: true

epithelial cell of lower respiratory tract
type: Class
equivalent class: Class
  intersection of: respiratory epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: lower respiratory tract
subclass of: respiratory epithelial cell
subclass of: Restriction
  on property: part_of
  some values from: lower respiratory tract
imported from: cl.owl
created by: tmeehan
creation date: 2011-06-21T12:29:31Z
has_obo_namespace: cell

Axiom
annotated source: epithelial cell of lower respiratory tract
annotated property: subClassOf
annotated target: respiratory epithelial cell
is inferred: true

respiratory basal cell
type: Class
subclass of: basal cell
subclass of: respiratory epithelial cell
definition: A basal cell in the respiratory tract.
imported from: cl.owl
created by: tmeehan
creation date: 2011-06-21T03:11:10Z
has exact synonym: airway basal cell
has exact synonym: airway basal stem cell
has_obo_namespace: cell

Axiom
annotated source: respiratory basal cell
annotated property: subClassOf
annotated target: basal cell
is inferred: true

Axiom
annotated source: respiratory basal cell
annotated property: subClassOf
annotated target: respiratory epithelial cell
is inferred: true

bronchioalveolar stem cell
type: Class
equivalent class: Class
  intersection of: respiratory basal cell
  intersection of: Restriction
    on property: part_of
    some values from: epithelium of respiratory bronchiole
  intersection of: Restriction
    on property: part_of
    some values from: terminal bronchiole epithelium
subclass of: basal cell of epithelium of terminal bronchiole
subclass of: basal cell of epithelium of respiratory bronchiole
subclass of: Restriction
  on property: part_of
  some values from: epithelium of respiratory bronchiole
subclass of: Restriction
  on property: part_of
  some values from: terminal bronchiole epithelium
definition: A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and Clara cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc.
imported from: cl.owl
created by: tmeehan
creation date: 2011-06-21T03:26:08Z
has exact synonym: BASC
has exact synonym: basal epithelial cell of bronchioalveolar duct junction
has_obo_namespace: cell

Axiom
annotated source: bronchioalveolar stem cell
annotated property: subClassOf
annotated target: basal cell of epithelium of terminal bronchiole
is inferred: true

Axiom
annotated source: bronchioalveolar stem cell
annotated property: subClassOf
annotated target: basal cell of epithelium of respiratory bronchiole
is inferred: true

amniotic stem cell
type: Class
subclass of: mesenchymal stem cell
subclass of: amniocyte
definition: An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue type such as skin, cartilage, cardiac tissue, nerves, muscle, and bone
imported from: cl.owl
created by: tmeehan
creation date: 2011-06-21T03:55:39Z
has_obo_namespace: cell
comment: Not clear to me if amniotic stem cell is a different cell type from amnion mesenchymal stem cells. They are treated as distinct in the literature as isolations methods are different, so I will keep them as separate terms for now.

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

Axiom
annotated source: amniotic stem cell
annotated property: subClassOf
annotated target: amniocyte
is inferred: true

amniotic epithelial stem cell
type: Class
subclass of: epithelial fate stem cell
definition: An epithelial fate stem cell derived form the amnion membrane.
imported from: cl.owl
created by: tmeehan
creation date: 2011-06-21T04:06:17Z
has_obo_namespace: cell

Axiom
annotated source: amniotic epithelial stem cell
annotated property: subClassOf
annotated target: epithelial fate stem cell
is inferred: true

glandular cell of stomach
type: Class
equivalent class: Class
  intersection of: glandular epithelial cell
  intersection of: Restriction
    on property: part_of
    some values from: stomach
subclass of: glandular epithelial cell
subclass of: epithelial cell of stomach
subclass of: Restriction
  on property: part_of
  some values from: stomach
definition: A glandular epithelial cell that is part of the stomach.
imported from: cl.owl
created by: tmeehan
creation date: 2011-07-11T01:20:35Z
database_cross_reference: CALOHA:TS-1284
database_cross_reference: FMA:86554
has_obo_namespace: cell

Axiom
annotated source: glandular cell of stomach
annotated property: subClassOf
annotated target: glandular epithelial cell
is inferred: true

Axiom
annotated source: glandular cell of stomach
annotated property: subClassOf
annotated target: epithelial cell of stomach
is inferred: true

cardioblast
type: Class
subclass of: multi fate stem cell
definition: A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart.
imported from: cl.owl
created by: tmeehan
creation date: 2011-07-11T03:15:38Z
has_obo_namespace: cell
comment: Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell.

Axiom
annotated source: cardioblast
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

retinal progenitor cell
type: Class
subclass of: multi fate stem cell
subclass of: Restriction
  on property: develops from
  some values from: neurectodermal cell
definition: A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells.
imported from: cl.owl
created by: tmeehan
creation date: 2011-08-16T02:38:01Z
has_obo_namespace: cell

Axiom
annotated source: retinal progenitor cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

neural crest derived neuroblast
type: Class
subclass of: neuroblast (sensu Vertebrata)
subclass of: Restriction
  on property: develops from
  some values from: migratory neural crest cell
definition: A neuroblast derived from a neural crest cell.
imported from: cl.owl
created by: tmeehan
creation date: 2011-08-22T09:24:15Z
has_obo_namespace: cell

Axiom
annotated source: neural crest derived neuroblast
annotated property: subClassOf
annotated target: neuroblast (sensu Vertebrata)
is inferred: true

lymphangioblast
type: Class
equivalent class: Class
  intersection of: multi fate stem cell
  intersection of: Restriction
    on property: adjacent to
    some values from: lymph vasculature
subclass of: multi fate stem cell
subclass of: Restriction
  on property: adjacent to
  some values from: lymph vasculature
definition: Lymphatic progenitor cells.
imported from: cl.owl
created by: Ceri
creation date: 2012-01-12T04:44:34Z
has_obo_namespace: cell
comment: Usually express Prox1, or prox1b.

Axiom
annotated source: lymphangioblast
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

mesenchymal lymphangioblast
type: Class
subclass of: mesenchymal stem cell
subclass of: lymphangioblast
definition: Mesenchymal derived lymphatic progenitor cells that give rise to the superficial lymphatics.
imported from: cl.owl
created by: Ceri
creation date: 2012-01-12T05:01:22Z
has_obo_namespace: cell

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

Axiom
annotated source: mesenchymal lymphangioblast
annotated property: subClassOf
annotated target: lymphangioblast
is inferred: true

vascular lymphangioblast
type: Class
equivalent class: Class
  intersection of: lymphangioblast
  intersection of: Restriction
    on property: adjacent to
    some values from: vein
subclass of: lymphangioblast
subclass of: Restriction
  on property: adjacent to
  some values from: vein
definition: Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells.
imported from: cl.owl
created by: Ceri
creation date: 2012-01-12T05:21:09Z
has_narrow_synonym: parachordal lymphangioblast
has_obo_namespace: cell

Axiom
annotated source: vascular lymphangioblast
annotated property: subClassOf
annotated target: lymphangioblast
is inferred: true

hepatoblast
type: Class
subclass of: multi fate stem cell
definition: Multi fate stem cell that gives rise to to both hepatocytes and cholangiocytes as descendants.
imported from: cl.owl

Axiom
annotated source: hepatoblast
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

premigratory neural crest cell
type: Class
subclass of: neural crest cell
subclass of: Restriction
  on property: part_of
  some values from: neural crest
subclass of: Restriction
  on property: develops from
  some values from: neurectodermal cell
definition: Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.
imported from: cl.owl
created by: haendel
creation date: 2012-06-27T08:27:35Z
has_obo_namespace: cell

Axiom
annotated source: premigratory neural crest cell
annotated property: subClassOf
annotated target: neural crest cell
is inferred: true

hematopoietic precursor cell
type: Class
subclass of: hematopoietic cell
definition: Any hematopoietic cell that is a precursor of some other hematopoietic cell type.
imported from: cl.owl

Axiom
annotated source: hematopoietic precursor cell
annotated property: subClassOf
annotated target: hematopoietic cell
is inferred: true

skeletal muscle satellite stem cell
type: Class
equivalent class: Class
  intersection of: skeletal muscle satellite cell
  intersection of: Restriction
    on property: bearer of
    some values from: unipotent
  intersection of: Restriction
    on property: capable of
    some values from: stem cell division
subclass of: single fate stem cell
subclass of: skeletal muscle satellite cell
subclass of: Restriction
  on property: bearer of
  some values from: unipotent
subclass of: Restriction
  on property: capable of
  some values from: stem cell division
definition: A skeletal muscle satellite cell that divides by stem cell division. A proportion of this population undergoes symmetric stem cell division, producing two skeletal muscle satellite stem cells. The rest undergo asymmetric stem cell division - retaining their identity while budding off a daughter cell that differentiates into an adult skeletal muscle myoblast.
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: skeletal muscle satellite stem cell
annotated property: subClassOf
annotated target: single fate stem cell
is inferred: true

Axiom
annotated source: skeletal muscle satellite stem cell
annotated property: subClassOf
annotated target: skeletal muscle satellite cell
is inferred: true

neural crest cell
type: Class
subclass of: multi fate stem cell
subclass of: embryonic cell
definition: A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: neural crest cell
annotated property: subClassOf
annotated target: multi fate stem cell
is inferred: true

Axiom
annotated source: neural crest cell
annotated property: subClassOf
annotated target: embryonic cell
is inferred: true

precursor cell
type: Class
equivalent class: Class
  intersection of: native cell
  intersection of: Restriction
    on property: capable of
    some values from: cell differentiation
subclass of: native cell
subclass of: Restriction
  on property: capable of
  some values from: cell differentiation
definition: A cell that, by division or terminal differentiation, can give rise to other cell types.
imported from: cl.owl
imported from: clo.owl
comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell.

Axiom
annotated source: precursor cell
annotated property: subClassOf
annotated target: native cell
is inferred: true

forebrain neuroblast
type: Class
equivalent class: Class
  intersection of: neuroblast
  intersection of: Restriction
    on property: part_of
    some values from: forebrain
subclass of: neuroblast
subclass of: Restriction
  on property: part_of
  some values from: forebrain
imported from: cl.owl

Axiom
annotated source: forebrain neuroblast
annotated property: subClassOf
annotated target: neuroblast
is inferred: true

stratified keratinized epithelial stem cell
type: Class
subclass of: stratified epithelial stem cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: stratified keratinized epithelial stem cell
annotated property: subClassOf
annotated target: stratified epithelial stem cell
is inferred: true

stratified non keratinized epithelial stem cell
type: Class
subclass of: stratified epithelial stem cell
imported from: cl.owl
has_obo_namespace: cell

Axiom
annotated source: stratified non keratinized epithelial stem cell
annotated property: subClassOf
annotated target: stratified epithelial stem cell
is inferred: true

basal cell of epithelium of trachea
type: Class
equivalent class: Class
  intersection of: respiratory basal cell
  intersection of: Restriction
    on property: part_of
    some values from: epithelium of trachea
subclass of: tracheal epithelial cell
subclass of: respiratory basal cell
subclass of: Restriction
  on property: part_of
  some values from: epithelium of trachea
definition: A basal cell that is part of the epithelium of trachea.
imported from: cl.owl
database_cross_reference: FMA:263118
has_obo_namespace: cell

Axiom
annotated source: basal cell of epithelium of trachea
annotated property: subClassOf
annotated target: tracheal epithelial cell
is inferred: true

Axiom
annotated source: basal cell of epithelium of trachea
annotated property: subClassOf
annotated target: respiratory basal cell
is inferred: true

basal cell of epithelium of bronchus
type: Class
equivalent class: Class
  intersection of: respiratory basal cell
  intersection of: Restriction
    on property: part_of
    some values from: epithelium of bronchus
subclass of: bronchial epithelial cell
subclass of: basal epithelial cell of tracheobronchial tree
subclass of: respiratory basal cell
subclass of: Restriction
  on property: part_of
  some values from: epithelium of bronchus
definition: A basal cell found in the bronchus epithelium.
imported from: cl.owl
has_alternative_id: CL:0002331
database_cross_reference: FMA:263120
has exact synonym: basal cell of bronchus
has_obo_namespace: cell

Axiom
annotated source: basal cell of epithelium of bronchus
annotated property: subClassOf
annotated target: bronchial epithelial cell
is inferred: true

Axiom
annotated source: basal cell of epithelium of bronchus
annotated property: subClassOf
annotated target: basal epithelial cell of tracheobronchial tree
is inferred: true

Axiom
annotated source: basal cell of epithelium of bronchus
annotated property: subClassOf
annotated target: respiratory basal cell
is inferred: true

basal cell of epithelium of terminal bronchiole
type: Class
equivalent class: Class
  intersection of: respiratory basal cell
  intersection of: Restriction
    on property: part_of
    some values from: terminal bronchiole epithelium
subclass of: basal cell of epithelium of lobular bronchiole
subclass of: Restriction
  on property: part_of
  some values from: terminal bronchiole epithelium
definition: A basal cell that is part of the epithelium of terminal bronchiole.
imported from: cl.owl
database_cross_reference: FMA:263122
has_obo_namespace: cell

Axiom
annotated source: basal cell of epithelium of terminal bronchiole
annotated property: subClassOf
annotated target: basal cell of epithelium of lobular bronchiole
is inferred: true

basal cell of epithelium of respiratory bronchiole
type: Class
equivalent class: Class
  intersection of: respiratory basal cell
  intersection of: Restriction
    on property: part_of
    some values from: epithelium of respiratory bronchiole
subclass of: basal cell of epithelium of lobular bronchiole
subclass of: Restriction
  on property: part_of
  some values from: epithelium of respiratory bronchiole
definition: A basal cell that is part of the epithelium of respiratory bronchiole.
imported from: cl.owl
database_cross_reference: FMA:263124
has_obo_namespace: cell

Axiom
annotated source: basal cell of epithelium of respiratory bronchiole
annotated property: subClassOf
annotated target: basal cell of epithelium of lobular bronchiole
is inferred: true

basal cell of epithelium of lobular bronchiole
type: Class
equivalent class: Class
  intersection of: respiratory basal cell
  intersection of: Restriction
    on property: part_of
    some values from: epithelium of bronchiole
subclass of: epithelial cell of lung
subclass of: basal cell of epithelium of bronchus
subclass of: Restriction
  on property: part_of
  some values from: epithelium of bronchiole
definition: A basal cell that is part of the epithelium of bronchiole.
imported from: cl.owl
database_cross_reference: FMA:263126
has_obo_namespace: cell

Axiom
annotated source: basal cell of epithelium of lobular bronchiole
annotated property: subClassOf
annotated target: epithelial cell of lung
is inferred: true

Axiom
annotated source: basal cell of epithelium of lobular bronchiole
annotated property: subClassOf
annotated target: basal cell of epithelium of bronchus
is inferred: true

stem cell of epidermis
type: Class
equivalent class: Class
  intersection of: somatic stem cell
  intersection of: Restriction
    on property: part_of
    some values from: skin epidermis
subclass of: somatic stem cell
subclass of: Restriction
  on property: part_of
  some values from: skin epidermis
definition: A somatic stem cell that is part of the epidermis.
imported from: cl.owl
database_cross_reference: FMA:70541
has exact synonym: epidermal stem cell
has_obo_namespace: cell

Axiom
annotated source: stem cell of epidermis
annotated property: subClassOf
annotated target: somatic stem cell
is inferred: true

epithelial cell of stratum germinativum of esophagus
type: Class
equivalent class: Class
  intersection of: basal cell
  intersection of: Restriction
    on property: part_of
    some values from: epithelium of esophagus
subclass of: basal cell
subclass of: Restriction
  on property: part_of
  some values from: epithelium of esophagus
definition: A basal cell that is part of the epithelium of esophagus.
imported from: cl.owl
database_cross_reference: FMA:70731
has exact synonym: basal cell of esophageal epithelium
has_obo_namespace: cell

Axiom
annotated source: epithelial cell of stratum germinativum of esophagus
annotated property: subClassOf
annotated target: basal cell
is inferred: true

basal cell of urothelium
type: Class
equivalent class: Class
  intersection of: basal cell
  intersection of: Restriction
    on property: part_of
    some values from: urothelium
subclass of: basal cell
subclass of: Restriction
  on property: part_of
  some values from: urothelium
definition: A basal cell that is part of the urothelium.
imported from: cl.owl
database_cross_reference: FMA:84150
has_obo_namespace: cell

Axiom
annotated source: basal cell of urothelium
annotated property: subClassOf
annotated target: basal cell
is inferred: true

bronchioalveolar stem cells
type: Class
subclass of: stem cell
subclass of: Restriction
  on property: part_of
  some values from: lung epithelium
definition: a respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole, which gives rise to alveolar cell types and Clara cells in response to lung injury.
imported from: cl.owl
has_obo_namespace: cl

Axiom
annotated source: bronchioalveolar stem cells
annotated property: subClassOf
annotated target: stem cell
is inferred: true

limb basal cell of epidermis
type: Class
equivalent class: Class
  intersection of: basal cell of epidermis
  intersection of: Restriction
    on property: part_of
    some values from: limb
subclass of: basal cell of epidermis
subclass of: Restriction
  on property: part_of
  some values from: limb
definition: Any basal cell of epidermis that is part of a limb.
imported from: cl.owl
created by: TermGenie
creation date: 2014-06-25T02:28:25Z
has_obo_namespace: cell
id: CL:2000033

Axiom
annotated source: limb basal cell of epidermis
annotated property: subClassOf
annotated target: basal cell of epidermis
is inferred: true

placental amniotic mesenchymal stromal cell
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell
  intersection of: Restriction
    on property: part_of
    some values from: placenta
subclass of: mesenchymal stem cell
subclass of: Restriction
  on property: part_of
  some values from: placenta
definition: Any mesenchymal stem cell that is part of a placenta.
imported from: cl.owl
created by: TermGenie
creation date: 2014-10-07T17:51:11Z
has_obo_namespace: cell
id: CL:2000061
comment: http://www.sciencellonline.com/site/productInformation.php

Axiom
annotated source: placental amniotic mesenchymal stromal cell
annotated property: subClassOf
annotated target: mesenchymal stem cell
is inferred: true

migratory cardiac neural crest cell
type: Class
equivalent class: Class
  intersection of: migratory neural crest cell
  intersection of: Restriction
    on property: part_of
    some values from: cardiac neural crest
subclass of: migratory neural crest cell
subclass of: Restriction
  on property: part_of
  some values from: cardiac neural crest
definition: Any migratory neural crest cell that is part of a cardiac neural crest.
imported from: cl.owl
created by: TermGenie
creation date: 2014-11-05T01:18:43Z
has_obo_namespace: cell
id: CL:2000073

Axiom
annotated source: migratory cardiac neural crest cell
annotated property: subClassOf
annotated target: migratory neural crest cell
is inferred: true

mesenchymal stem cell of femoral bone marrow
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell of the bone marrow
  intersection of: Restriction
    on property: part_of
    some values from: femur
subclass of: mesenchymal stem cell of the bone marrow
subclass of: Restriction
  on property: part_of
  some values from: femur
definition: Any mesenchymal stem cell of the bone marrow that is part of a femur.
imported from: cl.owl
created by: TermGenie
creation date: 2014-12-02T19:07:31Z
has_obo_namespace: cell
id: CL:2000079

Axiom
annotated source: mesenchymal stem cell of femoral bone marrow
annotated property: subClassOf
annotated target: mesenchymal stem cell of the bone marrow
is inferred: true

mesenchymal stem cell of abdominal adipose
type: Class
equivalent class: Class
  intersection of: mesenchymal stem cell of adipose
  intersection of: Restriction
    on property: part_of
    some values from: abdomen
subclass of: mesenchymal stem cell of adipose
subclass of: Restriction
  on property: part_of
  some values from: abdomen
definition: Any mesenchymal stem cell of adipose that is part of a abdomen.
imported from: cl.owl
created by: TermGenie
creation date: 2014-12-02T19:10:34Z
has_obo_namespace: cell
id: CL:2000080

Axiom
annotated source: mesenchymal stem cell of abdominal adipose
annotated property: subClassOf
annotated target: mesenchymal stem cell of adipose
is inferred: true

hair follicle dermal papilla cell of scalp
type: Class
equivalent class: Class
  intersection of: hair follicle dermal papilla cell
  intersection of: Restriction
    on property: part_of
    some values from: scalp
subclass of: hair follicle dermal papilla cell
subclass of: Restriction
  on property: part_of
  some values from: scalp
definition: Any hair follicle dermal papilla cell that is part of a scalp.
imported from: cl.owl
created by: TermGenie
creation date: 2014-12-02T19:10:50Z
has_obo_namespace: cell
id: CL:2000083

Axiom
annotated source: hair follicle dermal papilla cell of scalp
annotated property: subClassOf
annotated target: hair follicle dermal papilla cell
is inferred: true

cord blood hematopoietic stem cell
type: Class
equivalent class: Class
  intersection of: hematopoietic stem cell
  intersection of: Restriction
    on property: part_of
    some values from: umbilical cord blood
subclass of: peripheral blood stem cell
subclass of: gestational hematopoietic stem cell
subclass of: Restriction
  on property: part_of
  some values from: umbilical cord blood
definition: Any hematopoietic stem cell that is part of a umbilical cord blood.
imported from: cl.owl
created by: TermGenie
creation date: 2015-05-26T18:58:34Z
has_obo_namespace: cell
id: CL:2000095

Axiom
annotated source: cord blood hematopoietic stem cell
annotated property: subClassOf
annotated target: peripheral blood stem cell
is inferred: true

Axiom
annotated source: cord blood hematopoietic stem cell
annotated property: subClassOf
annotated target: gestational hematopoietic stem cell
is inferred: true

spinal muscular atrophy
type: Class
subclass of: motor neuron disease
subclass of: spinal cord disease
imported from: clo.owl
see also: URI: http://www.ebi.ac.uk/cellline#spinal_muscular_atrophy

Axiom
annotated source: spinal muscular atrophy
annotated property: subClassOf
annotated target: motor neuron disease
is inferred: true

Axiom
annotated source: spinal muscular atrophy
annotated property: subClassOf
annotated target: spinal cord disease
is inferred: true

degenerative disease
type: Class
subclass of: disease of biological process
alternative term: "degenerative disease" EXACT [NCI2004_11_17:C27090]
alternative term: "degenerative disorder (disorder)" EXACT [SNOMEDCT_2005_07_31:362975008]
imported from: clo.owl
comment: "A disease of biological process that results_in the progressive deterioration of tissue or organ function or structure, whether due to normal bodily wear or lifestyle choices." [url:http\://en.wikipedia.org/wiki/Degenerative_disease]
see also: URI: http://www.ebi.ac.uk/cellline#degenerative_disease

Axiom
annotated source: degenerative disease
annotated property: subClassOf
annotated target: disease of biological process
is inferred: true

hereditary motor neuropathy proximal type I
type: Class
subclass of: spinal muscular atrophy
alternative term: "HMN (Hereditary motor Neuropathy) Proximal type I" EXACT []
alternative term: "Werdnig-Hoffman disease" EXACT [SNOMEDCT_2005_07_31:155016008]
alternative term: "Werdnig-Hoffman disease" EXACT [SNOMEDCT_2005_07_31:267694009]
alternative term: "Werdnig-Hoffmann disease (disorder)" EXACT [SNOMEDCT_2005_07_31:64383006]
alternative term: "Werdnig-Hoffmann disease" EXACT [ICD9CM_2006:335.0]
alternative term: "infantile muscular atrophy" EXACT [CSP2005:2057-3620]
alternative term: "progressive muscular atrophy of infancy" EXACT [MTHICD9_2006:335.0]
imported from: clo.owl
see also: URI: http://www.ebi.ac.uk/cellline#hereditary_motor_neuropathy_proximal_type_I

Axiom
annotated source: hereditary motor neuropathy proximal type I
annotated property: subClassOf
annotated target: spinal muscular atrophy
is inferred: true

musculoskeletal system disease
type: Class
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that occurs in the muscular and/or skeletal system.
alternative term: "Musculo-skeletal disorder NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:274149006]
alternative term: "Musculo-skeletal disorder NOS" EXACT [SNOMEDCT_2005_07_31:156881000]
alternative term: "Musculo-skeletal disorder NOS" EXACT [SNOMEDCT_2005_07_31:268142006]
alternative term: "Musculoskeletal disease" EXACT [MTH:NOCODE]
alternative term: "Musuloskeletal disease" EXACT [SNOMEDCT_2005_07_31:268047003]
alternative term: "disorder of musculoskeletal system (disorder)" EXACT [SNOMEDCT_2005_07_31:928000]
alternative term: "musculoskeletal disorder" EXACT [CSP2005:4000-0257]
imported from: clo.owl
imported from: doid.owl
has db xref: MESH:D009140
has db xref: NCI:C107377
has db xref: SNOMEDCT_US_2016_03_01:156881000
has db xref: SNOMEDCT_US_2016_03_01:268047003
has db xref: SNOMEDCT_US_2016_03_01:268142006
has db xref: SNOMEDCT_US_2016_03_01:274149006
has db xref: SNOMEDCT_US_2016_03_01:928000
has db xref: UMLS_CUI:C0026857
has OBO namespace: disease_ontology
id: DOID:17
in subset: DO MGI slim
see also: URI: http://www.ebi.ac.uk/cellline#musculoskeletal_system_disease

Axiom
annotated source: musculoskeletal system disease
annotated property: subClassOf
annotated target: disease of anatomical entity
is inferred: true

motor neuron disease
type: Class
subclass of: anterior horn cell disease
subclass of: neurodegenerative disease
imported from: clo.owl
see also: URI: http://www.ebi.ac.uk/cellline#motor_neuron_disease

Axiom
annotated source: motor neuron disease
annotated property: subClassOf
annotated target: anterior horn cell disease
is inferred: true

Axiom
annotated source: motor neuron disease
annotated property: subClassOf
annotated target: neurodegenerative disease
is inferred: true

spinal cord disease
type: Class
subclass of: central nervous system disease
alternative term: "myelopathy" RELATED []
imported from: clo.owl
see also: URI: http://www.ebi.ac.uk/cellline#spinal_cord_disease

Axiom
annotated source: spinal cord disease
annotated property: subClassOf
annotated target: central nervous system disease
is inferred: true

central nervous system disease
type: Class
subclass of: nervous system disease
imported from: clo.owl
comment: "A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system." [url:http\://en.wikipedia.org/wiki/Central_nervous_system_disease]
see also: URI: http://www.ebi.ac.uk/cellline#central_nervous_system_disease

Axiom
annotated source: central nervous system disease
annotated property: subClassOf
annotated target: nervous system disease
is inferred: true

disease of biological process
type: Class
subclass of: EFO_0000408
imported from: clo.owl
comment: "A disease that involves any biological process (GO:0008150) specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms." [DO:wk\,ls]
see also: URI: http://www.ebi.ac.uk/cellline#disease_of_biological_process

Axiom
annotated source: disease of biological process
annotated property: subClassOf
annotated target: EFO_0000408
is inferred: true

disease
type: Class
subclass of: disposition
definition: A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
imported from: clo.owl
imported from: doid.owl
has db xref: MESH:D004194
has db xref: NCI:C2991
has db xref: SNOMEDCT_US_2016_03_01:64572001
has db xref: UMLS_CUI:C0012634
has OBO namespace: disease_ontology
id: DOID:4

Axiom
annotated source: disease
annotated property: subClassOf
annotated target: disposition
is inferred: true

tissue disease
type: Class
subclass of: musculoskeletal system disease
imported from: clo.owl
see also: URI: http://www.ebi.ac.uk/cellline#tissue_disease

Axiom
annotated source: tissue disease
annotated property: subClassOf
annotated target: musculoskeletal system disease
is inferred: true

neuromuscular disease
type: Class
subclass of: neuropathy
subclass of: EFO_0002970
imported from: clo.owl
see also: URI: http://www.ebi.ac.uk/cellline#neuromuscular_disease

Axiom
annotated source: neuromuscular disease
annotated property: subClassOf
annotated target: neuropathy
is inferred: true

Axiom
annotated source: neuromuscular disease
annotated property: subClassOf
annotated target: EFO_0002970
is inferred: true

hereditary degenerative disease of central nervous system
type: Class
subclass of: central nervous system disease
subclass of: neuromuscular disease
imported from: clo.owl
see also: URI: http://www.ebi.ac.uk/cellline#hereditary_degenerative_disease_of_central_nervous_system

Axiom
annotated source: hereditary degenerative disease of central nervous system
annotated property: subClassOf
annotated target: central nervous system disease
is inferred: true

Axiom
annotated source: hereditary degenerative disease of central nervous system
annotated property: subClassOf
annotated target: neuromuscular disease
is inferred: true

anterior horn cell disease
type: Class
subclass of: hereditary degenerative disease of central nervous system
imported from: clo.owl
see also: URI: http://www.ebi.ac.uk/cellline#anterior_horn_cell_disease

Axiom
annotated source: anterior horn cell disease
annotated property: subClassOf
annotated target: hereditary degenerative disease of central nervous system
is inferred: true

neurodegenerative disease
type: Class
subclass of: degenerative disease
subclass of: nervous system disease
alternative term: "Neurodegenerative disease" EXACT [NCI2004_11_17:C4802]
imported from: clo.owl
comment: "A degenerative disease that results_in the progressive loss of structure or function of neurons, including death of neurons." [url:http\://en.wikipedia.org/wiki/Neurodegeneration]
see also: URI: http://www.ebi.ac.uk/cellline#neurodegenerative_disease

Axiom
annotated source: neurodegenerative disease
annotated property: subClassOf
annotated target: degenerative disease
is inferred: true

Axiom
annotated source: neurodegenerative disease
annotated property: subClassOf
annotated target: nervous system disease
is inferred: true

muscle tissue disease
type: Class
subclass of: tissue disease
imported from: clo.owl
see also: URI: http://www.ebi.ac.uk/cellline#muscle_tissue_disease

Axiom
annotated source: muscle tissue disease
annotated property: subClassOf
annotated target: tissue disease
is inferred: true

disease of anatomical entity
type: Class
subclass of: disease
subclass of: EFO_0000408
definition: A disease that manifests in a defined anatomical structure.
alternative term: "acellular anatomical structure disease" EXACT []
alternative term: "disease of anatomical set" EXACT []
alternative term: "disease of anatomical structure" EXACT []
alternative term: "disease of material anatomical entity" EXACT []
alternative term: "disease of physical anatomical entity" EXACT []
alternative term: "disease of set of heterogenous clusters" EXACT []
imported from: clo.owl
imported from: doid.owl
has alternative id: DOID:1
has alternative id: DOID:2
has alternative id: DOID:5
has alternative id: DOID:71
has alternative id: DOID:72
has alternative id: DOID:8
has OBO namespace: disease_ontology
id: DOID:7
comment: "A disease that manifests in a defined anatomical structure." [DO:wk\,ls, URL:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic]
see also: URI: http://www.ebi.ac.uk/cellline#disease_of_anatomical_entity

Axiom
annotated source: disease of anatomical entity
annotated property: subClassOf
annotated target: disease
is inferred: true

Axiom
annotated source: disease of anatomical entity
annotated property: subClassOf
annotated target: EFO_0000408
is inferred: true

nervous system disease
type: Class
subclass of: disease of anatomical entity
imported from: clo.owl
see also: URI: http://www.ebi.ac.uk/cellline#nervous_system_disease

Axiom
annotated source: nervous system disease
annotated property: subClassOf
annotated target: disease of anatomical entity
is inferred: true

neuropathy
type: Class
subclass of: nervous system disease
alternative term: "Neuropathy (disorder)" EXACT [SNOMEDCT_2005_07_31:264554005]
alternative term: "Neuropathy (disorder)" EXACT [SNOMEDCT_2005_07_31:386033004]
alternative term: "Neuropathy" EXACT [MTH:NOCODE]
alternative term: "Neuropathy" EXACT [SNOMEDCT_2005_07_31:193167000]
alternative term: "Neuropathy" EXACT [SNOMEDCT_2005_07_31:277317008]
alternative term: "Neuropathy" EXACT [SNOMEDCT_2005_07_31:277878001]
alternative term: "Neuropathy, NOS" EXACT [SNOMEDCT_2005_07_31:42658009]
imported from: clo.owl
see also: URI: http://www.ebi.ac.uk/cellline#neuropathy

Axiom
annotated source: neuropathy
annotated property: subClassOf
annotated target: nervous system disease
is inferred: true

osteoblast differentiation
type: Class
subclass of: cell differentiation
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: osteoblast differentiation
annotated property: subClassOf
annotated target: cell differentiation
is inferred: true

hematopoietic progenitor cell differentiation
type: Class
subclass of: cell differentiation
imported from: cl.owl

Axiom
annotated source: hematopoietic progenitor cell differentiation
annotated property: subClassOf
annotated target: cell differentiation
is inferred: true

immune system process
type: Class
subclass of: biological_process
imported from: cl.owl

Axiom
annotated source: immune system process
annotated property: subClassOf
annotated target: biological_process
is inferred: true

production of molecular mediator of immune response
type: Class
subclass of: immune system process
imported from: cl.owl

Axiom
annotated source: production of molecular mediator of immune response
annotated property: subClassOf
annotated target: immune system process
is inferred: true

regulation of immune system process
type: Class
subclass of: regulation of biological process
imported from: cl.owl

Axiom
annotated source: regulation of immune system process
annotated property: subClassOf
annotated target: regulation of biological process
is inferred: true

positive regulation of immune system process
type: Class
subclass of: regulation of immune system process
subclass of: positive regulation of biological process
imported from: cl.owl

Axiom
annotated source: positive regulation of immune system process
annotated property: subClassOf
annotated target: regulation of immune system process
is inferred: true

Axiom
annotated source: positive regulation of immune system process
annotated property: subClassOf
annotated target: positive regulation of biological process
is inferred: true

regulation of leukocyte migration
type: Class
subclass of: regulation of immune system process
subclass of: regulation of cell migration
imported from: cl.owl

Axiom
annotated source: regulation of leukocyte migration
annotated property: subClassOf
annotated target: regulation of immune system process
is inferred: true

Axiom
annotated source: regulation of leukocyte migration
annotated property: subClassOf
annotated target: regulation of cell migration
is inferred: true

positive regulation of leukocyte migration
type: Class
subclass of: positive regulation of immune system process
subclass of: regulation of leukocyte migration
subclass of: positive regulation of cell migration
imported from: cl.owl

Axiom
annotated source: positive regulation of leukocyte migration
annotated property: subClassOf
annotated target: positive regulation of immune system process
is inferred: true

Axiom
annotated source: positive regulation of leukocyte migration
annotated property: subClassOf
annotated target: regulation of leukocyte migration
is inferred: true

Axiom
annotated source: positive regulation of leukocyte migration
annotated property: subClassOf
annotated target: positive regulation of cell migration
is inferred: true

regulation of leukocyte chemotaxis
type: Class
subclass of: regulation of leukocyte migration
subclass of: regulation of chemotaxis
imported from: cl.owl

Axiom
annotated source: regulation of leukocyte chemotaxis
annotated property: subClassOf
annotated target: regulation of leukocyte migration
is inferred: true

Axiom
annotated source: regulation of leukocyte chemotaxis
annotated property: subClassOf
annotated target: regulation of chemotaxis
is inferred: true

positive regulation of leukocyte chemotaxis
type: Class
subclass of: positive regulation of leukocyte migration
subclass of: regulation of leukocyte chemotaxis
subclass of: positive regulation of chemotaxis
imported from: cl.owl

Axiom
annotated source: positive regulation of leukocyte chemotaxis
annotated property: subClassOf
annotated target: positive regulation of leukocyte migration
is inferred: true

Axiom
annotated source: positive regulation of leukocyte chemotaxis
annotated property: subClassOf
annotated target: regulation of leukocyte chemotaxis
is inferred: true

Axiom
annotated source: positive regulation of leukocyte chemotaxis
annotated property: subClassOf
annotated target: positive regulation of chemotaxis
is inferred: true

antimicrobial peptide production
type: Class
subclass of: production of molecular mediator of immune response
imported from: cl.owl

Axiom
annotated source: antimicrobial peptide production
annotated property: subClassOf
annotated target: production of molecular mediator of immune response
is inferred: true

antimicrobial peptide secretion
type: Class
subclass of: peptide secretion
imported from: cl.owl

Axiom
annotated source: antimicrobial peptide secretion
annotated property: subClassOf
annotated target: peptide secretion
is inferred: true

peptide secretion
type: Class
subclass of: peptide transport
subclass of: secretion
imported from: cl.owl

Axiom
annotated source: peptide secretion
annotated property: subClassOf
annotated target: peptide transport
is inferred: true

Axiom
annotated source: peptide secretion
annotated property: subClassOf
annotated target: secretion
is inferred: true

developmental process involved in reproduction
type: Class
subclass of: reproductive process
subclass of: developmental process
imported from: cl.owl

Axiom
annotated source: developmental process involved in reproduction
annotated property: subClassOf
annotated target: reproductive process
is inferred: true

Axiom
annotated source: developmental process involved in reproduction
annotated property: subClassOf
annotated target: developmental process
is inferred: true

system process
type: Class
subclass of: multicellular organismal process
imported from: cl.owl

Axiom
annotated source: system process
annotated property: subClassOf
annotated target: multicellular organismal process
is inferred: true

cellular_component
type: Class
subclass of: material entity
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: cellular_component
annotated property: subClassOf
annotated target: material entity
is inferred: true

cell
type: Class
subclass of: anatomical structure
subclass of: cellular_component
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: cell
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: cell
annotated property: subClassOf
annotated target: cellular_component
is inferred: true

transport
type: Class
subclass of: establishment of localization
imported from: cl.owl

Axiom
annotated source: transport
annotated property: subClassOf
annotated target: establishment of localization
is inferred: true

movement of cell or subcellular component
type: Class
subclass of: cellular process
imported from: cl.owl
imported from: clo.owl
imported from: go.owl
imported from: uberon.owl
in subset: goslim pir
in subset: gosubset prok

Axiom
annotated source: movement of cell or subcellular component
annotated property: subClassOf
annotated target: cellular process
is inferred: true

gamete generation
type: Class
subclass of: multicellular organismal reproductive process
imported from: cl.owl

Axiom
annotated source: gamete generation
annotated property: subClassOf
annotated target: multicellular organismal reproductive process
is inferred: true

germ cell development
type: Class
subclass of: developmental process involved in reproduction
subclass of: cellular process involved in reproduction in multicellular organism
subclass of: cell development
imported from: cl.owl

Axiom
annotated source: germ cell development
annotated property: subClassOf
annotated target: developmental process involved in reproduction
is inferred: true

Axiom
annotated source: germ cell development
annotated property: subClassOf
annotated target: cellular process involved in reproduction in multicellular organism
is inferred: true

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

spermatogenesis
type: Class
subclass of: male gamete generation
imported from: cl.owl

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

female gamete generation
type: Class
subclass of: gamete generation
imported from: cl.owl

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

biological_process
type: Class
subclass of: process
editor preferred label: biological_process
definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
imported from: cl.owl
imported from: clo.owl
imported from: go.owl
imported from: obi.owl
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
database_cross_reference: Wikipedia:Biological_process
has exact synonym: biological process
has exact synonym: physiological process
has_obo_namespace: biological_process
id: GO:0008150
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim generic
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: goslim pombe
in subset: goslim yeast
in subset: gosubset prok
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.

Axiom
annotated source: biological_process
annotated property: subClassOf
annotated target: process
is inferred: true

detection of chemical stimulus
type: Class
subclass of: detection of stimulus
imported from: cl.owl

Axiom
annotated source: detection of chemical stimulus
annotated property: subClassOf
annotated target: detection of stimulus
is inferred: true

cellular process
type: Class
subclass of: biological_process
definition: Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
imported from: cl.owl
imported from: clo.owl
imported from: go.owl
imported from: uberon.owl
has_alternative_id: GO:0008151
has_alternative_id: GO:0050875
has exact synonym: cell physiology
has exact synonym: cellular physiological process
has_narrow_synonym: cell growth and/or maintenance
has_obo_namespace: biological_process
id: GO:0009987
in subset: goslim pir
in subset: goslim plant
in subset: gosubset prok

Axiom
annotated source: cellular process
annotated property: subClassOf
annotated target: biological_process
is inferred: true

peptide transport
type: Class
subclass of: amide transport
subclass of: organic substance transport
imported from: cl.owl

Axiom
annotated source: peptide transport
annotated property: subClassOf
annotated target: amide transport
is inferred: true

Axiom
annotated source: peptide transport
annotated property: subClassOf
annotated target: organic substance transport
is inferred: true

cell migration
type: Class
subclass of: cell motility
imported from: cl.owl
imported from: clo.owl
imported from: go.owl
imported from: uberon.owl

Axiom
annotated source: cell migration
annotated property: subClassOf
annotated target: cell motility
is inferred: true

stem cell division
type: Class
subclass of: cell division
imported from: cl.owl
imported from: clo.owl

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

transmission of nerve impulse
type: Class
subclass of: multicellular organismal signaling
subclass of: nervous system process
imported from: cl.owl

Axiom
annotated source: transmission of nerve impulse
annotated property: subClassOf
annotated target: multicellular organismal signaling
is inferred: true

Axiom
annotated source: transmission of nerve impulse
annotated property: subClassOf
annotated target: nervous system process
is inferred: true

cellular process involved in reproduction in multicellular organism
type: Class
subclass of: cellular process
subclass of: reproductive process
imported from: cl.owl

Axiom
annotated source: cellular process involved in reproduction in multicellular organism
annotated property: subClassOf
annotated target: cellular process
is inferred: true

Axiom
annotated source: cellular process involved in reproduction in multicellular organism
annotated property: subClassOf
annotated target: reproductive process
is inferred: true

reproductive process
type: Class
subclass of: biological_process
imported from: cl.owl

Axiom
annotated source: reproductive process
annotated property: subClassOf
annotated target: biological_process
is inferred: true

signaling
type: Class
subclass of: biological_process
imported from: cl.owl

Axiom
annotated source: signaling
annotated property: subClassOf
annotated target: biological_process
is inferred: true

cell differentiation
type: Class
subclass of: cellular developmental process
imported from: cl.owl
imported from: clo.owl
imported from: go.owl
imported from: uberon.owl
in subset: goslim generic
in subset: goslim plant
in subset: gosubset prok

Axiom
annotated source: cell differentiation
annotated property: subClassOf
annotated target: cellular developmental process
is inferred: true

neuron differentiation
type: Class
subclass of: cell differentiation
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: neuron differentiation
annotated property: subClassOf
annotated target: cell differentiation
is inferred: true

regulation of cell migration
type: Class
subclass of: regulation of cell motility
imported from: cl.owl

Axiom
annotated source: regulation of cell migration
annotated property: subClassOf
annotated target: regulation of cell motility
is inferred: true

positive regulation of cell migration
type: Class
subclass of: regulation of cell migration
subclass of: positive regulation of cell motility
imported from: cl.owl

Axiom
annotated source: positive regulation of cell migration
annotated property: subClassOf
annotated target: regulation of cell migration
is inferred: true

Axiom
annotated source: positive regulation of cell migration
annotated property: subClassOf
annotated target: positive regulation of cell motility
is inferred: true

epithelial cell differentiation
type: Class
subclass of: cell differentiation
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: epithelial cell differentiation
annotated property: subClassOf
annotated target: cell differentiation
is inferred: true

regulation of response to external stimulus
type: Class
subclass of: regulation of response to stimulus
imported from: cl.owl

Axiom
annotated source: regulation of response to external stimulus
annotated property: subClassOf
annotated target: regulation of response to stimulus
is inferred: true

positive regulation of response to external stimulus
type: Class
subclass of: regulation of response to external stimulus
subclass of: positive regulation of response to stimulus
imported from: cl.owl

Axiom
annotated source: positive regulation of response to external stimulus
annotated property: subClassOf
annotated target: regulation of response to external stimulus
is inferred: true

Axiom
annotated source: positive regulation of response to external stimulus
annotated property: subClassOf
annotated target: positive regulation of response to stimulus
is inferred: true

multicellular organismal process
type: Class
subclass of: biological_process
imported from: cl.owl

Axiom
annotated source: multicellular organismal process
annotated property: subClassOf
annotated target: biological_process
is inferred: true

developmental process
type: Class
subclass of: biological_process
imported from: cl.owl
imported from: clo.owl
imported from: go.owl
imported from: uberon.owl
in subset: goslim aspergillus
in subset: goslim pir
in subset: gosubset prok

Axiom
annotated source: developmental process
annotated property: subClassOf
annotated target: biological_process
is inferred: true

regulation of localization
type: Class
subclass of: regulation of biological process
imported from: cl.owl

Axiom
annotated source: regulation of localization
annotated property: subClassOf
annotated target: regulation of biological process
is inferred: true

secretion by cell
type: Class
subclass of: cellular process
subclass of: secretion
imported from: cl.owl

Axiom
annotated source: secretion by cell
annotated property: subClassOf
annotated target: cellular process
is inferred: true

Axiom
annotated source: secretion by cell
annotated property: subClassOf
annotated target: secretion
is inferred: true

macromolecular complex
type: Class
subclass of: cellular_component
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: macromolecular complex
annotated property: subClassOf
annotated target: cellular_component
is inferred: true

cardiocyte differentiation
type: Class
subclass of: cell differentiation
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: cardiocyte differentiation
annotated property: subClassOf
annotated target: cell differentiation
is inferred: true

multicellular organismal signaling
type: Class
subclass of: signaling
subclass of: multicellular organismal process
imported from: cl.owl

Axiom
annotated source: multicellular organismal signaling
annotated property: subClassOf
annotated target: signaling
is inferred: true

Axiom
annotated source: multicellular organismal signaling
annotated property: subClassOf
annotated target: multicellular organismal process
is inferred: true

locomotion
type: Class
subclass of: biological_process
definition: Self-propelled movement of a cell or organism from one location to another.
imported from: cl.owl
imported from: clo.owl
imported from: go.owl
imported from: uberon.owl
has_obo_namespace: biological_process
id: GO:0040011
in subset: goslim chembl
in subset: goslim generic
in subset: goslim pir
in subset: gosubset prok

Axiom
annotated source: locomotion
annotated property: subClassOf
annotated target: biological_process
is inferred: true

regulation of locomotion
type: Class
subclass of: regulation of biological process
imported from: cl.owl

Axiom
annotated source: regulation of locomotion
annotated property: subClassOf
annotated target: regulation of biological process
is inferred: true

positive regulation of locomotion
type: Class
subclass of: regulation of locomotion
subclass of: positive regulation of biological process
imported from: cl.owl

Axiom
annotated source: positive regulation of locomotion
annotated property: subClassOf
annotated target: regulation of locomotion
is inferred: true

Axiom
annotated source: positive regulation of locomotion
annotated property: subClassOf
annotated target: positive regulation of biological process
is inferred: true

MHC protein complex
type: Class
subclass of: plasma membrane protein complex
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: MHC protein complex
annotated property: subClassOf
annotated target: plasma membrane protein complex
is inferred: true

MHC class II protein complex
type: Class
subclass of: MHC protein complex
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: MHC class II protein complex
annotated property: subClassOf
annotated target: MHC protein complex
is inferred: true

muscle cell differentiation
type: Class
subclass of: cell differentiation
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: muscle cell differentiation
annotated property: subClassOf
annotated target: cell differentiation
is inferred: true

amide transport
type: Class
subclass of: nitrogen compound transport
imported from: cl.owl

Axiom
annotated source: amide transport
annotated property: subClassOf
annotated target: nitrogen compound transport
is inferred: true

protein complex
type: Class
subclass of: macromolecular complex
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: protein complex
annotated property: subClassOf
annotated target: macromolecular complex
is inferred: true

membrane part
type: Class
subclass of: cellular_component
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: membrane part
annotated property: subClassOf
annotated target: cellular_component
is inferred: true

plasma membrane part
type: Class
subclass of: membrane part
subclass of: cell part
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: plasma membrane part
annotated property: subClassOf
annotated target: membrane part
is inferred: true

Axiom
annotated source: plasma membrane part
annotated property: subClassOf
annotated target: cell part
is inferred: true

cell part
type: Class
subclass of: cell part
subclass of: cellular_component
imported from: cl.owl
imported from: clo.owl
imported from: go.owl
imported from: uberon.owl
in subset: goslim pir
in subset: gosubset prok
in subset: high level annotation qc

Axiom
annotated source: cell part
annotated property: subClassOf
annotated target: cell part
is inferred: true

Axiom
annotated source: cell part
annotated property: subClassOf
annotated target: cellular_component
is inferred: true

fat cell differentiation
type: Class
subclass of: cell differentiation
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: fat cell differentiation
annotated property: subClassOf
annotated target: cell differentiation
is inferred: true

secretion
type: Class
subclass of: transport
imported from: cl.owl

Axiom
annotated source: secretion
annotated property: subClassOf
annotated target: transport
is inferred: true

somatic stem cell division
type: Class
subclass of: stem cell division
imported from: cl.owl

Axiom
annotated source: somatic stem cell division
annotated property: subClassOf
annotated target: stem cell division
is inferred: true

male gamete generation
type: Class
subclass of: gamete generation
imported from: cl.owl

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

cell development
type: Class
subclass of: anatomical structure development
subclass of: cellular developmental process
imported from: cl.owl

Axiom
annotated source: cell development
annotated property: subClassOf
annotated target: anatomical structure development
is inferred: true

Axiom
annotated source: cell development
annotated property: subClassOf
annotated target: cellular developmental process
is inferred: true

oogenesis
type: Class
subclass of: germ cell development
subclass of: female gamete generation
imported from: cl.owl

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

Axiom
annotated source: oogenesis
annotated property: subClassOf
annotated target: female gamete generation
is inferred: true

positive regulation of biological process
type: Class
subclass of: regulation of biological process
imported from: cl.owl

Axiom
annotated source: positive regulation of biological process
annotated property: subClassOf
annotated target: regulation of biological process
is inferred: true

positive regulation of cellular process
type: Class
subclass of: positive regulation of biological process
subclass of: regulation of cellular process
imported from: cl.owl

Axiom
annotated source: positive regulation of cellular process
annotated property: subClassOf
annotated target: positive regulation of biological process
is inferred: true

Axiom
annotated source: positive regulation of cellular process
annotated property: subClassOf
annotated target: regulation of cellular process
is inferred: true

regulation of response to stimulus
type: Class
subclass of: regulation of biological process
imported from: cl.owl

Axiom
annotated source: regulation of response to stimulus
annotated property: subClassOf
annotated target: regulation of biological process
is inferred: true

positive regulation of response to stimulus
type: Class
subclass of: positive regulation of biological process
subclass of: regulation of response to stimulus
imported from: cl.owl

Axiom
annotated source: positive regulation of response to stimulus
annotated property: subClassOf
annotated target: positive regulation of biological process
is inferred: true

Axiom
annotated source: positive regulation of response to stimulus
annotated property: subClassOf
annotated target: regulation of response to stimulus
is inferred: true

multicellular organismal reproductive process
type: Class
subclass of: reproductive process
imported from: cl.owl

Axiom
annotated source: multicellular organismal reproductive process
annotated property: subClassOf
annotated target: reproductive process
is inferred: true

anatomical structure development
type: Class
subclass of: developmental process
imported from: cl.owl

Axiom
annotated source: anatomical structure development
annotated property: subClassOf
annotated target: developmental process
is inferred: true

cellular developmental process
type: Class
subclass of: cellular process
subclass of: developmental process
imported from: cl.owl
imported from: clo.owl
imported from: go.owl
imported from: uberon.owl
in subset: gosubset prok

Axiom
annotated source: cellular developmental process
annotated property: subClassOf
annotated target: cellular process
is inferred: true

Axiom
annotated source: cellular developmental process
annotated property: subClassOf
annotated target: developmental process
is inferred: true

cell motility
type: Class
subclass of: movement of cell or subcellular component
subclass of: locomotion
imported from: cl.owl
imported from: clo.owl
imported from: go.owl
imported from: uberon.owl
in subset: goslim generic
in subset: goslim metagenomics
in subset: gosubset prok

Axiom
annotated source: cell motility
annotated property: subClassOf
annotated target: movement of cell or subcellular component
is inferred: true

Axiom
annotated source: cell motility
annotated property: subClassOf
annotated target: locomotion
is inferred: true

regulation of biological process
type: Class
subclass of: biological regulation
imported from: cl.owl

Axiom
annotated source: regulation of biological process
annotated property: subClassOf
annotated target: biological regulation
is inferred: true

regulation of cellular process
type: Class
subclass of: regulation of biological process
imported from: cl.owl

Axiom
annotated source: regulation of cellular process
annotated property: subClassOf
annotated target: regulation of biological process
is inferred: true

nervous system process
type: Class
subclass of: system process
imported from: cl.owl

Axiom
annotated source: nervous system process
annotated property: subClassOf
annotated target: system process
is inferred: true

response to stimulus
type: Class
subclass of: biological_process
imported from: cl.owl

Axiom
annotated source: response to stimulus
annotated property: subClassOf
annotated target: biological_process
is inferred: true

detection of stimulus involved in sensory perception
type: Class
subclass of: detection of stimulus
imported from: cl.owl

Axiom
annotated source: detection of stimulus involved in sensory perception
annotated property: subClassOf
annotated target: detection of stimulus
is inferred: true

detection of chemical stimulus involved in sensory perception
type: Class
subclass of: detection of chemical stimulus
subclass of: detection of stimulus involved in sensory perception
imported from: cl.owl

Axiom
annotated source: detection of chemical stimulus involved in sensory perception
annotated property: subClassOf
annotated target: detection of chemical stimulus
is inferred: true

Axiom
annotated source: detection of chemical stimulus involved in sensory perception
annotated property: subClassOf
annotated target: detection of stimulus involved in sensory perception
is inferred: true

detection of chemical stimulus involved in sensory perception of taste
type: Class
subclass of: detection of chemical stimulus involved in sensory perception
imported from: cl.owl

Axiom
annotated source: detection of chemical stimulus involved in sensory perception of taste
annotated property: subClassOf
annotated target: detection of chemical stimulus involved in sensory perception
is inferred: true

regulation of chemotaxis
type: Class
subclass of: regulation of response to external stimulus
subclass of: regulation of locomotion
imported from: cl.owl

Axiom
annotated source: regulation of chemotaxis
annotated property: subClassOf
annotated target: regulation of response to external stimulus
is inferred: true

Axiom
annotated source: regulation of chemotaxis
annotated property: subClassOf
annotated target: regulation of locomotion
is inferred: true

positive regulation of chemotaxis
type: Class
subclass of: positive regulation of response to external stimulus
subclass of: positive regulation of locomotion
subclass of: regulation of chemotaxis
imported from: cl.owl

Axiom
annotated source: positive regulation of chemotaxis
annotated property: subClassOf
annotated target: positive regulation of response to external stimulus
is inferred: true

Axiom
annotated source: positive regulation of chemotaxis
annotated property: subClassOf
annotated target: positive regulation of locomotion
is inferred: true

Axiom
annotated source: positive regulation of chemotaxis
annotated property: subClassOf
annotated target: regulation of chemotaxis
is inferred: true

striated muscle cell differentiation
type: Class
subclass of: muscle cell differentiation
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: striated muscle cell differentiation
annotated property: subClassOf
annotated target: muscle cell differentiation
is inferred: true

localization
type: Class
subclass of: biological_process
imported from: cl.owl

Axiom
annotated source: localization
annotated property: subClassOf
annotated target: biological_process
is inferred: true

establishment of localization
type: Class
subclass of: localization
imported from: cl.owl

Axiom
annotated source: establishment of localization
annotated property: subClassOf
annotated target: localization
is inferred: true

regulation of cellular component movement
type: Class
subclass of: regulation of localization
subclass of: regulation of cellular process
imported from: cl.owl

Axiom
annotated source: regulation of cellular component movement
annotated property: subClassOf
annotated target: regulation of localization
is inferred: true

Axiom
annotated source: regulation of cellular component movement
annotated property: subClassOf
annotated target: regulation of cellular process
is inferred: true

positive regulation of cellular component movement
type: Class
subclass of: positive regulation of cellular process
subclass of: regulation of cellular component movement
imported from: cl.owl

Axiom
annotated source: positive regulation of cellular component movement
annotated property: subClassOf
annotated target: positive regulation of cellular process
is inferred: true

Axiom
annotated source: positive regulation of cellular component movement
annotated property: subClassOf
annotated target: regulation of cellular component movement
is inferred: true

cell division
type: Class
subclass of: cellular process
imported from: cl.owl
imported from: clo.owl
imported from: go.owl
imported from: uberon.owl
in subset: goslim generic
in subset: goslim metagenomics
in subset: goslim pir
in subset: gosubset prok

Axiom
annotated source: cell division
annotated property: subClassOf
annotated target: cellular process
is inferred: true

detection of stimulus
type: Class
subclass of: response to stimulus
imported from: cl.owl

Axiom
annotated source: detection of stimulus
annotated property: subClassOf
annotated target: response to stimulus
is inferred: true

cardiac muscle cell differentiation
type: Class
subclass of: cardiocyte differentiation
subclass of: striated muscle cell differentiation
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: cardiac muscle cell differentiation
annotated property: subClassOf
annotated target: cardiocyte differentiation
is inferred: true

Axiom
annotated source: cardiac muscle cell differentiation
annotated property: subClassOf
annotated target: striated muscle cell differentiation
is inferred: true

chondroblast differentiation
type: Class
subclass of: cell differentiation
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: chondroblast differentiation
annotated property: subClassOf
annotated target: cell differentiation
is inferred: true

biological regulation
type: Class
subclass of: biological_process
imported from: cl.owl

Axiom
annotated source: biological regulation
annotated property: subClassOf
annotated target: biological_process
is inferred: true

regulation of granulocyte chemotaxis
type: Class
subclass of: regulation of leukocyte chemotaxis
imported from: cl.owl

Axiom
annotated source: regulation of granulocyte chemotaxis
annotated property: subClassOf
annotated target: regulation of leukocyte chemotaxis
is inferred: true

positive regulation of granulocyte chemotaxis
type: Class
subclass of: positive regulation of leukocyte chemotaxis
subclass of: regulation of granulocyte chemotaxis
imported from: cl.owl

Axiom
annotated source: positive regulation of granulocyte chemotaxis
annotated property: subClassOf
annotated target: positive regulation of leukocyte chemotaxis
is inferred: true

Axiom
annotated source: positive regulation of granulocyte chemotaxis
annotated property: subClassOf
annotated target: regulation of granulocyte chemotaxis
is inferred: true

organic substance transport
type: Class
subclass of: transport
imported from: cl.owl

Axiom
annotated source: organic substance transport
annotated property: subClassOf
annotated target: transport
is inferred: true

nitrogen compound transport
type: Class
subclass of: transport
imported from: cl.owl

Axiom
annotated source: nitrogen compound transport
annotated property: subClassOf
annotated target: transport
is inferred: true

regulation of neutrophil chemotaxis
type: Class
subclass of: regulation of granulocyte chemotaxis
subclass of: regulation of neutrophil migration
imported from: cl.owl

Axiom
annotated source: regulation of neutrophil chemotaxis
annotated property: subClassOf
annotated target: regulation of granulocyte chemotaxis
is inferred: true

Axiom
annotated source: regulation of neutrophil chemotaxis
annotated property: subClassOf
annotated target: regulation of neutrophil migration
is inferred: true

positive regulation of neutrophil chemotaxis
type: Class
subclass of: positive regulation of granulocyte chemotaxis
subclass of: regulation of neutrophil chemotaxis
subclass of: positive regulation of neutrophil migration
imported from: cl.owl

Axiom
annotated source: positive regulation of neutrophil chemotaxis
annotated property: subClassOf
annotated target: positive regulation of granulocyte chemotaxis
is inferred: true

Axiom
annotated source: positive regulation of neutrophil chemotaxis
annotated property: subClassOf
annotated target: regulation of neutrophil chemotaxis
is inferred: true

Axiom
annotated source: positive regulation of neutrophil chemotaxis
annotated property: subClassOf
annotated target: positive regulation of neutrophil migration
is inferred: true

membrane protein complex
type: Class
subclass of: protein complex
subclass of: membrane part
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: membrane protein complex
annotated property: subClassOf
annotated target: protein complex
is inferred: true

Axiom
annotated source: membrane protein complex
annotated property: subClassOf
annotated target: membrane part
is inferred: true

plasma membrane protein complex
type: Class
subclass of: plasma membrane part
subclass of: membrane protein complex
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: plasma membrane protein complex
annotated property: subClassOf
annotated target: plasma membrane part
is inferred: true

Axiom
annotated source: plasma membrane protein complex
annotated property: subClassOf
annotated target: membrane protein complex
is inferred: true

regulation of neutrophil migration
type: Class
subclass of: regulation of leukocyte migration
imported from: cl.owl

Axiom
annotated source: regulation of neutrophil migration
annotated property: subClassOf
annotated target: regulation of leukocyte migration
is inferred: true

positive regulation of neutrophil migration
type: Class
subclass of: positive regulation of leukocyte migration
subclass of: regulation of neutrophil migration
imported from: cl.owl

Axiom
annotated source: positive regulation of neutrophil migration
annotated property: subClassOf
annotated target: positive regulation of leukocyte migration
is inferred: true

Axiom
annotated source: positive regulation of neutrophil migration
annotated property: subClassOf
annotated target: regulation of neutrophil migration
is inferred: true

regulation of cell motility
type: Class
subclass of: regulation of locomotion
subclass of: regulation of cellular component movement
imported from: cl.owl

Axiom
annotated source: regulation of cell motility
annotated property: subClassOf
annotated target: regulation of locomotion
is inferred: true

Axiom
annotated source: regulation of cell motility
annotated property: subClassOf
annotated target: regulation of cellular component movement
is inferred: true

positive regulation of cell motility
type: Class
subclass of: positive regulation of locomotion
subclass of: positive regulation of cellular component movement
subclass of: regulation of cell motility
imported from: cl.owl

Axiom
annotated source: positive regulation of cell motility
annotated property: subClassOf
annotated target: positive regulation of locomotion
is inferred: true

Axiom
annotated source: positive regulation of cell motility
annotated property: subClassOf
annotated target: positive regulation of cellular component movement
is inferred: true

Axiom
annotated source: positive regulation of cell motility
annotated property: subClassOf
annotated target: regulation of cell motility
is inferred: true

measurement unit label
type: Class
subclass of: datum label
editor preferred label: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
has curation status: IAO_0000125
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
imported from: obi.owl

Axiom
annotated source: measurement unit label
annotated property: subClassOf
annotated target: datum label
is inferred: true

objective specification
type: Class
subclass of: directive information entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: IAO_0000122
has curation status: IAO_0000125
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: objective specification
annotated property: subClassOf
annotated target: directive information entity
is inferred: true

action specification
type: Class
subclass of: directive information entity
editor preferred label: action specification
example of usage: Pour the contents of flask 1 into flask 2
has curation status: IAO_0000122
has curation status: IAO_0000123
definition: a directive information entity that describes an action the bearer will take
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: action specification
annotated property: subClassOf
annotated target: directive information entity
is inferred: true

datum label
type: Class
subclass of: information content entity
editor preferred label: datum label
has curation status: IAO_0000123
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
definition editor: GROUP: IAO
curator note: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
imported from: obi.owl

Axiom
annotated source: datum label
annotated property: subClassOf
annotated target: information content entity
is inferred: true

data item
type: Class
subclass of: information content entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: IAO_0000125
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data
imported from: clo.owl
imported from: iao.owl
imported from: obi.owl
imported from: omrse.owl

Axiom
annotated source: data item
annotated property: subClassOf
annotated target: information content entity
is inferred: true

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: IAO_0000122
has curation status: IAO_0000125
definition: A generically dependent continuant that is about some thing.
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: clo.owl
imported from: iao.owl
imported from: obi.owl
imported from: omrse.owl

Axiom
annotated source: information content entity
annotated property: subClassOf
annotated target: generically dependent continuant
is inferred: true

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: scalar value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
example of usage: 10 feet. 3 ml.
has curation status: IAO_0000120
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
imported from: obi.owl

Axiom
annotated source: scalar measurement datum
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
editor preferred label: directive information entity
has curation status: IAO_0000122
has curation status: IAO_0000123
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
imported from: clo.owl
imported from: iao.owl
imported from: obi.owl

Axiom
annotated source: directive information entity
annotated property: subClassOf
annotated target: information content entity
is inferred: true

graph
type: Class
subclass of: diagram
editor preferred label: graph
has curation status: IAO_0000125
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
definition editor: PERSON: Lawrence Hunter
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
definition source: OBI_0000240
definition source: group:OBI
imported from: obi.owl

Axiom
annotated source: graph
annotated property: subClassOf
annotated target: diagram
is inferred: true

algorithm
type: Class
subclass of: plan specification
editor preferred label: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: IAO_0000120
definition: A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
definition editor: Philippe Rocca-Serra
definition editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
imported from: obi.owl

Axiom
annotated source: algorithm
annotated property: subClassOf
annotated target: plan specification
is inferred: true

curation status specification
type: Class
equivalent class: Class
  one of: IAO_0000002
  one of: IAO_0000120
  one of: IAO_0000121
  one of: IAO_0000122
  one of: IAO_0000123
  one of: IAO_0000124
  one of: IAO_0000125
  one of: IAO_0000423
  one of: IAO_0000428
subclass of: data about an ontology part
editor preferred label: curation status specification
has curation status: IAO_0000125
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
imported from: clo.owl
imported from: obi.owl
imported from: omrse.owl

Axiom
annotated source: curation status specification
annotated property: subClassOf
annotated target: data about an ontology part
is inferred: true

data about an ontology part
type: Class
subclass of: data item
editor preferred label: data about an ontology part
definition: data about an ontology part is a data item about a part of an ontology, for example a term
definition editor: Person:Alan Ruttenberg
imported from: clo.owl
imported from: obi.owl
imported from: omrse.owl

Axiom
annotated source: data about an ontology part
annotated property: subClassOf
annotated target: data item
is inferred: true

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: IAO_0000120
has curation status: IAO_0000122
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: clo.owl
imported from: obi.owl
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

Axiom
annotated source: plan specification
annotated property: subClassOf
annotated target: directive information entity
is inferred: true

measurement datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: value specification
editor preferred label: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
has curation status: IAO_0000125
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
definition editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: obi.owl

Axiom
annotated source: measurement datum
annotated property: subClassOf
annotated target: data item
is inferred: true

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
editor preferred label: material information bearer
example of usage: A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
example of usage: a brain
example of usage: a hard drive
has curation status: IAO_0000122
definition: A material entity in which a concretization of an information content entity inheres.
definition editor: GROUP: IAO
imported from: obi.owl

Axiom
annotated source: material information bearer
annotated property: subClassOf
annotated target: material entity
is inferred: true

figure
type: Class
subclass of: information content entity
editor preferred label: figure
example of usage: Any picture, diagram or table
has curation status: IAO_0000120
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
definition editor: PERSON: Lawrence Hunter
imported from: obi.owl

Axiom
annotated source: figure
annotated property: subClassOf
annotated target: information content entity
is inferred: true

diagram
type: Class
subclass of: figure
editor preferred label: diagram
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
has curation status: IAO_0000120
definition: A figure that expresses one or more propositions
definition editor: PERSON: Lawrence Hunter
imported from: obi.owl

Axiom
annotated source: diagram
annotated property: subClassOf
annotated target: figure
is inferred: true

document
type: Class
subclass of: information content entity
editor preferred label: document
example of usage: A journal article, patent application, laboratory notebook, or a book
has curation status: IAO_0000120
definition: A collection of information content entities intended to be understood together as a whole
definition editor: PERSON: Lawrence Hunter
imported from: obi.owl
imported from: omrse.owl

Axiom
annotated source: document
annotated property: subClassOf
annotated target: information content entity
is inferred: true

length measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000001
subclass of: Restriction
  on property: is quality measurement of
  some values from: length
has curation status: IAO_0000123
definition: A scalar measurement datum that is the result of measurement of length quality
definition editor: Alan Ruttenberg
imported from: obi.owl

Axiom
annotated source: length measurement datum
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

mass measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: UO_0000002
  intersection of: Restriction
    on property: is quality measurement of
    all values from: mass
has curation status: IAO_0000123
definition: A scalar measurement datum that is the result of measurement of mass quality
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg
imported from: obi.owl

Axiom
annotated source: mass measurement datum
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

time measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: UO_0000003
  intersection of: Restriction
    on property: is duration of
    all values from: process
has curation status: IAO_0000123
definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg
imported from: obi.owl

Axiom
annotated source: time measurement datum
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

documenting
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: document
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
has curation status: IAO_0000125
definition: a planned process in which a document is created or added to by including the specified input in it.
editor note: 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
definition editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
imported from: obi.owl

Axiom
annotated source: documenting
annotated property: subClassOf
annotated target: planned process
is inferred: true

line graph
type: Class
subclass of: graph
editor preferred label: line graph
has curation status: IAO_0000122
definition: A line graph is a type of graph created by connecting a series of data points together with a line.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:Melanie Courtot
alternative term: line chart
definition source: GROUP:OBI
definition source: WEB: http://en.wikipedia.org/wiki/Line_chart
imported from: obi.owl

Axiom
annotated source: line graph
annotated property: subClassOf
annotated target: graph
is inferred: true

time stamped measurement datum
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has time stamp
    some values from: time measurement datum
  intersection of: Restriction
    on property: has measurement datum
    some values from: measurement datum
has curation status: IAO_0000123
imported from: obi.owl

Axiom
annotated source: time stamped measurement datum
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

identity document
type: Class
equivalent class: Class
  intersection of: document
  intersection of: Restriction
    on property: is about
    some values from: documented identity
  intersection of: Restriction
    on property: is concretized as
    some values from: Class
      intersection of: specifically dependent continuant
      intersection of: Restriction
        on property: inheres in
        some values from: Restriction
  intersection of: Restriction
    on property: is concretized as
    all values from: Class
      intersection of: specifically dependent continuant
      intersection of: Restriction
        on property: inheres in
        some values from: Restriction
subclass of: document
definition: a document that denotes some identity and is concretized by the bearer of some credential role
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: identity document
annotated property: subClassOf
annotated target: document
is inferred: true

documented identity
type: Class
subclass of: information content entity
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: information content entity
  intersection of: Restriction
    on property:
      inverse of: is about
    some values from: identity document
  intersection of: Restriction
    on property: has part
    all values from: information content entity
definition: a documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents.
definition editor: Amanda Hicks
imported from: omrse.owl
comment: is an aggregate of ICEs also an ICE? yes Is part_of the appropriate relation to use for data items and documented identities?

Axiom
annotated source: documented identity
annotated property: subClassOf
annotated target: information content entity
is inferred: true

authentication
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: realizes
    some values from: credential role
  intersection of: Restriction
    on property: has_participant
    some values from: data item
  intersection of: Restriction
    on property: has_participant
    some values from: Restriction
      on property:
        inverse of: is about
      some values from: data item
example of usage: I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database.
definition: Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit).
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: authentication
annotated property: subClassOf
annotated target: process
is inferred: true

credential role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: realized in
    some values from: authentication
  intersection of: Restriction
    on property: inheres in
    some values from: Restriction
      on property: bearer of
      some values from: Restriction
        on property: concretizes
        some values from: identity document
subclass of: role
definition: a role that inheres in a concretization of an identity document and is realized by an authentication process
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: credential role
annotated property: subClassOf
annotated target: role
is inferred: true

social act
type: Class
subclass of: process
example of usage: Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
definition: A process that is carried out by a conscious being or an aggregate of conscious beings and is spontaneous, directed towards other conscious beings and aggregates thereof and needs to be perceived.
definition editor: Mathias Brochhausen
imported from: omrse.owl
comment: MB: Regarding the use of the term 'sponteneous' in the definition: The term is used in the following meaning of being self generated. It does not stand in contrast to being planned.

Axiom
annotated source: social act
annotated property: subClassOf
annotated target: process
is inferred: true

Muridae
type: Class
subclass of: Muroidea
editor preferred label: Muridae
imported from: clo.owl
imported from: ncbitaxon.owl

Axiom
annotated source: Muridae
annotated property: subClassOf
annotated target: Muroidea
is inferred: true

Mus musculus
type: Class
subclass of: Murinae
editor preferred label: Mus musculus
alternative term: "Mus muscaris" RELATED misnomer []
alternative term: "house mouse" EXACT genbank_common_name []
alternative term: "mice C57BL/6xCBA/CaJ hybrid" RELATED misspelling []
alternative term: "mouse" EXACT common_name []
alternative term: house mouse
alternative term: mouse
imported from: clo.owl
imported from: ncbitaxon.owl
see also: URI: http://www.ebi.ac.uk/cellline#Mus_musculus

Axiom
annotated source: Mus musculus
annotated property: subClassOf
annotated target: Murinae
is inferred: true

Viruses
type: Class
subclass of: organism
editor preferred label: Viruses
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl

Axiom
annotated source: Viruses
annotated property: subClassOf
annotated target: organism
is inferred: true

Euteleostomi
type: Class
subclass of: Vertebrata <Metazoa>
subclass of: Craniata <chordata>
editor preferred label: Euteleostomi
alternative term: bony vertebrates
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: uberon.owl
imported from: taxslim.owl

Axiom
annotated source: Euteleostomi
annotated property: subClassOf
annotated target: Vertebrata <Metazoa>
is inferred: true

Axiom
annotated source: Euteleostomi
annotated property: subClassOf
annotated target: Craniata <chordata>
is inferred: true

Bacteria
type: Class
subclass of: organism
editor preferred label: Bacteria
alternative term: eubacteria
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl

Axiom
annotated source: Bacteria
annotated property: subClassOf
annotated target: organism
is inferred: true

Homininae
type: Class
subclass of: Hominidae
editor preferred label: Homininae
imported from: clo.owl
imported from: ncbitaxon.owl

Axiom
annotated source: Homininae
annotated property: subClassOf
annotated target: Hominidae
is inferred: true

Archaea
type: Class
subclass of: organism
editor preferred label: Archaea
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl

Axiom
annotated source: Archaea
annotated property: subClassOf
annotated target: organism
is inferred: true

Eukaryota
type: Class
subclass of: organism
subclass of: Restriction
  on property: has part
  some values from: genome of Eukaryota
editor preferred label: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: ogg.owl
imported from: uberon.owl
imported from: taxslim.owl
has_rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:1
database_cross_reference: PMID:23020233
has exact synonym: eucaryotes
has exact synonym: eukaryotes
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Eucarya
has_related_synonym: Eucaryotae
has_related_synonym: Eukarya
has_related_synonym: Eukaryotae
has_related_synonym: eukaryotes

Axiom
annotated source: Eukaryota
annotated property: subClassOf
annotated target: organism
is inferred: true

Euarchontoglires
type: Class
subclass of: Mammalia
subclass of: Eutheria
editor preferred label: Euarchontoglires
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl

Axiom
annotated source: Euarchontoglires
annotated property: subClassOf
annotated target: Mammalia
is inferred: true

Axiom
annotated source: Euarchontoglires
annotated property: subClassOf
annotated target: Eutheria
is inferred: true

Glires
type: Class
subclass of: Euarchontoglires
editor preferred label: Glires
alternative term: "Rodents and rabbits" EXACT genbank_common_name []
alternative term: Rodents and rabbits
imported from: clo.owl
imported from: ncbitaxon.owl
see also: URI: http://www.ebi.ac.uk/cellline#Glires

Axiom
annotated source: Glires
annotated property: subClassOf
annotated target: Euarchontoglires
is inferred: true

Simiiformes
type: Class
subclass of: Primates
editor preferred label: Simiiformes
imported from: clo.owl
imported from: ncbitaxon.owl

Axiom
annotated source: Simiiformes
annotated property: subClassOf
annotated target: Primates
is inferred: true

Hominoidea
type: Class
subclass of: Catarrhini
editor preferred label: Hominoidea
alternative term: "ape" EXACT common_name []
alternative term: "apes" EXACT common_name []
alternative term: ape
alternative term: apes
imported from: clo.owl
imported from: ncbitaxon.owl
see also: URI: http://www.ebi.ac.uk/cellline#Hominoidea

Axiom
annotated source: Hominoidea
annotated property: subClassOf
annotated target: Catarrhini
is inferred: true

Tetrapoda
type: Class
subclass of: Euteleostomi
editor preferred label: Tetrapoda
alternative term: tetrapods
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: uberon.owl
imported from: taxslim.owl

Axiom
annotated source: Tetrapoda
annotated property: subClassOf
annotated target: Euteleostomi
is inferred: true

Amniota
type: Class
subclass of: Tetrapoda
editor preferred label: Amniota
alternative term: amniotes
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: uberon.owl
imported from: taxslim.owl

Axiom
annotated source: Amniota
annotated property: subClassOf
annotated target: Tetrapoda
is inferred: true

Theria <Mammalia>
type: Class
subclass of: Amniota
editor preferred label: Theria <Mammalia>
alternative term: Theria
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: uberon.owl
imported from: taxslim.owl

Axiom
annotated source: Theria <Mammalia>
annotated property: subClassOf
annotated target: Amniota
is inferred: true

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred label: Opisthokonta
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: uberon.owl
imported from: taxslim.owl

Axiom
annotated source: Opisthokonta
annotated property: subClassOf
annotated target: Eukaryota
is inferred: true

Bilateria
type: Class
subclass of: Opisthokonta
editor preferred label: Bilateria
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: uberon.owl
imported from: taxslim.owl

Axiom
annotated source: Bilateria
annotated property: subClassOf
annotated target: Opisthokonta
is inferred: true

Sciurognathi
type: Class
subclass of: Rodentia
editor preferred label: Sciurognathi
imported from: clo.owl
imported from: ncbitaxon.owl

Axiom
annotated source: Sciurognathi
annotated property: subClassOf
annotated target: Rodentia
is inferred: true

Muroidea
type: Class
subclass of: Sciurognathi
editor preferred label: Muroidea
imported from: clo.owl
imported from: ncbitaxon.owl

Axiom
annotated source: Muroidea
annotated property: subClassOf
annotated target: Sciurognathi
is inferred: true

Murinae
type: Class
subclass of: Muridae
editor preferred label: Murinae
imported from: clo.owl
imported from: ncbitaxon.owl

Axiom
annotated source: Murinae
annotated property: subClassOf
annotated target: Muridae
is inferred: true

Mammalia
type: Class
subclass of: Amniota
editor preferred label: Mammalia
alternative term: "mammals" EXACT genbank_common_name []
alternative term: "mammals" RELATED blast_name []
alternative term: mammals
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: uberon.owl
imported from: taxslim.owl
see also: URI: http://www.ebi.ac.uk/cellline#Mammalia

Axiom
annotated source: Mammalia
annotated property: subClassOf
annotated target: Amniota
is inferred: true

Vertebrata <Metazoa>
type: Class
subclass of: Bilateria
editor preferred label: Vertebrata <Metazoa>
alternative term: Vertebrata
alternative term: vertebrates
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: uberon.owl
imported from: taxslim.owl

Axiom
annotated source: Vertebrata <Metazoa>
annotated property: subClassOf
annotated target: Bilateria
is inferred: true

Craniata <chordata>
type: Class
subclass of: Bilateria
editor preferred label: Craniata <chordata>
alternative term: Craniata
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: uberon.owl
imported from: taxslim.owl

Axiom
annotated source: Craniata <chordata>
annotated property: subClassOf
annotated target: Bilateria
is inferred: true

Eutheria
type: Class
subclass of: Theria <Mammalia>
editor preferred label: Eutheria
alternative term: eutherian mammals
alternative term: placental mammals
alternative term: placentals
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: uberon.owl
imported from: taxslim.owl

Axiom
annotated source: Eutheria
annotated property: subClassOf
annotated target: Theria <Mammalia>
is inferred: true

Primates
type: Class
subclass of: Euarchontoglires
editor preferred label: Primates
alternative term: "Primata" RELATED synonym []
alternative term: "primate" EXACT equivalent_name []
alternative term: "primates" RELATED blast_name []
alternative term: primate
imported from: clo.owl
imported from: ncbitaxon.owl
see also: URI: http://www.ebi.ac.uk/cellline#Primates

Axiom
annotated source: Primates
annotated property: subClassOf
annotated target: Euarchontoglires
is inferred: true

Catarrhini
type: Class
subclass of: Simiiformes
editor preferred label: Catarrhini
imported from: clo.owl
imported from: ncbitaxon.owl

Axiom
annotated source: Catarrhini
annotated property: subClassOf
annotated target: Simiiformes
is inferred: true

Hominidae
type: Class
subclass of: Hominoidea
editor preferred label: Hominidae
alternative term: "Pongidae" RELATED synonym []
alternative term: "great apes" EXACT common_name []
alternative term: great apes
imported from: clo.owl
imported from: ncbitaxon.owl
see also: URI: http://www.ebi.ac.uk/cellline#Hominidae

Axiom
annotated source: Hominidae
annotated property: subClassOf
annotated target: Hominoidea
is inferred: true

Homo sapiens
type: Class
subclass of: Homininae
subclass of: Restriction
  on property: has part
  some values from: genome of Homo sapiens
editor preferred label: Homo sapiens
alternative term: "human" EXACT genbank_common_name []
alternative term: human
alternative term: human being
alternative term: man
imported from: clo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has exact synonym: human
has exact synonym: man
has_obo_namespace: ncbi_taxonomy
see also: URI: http://www.ebi.ac.uk/cellline#Homo_sapiens

Axiom
annotated source: Homo sapiens
annotated property: subClassOf
annotated target: Homininae
is inferred: true

Rodentia
type: Class
subclass of: Glires
editor preferred label: Rodentia
alternative term: "rodents" EXACT genbank_common_name []
alternative term: "rodents" RELATED blast_name []
alternative term: rodents
imported from: clo.owl
imported from: ncbitaxon.owl
see also: URI: http://www.ebi.ac.uk/cellline#Rodentia

Axiom
annotated source: Rodentia
annotated property: subClassOf
annotated target: Glires
is inferred: true

Cell Density
type: Class
subclass of: scalar measurement datum
definition: A measurement of the number of cells per unit volume or area.
imported from: ncit.owl
code: C120538
Semantic_Type: Quantitative Concept
Preferred_Name: Cell Density
UMLS_CUI: C0162339
Contributing_Source: CDISC
ALT_DEFINITION: A measurement of the number of cells contained in a unit of volume.
has exact synonym: CELLDENS
has exact synonym: Cell Density
in subset: NCIT C117742
in subset: NCIT C117743
in subset: NCIT C61410
in subset: NCIT C66830

Axiom
annotated source: Cell Density
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

HLA Typing
type: Class
subclass of: analyte assay
definition: A process in which blood or tissue samples are analyzed to determine their human leukocyte antigen (HLA) profiles.
imported from: ncit.owl
code: C71329
Semantic_Type: Laboratory Procedure
Preferred_Name: HLA Typing
UMLS_CUI: C0242318
Legacy_Concept_Name: HLA_Typing
has exact synonym: HLA Testing
has exact synonym: HLA Typing

Axiom
annotated source: HLA Typing
annotated property: subClassOf
annotated target: analyte assay
is inferred: true

fluorescent reporter intensity
type: Class
subclass of: measurement datum
editor preferred label: fluorescent reporter intensity
has curation status: IAO_0000125
definition: A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
definition editor: person:Chris Stoeckert
definition source: group:OBI
curator note: From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem.
imported from: obi.owl

Axiom
annotated source: fluorescent reporter intensity
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: IAO_0000122
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
definition editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: clo.owl
imported from: obi.owl
imported from: omrse.owl

Axiom
annotated source: planned process
annotated property: subClassOf
annotated target: process
is inferred: true

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
editor preferred label: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: IAO_0000122
definition: Is a material entity that is created or changed during material processing.
definition editor: PERSON: Alan Ruttenberg
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: processed material
annotated property: subClassOf
annotated target: material entity
is inferred: true

ratio of collected to emitted light
type: Class
subclass of: measurement datum
editor preferred label: ratio of collected to emitted light
example of usage: 10%
has curation status: IAO_0000120
definition: A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role
definition editor: person:Chris Stoeckert
definition editor: person:Kevin Clancy
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
imported from: obi.owl

Axiom
annotated source: ratio of collected to emitted light
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

investigation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: documenting
subclass of: Restriction
  on property: has part
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: has part
  some values from: study design execution
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has_specified_output
      some values from: study design
editor preferred label: investigation
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has curation status: IAO_0000122
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
definition editor: Bjoern Peters
definition source: OBI branch derived
curator note: Could add specific objective specification
curator note: Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: obi.owl
ISA alternative term: study

Axiom
annotated source: investigation
annotated property: subClassOf
annotated target: planned process
is inferred: true

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred label: evaluant role
example of usage: When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
has curation status: IAO_0000122
definition: a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
editor note: Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
definition editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

Axiom
annotated source: evaluant role
annotated property: subClassOf
annotated target: role
is inferred: true

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred label: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: IAO_0000122
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
definition editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
imported from: obi.owl
ISA alternative term: study assay
IEDB alternative term: any method

Axiom
annotated source: assay
annotated property: subClassOf
annotated target: planned process
is inferred: true

culture medium
type: Class
subclass of: processed material
editor preferred label: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
has curation status: IAO_0000120
has curation status: IAO_0000122
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
definition editor: Person: Jennifer Fostel, Jie Zheng
definition source: OBI
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: culture medium
annotated property: subClassOf
annotated target: processed material
is inferred: true

reagent role
type: Class
subclass of: role
editor preferred label: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: IAO_0000120
definition: A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
definition editor: PERSON:Matthew Brush
alternative term: reagent
definition source: PERSON:Matthew Brush
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
imported from: obi.owl
comment: (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is t…

Axiom
annotated source: reagent role
annotated property: subClassOf
annotated target: role
is inferred: true

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
subclass of: Restriction
  on property: has_specified_output
  all values from: material entity
editor preferred label: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
has curation status: IAO_0000122
definition: A planned process which results in physical changes in a specified input material
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca Serra
alternative term: material transformation
definition source: OBI branch derived
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: material processing
annotated property: subClassOf
annotated target: planned process
is inferred: true

measured expression level
type: Class
subclass of: measurement datum
editor preferred label: measured expression level
example of usage: Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
has curation status: IAO_0000120
definition: A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts.
definition editor: person:Chris Stoeckert
definition source: OBI Data Transformation branch
imported from: obi.owl

Axiom
annotated source: measured expression level
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
editor preferred label: specimen role
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
has curation status: IAO_0000122
definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
definition editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

Axiom
annotated source: specimen role
annotated property: subClassOf
annotated target: role
is inferred: true

number of particles in subset
type: Class
subclass of: measurement datum
editor preferred label: number of particles in subset
example of usage: 500, 200, 0
has curation status: IAO_0000120
definition: A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
definition editor: person:Kevin Clancy
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
imported from: obi.owl

Axiom
annotated source: number of particles in subset
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

number of lost events electronic
type: Class
subclass of: measurement datum
editor preferred label: number of lost events electronic
example of usage: 74, 0, 14 events lost due to data acquisition electronic coincidence.
has curation status: IAO_0000120
definition: A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role.
definition editor: person:Kevin Clancy
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
imported from: obi.owl

Axiom
annotated source: number of lost events electronic
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

parameter threshold
type: Class
subclass of: measurement datum
editor preferred label: parameter threshold
example of usage: 0.01, 0.03
has curation status: IAO_0000120
definition: A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role
definition editor: person:Kevin Clancy
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
imported from: obi.owl

Axiom
annotated source: parameter threshold
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

organization
type: Class
subclass of: material entity
editor preferred label: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status: IAO_0000122
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
definition editor: James Malone
definition editor: Jie Zheng
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
definition editor: Tomasz Adamusiak
alternative term: organisation
definition source: GROUP: OBI
definition source: MO_177
imported from: clo.owl
imported from: obi.owl
comment: An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
see also: EFO_URI: http://www.ebi.ac.uk/efo/EFO_0002010

Axiom
annotated source: organization
annotated property: subClassOf
annotated target: material entity
is inferred: true

number of lost events computer
type: Class
subclass of: measurement datum
editor preferred label: number of lost events computer
example of usage: 0, 125, 787 events lost due to computer busy.
has curation status: IAO_0000120
definition: A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role
definition editor: person:Kevin Clancy
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
imported from: obi.owl

Axiom
annotated source: number of lost events computer
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

protocol
type: Class
subclass of: plan specification
editor preferred label: protocol
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has curation status: IAO_0000122
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
imported from: obi.owl
ISA alternative term: study protocol

Axiom
annotated source: protocol
annotated property: subClassOf
annotated target: plan specification
is inferred: true

analyte role
type: Class
subclass of: measurand role
subclass of: Restriction
  on property: role of
  some values from: Class
    union of: molecular entity
    union of: atom
subclass of: Restriction
  on property: realized in
  all values from: analyte assay
editor preferred label: analyte role
example of usage: Glucose in blood (measured in an assay to determine the concentration of glucose).
has curation status: IAO_0000122
definition: A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
editor note: interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
editor note: pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
editor note: qualities such as weight, color are not assayed but measured, so they do not fall into this category.
definition editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

Axiom
annotated source: analyte role
annotated property: subClassOf
annotated target: measurand role
is inferred: true

material to be added role
type: Class
subclass of: role
editor preferred label: material to be added role
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
has curation status: IAO_0000120
definition: material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
definition editor: Role Branch
definition source: OBI
curator note: 9 March 09 from discussion with PA branch
imported from: obi.owl

Axiom
annotated source: material to be added role
annotated property: subClassOf
annotated target: role
is inferred: true

drawing a conclusion based on data
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: conclusion based on data
editor preferred label: interpreting data
example of usage: Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
has curation status: IAO_0000122
definition: A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
definition source: Bjoern Peters
imported from: obi.owl

Axiom
annotated source: drawing a conclusion based on data
annotated property: subClassOf
annotated target: planned process
is inferred: true

planning
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: has_participant
    some values from: plan specification
editor preferred label: planning
example of usage: The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
has curation status: IAO_0000122
definition: a process of creating or modifying a plan specification
editor note: 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
definition editor: Bjoern Peters
definition source: Bjoern Peters
definition source: Plans and Planned Processes Branch
imported from: obi.owl

Axiom
annotated source: planning
annotated property: subClassOf
annotated target: process
is inferred: true

information processor function
type: Class
subclass of: function
subclass of: Restriction
  on property: has part
  some values from: measure function
subclass of: Restriction
  on property: has part
  some values from: consume data function
editor preferred label: information processor function
has curation status: IAO_0000122
definition: An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
definition editor: Frank Gibson
alternative term: data processor function
imported from: obi.owl

Axiom
annotated source: information processor function
annotated property: subClassOf
annotated target: function
is inferred: true

analyte measurement objective
type: Class
subclass of: assay objective
editor preferred label: analyte measurement objective
example of usage: The objective to measure the concentration of glucose in a blood sample
has curation status: IAO_0000122
definition: an assay objective to determine the presence or concentration of an analyte in the evaluant
definition editor: PERSON: Bjoern Peters
definition source: PPPB branch
imported from: obi.owl

Axiom
annotated source: analyte measurement objective
annotated property: subClassOf
annotated target: assay objective
is inferred: true

assay objective
type: Class
subclass of: objective specification
editor preferred label: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: IAO_0000122
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
definition editor: PPPB branch
definition source: PPPB branch
imported from: obi.owl

Axiom
annotated source: assay objective
annotated property: subClassOf
annotated target: objective specification
is inferred: true

analyte assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
subclass of: assay
subclass of: Restriction
  on property: realizes
  some values from: analyte role
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
editor preferred label: analyte assay
example of usage: example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
has curation status: IAO_0000122
definition: An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
editor note: 2013-09-23: simplify equivalent axiom
editor note: Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
editor note: logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration'))
definition editor: PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
definition source: PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch
imported from: obi.owl

Axiom
annotated source: analyte assay
annotated property: subClassOf
annotated target: assay
is inferred: true

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: processed material
subclass of: Restriction
  on property: realized in
  all values from: Restriction
    on property: has_specified_output
    some values from: measurement datum
editor preferred label: measure function
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
has curation status: IAO_0000122
definition: Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
definition editor: PERSON: Daniel Schober
definition editor: PERSON: Helen Parkinson
definition editor: PERSON: Melanie Courtot
definition editor: PERSON:Frank Gibson
imported from: obi.owl

Axiom
annotated source: measure function
annotated property: subClassOf
annotated target: function
is inferred: true

consume data function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: material entity
editor preferred label: consume data function
has curation status: IAO_0000122
definition: Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data.
definition editor: PERSON: Daniel Schober
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Melanie Courtot
imported from: obi.owl

Axiom
annotated source: consume data function
annotated property: subClassOf
annotated target: function
is inferred: true

material transformation objective
type: Class
subclass of: objective specification
editor preferred label: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: IAO_0000122
definition: an objective specifiction that creates an specific output object from input materials.
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
alternative term: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: material transformation objective
annotated property: subClassOf
annotated target: objective specification
is inferred: true

study design execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: study design
subclass of: planned process
editor preferred label: study design execution
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
has curation status: IAO_0000122
definition: a planned process that carries out a study design
editor note: removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
definition source: branch derived
curator note: 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
imported from: obi.owl

Axiom
annotated source: study design execution
annotated property: subClassOf
annotated target: planned process
is inferred: true

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
editor preferred label: material separation objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
has curation status: IAO_0000122
definition: is an objective to transform a material entity into spatially separated components.
definition editor: PPPB branch
definition source: PPPB branch
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: material separation objective
annotated property: subClassOf
annotated target: material transformation objective
is inferred: true

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
editor preferred label: specimen collection process
example of usage: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
has curation status: IAO_0000122
definition: A planned process with the objective of collecting a specimen.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
definition editor: Bjoern Peters
alternative term: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop
imported from: obi.owl

Axiom
annotated source: specimen collection process
annotated property: subClassOf
annotated target: planned process
is inferred: true

portioning objective
type: Class
subclass of: material separation objective
editor preferred label: portioning objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
has curation status: IAO_0000123
definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: portioning objective
annotated property: subClassOf
annotated target: material separation objective
is inferred: true

separation into different composition objective
type: Class
subclass of: material separation objective
editor preferred label: separation into different composition objective
example of usage: The objective to obtain cells contained in a sample of blood.
has curation status: IAO_0000120
definition: A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: separation into different composition objective
annotated property: subClassOf
annotated target: material separation objective
is inferred: true

specimen collection objective
type: Class
subclass of: objective specification
editor preferred label: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: IAO_0000122
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
definition editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl

Axiom
annotated source: specimen collection objective
annotated property: subClassOf
annotated target: objective specification
is inferred: true

survival rate
type: Class
subclass of: measurement datum
editor preferred label: survival rate
has curation status: IAO_0000120
definition: A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
definition editor: Oliver He
definition source: adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate
imported from: obi.owl

Axiom
annotated source: survival rate
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

spike train datum
type: Class
subclass of: measurement datum
editor preferred label: spike train datum
example of usage: Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog
has curation status: IAO_0000120
definition: A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time.
editor note: needs more work to see exactly what the data set looks like - HP
definition editor: Helen Parkinson, Alan Ruttenberg
alternative term: spike train measurement
definition source: Jessica Turner, NIF
imported from: obi.owl

Axiom
annotated source: spike train datum
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

material maintenance objective
type: Class
subclass of: objective specification
editor preferred label: material maintenance objective
has curation status: IAO_0000122
has curation status: IAO_0000123
definition: An objective specification maintains some or all of the qualities of a material over time.
definition editor: PERSON: Bjoern Peters
definition source: PERSON: Bjoern Peters
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: material maintenance objective
annotated property: subClassOf
annotated target: objective specification
is inferred: true

primary structure of DNA macromolecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres in
    some values from: deoxyribonucleic acid
subclass of: region
editor preferred label: primary structure of DNA macromolecule
has curation status: IAO_0000123
definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
definition editor: BP et al
imported from: obi.owl

Axiom
annotated source: primary structure of DNA macromolecule
annotated property: subClassOf
annotated target: region
is inferred: true

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
editor preferred label: material maintenance
has curation status: IAO_0000123
definition: a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: material maintenance
annotated property: subClassOf
annotated target: planned process
is inferred: true

categorical measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: categorical value specification
editor preferred label: categorical measurement datum
has curation status: IAO_0000120
definition: A measurement datum that is reported on a categorical scale
definition editor: Bjoern Peters
alternative term: nominal mesurement datum
definition source: Bjoern Peters
imported from: obi.owl

Axiom
annotated source: categorical measurement datum
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

handedness assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: handedness
subclass of: assay
editor preferred label: handedness assay
example of usage: The Edinburgh handedness assay is a specific method of determing handedness
has curation status: IAO_0000120
definition: A handedness assay measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure.
definition editor: Helen Parkinson
alternative term: handedness test
definition source: http://en.wikipedia.org/wiki/Handedness
imported from: obi.owl

Axiom
annotated source: handedness assay
annotated property: subClassOf
annotated target: assay
is inferred: true

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: specimen
subclass of: processed material
subclass of: specimen
editor preferred label: processed specimen
example of usage: A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
has curation status: IAO_0000122
definition: A specimen that has been intentionally physically modified.
definition editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl
comment: A tissue sample that has been sliced and stained for a histology study.

Axiom
annotated source: processed specimen
annotated property: subClassOf
annotated target: processed material
is inferred: true

Axiom
annotated source: processed specimen
annotated property: subClassOf
annotated target: specimen
is inferred: true

categorical label
type: Class
subclass of: datum label
editor preferred label: categorical label
example of usage: The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
has curation status: IAO_0000120
definition: A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
definition editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl

Axiom
annotated source: categorical label
annotated property: subClassOf
annotated target: datum label
is inferred: true

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
subclass of: Restriction
  on property: has function
  some values from: function
editor preferred label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: IAO_0000122
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
definition editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.
imported from: obi.owl

Axiom
annotated source: device
annotated property: subClassOf
annotated target: processed material
is inferred: true

scalar score from composite inputs
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: is_specified_output_of
  some values from: data transformation
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
editor preferred label: scalar score from composite inputs
has curation status: IAO_0000120
definition: A measurement datum which is the result of combining multiple datum. For example, a mean or summary score.
editor note: JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question.
definition editor: Person: Jessica Turner
alternative term: questionaire score
definition source: Person: Jessica Turner
curator note: JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation?
imported from: obi.owl

Axiom
annotated source: scalar score from composite inputs
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

sequence data
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is about
    some values from: region
editor preferred label: sequence data
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
has curation status: IAO_0000120
definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
definition editor: Person:Chris Stoeckert
definition source: GROUP: OBI
imported from: obi.owl

Axiom
annotated source: sequence data
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

handedness categorical measurement datum
type: Class
subclass of: categorical measurement datum
subclass of: Restriction
  on property: is quality measurement of
  some values from: handedness
subclass of: Restriction
  on property: has category label
  some values from: Class
    one of: OBI_0000958
    one of: OBI_0000979
    one of: OBI_0000998
editor preferred label: handedness categorical measurement datum
has curation status: IAO_0000123
definition: A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Jessica Turner
imported from: obi.owl

Axiom
annotated source: handedness categorical measurement datum
annotated property: subClassOf
annotated target: categorical measurement datum
is inferred: true

dose
type: Class
subclass of: measurement datum
editor preferred label: dose
example of usage: An organism has been injected 1ml of vaccine
has curation status: IAO_0000123
definition: A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
imported from: obi.owl

Axiom
annotated source: dose
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

Edinburgh score
type: Class
subclass of: scalar score from composite inputs
subclass of: Restriction
  on property: is quality measurement of
  some values from: handedness
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Edinburgh handedness assay
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
editor preferred label: Edinburgh score
has curation status: IAO_0000123
definition: A score that measures the dominance of a person's right or left hand in everyday activities.
definition editor: Person: Alan Ruttenberg
definition editor: Person:Jessica Turner
definition source: PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
definition source: WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html
imported from: obi.owl

Axiom
annotated source: Edinburgh score
annotated property: subClassOf
annotated target: scalar score from composite inputs
is inferred: true

questionnaire
type: Class
subclass of: document
editor preferred label: questionnaire
has curation status: IAO_0000120
definition: A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
editor note: JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
editor note: Need to clarify if this is a document or a directive information entity (or what their connection is))
definition editor: PERSON: Jessica Turner
definition source: Merriam-Webster
imported from: obi.owl

Axiom
annotated source: questionnaire
annotated property: subClassOf
annotated target: document
is inferred: true

Edinburgh handedness assay
type: Class
subclass of: handedness assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Edinburgh score
subclass of: Restriction
  on property: has_specified_input
  has value: OBI_0001004
editor preferred label: Edinburgh handedness assay
has curation status: IAO_0000120
definition: The Edinburgh Handedness assay is an assay in which a set of questions = the Edinburgh Handedness inventory - is asked and the answers to these questions are turned into a score, used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand.
definition editor: PERSON:Jessica Turner
definition editor: Person:Alan Ruttenberg
definition source: WEB:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory
imported from: obi.owl

Axiom
annotated source: Edinburgh handedness assay
annotated property: subClassOf
annotated target: handedness assay
is inferred: true

binding constant
type: Class
equivalent class: Class
  union of: equilibrium dissociation constant (KD)
  union of: equilibrium association constant (KA)
  union of: equilibrium dissociation constant (KD) approximated by IC50
  union of: equilibrium dissociation constant (KD) approximated by EC50
  union of: half life of binding datum
  union of: binding off rate measurement datum (koff)
  union of: binding on rate measurement datum (kon)
subclass of: binding datum
editor preferred label: binding constant
example of usage: The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes".
has curation status: IAO_0000123
definition: A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process
editor note: 10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class.
definition editor: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
imported from: obi.owl

Axiom
annotated source: binding constant
annotated property: subClassOf
annotated target: binding datum
is inferred: true

3D structural organization datum
type: Class
subclass of: measurement datum
editor preferred label: 3D structural organization datum
example of usage: The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR.
has curation status: IAO_0000123
definition: A measurement datum that describes the structural orientation of a material entity in 3D space.
definition editor: PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters
imported from: obi.owl

Axiom
annotated source: 3D structural organization datum
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

age since planting measurement datum
type: Class
subclass of: age measurement datum
editor preferred label: age since planting measurement datum
has curation status: IAO_0000120
definition: An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
definition editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_495 planting
curator note: Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call
imported from: obi.owl

Axiom
annotated source: age since planting measurement datum
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

age since hatching measurement datum
type: Class
subclass of: age measurement datum
editor preferred label: age since hatching measurement datum
has curation status: IAO_0000120
definition: An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
definition editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_745 hatching
imported from: obi.owl

Axiom
annotated source: age since hatching measurement datum
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

age measurement assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: age measurement datum
editor preferred label: age measurement assay
has curation status: IAO_0000120
definition: An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted.
editor note: This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature.
definition editor: PERSON: Alan Ruttenberg
definition source: OBI group
imported from: obi.owl

Axiom
annotated source: age measurement assay
annotated property: subClassOf
annotated target: assay
is inferred: true

age since egg laying measurement datum
type: Class
subclass of: age measurement datum
editor preferred label: age since egg laying measurement datum
has curation status: IAO_0000120
definition: An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
definition editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_767 egg laying
imported from: obi.owl

Axiom
annotated source: age since egg laying measurement datum
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

age since germination measurement datum
type: Class
subclass of: age measurement datum
editor preferred label: age since germination measurement datum
has curation status: IAO_0000120
definition: An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
editor note: Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
definition editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_590 germination
imported from: obi.owl

Axiom
annotated source: age since germination measurement datum
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

age since eclosion measurement datum
type: Class
subclass of: age measurement datum
editor preferred label: age since eclosion measurement datum
has curation status: IAO_0000120
definition: An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
definition editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_876 eclosion
imported from: obi.owl

Axiom
annotated source: age since eclosion measurement datum
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

age since sowing measurement datum
type: Class
subclass of: age measurement datum
editor preferred label: age since sowing measurement datum
has curation status: IAO_0000120
definition: An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
definition editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_748 sowing
imported from: obi.owl

Axiom
annotated source: age since sowing measurement datum
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

age since coitus measurement datum
type: Class
subclass of: age measurement datum
editor preferred label: age since coitus measurement datum
has curation status: IAO_0000120
definition: An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
definition editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_783 coitus
imported from: obi.owl

Axiom
annotated source: age since coitus measurement datum
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

age measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is quality measurement of
  some values from: age
subclass of: Restriction
  on property: is_specified_output_of
  some values from: age measurement assay
editor preferred label: age measurement datum
has curation status: IAO_0000120
definition: A time measurement datum that is the result of measurement of age of an organism
editor note: note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage
definition editor: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
definition source: MO_178 Age
curator note: In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
curator note: discussed on Nov 15, dev call All subtype will be defined by textual definition now.
imported from: obi.owl

Axiom
annotated source: age measurement datum
annotated property: subClassOf
annotated target: time measurement datum
is inferred: true

age since fertilization measurement datum
type: Class
subclass of: age measurement datum
editor preferred label: age since fertilization measurement datum
has curation status: IAO_0000120
definition: An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
editor note: Definition of fertilization comes from GO.
definition editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_701 fertilization
imported from: obi.owl

Axiom
annotated source: age since fertilization measurement datum
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

age since birth measurement datum
type: Class
subclass of: age measurement datum
editor preferred label: age since birth measurement datum
has curation status: IAO_0000120
definition: An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
definition editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_710 birth
imported from: obi.owl

Axiom
annotated source: age since birth measurement datum
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

half life datum (t 1/2)
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000003
editor preferred label: half life datum (t 1/2)
has curation status: IAO_0000120
definition: The time it takes for 50% of a class of stochastic processes to occur.
definition editor: Bjoern Peters
alternative term: t 1/2
definition source: Bjoern Peters
imported from: obi.owl

Axiom
annotated source: half life datum (t 1/2)
annotated property: subClassOf
annotated target: time measurement datum
is inferred: true

dose response curve
type: Class
subclass of: line graph
editor preferred label: dose response curve
has curation status: IAO_0000120
definition: A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
definition editor: Bjoern Peters; Randi Vita
imported from: obi.owl

Axiom
annotated source: dose response curve
annotated property: subClassOf
annotated target: line graph
is inferred: true

half maximal effective concentration (EC50)
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
subclass of: Restriction
  on property: is about
  some values from: dose response curve
editor preferred label: half maximal effective concentration (EC50)
example of usage: Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed.
has curation status: IAO_0000120
definition: half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time.
definition editor: Bjoern Peters; Randi Vita
definition source: wikipedia
imported from: obi.owl

Axiom
annotated source: half maximal effective concentration (EC50)
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

binding datum
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: binding
subclass of: data item
editor preferred label: binding datum
has curation status: IAO_0000120
definition: A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is.
definition editor: Bjoern Peters; Randi Vita
imported from: obi.owl

Axiom
annotated source: binding datum
annotated property: subClassOf
annotated target: data item
is inferred: true

half maximal inhibitory concentration (IC50)
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
subclass of: Restriction
  on property: is about
  some values from: dose response curve
editor preferred label: half maximal inhibitory concentration (IC50)
example of usage: Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
has curation status: IAO_0000120
definition: Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect.
definition editor: Bjoern Peters; Randi Vita
definition source: wikipedia
imported from: obi.owl

Axiom
annotated source: half maximal inhibitory concentration (IC50)
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

sampling time measurement datum
type: Class
subclass of: time measurement datum
editor preferred label: sampling time measurement datum
has curation status: IAO_0000120
definition: A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
definition editor: Person: Chris Stoeckert
alternative term: time point
definition source: MO_738 timepoint
imported from: obi.owl

Axiom
annotated source: sampling time measurement datum
annotated property: subClassOf
annotated target: time measurement datum
is inferred: true

minimal inhibitory concentration
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
subclass of: Restriction
  on property: is about
  some values from: dose response curve
editor preferred label: minimal inhibitory concentration
has curation status: IAO_0000120
definition: A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound.
editor note: Created following request by Albert Goldfain
definition editor: PERSON:Bjoern Peters
definition source: Bjoern Peters, coordinated with Albert Goldfain
imported from: obi.owl

Axiom
annotated source: minimal inhibitory concentration
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

sequence assembly algorithm
type: Class
subclass of: algorithm
editor preferred label: sequence assembly algorithm
has curation status: IAO_0000120
definition: An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
NIAID GSCID-BRC alternative term: Assembly Algorithm
Source: NIAID GSCID-BRC

Axiom
annotated source: sequence assembly algorithm
annotated property: subClassOf
annotated target: algorithm
is inferred: true

PDB file
type: Class
subclass of: 3D structural organization datum
editor preferred label: PDB file
example of usage: The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4
has curation status: IAO_0000120
definition: A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned.
definition editor: PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum
imported from: obi.owl

Axiom
annotated source: PDB file
annotated property: subClassOf
annotated target: 3D structural organization datum
is inferred: true

equilibrium dissociation constant (KD)
type: Class
subclass of: binding constant
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
editor preferred label: equilibrium dissociation constant (KD)
example of usage: KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb
has curation status: IAO_0000120
definition: A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate)
definition editor: PERSON: Bjoern Peters, Randi Vita
definition source: IEDB
imported from: obi.owl

Axiom
annotated source: equilibrium dissociation constant (KD)
annotated property: subClassOf
annotated target: binding constant
is inferred: true

equilibrium association constant (KA)
type: Class
subclass of: binding constant
editor preferred label: equilibrium association constant (KA)
example of usage: KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens.
has curation status: IAO_0000120
definition: A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate)
definition editor: PERSON: Bjoern Peters, Randi Vita
definition source: IEDB
imported from: obi.owl

Axiom
annotated source: equilibrium association constant (KA)
annotated property: subClassOf
annotated target: binding constant
is inferred: true

rate measurement datum
type: Class
subclass of: scalar measurement datum
editor preferred label: rate measurement datum
example of usage: The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
has curation status: IAO_0000120
definition: A scalar measurement datum that represents the number of events occuring over a time interval
definition editor: PERSON: Bjoern Peters, Randi Vita
definition source: IEDB
imported from: obi.owl

Axiom
annotated source: rate measurement datum
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

equilibrium dissociation constant (KD) approximated by IC50
type: Class
subclass of: binding constant
subclass of: half maximal inhibitory concentration (IC50)
editor preferred label: equilibrium dissociation constant (KD) approximated by IC50
has curation status: IAO_0000120
definition: A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor.
definition editor: PERSON: Bjoern Peters, Randi Vita
definition source: http://dx.doi.org/10.1016/0006-2952(73)90196-2
imported from: obi.owl

Axiom
annotated source: equilibrium dissociation constant (KD) approximated by IC50
annotated property: subClassOf
annotated target: binding constant
is inferred: true

Axiom
annotated source: equilibrium dissociation constant (KD) approximated by IC50
annotated property: subClassOf
annotated target: half maximal inhibitory concentration (IC50)
is inferred: true

DNA sequence data
type: Class
subclass of: sequence data
subclass of: Restriction
  on property: is about
  some values from: primary structure of DNA macromolecule
editor preferred label: DNA sequence data
example of usage: The part of a FASTA file that contains the letters ACTGGGAA
has curation status: IAO_0000120
definition: A sequence data item that is about the primary structure of DNA
definition editor: OBI call; Bjoern Peters
definition source: OBI call; Melanie Courtout
curator note: 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
imported from: obi.owl

Axiom
annotated source: DNA sequence data
annotated property: subClassOf
annotated target: sequence data
is inferred: true

equilibrium dissociation constant (KD) approximated by EC50
type: Class
subclass of: binding constant
subclass of: half maximal effective concentration (EC50)
editor preferred label: equilibrium dissociation constant (KD) approximated by EC50
has curation status: IAO_0000120
definition: A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand.
definition editor: PERSON: Bjoern Peters, Randi Vita
definition source: Assay Development: Fundamentals and Practices, By Ge Wu, page 74
imported from: obi.owl

Axiom
annotated source: equilibrium dissociation constant (KD) approximated by EC50
annotated property: subClassOf
annotated target: binding constant
is inferred: true

Axiom
annotated source: equilibrium dissociation constant (KD) approximated by EC50
annotated property: subClassOf
annotated target: half maximal effective concentration (EC50)
is inferred: true

half life of binding datum
type: Class
subclass of: binding constant
subclass of: half life datum (t 1/2)
editor preferred label: half life of binding datum
example of usage: The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate.
has curation status: IAO_0000120
definition: A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association.
definition editor: PERSON: Bjoern Peters, Randi Vita
definition source: IEDB
imported from: obi.owl

Axiom
annotated source: half life of binding datum
annotated property: subClassOf
annotated target: binding constant
is inferred: true

Axiom
annotated source: half life of binding datum
annotated property: subClassOf
annotated target: half life datum (t 1/2)
is inferred: true

binding
type: Class
subclass of: biological_process
editor preferred label: binding
example of usage: A peptide binding to an MHC molecule to form a complex.
has curation status: IAO_0000120
definition: The process of material entities forming complexes.
editor note: 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.
definition editor: PERSON: Bjoern Peters, Randi Vita
definition source: IEDB
imported from: obi.owl

Axiom
annotated source: binding
annotated property: subClassOf
annotated target: biological_process
is inferred: true

PDB file chain
type: Class
subclass of: 3D structural organization datum
subclass of: Restriction
  on property: part_of
  some values from: PDB file
editor preferred label: PDB file chain
example of usage: The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex
has curation status: IAO_0000120
definition: A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities
definition editor: PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum
definition source: IEDB
imported from: obi.owl

Axiom
annotated source: PDB file chain
annotated property: subClassOf
annotated target: 3D structural organization datum
is inferred: true

binding off rate measurement datum (koff)
type: Class
subclass of: binding constant
subclass of: rate measurement datum
editor preferred label: binding off rate measurement datum (koff)
has curation status: IAO_0000120
definition: A rate measurement datum of how quickly bound complexes disassociate
definition editor: PERSON: Bjoern Peters, Randi Vita
definition source: IEDB
imported from: obi.owl

Axiom
annotated source: binding off rate measurement datum (koff)
annotated property: subClassOf
annotated target: binding constant
is inferred: true

Axiom
annotated source: binding off rate measurement datum (koff)
annotated property: subClassOf
annotated target: rate measurement datum
is inferred: true

binding on rate measurement datum (kon)
type: Class
subclass of: binding constant
subclass of: rate measurement datum
editor preferred label: binding on rate measurement datum (kon)
has curation status: IAO_0000120
definition: A rate measurement datum of how quickly bound complexes form
definition editor: PERSON: Bjoern Peters, Randi Vita
definition source: IEDB
imported from: obi.owl

Axiom
annotated source: binding on rate measurement datum (kon)
annotated property: subClassOf
annotated target: binding constant
is inferred: true

Axiom
annotated source: binding on rate measurement datum (kon)
annotated property: subClassOf
annotated target: rate measurement datum
is inferred: true

specimen collection time measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: process boundary
    intersection of: Restriction
      on property: starts
      some values from: specimen collection process
editor preferred label: specimen collection time measurement datum
has curation status: IAO_0000120
definition: A time measurement datum that is the measure of the time when the specimens are collected.
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative term: collection date
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
NIAID GSCID-BRC alternative term: Specimen Collection Date
Source: NIAID GSCID-BRC

Axiom
annotated source: specimen collection time measurement datum
annotated property: subClassOf
annotated target: time measurement datum
is inferred: true

latitude coordinate measurement datum
type: Class
subclass of: measurement datum
editor preferred label: latitude coordinate measurement datum
has curation status: IAO_0000120
definition: A measurement datum that is the measure of the latitude coordinate of a site.
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative term: latitude
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
NIAID GSCID-BRC alternative term: Specimen Collection Location - Latitude
Source: NIAID GSCID-BRC

Axiom
annotated source: latitude coordinate measurement datum
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

longitude coordinate measurement datum
type: Class
subclass of: measurement datum
editor preferred label: longitude coordinate measurement datum
has curation status: IAO_0000120
definition: A measurement datum that is the measure of the longitude coordinate of a site.
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative term: longitude
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
NIAID GSCID-BRC alternative term: Specimen Collection Location - Longitude
Source: NIAID GSCID-BRC

Axiom
annotated source: longitude coordinate measurement datum
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

secondary cultured cell
type: Class
subclass of: cultured cell
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: cell culture splitting
  union of: Restriction
    on property: derives_from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: cell culture splitting
subclass of: Restriction
  on property: derives_from
  some values from: primary cultured cell
editor preferred label: secondary cultured cell
has curation status: IAO_0000120
definition: A cultured cell that has been passaged or derives from a cell that has been passaged in culture.
editor note: The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
definition editor: Person: Matthew Brush
definition source: PERSON: Matthew Brush
imported from: clo.owl
imported from: obi.owl
comment: A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.

Axiom
annotated source: secondary cultured cell
annotated property: subClassOf
annotated target: cultured cell
is inferred: true

establishing cell line
type: Class
subclass of: establishing cell culture
subclass of: Restriction
  on property: has_specified_output
  some values from: cell line
editor preferred label: establishing cell line
has curation status: IAO_0000120
definition: a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
editor note: 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time.
definition editor: Person: Matthew Brush
definition source: PERSON:Matthew Brush
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: establishing cell line
annotated property: subClassOf
annotated target: establishing cell culture
is inferred: true

sequence assembly process
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: sequence assembly algorithm
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: genome coverage
subclass of: Restriction
  on property: has_specified_output
  some values from: N50
editor preferred label: sequence assembly process
has curation status: IAO_0000122
definition: A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs).
editor note: PRS/AGB: changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly.
definition editor: Alejandra Gonzalez-Beltran
definition editor: PERSON: Jie Zheng, Chris Stoeckert
definition editor: Philippe Rocca-Serra
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
Source: NIAID GSCID-BRC

Axiom
annotated source: sequence assembly process
annotated property: subClassOf
annotated target: data transformation
is inferred: true

number of errors
type: Class
subclass of: data item
subclass of: value specification
subclass of: Restriction
  on property: is about
  some values from: process
subclass of: Restriction
  on property: has specified numeric value
  some values from: integer
editor preferred label: number of errors
example of usage: Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. see table2
has curation status: IAO_0000122
definition: a data item that is the number of times that a given process failed, as an integer
definition editor: Alejandra Gonzalez-Beltran
definition editor: Philippe Rocca-Serra
definition source: PRS, AGB
imported from: obi.owl

Axiom
annotated source: number of errors
annotated property: subClassOf
annotated target: data item
is inferred: true

Axiom
annotated source: number of errors
annotated property: subClassOf
annotated target: value specification
is inferred: true

random access memory size
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: random access memory
    intersection of: Restriction
      on property: part_of
      some values from: computer
editor preferred label: random access memory size
example of usage: Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "However, the error correction module in SOAPdenovo was designed for short Illumina reads (35-50 bp), which consumes an excessive amount of computational time and memory on longer reads, for example, over 150 GB memory running for two days using 40-fold 100 bp paired-end Illumina HiSeq 2000 reads"
has curation status: IAO_0000125
definition: random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation
definition editor: Alejandra Gonzalez-Beltran
definition editor: Philippe Rocca-Serra
definition source: PRS, AGB
imported from: obi.owl

Axiom
annotated source: random access memory size
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

random access memory
type: Class
subclass of: material information bearer
editor preferred label: random access memory
has curation status: IAO_0000125
definition: Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location
definition editor: Alejandra Gonzalez-Beltran
definition editor: Philippe Rocca-Serra
alternative term: RAM
definition source: http://en.wikipedia.org/wiki/RAM last accessed: 2013-12-02
imported from: obi.owl

Axiom
annotated source: random access memory
annotated property: subClassOf
annotated target: material information bearer
is inferred: true

reagent
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: reagent role
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred label: reagent
has curation status: IAO_0000120
definition: A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
editor note: 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device.
definition editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
imported from: obi.owl
comment: (copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some…

Axiom
annotated source: reagent
annotated property: subClassOf
annotated target: processed material
is inferred: true

secondary cultured cell population
type: Class
subclass of: cultured cell population
subclass of: Restriction
  on property: is_specified_output_of
  some values from: cell culture splitting
subclass of: Restriction
  on property: has grain
  some values from: secondary cultured cell
subclass of: Restriction
  on property: has grain
  all values from: secondary cultured cell
editor preferred label: secondary cultured cell population
has curation status: IAO_0000120
definition: A cultured cell population that is derived through one or more passages in culture.
editor note: The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
definition editor: PERSON:Matthew Brush
alternative term: secondary cell culture sample
definition source: PERSON:Matthew Brush
imported from: clo.owl
imported from: obi.owl
comment: The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.

Axiom
annotated source: secondary cultured cell population
annotated property: subClassOf
annotated target: cultured cell population
is inferred: true

testable hypothesis
type: Class
subclass of: information content entity
editor preferred label: testable hypothesis
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: IAO_0000122
definition: An information content entity that expresses an assertion that is intended to be tested.
editor note: In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
definition editor: Group:2013 Philly Workshop group
alternative term: hypothesis
definition source: Group:2013 Philly Workshop group
imported from: obi.owl

Axiom
annotated source: testable hypothesis
annotated property: subClassOf
annotated target: information content entity
is inferred: true

conclusion based on data
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor preferred label: conclusion based on data
example of usage: The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
has curation status: IAO_0000122
definition: An information content entity that is inferred from data.
editor note: In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
definition editor: Group:2013 Philly Workshop group
definition source: Group:2013 Philly Workshop group
imported from: obi.owl

Axiom
annotated source: conclusion based on data
annotated property: subClassOf
annotated target: information content entity
is inferred: true

cell freezing medium
type: Class
subclass of: processed material
editor preferred label: cell freezing medium
example of usage: culture media or serum + 10% DMSO is often used as cell freezing media.
has curation status: IAO_0000120
definition: A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
definition editor: PERSON: Matthew Brush
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: cell freezing medium
annotated property: subClassOf
annotated target: processed material
is inferred: true

computation run time
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is duration of
  some values from: data transformation
editor preferred label: computation run time
example of usage: Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. See Table 4
has curation status: IAO_0000125
definition: computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency.
definition editor: Alejandra Gonzalez-Beltran
definition editor: Philippe Rocca-Serra
alternative term: computation run time datum
definition source: PRS,AGB
imported from: obi.owl

Axiom
annotated source: computation run time
annotated property: subClassOf
annotated target: time measurement datum
is inferred: true

mass value specification
type: Class
subclass of: scalar value specification
subclass of: Restriction
  on property: specifies value of
  some values from: mass
subclass of: Restriction
  on property: has measurement unit label
  all values from: UO_0000002
editor preferred label: mass value specification
has curation status: IAO_0000123
definition: A value specification that specifies the mass of some thing.
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

Axiom
annotated source: mass value specification
annotated property: subClassOf
annotated target: scalar value specification
is inferred: true

categorical value specification
type: Class
subclass of: value specification
editor preferred label: categorical value specification
has curation status: IAO_0000123
definition: A value specification that is specifies one category out of a fixed number of nominal categories
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

Axiom
annotated source: categorical value specification
annotated property: subClassOf
annotated target: value specification
is inferred: true

scalar value specification
type: Class
subclass of: value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has specified numeric value
  min cardinality: 1
editor preferred label: scalar value specification
has curation status: IAO_0000123
definition: A value specification that consists of two parts: a numeral and a unit label
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

Axiom
annotated source: scalar value specification
annotated property: subClassOf
annotated target: value specification
is inferred: true

value specification
type: Class
subclass of: information content entity
editor preferred label: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: IAO_0000122
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

Axiom
annotated source: value specification
annotated property: subClassOf
annotated target: information content entity
is inferred: true

genome coverage
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: assembly
subclass of: Restriction
  on property: is_specified_output_of
  some values from: sequence assembly process
editor preferred label: genome coverage
example of usage: Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "The genome coverage increased from 81.16% to 93.91%"
has curation status: IAO_0000122
definition: A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%.
definition editor: Alejandra Gonzalez-Beltran
definition editor: Philippe Rocca-Serra
definition source: A beginner's guide to eukaryotic genome annotation. Yandell M, Ence D. Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174. PMID: 22510764
imported from: obi.owl

Axiom
annotated source: genome coverage
annotated property: subClassOf
annotated target: data item
is inferred: true

N50
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: measurement unit label
subclass of: Restriction
  on property: is about
  some values from: assembly
subclass of: Restriction
  on property: is_specified_output_of
  some values from: sequence assembly process
editor preferred label: N50
example of usage: Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
has curation status: IAO_0000125
definition: the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly
definition editor: Alejandra Gonzalez-Beltran
definition editor: Philippe Rocca-Serra
alternative term: weighted median item size
definition source: adapted from: "http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" (from table 7) and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html"
imported from: obi.owl

Axiom
annotated source: N50
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

contig N50
type: Class
subclass of: N50
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: contig
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: sequence assembly process
editor preferred label: contig N50
example of usage: Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
has curation status: IAO_0000125
definition: N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list.
definition editor: Alejandra Gonzalez-Beltran
definition editor: Philippe Rocca-Serra
definition source: adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
imported from: obi.owl

Axiom
annotated source: contig N50
annotated property: subClassOf
annotated target: N50
is inferred: true

scaffold N50
type: Class
subclass of: N50
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: supercontig
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: sequence assembly process
editor preferred label: scaffold N50
example of usage: Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
has curation status: IAO_0000125
definition: N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information
definition editor: Alejandra Gonzalez-Beltran
definition editor: Philippe Rocca-Serra
definition source: adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
imported from: obi.owl

Axiom
annotated source: scaffold N50
annotated property: subClassOf
annotated target: N50
is inferred: true

RNA Integrity Number value specification
type: Class
subclass of: value specification
editor preferred label: RNA Integrity Number value specification
has curation status: IAO_0000122
definition: A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact).
definition editor: Chris Stoeckert, Bjoern Peters
alternative term: RIN value specification
definition source: OBI
imported from: obi.owl

Axiom
annotated source: RNA Integrity Number value specification
annotated property: subClassOf
annotated target: value specification
is inferred: true

temperature value specification
type: Class
subclass of: value specification
subclass of: Class
  intersection of: Restriction
    on property: specifies value of
    some values from: temperature
  intersection of: Restriction
    on property: has measurement unit label
    all values from: UO_0000005
editor preferred label: temperature value specification
has curation status: IAO_0000122
definition: A value specification that specifies the temperature of some thing.
definition editor: Chris Stoeckert
definition source: OBI
imported from: obi.owl

Axiom
annotated source: temperature value specification
annotated property: subClassOf
annotated target: value specification
is inferred: true

volume value specification
type: Class
subclass of: value specification
subclass of: Class
  intersection of: Restriction
    on property: specifies value of
    some values from: volume
  intersection of: Restriction
    on property: has measurement unit label
    all values from: UO_0000095
editor preferred label: volume value specification
has curation status: IAO_0000122
definition: A value specification that specifies the volume of some thing.
definition editor: Chris Stoeckert
definition source: OBI
imported from: obi.owl

Axiom
annotated source: volume value specification
annotated property: subClassOf
annotated target: value specification
is inferred: true

tissue section thickness
type: Class
subclass of: length measurement datum
editor preferred label: tissue section thickness
has curation status: IAO_0000122
definition: A length measurement datum that is the result of an assay measuring the thickness of a tissue section.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: tissue section thickness
annotated property: subClassOf
annotated target: length measurement datum
is inferred: true

histologic grade according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade according to AJCC 7th edition
example of usage: G4: Undifferentiated
example of usage: G1:Well differentiated
has curation status: IAO_0000120
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: histologic grade according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

histologic grade according to the Fuhrman Nuclear Grading System
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade according to the Fuhrman Nuclear Grading System
has curation status: IAO_0000120
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Histologic Grade (Fuhrman Nuclear Grading System)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: histologic grade according to the Fuhrman Nuclear Grading System
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

histologic grade for ovarian tumor
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade for ovarian tumor
has curation status: IAO_0000120
definition: A categorical value specification that is a histologic grade assigned to a ovarian tumor.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: histologic grade for ovarian tumor
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

histologic grade for ovarian tumor according to a two-tier grading system
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred label: histologic grade for ovarian tumor according to a two-tier grading system
has curation status: IAO_0000120
definition: A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: histologic grade for ovarian tumor according to a two-tier grading system
annotated property: subClassOf
annotated target: histologic grade for ovarian tumor
is inferred: true

histologic grade for ovarian tumor according to the World Health Organization
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred label: histologic grade for ovarian tumor according to the World Health Organization
has curation status: IAO_0000120
definition: A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: histologic grade for ovarian tumor according to the World Health Organization
annotated property: subClassOf
annotated target: histologic grade for ovarian tumor
is inferred: true

pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

pathologic primary tumor stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for lung according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic primary tumor stage for lung according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

pathologic primary tumor stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for kidney according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic primary tumor stage for kidney according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

pathologic primary tumor stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for ovary according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic primary tumor stage for ovary according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

pathologic lymph node stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

pathologic lymph node stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for lung according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic lymph node stage for lung according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

pathologic lymph node stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for kidney according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic lymph node stage for kidney according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

pathologic lymph node stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for ovary according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic lymph node stage for ovary according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

pathologic distant metastases stage for colon according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for colon according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: M: colon distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic distant metastases stage for colon according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

pathologic distant metastases stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for lung according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: M: lung distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic distant metastases stage for lung according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

pathologic distant metastases stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for kidney according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: M: kidney distant Metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic distant metastases stage for kidney according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

pathologic distant metastases stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for ovary according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: M: ovarian distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: pathologic distant metastases stage for ovary according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

clinical tumor stage group according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: clinical tumor stage group according to AJCC 7th edition
has curation status: IAO_0000120
definition: A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Clinical tumor stage group (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: clinical tumor stage group according to AJCC 7th edition
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

International Federation of Gynecology and Obstetrics cervical cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred label: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
has curation status: IAO_0000120
definition: A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Clinical FIGO stage
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred label: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
has curation status: IAO_0000120
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

performance status value specification
type: Class
subclass of: categorical value specification
editor preferred label: performance status value specification
has curation status: IAO_0000120
definition: A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Performance Status Scale
definition source: https://en.wikipedia.org/wiki/Performance_status
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: performance status value specification
annotated property: subClassOf
annotated target: categorical value specification
is inferred: true

Eastern Cooperative Oncology Group score value specification
type: Class
subclass of: performance status value specification
editor preferred label: Eastern Cooperative Oncology Group score value specification
has curation status: IAO_0000120
definition: A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: ECOG score
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: Eastern Cooperative Oncology Group score value specification
annotated property: subClassOf
annotated target: performance status value specification
is inferred: true

Karnofsky score vaue specification
type: Class
subclass of: performance status value specification
editor preferred label: Karnofsky score vaue specification
has curation status: IAO_0000120
definition: A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Karnofsky Score
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: Karnofsky score vaue specification
annotated property: subClassOf
annotated target: performance status value specification
is inferred: true

number of pregnancies
type: Class
subclass of: measurement datum
editor preferred label: number of pregnancies
has curation status: IAO_0000120
definition: A measurement datum of the total number of pregnancies a woman has had.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: number of pregnancies
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

number of live births
type: Class
subclass of: measurement datum
editor preferred label: number of live births
has curation status: IAO_0000120
definition: A measurement datum of the total number of live births a female has had.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: number of live births
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

age when gave birth to first child
type: Class
subclass of: age measurement datum
editor preferred label: age when gave birth to first child
has curation status: IAO_0000120
definition: An age measurement datum performed on a female when her first biological child was born.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: obi.owl

Axiom
annotated source: age when gave birth to first child
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

measurand role
type: Class
subclass of: role
subclass of: Restriction
  on property: role of
  some values from: material entity
editor preferred label: measurand role
has curation status: IAO_0000120
definition: A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
definition editor: Person: Alan Ruttenberg, Jie Zheng
definition source: https://en.wiktionary.org/wiki/measurand
term tracker item: https://github.com/obi-ontology/obi/issues/778
imported from: obi.owl

Axiom
annotated source: measurand role
annotated property: subClassOf
annotated target: role
is inferred: true

age since culture seeding measurement datum
type: Class
subclass of: age measurement datum
editor preferred label: age since culture seeding measurement datum
has curation status: IAO_0000123
definition: An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish).
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
alternative term: age of culture
imported from: obi.owl

Axiom
annotated source: age since culture seeding measurement datum
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

sequence read length measurement datum
type: Class
subclass of: measurement datum
editor preferred label: sequence read length measurement datum
has curation status: IAO_0000123
definition: A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
alternative term: read length, read length measurement datum
imported from: obi.owl

Axiom
annotated source: sequence read length measurement datum
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

sequencing library input quantity measurement datum
type: Class
subclass of: scalar measurement datum
editor preferred label: sequencing library input quantity measurement datum
has curation status: IAO_0000123
definition: A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer.
definition editor: Stephen A. Fisher, Junhyong Kim
alternative term: library input amount
imported from: obi.owl

Axiom
annotated source: sequencing library input quantity measurement datum
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

specimen harvest quantity
type: Class
subclass of: measurement datum
editor preferred label: specimen harvest quantity
has curation status: IAO_0000123
definition: A scalar measurement datum that indicates the amount of specimen collected.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
alternative term: harvest quantity
imported from: obi.owl

Axiom
annotated source: specimen harvest quantity
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

minimum age value specification
type: Class
subclass of: value specification
editor preferred label: minimum age value specification
has curation status: IAO_0000123
definition: A value specifcation that specifies the youngest age when specifying an age range.
definition editor: Mathias Brochhausen
imported from: obi.owl

Axiom
annotated source: minimum age value specification
annotated property: subClassOf
annotated target: value specification
is inferred: true

maximum age value specification
type: Class
subclass of: value specification
editor preferred label: maximum age value specification
has curation status: IAO_0000123
definition: A value specifcation that specifies the oldest age when specifying an age range.
definition editor: Mathias Brochhausen
imported from: obi.owl

Axiom
annotated source: maximum age value specification
annotated property: subClassOf
annotated target: value specification
is inferred: true

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: genome
editor preferred label: organism
example of usage: Drosophila melanogaster
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: IAO_0000121
has curation status: IAO_0000122
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
definition editor: GROUP: OBI Biomaterial Branch
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
definition source: MO_508
definition source: NIFSTD:birnlex_376
definition source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: clo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: omrse.owl
comment: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
comment: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. E.g Drosophila melanogaster
see also: EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000634

Axiom
annotated source: organism
annotated property: subClassOf
annotated target: material entity
is inferred: true

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
editor preferred label: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
has curation status: IAO_0000122
definition: A material entity that has the specimen role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
definition editor: PERSON: James Malone
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch
imported from: obi.owl

Axiom
annotated source: specimen
annotated property: subClassOf
annotated target: material entity
is inferred: true

cultured cell population
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: maintaining cell culture
subclass of: Restriction
  on property: has grain
  some values from: cultured cell
subclass of: Restriction
  on property: has grain
  all values from: cultured cell
editor preferred label: cultured cell population
example of usage: A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
has curation status: IAO_0000120
definition: A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
editor note: 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
definition editor: PERSON:Matthew Brush
alternative term: cell culture sample
definition source: PERSON:Matthew Brush
imported from: clo.owl
imported from: obi.owl
comment: The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.

Axiom
annotated source: cultured cell population
annotated property: subClassOf
annotated target: processed material
is inferred: true

data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: algorithm
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
subclass of: Restriction
  on property: has_specified_output
  all values from: data item
editor preferred label: data transformation
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
has curation status: IAO_0000122
definition: A planned process that produces output data from input data.
definition editor: Elisabetta Manduchi
definition editor: Helen Parkinson
definition editor: James Malone
definition editor: Melanie Courtot
definition editor: Philippe Rocca-Serra
definition editor: Richard Scheuermann
definition editor: Ryan Brinkman
definition editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
definition source: Branch editors
imported from: obi.owl

Axiom
annotated source: data transformation
annotated property: subClassOf
annotated target: planned process
is inferred: true

data transformation objective
type: Class
subclass of: objective specification
editor preferred label: data transformation objective
example of usage: normalize objective
has curation status: IAO_0000122
definition: An objective specification to transformation input data into output data
editor note: Modified definition in 2013 Philly OBI workshop
definition editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

Axiom
annotated source: data transformation objective
annotated property: subClassOf
annotated target: objective specification
is inferred: true

computer
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: information processor function
editor preferred label: computer
example of usage: Apple PowerBook, Dell OptiPlex
has curation status: IAO_0000122
definition: A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
definition editor: Melanie Courtot
definition editor: Trish Whetzel
definition source: http://en.wikipedia.org/wiki/Computer
imported from: obi.owl

Axiom
annotated source: computer
annotated property: subClassOf
annotated target: device
is inferred: true

study design
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: protocol
editor preferred label: study design
example of usage: a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
has curation status: IAO_0000122
definition: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor note: Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
definition editor: PERSON: Chris Stoeckert
alternative term: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: obi.owl

Axiom
annotated source: study design
annotated property: subClassOf
annotated target: plan specification
is inferred: true

material component separation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor preferred label: material component separation
example of usage: Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
has curation status: IAO_0000122
definition: a material processing in which components of an input material become segregated in space
definition editor: Bjoern Peters
definition source: IEDB
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: material component separation
annotated property: subClassOf
annotated target: material processing
is inferred: true

maintaining cell culture
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: culture medium
    union of: cell freezing medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: maintaining cell culture
example of usage: When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
has curation status: IAO_0000125
definition: a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: clo.owl
imported from: obi.owl

Axiom
annotated source: maintaining cell culture
annotated property: subClassOf
annotated target: material maintenance
is inferred: true

establishing cell culture
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: cell type
subclass of: Restriction
  on property: has_specified_input
  some values from: culture medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: establishing cell culture
has curation status: IAO_0000120
definition: a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
definition editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
imported from: clo.owl
imported from: obi.owl
comment: A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.

Axiom
annotated source: establishing cell culture
annotated property: subClassOf
annotated target: material processing
is inferred: true

cell culture splitting
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: portioning objective
editor preferred label: cell culture splitting
example of usage: The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
has curation status: IAO_0000125
definition: The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
definition editor: PlanAndPlannedProcess Branch
alternative term: cell culture passaging
definition source: OBI branch derived
imported from: clo.owl
imported from: obi.owl
comment: An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone.

Axiom
annotated source: cell culture splitting
annotated property: subClassOf
annotated target: material component separation
is inferred: true

donor
type: Class
subclass of: role
editor preferred label: donor
example of usage: A T cell line from a PPD(+) donor.
has curation status: IAO_0000120
definition: A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
definition editor: IEDB
alternative term: donor role
definition source: IEDB
curator note: Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.
imported from: obi.owl

Axiom
annotated source: donor
annotated property: subClassOf
annotated target: role
is inferred: true

genome
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: gene
definition: A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA.
definition editor: Oliver He
definition source: Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311
definition source: WEB: http://en.wikipedia.org/wiki/Genome
imported from: ogg.owl

Axiom
annotated source: genome
annotated property: subClassOf
annotated target: material entity
is inferred: true

gene
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has disposition at all times
  some values from: gene disposition
definition: A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
definition editor: Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
imported from: ogg.owl
comment: In addition to the coding regions (exons), a gene includes transcription-control regions and sometimes introns. Although the majority of genes encode proteins, some encode tRNAs, rRNAs, and other types of RNA.

Axiom
annotated source: gene
annotated property: subClassOf
annotated target: material entity
is inferred: true

gene disposition
type: Class
subclass of: disposition
definition: a disposition that a gene can be used as a blueprint for generating a new form of product such as protein.
definition editor: Yongqun He
definition source: WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
imported from: ogg.owl
comment: YH: According to NCBI Gene project, there are two gene types: unknown (0) , tRNA (1) , rRNA (2) , snRNA (3) , scRNA (4) , snoRNA (5) , protein-coding (6) , pseudo (7) , transposon (8) , miscRNA (9) , ncRNA (10) , other (255). Therefore, we have generated corresponding gene dispositions. Note that we don't use the term "gene type" here to differentiate the meanings of "type" and "disposition".

Axiom
annotated source: gene disposition
annotated property: subClassOf
annotated target: disposition
is inferred: true

protein-coding gene disposition
type: Class
subclass of: gene disposition
definition: a gene disposition that a gene can be used as a blueprint for generating a protein (i.e., a gene encodes for a protein).
definition editor: Yongqun He
definition source: WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
imported from: ogg.owl

Axiom
annotated source: protein-coding gene disposition
annotated property: subClassOf
annotated target: gene disposition
is inferred: true

pseudo gene disposition
type: Class
subclass of: gene disposition
definition: a gene disposition that represents the disposition of gene being "pseudo", i.e., the gene is a pseudogene.
definition editor: Yongqun He
definition source: WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
imported from: ogg.owl

Axiom
annotated source: pseudo gene disposition
annotated property: subClassOf
annotated target: gene disposition
is inferred: true

genome of Eukaryota
type: Class
subclass of: genome
subclass of: Restriction
  on property: has part
  some values from: gene of Eukaryota
subclass of: Restriction
  on property: is genome of organism
  some values from: Eukaryota
definition: The genome of an organism of Eukaryota
definition editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 2759

Axiom
annotated source: genome of Eukaryota
annotated property: subClassOf
annotated target: genome
is inferred: true

genome of Homo sapiens
type: Class
subclass of: genome of Eukaryota
subclass of: Restriction
  on property: has part
  some values from: gene of Homo sapiens
subclass of: Restriction
  on property: is genome of organism
  some values from: Homo sapiens
definition: The genome of an organism of Homo sapiens
definition editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 9606

Axiom
annotated source: genome of Homo sapiens
annotated property: subClassOf
annotated target: genome of Eukaryota
is inferred: true

gene of Eukaryota
type: Class
subclass of: gene
subclass of: Restriction
  on property: is gene of organism
  some values from: Eukaryota
definition: A gene of an organism of Eukaryota
definition editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 2759

Axiom
annotated source: gene of Eukaryota
annotated property: subClassOf
annotated target: gene
is inferred: true

gene of Homo sapiens
type: Class
subclass of: gene of Eukaryota
subclass of: Restriction
  on property: is gene of organism
  some values from: Homo sapiens
definition: A gene of an organism of Homo sapiens
definition editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 9606

Axiom
annotated source: gene of Homo sapiens
annotated property: subClassOf
annotated target: gene of Eukaryota
is inferred: true

protein-coding gene of Homo sapiens
type: Class
subclass of: gene of Homo sapiens
subclass of: Restriction
  on property: has disposition at all times
  some values from: protein-coding gene disposition
definition: A gene of Homo sapiens that has a protein-coding gene disposition
definition editor: Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 9606

Axiom
annotated source: protein-coding gene of Homo sapiens
annotated property: subClassOf
annotated target: gene of Homo sapiens
is inferred: true

pseudo gene of Homo sapiens
type: Class
subclass of: gene of Homo sapiens
subclass of: Restriction
  on property: has disposition at all times
  some values from: pseudo gene disposition
definition: A gene of Homo sapiens that has a pseudo gene disposition
definition editor: Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 9606

Axiom
annotated source: pseudo gene of Homo sapiens
annotated property: subClassOf
annotated target: gene of Homo sapiens
is inferred: true

ACTA2
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: AAT6
alternative term: ACTSA
alternative term: MYMY5
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28117838
imported from: ogg.owl
symbol from nomenclature authority: ACTA2
full name from nomenclature authority: actin, alpha 2, smooth muscle, aorta
NCBI GeneID: 59
NCBI LocusTag: GIG46
gene map location: 10q23.3
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 10
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0005524 (EC: IEA); GO_0005615 (EC: IDA); GO_0005737 (EC: IDA, PMID: 12355421); GO_0005829 (EC: TAS); GO_0006936 (EC: TAS); GO_0008217 (EC: IEA); GO_0009615 (EC: IEP, PMID: 16548883); GO_0014829 (EC: IEA); GO_0015629 (EC: IEA); GO_0030485 (EC: IEA); GO_0043234 (EC: IDA, PMID: 18468998); GO_0072144 (EC: IEP, PMID: 17464107)
has PubMed association: PMID: 1540415; 1555776; 1907279; 1939373; 1969628; 1991513; 2022339; 2295650; 2398629; 2612915; 2701935; 3842206; 6330528; 6725286; 7780165; 8138584; 8997639; 9512352; 9546431; 9841925; 10341211; 10556093; 10628374; 11037796; 11580270; 11707283; 11812134; 12119014; 12355421; 12477932; 12777385; 14530271; 14627618; 14694110; 15032605; 15164054; 15342556; 15489334; 15555551; 15588509; 15618548; 15703204; 15862967; 16051665; 16115228; 16289162; 16385451; 16526095; 16548883; 16573163; 17360745; 17411366; 17464107; 17504171; 17626241; 17786474; 17994018; 18443296; 18468998; 18775311; 18781797; 19261809; 19285011; 19409525; 19531499; 19639585; 19639654; 19654303; 19683985; 19745835; 19788615; 19883584; 19913121; 20128380; 20132408; 20147394; 20237496; 20301299; 20381122; 20618440; 20628086; 20628268; 20639865; 20689142; 20694011; 20734336; 20876399; 20970362; 20972266; 21131735; 21139048; 21145461; 21212136; 21233699; 21248741; 21288906; 21343850; 21477997; 21496259; 21530503; 21553326; 21612641; 21617610; 21815248; 21890473; 21906983; 21917091; 21923909; 21937134; 21937873; 21963094; 21987572; 21996542; 22001912; 22004035; 22053931; 22133903; 22138123; 22232431; 22395512; 22460095; 22465675; 22479424; 22505724; 22535526; 22543453; 22619371; 22790431; 22810585; 22831780; 22939629; 22946110; 22960022; 22989508; 23000965; 23020218; 23068445; 23116162; 23182716; 23246001; 23770605; 23788249; 23794425; 23982059; 24244333
description: actin, alpha 2, smooth muscle, aorta
database_cross_reference: Ensembl:ENSG00000107796
database_cross_reference: HGNC:130
database_cross_reference: HPRD:00031
database_cross_reference: MIM:102620
database_cross_reference: Vega:OTTHUMG00000018700
comment: Other designations: actin, aortic smooth muscle|alpha-cardiac actin|cell growth-inhibiting gene 46 protein
comment: This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: ACTA2
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

ANK1
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: ANK
alternative term: SPH1
alternative term: SPH2
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: ANK1
full name from nomenclature authority: ankyrin 1, erythrocytic
NCBI GeneID: 286
gene map location: 8p11.1
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 8
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0005198 (EC: NAS, PMID: 9430667); GO_0005200 (EC: TAS, PMID: 8640229); GO_0005515 (EC: IPI, PMID: 12527750); GO_0005634 (EC: IEA); GO_0005829 (EC: TAS); GO_0005856 (EC: NAS, PMID: 1833445); GO_0005886 (EC: IDA, PMID: 379653); GO_0005886 (EC: NAS, PMID: 9430667); GO_0006779 (EC: IEA); GO_0006887 (EC: NAS, PMID: 1833445); GO_0006888 (EC: IDA, PMID: 18768923); GO_0007010 (EC: NAS, PMID: 9430667); GO_0007165 (EC: IEA); GO_0007411 (EC: TAS); GO_0008093 (EC: IDA, PMID: 379653); GO_0008093 (EC: TAS, PMID: 11427698); GO_0010638 (EC: IEA); GO_0014731 (EC: IDA, PMID: 379653); GO_0015672 (EC: IEA); GO_0016323 (EC: NAS, PMID: 12409278); GO_0016529 (EC: IEA); GO_0019899 (EC: IPI); GO_0019899 (EC: TAS, PMID: 11427698); GO_0030018 (EC: IEA); GO_0030507 (EC: IDA, PMID: 379653); GO_0030507 (EC: IPI, PMID: 8159688); GO_0030507 (EC: NAS, PMID: 8640229); GO_0030673 (EC: IEA); GO_0030863 (EC: IEA); GO_0031430 (EC: IEA); GO_0042383 (EC: IEA); GO_0045199 (EC: TAS, PMID: 11427698); GO_0045211 (EC: IEA); GO_0048821 (EC: IEA); GO_0051117 (EC: IPI, PMID: 8159688); GO_0072661 (EC: IMP, PMID: 18768923)
has PubMed association: PMID: 379653; 492324; 1689849; 1833445; 2137557; 2141335; 2968981; 2970468; 2971657; 6449514; 7505012; 8125298; 8159688; 8227202; 8385102; 8640229; 8681137; 8703812; 9024692; 9235914; 9430667; 9519902; 9587054; 9628825; 9804856; 10893266; 10910934; 11222639; 11372755; 11427698; 12019270; 12130521; 12409278; 12444090; 12456646; 12477932; 12527750; 12543979; 12631729; 12719424; 15040428; 15051494; 15489334; 15929114; 16580865; 16597699; 16718373; 16762928; 16962094; 17128827; 17207965; 17520478; 17716929; 17720975; 18768923; 18987618; 20379614; 20479128; 20858683; 21071415; 21099109; 21177872; 21493712; 22348230; 22424883; 22456796; 22573887; 22968456; 23013433; 23457408
description: ankyrin 1, erythrocytic
database_cross_reference: Ensembl:ENSG00000029534
database_cross_reference: HGNC:492
database_cross_reference: HPRD:01693
database_cross_reference: MIM:612641
database_cross_reference: Vega:OTTHUMG00000150281
comment: Other designations: ANK-1|ankyrin-1|ankyrin-R|erythrocyte ankyrin
comment: This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: ANK1
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

TAGLN
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: SM22
alternative term: SMCC
alternative term: TAGLN1
alternative term: WS3-10
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: TAGLN
full name from nomenclature authority: transgelin
NCBI GeneID: 6876
gene map location: 11q23.2
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 11
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0003779 (EC: IEA); GO_0005515 (EC: IPI); GO_0005737 (EC: IEA); GO_0007517 (EC: TAS, PMID: 9615232); GO_0030855 (EC: IDA)
has PubMed association: PMID: 1520290; 1872880; 7788527; 8117285; 8125298; 9242426; 9276683; 9384215; 9615232; 11053353; 11773051; 12200029; 12477932; 12521938; 15489334; 16009940; 17082327; 17305610; 17353931; 17629319; 18245174; 18291675; 18378184; 18446369; 19011151; 19188659; 19329940; 19724680; 19796641; 19848416; 19913121; 20012321; 20066125; 20098441; 20336793; 20379614; 20540360; 20628086; 20705054; 20707403; 21044950; 21051832; 21092460; 21139048; 21677441; 21763649; 21943158; 22245152; 22257561; 22365974; 22939629; 23138394; 23174934; 23331552; 23538046; 23824909
description: transgelin
database_cross_reference: Ensembl:ENSG00000149591
database_cross_reference: HGNC:11553
database_cross_reference: HPRD:02891
database_cross_reference: MIM:600818
database_cross_reference: Vega:OTTHUMG00000167067
comment: Other designations: 22 kDa actin-binding protein|SM22-alpha|smooth muscle protein 22-alpha|transgelin variant 2
comment: This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: TAGLN
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

VGF
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: VGF
full name from nomenclature authority: VGF nerve growth factor inducible
NCBI GeneID: 7425
gene map location: 7q22.1
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 7
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0001541 (EC: IEA); GO_0002021 (EC: IEA); GO_0003674 (EC: ND); GO_0005184 (EC: IEA); GO_0005615 (EC: IDA, PMID: 15706611); GO_0006091 (EC: IEA); GO_0008083 (EC: IEA); GO_0009409 (EC: IEA); GO_0019953 (EC: IEA); GO_0030073 (EC: IEA); GO_0030133 (EC: IEA); GO_0031410 (EC: IDA, PMID: 17440014); GO_0032868 (EC: IEA); GO_0042593 (EC: IEA); GO_0042742 (EC: IEA); GO_0051591 (EC: IEP, PMID: 10381005)
has PubMed association: PMID: 8125298; 9084409; 9344675; 10381005; 12477932; 15706611; 16481598; 17440014; 17684500; 18432310; 19598235; 20164831; 20471433; 20631166; 21151573; 21621608; 22808091; 24244333; 24250222; 24457600
description: VGF nerve growth factor inducible
comment: Other designations: neuro-endocrine specific protein VGF|neurosecretory protein VGF
comment: This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: VGF
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

RGS5
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: MST092
alternative term: MST106
alternative term: MST129
alternative term: MSTP032
alternative term: MSTP092
alternative term: MSTP106
alternative term: MSTP129
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: RGS5
full name from nomenclature authority: regulator of G-protein signaling 5
NCBI GeneID: 8490
NCBI LocusTag: RP11-267N12.3
gene map location: 1q23.1
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 1
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0005096 (EC: IBA); GO_0005737 (EC: IDA); GO_0005886 (EC: IBA); GO_0007165 (EC: IEA); GO_0008277 (EC: TAS, PMID: 10471929); GO_0038032 (EC: IEA); GO_0043547 (EC: IBA); GO_0043547 (EC: TAS, PMID: 10471929)
has PubMed association: PMID: 9079700; 9747037; 10471929; 11009569; 11076863; 11230166; 11253162; 12477932; 14755443; 15342556; 15459006; 15489334; 15489336; 15670159; 16293795; 16344560; 16381901; 16710414; 17100651; 17220356; 17762159; 17939118; 18029348; 18262772; 18676680; 19170196; 19488044; 19536175; 19564336; 19625176; 19692168; 19863299; 20379614; 20453000; 20627871; 20643937; 21105200; 21278382; 21393447; 21780128; 21832049; 21881522; 22130514; 23464602; 23868206; 24009623; 24124411; 24297163
description: regulator of G-protein signaling 5
database_cross_reference: Ensembl:ENSG00000143248
database_cross_reference: Ensembl:ENSG00000232995
database_cross_reference: HGNC:10001
database_cross_reference: HPRD:04471
database_cross_reference: MIM:603276
database_cross_reference: Vega:OTTHUMG00000034441
comment: This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: RGS5
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

GABBR2
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: GABABR2
alternative term: GPR51
alternative term: GPRC3B
alternative term: HG20
alternative term: HRIHFB2099
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: GABBR2
full name from nomenclature authority: gamma-aminobutyric acid (GABA) B receptor, 2
NCBI GeneID: 9568
gene map location: 9q22.1-q22.3
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 9
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0004965 (EC: IDA, Qualifier: contributes_to, PMID: 9872316); GO_0005515 (EC: IPI, PMID: 16724110); GO_0005737 (EC: IEA); GO_0005886 (EC: TAS); GO_0005887 (EC: IDA, PMID: 9872316); GO_0007186 (EC: TAS, PMID: 9872316); GO_0007194 (EC: TAS, PMID: 10328880); GO_0007214 (EC: IDA, PMID: 9872316); GO_0007268 (EC: TAS); GO_0030054 (EC: IEA); GO_0038039 (EC: IPI, PMID: 9872316); GO_0043005 (EC: IEA); GO_0045211 (EC: IEA)
has PubMed association: PMID: 2834384; 7494864; 9872316; 9872317; 10075644; 10087195; 10328880; 10727622; 10773016; 11087824; 11850456; 11854302; 12477932; 14625043; 14961561; 14966130; 14978362; 15164053; 15489334; 15660124; 15822905; 16169070; 16724110; 16829628; 17145756; 17185339; 18482426; 18577758; 18978678; 19002745; 19086053; 19308021; 19336370; 19744961; 19763258; 20379614; 20424473; 20467438; 20557420; 20583170; 20634891; 20734064; 21303731; 21724853; 21971078; 22169202; 22613715; 22660477; 23726511; 23864651
description: gamma-aminobutyric acid (GABA) B receptor, 2
database_cross_reference: Ensembl:ENSG00000136928
database_cross_reference: HGNC:4507
database_cross_reference: HPRD:09552
database_cross_reference: MIM:607340
database_cross_reference: Vega:OTTHUMG00000020345
comment: Other designations: G protein-coupled receptor 51|G-protein coupled receptor 51|GABA-B receptor 2|GABA-B receptor, R2 subunit|GABA-B-R2|GABA-BR2|gamma-aminobutyric acid B receptor 2|gamma-aminobutyric acid type B receptor subunit 2|gb2
comment: This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: GABBR2
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

COL5A3
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: COL5A3
full name from nomenclature authority: collagen, type V, alpha 3
NCBI GeneID: 50509
gene map location: 19p13.2
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 19
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0005201 (EC: NAS, PMID: 10722718); GO_0005518 (EC: NAS, PMID: 10722718); GO_0005576 (EC: TAS); GO_0005588 (EC: NAS, PMID: 10722718); GO_0005788 (EC: TAS); GO_0007160 (EC: IEA); GO_0007411 (EC: TAS); GO_0008201 (EC: IEA); GO_0022617 (EC: TAS); GO_0030198 (EC: TAS); GO_0030199 (EC: NAS, PMID: 10722718); GO_0030574 (EC: TAS); GO_0043394 (EC: IEA); GO_0043588 (EC: NAS, PMID: 10722718)
has PubMed association: PMID: 1571108; 1916105; 6501291; 7115902; 7346227; 8535602; 9443080; 10722718; 11423559; 15136578; 15316020; 19012342
description: collagen, type V, alpha 3
comment: Other designations: collagen alpha-3(V) chain|pro-(alpha)3(V) collagen
comment: This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: COL5A3
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

NLRP2
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: iPSC marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: CLR19.9
alternative term: NALP2
alternative term: NBS1
alternative term: PAN1
alternative term: PYPAF2
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28117838
imported from: ogg.owl
symbol from nomenclature authority: NLRP2
full name from nomenclature authority: NLR family, pyrin domain containing 2
NCBI GeneID: 55655
NCBI LocusTag: XXbac-BPG230H20.8
gene map location: 19q13.42
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 19
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0005515 (EC: IPI, PMID: 15030775); GO_0005524 (EC: IEA); GO_0005737 (EC: IDA, PMID: 15030775); GO_0032090 (EC: IPI, PMID: 15030775); GO_0043280 (EC: IDA, PMID: 15030775); GO_0050718 (EC: IDA, PMID: 15030775)
has PubMed association: PMID: 8125298; 11250163; 11270363; 12019269; 12387869; 12477932; 12563287; 14702039; 15030775; 15456791; 15489334; 15817483; 16344560; 17046979; 17178784; 17420470; 17435760; 18056399; 18285453; 18369178; 18772453; 19074885; 19103770; 19300480; 19534089; 19900269; 20403135; 20800603; 21832049; 21906983; 21976665; 22909446; 23128233; 23360675; 23625868; 23644288
description: NLR family, pyrin domain containing 2
database_cross_reference: Ensembl:ENSG00000022556
database_cross_reference: HGNC:22948
database_cross_reference: HPRD:14805
database_cross_reference: MIM:609364
database_cross_reference: Vega:OTTHUMG00000167763
comment: Other designations: NACHT, LRR and PYD containing protein 2|NACHT, LRR and PYD domains-containing protein 2|NACHT, leucine rich repeat and PYD containing 2|PYRIN domain and NACHT domain-containing protein 1|PYRIN-containing APAF1-like protein 2|nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2|nucleotide-binding site protein 1
comment: This gene is upregulated at neural stem cell stage and at iPSC stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: NLRP2
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

PAG1
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: CBP
alternative term: PAG
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: PAG1
full name from nomenclature authority: phosphoprotein associated with glycosphingolipid microdomains 1
NCBI GeneID: 55824
gene map location: 8q21.13
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 8
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0005070 (EC: NAS, PMID: 10790433); GO_0005515 (EC: IPI, PMID: 10790433); GO_0005886 (EC: IDA, PMID: 10790433); GO_0005886 (EC: TAS); GO_0007165 (EC: TAS, PMID: 10790433); GO_0007173 (EC: TAS); GO_0009967 (EC: NAS, PMID: 10790433); GO_0016021 (EC: IEA); GO_0035556 (EC: IDA, PMID: 10790433); GO_0042169 (EC: IDA, PMID: 10790433); GO_0045121 (EC: IDA, PMID: 10790433); GO_0050852 (EC: TAS); GO_0050863 (EC: IDA, PMID: 10790433); GO_0050868 (EC: IEA)
has PubMed association: PMID: 9334312; 10790433; 11163757; 11684085; 12477932; 12665526; 14665621; 14702039; 15489334; 16160011; 16413409; 16636672; 16947079; 17143285; 17389760; 18056706; 18070987; 19581936; 19913121; 20379614; 20388373; 20561033; 20628086; 21092590; 21156787; 21388951; 21822266; 22027792; 22659621; 22994656; 23022100; 23671581
description: phosphoprotein associated with glycosphingolipid microdomains 1
database_cross_reference: Ensembl:ENSG00000076641
database_cross_reference: HGNC:30043
database_cross_reference: HPRD:05772
database_cross_reference: HPRD:16944
database_cross_reference: MIM:605767
database_cross_reference: Vega:OTTHUMG00000164592
comment: Other designations: Csk-binding protein|phosphoprotein associated with glycosphingolipid-enriched microdomains 1|transmembrane adapter protein PAG|transmembrane adaptor protein PAG|transmembrane phosphoprotein Cbp
comment: This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: PAG1
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

PPP1R14C
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: CPI17-like
alternative term: KEPI
alternative term: NY-BR-81
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: PPP1R14C
full name from nomenclature authority: protein phosphatase 1, regulatory (inhibitor) subunit 14C
NCBI GeneID: 81706
gene map location: 6q24.3-q25.3
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 6
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0004865 (EC: IEA); GO_0005737 (EC: IEA); GO_0016020 (EC: IEA); GO_0042325 (EC: IEA)
has PubMed association: PMID: 11564868; 11812771; 11948623; 12477932; 12747765; 14574404; 14702039; 15489334; 16449650; 19132087; 19475667; 20592344; 21946350; 22939629; 23284291
description: protein phosphatase 1, regulatory (inhibitor) subunit 14C
database_cross_reference: Ensembl:ENSG00000198729
database_cross_reference: HGNC:14952
database_cross_reference: HPRD:17890
database_cross_reference: MIM:613242
database_cross_reference: Vega:OTTHUMG00000015818
comment: Other designations: PKC-potentiated PP1 inhibitory protein|kinase C-enhanced PP1 inhibitor|kinase-enhanced PP1 inhibitor|protein phosphatase 1 regulatory subunit 14C|serologically defined breast cancer antigen NY-BR-81
comment: This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: PPP1R14C
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

CEACAM21
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: CEACAM3
alternative term: R29124_1
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: CEACAM21
full name from nomenclature authority: carcinoembryonic antigen-related cell adhesion molecule 21
NCBI GeneID: 90273
NCBI LocusTag: UNQ3098/PRO10075
gene map location: 19q13.2
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 19
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0016021 (EC: IEA)
has PubMed association: PMID: 12477932; 12975309; 14702039; 21682944; 23065704
description: carcinoembryonic antigen-related cell adhesion molecule 21
database_cross_reference: Ensembl:ENSG00000007129
database_cross_reference: HGNC:28834
database_cross_reference: HPRD:10179
database_cross_reference: Vega:OTTHUMG00000151062
comment: This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: CEACAM21
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

DNER
type: Class
subclass of: protein-coding gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: neural stem cell marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: UNQ26
alternative term: bet
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: DNER
full name from nomenclature authority: delta/notch-like EGF repeat containing
NCBI GeneID: 92737
NCBI LocusTag: UNQ262/PRO299
gene map location: 2q36.3
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 2
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0001764 (EC: NAS, PMID: 11950833); GO_0004888 (EC: TAS, PMID: 11950833); GO_0005112 (EC: IEA); GO_0005509 (EC: NAS, PMID: 11950833); GO_0005515 (EC: IPI, PMID: 11950833); GO_0005769 (EC: IDA, PMID: 11950833); GO_0005886 (EC: IDA, PMID: 11950833); GO_0006897 (EC: NAS, PMID: 11950833); GO_0007219 (EC: TAS); GO_0007220 (EC: IEA); GO_0007416 (EC: NAS, PMID: 11950833); GO_0007417 (EC: IEP, PMID: 11950833); GO_0010001 (EC: IEA); GO_0016021 (EC: IEA); GO_0030276 (EC: TAS, PMID: 11950833); GO_0030425 (EC: IDA, PMID: 11950833); GO_0043025 (EC: IEA); GO_0048741 (EC: IEA)
has PubMed association: PMID: 9847074; 11950833; 11997712; 12477932; 12975309; 15489334; 15815621; 16344560; 16740002; 20070733; 20237496; 20367751; 23284291; 23382691; 24101674
description: delta/notch-like EGF repeat containing
database_cross_reference: Ensembl:ENSG00000187957
database_cross_reference: HGNC:24456
database_cross_reference: HPRD:09531
database_cross_reference: MIM:607299
database_cross_reference: Vega:OTTHUMG00000153637
comment: Other designations: H_NH0150O02.1|WUGSC:H_NH0150O02.1|delta and Notch-like epidermal growth factor-related receptor|delta-notch-like EGF repeat-containing transmembrane
comment: This gene is upregulated at neural stem cell stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: DNER
annotated property: subClassOf
annotated target: protein-coding gene of Homo sapiens
is inferred: true

EEF1A1P16
type: Class
subclass of: pseudo gene of Homo sapiens
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: gene marker role
    intersection of: Restriction
      on property: realized in
      some values from: iPSC marker process
definition editor: Bin Zhao, Yue Liu, Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: EEF1A1P16
full name from nomenclature authority: eukaryotic translation elongation factor 1 alpha 1 pseudogene 16
NCBI GeneID: 387845
gene map location: 12p12.3
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 12
type of gene: pseudo
nomenclature status: Official from a nomenclature committee
description: eukaryotic translation elongation factor 1 alpha 1 pseudogene 16
comment: This gene is upregulated at iPSC stage. Ref: https://www.ncbi.nlm.nih.gov/pubmed/28117838

Axiom
annotated source: EEF1A1P16
annotated property: subClassOf
annotated target: pseudo gene of Homo sapiens
is inferred: true

OMB ethnic identity datum
type: Class
subclass of: ethnic identity datum
definition: An ethnic identity datum that is the output of an ethnic identification process that uses OMB terminology for ethnicity or terminology that is mapped the OMB ethnicity terms.
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: OMB ethnic identity datum
annotated property: subClassOf
annotated target: ethnic identity datum
is inferred: true

racial identity datum
type: Class
equivalent class: Class
  intersection of: identity datum
  intersection of: Restriction
    on property: part_of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: racial identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: identity datum
definition: A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
imported from: omrse.owl

Axiom
annotated source: racial identity datum
annotated property: subClassOf
annotated target: identity datum
is inferred: true

racial identification process
type: Class
subclass of: identification process
subclass of: Class
  intersection of: identification process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: part_of
      some values from: racial identity datum
imported from: omrse.owl

Axiom
annotated source: racial identification process
annotated property: subClassOf
annotated target: identification process
is inferred: true

ethnic identity datum
type: Class
equivalent class: Class
  intersection of: identity datum
  intersection of: Restriction
    on property: part_of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: ethnic identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: identity datum
definition: An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: ethnic identity datum
annotated property: subClassOf
annotated target: identity datum
is inferred: true

ethnic identification process
type: Class
subclass of: identification process
subclass of: Class
  intersection of: identification process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: part_of
      some values from: ethnic identity datum
imported from: omrse.owl

Axiom
annotated source: ethnic identification process
annotated property: subClassOf
annotated target: identification process
is inferred: true

hispanic or latino identity datum
type: Class
subclass of: OMB ethnic identity datum
definition: An OMB ethnic identity datum that indicates the person identified is of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: hispanic or latino identity datum
annotated property: subClassOf
annotated target: OMB ethnic identity datum
is inferred: true

not hispanic or latino identity datum
type: Class
subclass of: OMB ethnic identity datum
definition: An OMB ethnic identity datum that indicates the person identified is not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: not hispanic or latino identity datum
annotated property: subClassOf
annotated target: OMB ethnic identity datum
is inferred: true

identity datum
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: part_of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: information content entity
definition: An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method.
imported from: omrse.owl
creator: Amanda Hicks

Axiom
annotated source: identity datum
annotated property: subClassOf
annotated target: information content entity
is inferred: true

gender identity datum
type: Class
equivalent class: Class
  intersection of: identity datum
  intersection of: Restriction
    on property: part_of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: gender identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: identity datum
definition: A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method.
imported from: omrse.owl
creator: Amanda Hicks

Axiom
annotated source: gender identity datum
annotated property: subClassOf
annotated target: identity datum
is inferred: true

identification process
type: Class
subclass of: social act
subclass of: planned process
imported from: omrse.owl
creator: Amanda Hicks

Axiom
annotated source: identification process
annotated property: subClassOf
annotated target: social act
is inferred: true

Axiom
annotated source: identification process
annotated property: subClassOf
annotated target: planned process
is inferred: true

gender identification process
type: Class
subclass of: identification process
subclass of: Class
  intersection of: identification process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: part_of
      some values from: gender identity datum
imported from: omrse.owl

Axiom
annotated source: gender identification process
annotated property: subClassOf
annotated target: identification process
is inferred: true

female gender identity datum
type: Class
subclass of: gender identity datum
definition: a gender identity datum resulting from a gender identification process in which ‘female’ is selected based on the participant's subjective sense of gender
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: female gender identity datum
annotated property: subClassOf
annotated target: gender identity datum
is inferred: true

male gender identity datum
type: Class
subclass of: gender identity datum
definition: a gender identity datum resulting from a gender identification process in which ‘male’ is selected based on the participant's subjective sense of gender
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: male gender identity datum
annotated property: subClassOf
annotated target: gender identity datum
is inferred: true

American Indian or Alaska Native identity datum
type: Class
subclass of: OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: American Indian or Alaska Native identity datum
annotated property: subClassOf
annotated target: OMB racial identity datum
is inferred: true

Asian identity datum
type: Class
subclass of: OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: Asian identity datum
annotated property: subClassOf
annotated target: OMB racial identity datum
is inferred: true

black or African American identity datum
type: Class
subclass of: OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the black racial groups of Africa.
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: black or African American identity datum
annotated property: subClassOf
annotated target: OMB racial identity datum
is inferred: true

Native Hawaiian or other Pacific Islander identity datum
type: Class
subclass of: OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: Native Hawaiian or other Pacific Islander identity datum
annotated property: subClassOf
annotated target: OMB racial identity datum
is inferred: true

white identity datum
type: Class
subclass of: OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Europe, the Middle East, or North Africa.
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: white identity datum
annotated property: subClassOf
annotated target: OMB racial identity datum
is inferred: true

OMB racial identity datum
type: Class
subclass of: racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms.
definition editor: Amanda Hicks
imported from: omrse.owl

Axiom
annotated source: OMB racial identity datum
annotated property: subClassOf
annotated target: racial identity datum
is inferred: true

cell cutlture passage number
type: Class
subclass of: measurement datum
definition: A measurement datum that records how many times a cell culture has been subcultured.
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T21:47:04Z

Axiom
annotated source: cell cutlture passage number
annotated property: subClassOf
annotated target: measurement datum
is inferred: true

gene marker role
type: Class
subclass of: role

Axiom
annotated source: gene marker role
annotated property: subClassOf
annotated target: role
is inferred: true

stem cell marker process
type: Class
subclass of: biological_process

Axiom
annotated source: stem cell marker process
annotated property: subClassOf
annotated target: biological_process
is inferred: true

neural stem cell marker process
type: Class
subclass of: stem cell marker process

Axiom
annotated source: neural stem cell marker process
annotated property: subClassOf
annotated target: stem cell marker process
is inferred: true

iPSC marker process
type: Class
subclass of: stem cell marker process

Axiom
annotated source: iPSC marker process
annotated property: subClassOf
annotated target: stem cell marker process
is inferred: true

stem cell producer
type: Class
subclass of: organization
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:04:02Z

Axiom
annotated source: stem cell producer
annotated property: subClassOf
annotated target: organization
is inferred: true

stem cell provider
type: Class
subclass of: organization
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:05:33Z

Axiom
annotated source: stem cell provider
annotated property: subClassOf
annotated target: organization
is inferred: true

age of donor at time of donation
type: Class
subclass of: age measurement datum
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:44:27Z

Axiom
annotated source: age of donor at time of donation
annotated property: subClassOf
annotated target: age measurement datum
is inferred: true

cell line testing laboratory
type: Class
subclass of: organization
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T22:49:56Z

Axiom
annotated source: cell line testing laboratory
annotated property: subClassOf
annotated target: organization
is inferred: true

feeder cell role
type: Class
subclass of: role
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T23:01:40Z

Axiom
annotated source: feeder cell role
annotated property: subClassOf
annotated target: role
is inferred: true

feeder cell
type: Class
equivalent class: Class
  intersection of: cell type
  intersection of: Restriction
    on property: has role
    some values from: feeder cell role
subclass of: cell type
subclass of: cell
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T23:03:57Z

Axiom
annotated source: feeder cell
annotated property: subClassOf
annotated target: cell type
is inferred: true

Axiom
annotated source: feeder cell
annotated property: subClassOf
annotated target: cell
is inferred: true

feeder cell preparation protocol
type: Class
subclass of: protocol
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T23:05:48Z

Axiom
annotated source: feeder cell preparation protocol
annotated property: subClassOf
annotated target: protocol
is inferred: true

source cell storage/master cell banking protocol
type: Class
subclass of: protocol
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T23:08:01Z

Axiom
annotated source: source cell storage/master cell banking protocol
annotated property: subClassOf
annotated target: protocol
is inferred: true

source cell procurement protocol
type: Class
subclass of: protocol
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T23:09:23Z

Axiom
annotated source: source cell procurement protocol
annotated property: subClassOf
annotated target: protocol
is inferred: true

material transferring protocol
type: Class
subclass of: protocol
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T23:10:11Z

Axiom
annotated source: material transferring protocol
annotated property: subClassOf
annotated target: protocol
is inferred: true

cell passage protocol
type: Class
subclass of: protocol
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T23:10:35Z

Axiom
annotated source: cell passage protocol
annotated property: subClassOf
annotated target: protocol
is inferred: true

establishment protocol (molecular induction protocol)
type: Class
subclass of: protocol
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T23:11:25Z

Axiom
annotated source: establishment protocol (molecular induction protocol)
annotated property: subClassOf
annotated target: protocol
is inferred: true

cell culture protocol
type: Class
subclass of: protocol
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-05-31T23:12:12Z

Axiom
annotated source: cell culture protocol
annotated property: subClassOf
annotated target: protocol
is inferred: true

donor
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: donor
subclass of: organism
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-06-05T17:59:34Z

Axiom
annotated source: donor
annotated property: subClassOf
annotated target: organism
is inferred: true

TeSR
type: Class
subclass of: culture medium
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-06-05T19:08:22Z

Axiom
annotated source: TeSR
annotated property: subClassOf
annotated target: culture medium
is inferred: true

DMEM
type: Class
subclass of: culture medium
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-06-05T19:08:39Z

Axiom
annotated source: DMEM
annotated property: subClassOf
annotated target: culture medium
is inferred: true

F12
type: Class
subclass of: culture medium
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-06-05T19:08:58Z

Axiom
annotated source: F12
annotated property: subClassOf
annotated target: culture medium
is inferred: true

cell culture additive role
type: Class
subclass of: material to be added role
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-06-05T19:15:48Z

Axiom
annotated source: cell culture additive role
annotated property: subClassOf
annotated target: material to be added role
is inferred: true

cell culture medium additive
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: Restriction
    on property: has role
    some values from: cell culture additive role
subclass of: processed material
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-06-05T19:18:35Z

Axiom
annotated source: cell culture medium additive
annotated property: subClassOf
annotated target: processed material
is inferred: true

concentration measurment datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-06-05T19:24:37Z

Axiom
annotated source: concentration measurment datum
annotated property: subClassOf
annotated target: scalar measurement datum
is inferred: true

age
type: Class
subclass of: quality of a single physical entity
editor preferred label: age
definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.
imported from: obi.owl
imported from: pato.owl

Axiom
annotated source: age
annotated property: subClassOf
annotated target: quality of a single physical entity
is inferred: true

biological sex
type: Class
subclass of: organismal quality
editor preferred label: biological sex
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
alternative term: biological sex
alternative term: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sex
definition source: MO_680
definition source: NCIt:C28421
definition source: PATO:0000047
imported from: clo.owl
imported from: pato.owl
comment: An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
comment: Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.
comment: The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female.
label: sex
see also: EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000695

Axiom
annotated source: biological sex
annotated property: subClassOf
annotated target: organismal quality
is inferred: true

length
type: Class
subclass of: quality
editor preferred label: length
definition: A 1-D extent quality which is equal to the distance between two points.
imported from: obi.owl
imported from: pato.owl

Axiom
annotated source: length
annotated property: subClassOf
annotated target: quality
is inferred: true

mass
type: Class
subclass of: quality
editor preferred label: mass
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
imported from: obi.owl
imported from: pato.owl

Axiom
annotated source: mass
annotated property: subClassOf
annotated target: quality
is inferred: true

temperature
type: Class
subclass of: quality of a single physical entity
editor preferred label: temperature
definition: A physical quality of the thermal energy of a system.
imported from: obi.owl
imported from: pato.owl

Axiom
annotated source: temperature
annotated property: subClassOf
annotated target: quality of a single physical entity
is inferred: true

behavioral quality
type: Class
subclass of: quality of a single physical entity
editor preferred label: behavioral quality
definition: An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
imported from: obi.owl
imported from: pato.owl

Axiom
annotated source: behavioral quality
annotated property: subClassOf
annotated target: quality of a single physical entity
is inferred: true

male
type: Class
subclass of: biological sex
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
alternative term: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#male
definition source: CARO:0000027
definition source: MO_652
definition source: PATO:0000384
imported from: clo.owl
comment: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.

Axiom
annotated source: male
annotated property: subClassOf
annotated target: biological sex
is inferred: true

volume
type: Class
subclass of: quality of a single physical entity
editor preferred label: volume
definition: A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
imported from: obi.owl
imported from: pato.owl

Axiom
annotated source: volume
annotated property: subClassOf
annotated target: quality of a single physical entity
is inferred: true

quality of a single physical entity
type: Class
subclass of: quality
editor preferred label: quality of a single physical entity
definition: A physical object quality which inheres in a single-bearer.
imported from: obi.owl
imported from: pato.owl

Axiom
annotated source: quality of a single physical entity
annotated property: subClassOf
annotated target: quality
is inferred: true

physical object quality
type: Class
subclass of: quality
editor preferred label: physical object quality
imported from: cl.owl
imported from: clo.owl
imported from: pato.owl
imported from: uberon.owl

Axiom
annotated source: physical object quality
annotated property: subClassOf
annotated target: quality
is inferred: true

cellular quality
type: Class
subclass of: physical object quality
imported from: cl.owl
imported from: clo.owl

Axiom
annotated source: cellular quality
annotated property: subClassOf
annotated target: physical object quality
is inferred: true

cellular potency
type: Class
subclass of: cellular quality
editor preferred label: cellular potency
imported from: cl.owl
imported from: clo.owl
imported from: pato.owl

Axiom
annotated source: cellular potency
annotated property: subClassOf
annotated target: cellular quality
is inferred: true

unipotent
type: Class
subclass of: cellular potency
imported from: cl.owl

Axiom
annotated source: unipotent
annotated property: subClassOf
annotated target: cellular potency
is inferred: true

multipotent
type: Class
subclass of: cellular potency
editor preferred label: multipotent
imported from: cl.owl
imported from: clo.owl
imported from: pato.owl

Axiom
annotated source: multipotent
annotated property: subClassOf
annotated target: cellular potency
is inferred: true

pluripotent
type: Class
subclass of: cellular potency
editor preferred label: pluripotent
imported from: clo.owl
imported from: pato.owl

Axiom
annotated source: pluripotent
annotated property: subClassOf
annotated target: cellular potency
is inferred: true

organismal quality
type: Class
subclass of: physical object quality
editor preferred label: organismal quality
imported from: cl.owl
imported from: clo.owl
imported from: pato.owl

Axiom
annotated source: organismal quality
annotated property: subClassOf
annotated target: physical object quality
is inferred: true

handedness
type: Class
subclass of: behavioral quality
editor preferred label: handedness
definition: A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet.
imported from: obi.owl
imported from: pato.owl

Axiom
annotated source: handedness
annotated property: subClassOf
annotated target: behavioral quality
is inferred: true

left handedness
type: Class
subclass of: handedness
editor preferred label: left handedness
definition: Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
imported from: obi.owl
imported from: pato.owl

Axiom
annotated source: left handedness
annotated property: subClassOf
annotated target: handedness
is inferred: true

right handedness
type: Class
subclass of: handedness
editor preferred label: right handedness
definition: Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
imported from: obi.owl
imported from: pato.owl

Axiom
annotated source: right handedness
annotated property: subClassOf
annotated target: handedness
is inferred: true

ambidextrous handedness
type: Class
subclass of: handedness
editor preferred label: ambidextrous handedness
definition: Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot.
imported from: obi.owl
imported from: pato.owl

Axiom
annotated source: ambidextrous handedness
annotated property: subClassOf
annotated target: handedness
is inferred: true

protein
type: Class
subclass of: amino acid chain
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
imported from: cl.owl
imported from: clo.owl
imported from: pr.owl
imported from: uberon.owl

Axiom
annotated source: protein
annotated property: subClassOf
annotated target: amino acid chain
is inferred: true

CD19 molecule
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction.
imported from: cl.owl
has exact synonym: B-lymphocyte surface antigen B4
has exact synonym: CD19
has exact synonym: T-cell surface antigen Leu-12
has exact synonym: differentiation antigen CD19

Axiom
annotated source: CD19 molecule
annotated property: subClassOf
annotated target: protein
is inferred: true

CD34 molecule
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved.
imported from: cl.owl
imported from: clo.owl
has exact synonym: CD34
has exact synonym: hematopoietic progenitor cell antigen CD34

Axiom
annotated source: CD34 molecule
annotated property: subClassOf
annotated target: protein
is inferred: true

CD4 molecule
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence.
imported from: cl.owl
has exact synonym: CD4
has exact synonym: T-cell differentiation antigen L3T4
has exact synonym: T-cell surface antigen T4/Leu-3
has exact synonym: T-cell surface glycoprotein CD4

Axiom
annotated source: CD4 molecule
annotated property: subClassOf
annotated target: protein
is inferred: true

integrin alpha with A domain
type: Class
subclass of: integrin alpha
definition: An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage.
imported from: cl.owl
has exact synonym: integrin alpha with I domain

Axiom
annotated source: integrin alpha with A domain
annotated property: subClassOf
annotated target: integrin alpha
is inferred: true

receptor-type tyrosine-protein phosphatase C
type: Class
subclass of: protein
definition: A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule.
imported from: cl.owl
imported from: clo.owl
has_broad_synonym: T200
has exact synonym: CD45
has exact synonym: L-CA
has exact synonym: PTPRC
has exact synonym: leukocyte common antigen
has exact synonym: ly-5
has exact synonym: lymphocyte antigen 5

Axiom
annotated source: receptor-type tyrosine-protein phosphatase C
annotated property: subClassOf
annotated target: protein
is inferred: true

integrin alpha-M
type: Class
subclass of: integrin alpha with A domain
definition: An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1.
imported from: cl.owl
has exact synonym: CD11 antigen-like family member B
has exact synonym: CD11b
has exact synonym: CR-3 alpha chain
has exact synonym: ITGAM
has exact synonym: cell surface glycoprotein MAC-1 subunit alpha
has exact synonym: leukocyte adhesion receptor MO1
has exact synonym: neutrophil adherence receptor
has_related_synonym: CR3A

Axiom
annotated source: integrin alpha-M
annotated property: subClassOf
annotated target: integrin alpha with A domain
is inferred: true

receptor-type tyrosine-protein phosphatase C isoform CD45R
type: Class
subclass of: receptor-type tyrosine-protein phosphatase C
definition: A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that includes the region encoded by the variable exons 4(A), 5(B), and 6(C). Example: UniProtKB:P08575-1.
imported from: cl.owl
has exact synonym: CD45R
has exact synonym: CD45RABC
has exact synonym: PTPRC/iso:CD45R
has_related_synonym: B220

Axiom
annotated source: receptor-type tyrosine-protein phosphatase C isoform CD45R
annotated property: subClassOf
annotated target: receptor-type tyrosine-protein phosphatase C
is inferred: true

CD3 subunit with immunoglobulin domain
type: Class
subclass of: protein
definition: A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.
imported from: cl.owl
has exact synonym: CD3 subunit with Ig-like domain

Axiom
annotated source: CD3 subunit with immunoglobulin domain
annotated property: subClassOf
annotated target: protein
is inferred: true

CD3 epsilon
type: Class
subclass of: CD3 subunit with immunoglobulin domain
definition: A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD3E
has exact synonym: CD3e
has exact synonym: T-cell surface antigen T3/Leu-4 epsilon chain
has_related_synonym: T3E

Axiom
annotated source: CD3 epsilon
annotated property: subClassOf
annotated target: CD3 subunit with immunoglobulin domain
is inferred: true

neural cell adhesion molecule
type: Class
subclass of: protein
definition: A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain.
imported from: cl.owl

Axiom
annotated source: neural cell adhesion molecule
annotated property: subClassOf
annotated target: protein
is inferred: true

neural cell adhesion molecule NCAM
type: Class
subclass of: neural cell adhesion molecule
definition: A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration.
imported from: cl.owl

Axiom
annotated source: neural cell adhesion molecule NCAM
annotated property: subClassOf
annotated target: neural cell adhesion molecule
is inferred: true

neural cell adhesion molecule 1
type: Class
subclass of: neural cell adhesion molecule NCAM
definition: A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD56
has exact synonym: N-CAM-1
has exact synonym: NCAM-1
has exact synonym: NCAM1
has_related_synonym: NCAM

Axiom
annotated source: neural cell adhesion molecule 1
annotated property: subClassOf
annotated target: neural cell adhesion molecule NCAM
is inferred: true

CD2 molecule
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD2
has exact synonym: LFA-2
has exact synonym: LFA-3 receptor
has exact synonym: T-cell surface antigen CD2
has exact synonym: T-cell surface antigen T11/Leu-5
has exact synonym: T-cell surface glycoprotein CD2
has exact synonym: erythrocyte receptor
has exact synonym: ly-37
has exact synonym: lymphocyte antigen 37
has exact synonym: rosette receptor
has_related_synonym: SRBC

Axiom
annotated source: CD2 molecule
annotated property: subClassOf
annotated target: protein
is inferred: true

T-cell surface glycoprotein CD8 alpha chain
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain.
imported from: cl.owl
has exact synonym: CD8A
has exact synonym: CD8a
has exact synonym: T-cell surface glycoprotein Lyt-2
has exact synonym: T-lymphocyte differentiation antigen T8/Leu-2
has_related_synonym: Lyt-2
has_related_synonym: Lyt2
has_related_synonym: MAL

Axiom
annotated source: T-cell surface glycoprotein CD8 alpha chain
annotated property: subClassOf
annotated target: protein
is inferred: true

ADP-ribosyl cyclase
type: Class
subclass of: protein
definition: A protein that contains the ADP-ribosyl cyclase domain (Pfam:PF02267).
imported from: cl.owl

Axiom
annotated source: ADP-ribosyl cyclase
annotated property: subClassOf
annotated target: protein
is inferred: true

membrane-spanning 4-domains subfamily A member 1
type: Class
subclass of: protein
definition: A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: B-cell differentiation antigen Ly-44
has exact synonym: B-cell surface antigen CD20
has exact synonym: B-lymphocyte antigen CD20
has exact synonym: B-lymphocyte surface antigen B1
has exact synonym: Bp35
has exact synonym: CD20
has exact synonym: MS4A1
has exact synonym: leukocyte surface antigen Leu-16
has exact synonym: lymphocyte antigen 44
has_related_synonym: Ly-44
has_related_synonym: Ms4a2

Axiom
annotated source: membrane-spanning 4-domains subfamily A member 1
annotated property: subClassOf
annotated target: protein
is inferred: true

CD44 molecule
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD44
has exact synonym: CD44 antigen
has exact synonym: CDw44
has exact synonym: ECMR-III
has exact synonym: GP90 lymphocyte homing/adhesion receptor
has exact synonym: HUTCH-I
has exact synonym: PGP-1
has exact synonym: epican
has exact synonym: extracellular matrix receptor III
has exact synonym: heparan sulfate proteoglycan
has exact synonym: hermes antigen
has exact synonym: hyaluronate receptor
has exact synonym: ly-24
has exact synonym: lymphocyte antigen 24
has exact synonym: phagocytic glycoprotein 1
has exact synonym: phagocytic glycoprotein I
has_related_synonym: LHR
has_related_synonym: MDU2
has_related_synonym: MDU3
has_related_synonym: MIC4
has_related_synonym: PGP-I

Axiom
annotated source: CD44 molecule
annotated property: subClassOf
annotated target: protein
is inferred: true

CD48 molecule
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD48 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: B-lymphocyte activation marker BLAST-1
has exact synonym: BCM1 surface antigen
has exact synonym: BLAST-1
has exact synonym: CD48
has exact synonym: CD48 antigen
has exact synonym: HM48-1
has exact synonym: MRC OX-45 surface antigen
has exact synonym: TCT.1
has exact synonym: leukocyte antigen MEM-102
has exact synonym: sgp-60
has_related_synonym: BCM1
has_related_synonym: BLAST1
has_related_synonym: Bcm-1

Axiom
annotated source: CD48 molecule
annotated property: subClassOf
annotated target: protein
is inferred: true

cadherin
type: Class
subclass of: protein
definition: A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues.
imported from: cl.owl

Axiom
annotated source: cadherin
annotated property: subClassOf
annotated target: protein
is inferred: true

endoglin
type: Class
subclass of: protein
definition: A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof.
imported from: cl.owl
imported from: clo.owl
has exact synonym: CD105
has exact synonym: ENG
has exact synonym: cell surface MJ7/18 antigen
has_related_synonym: END
has_related_synonym: Edg

Axiom
annotated source: endoglin
annotated property: subClassOf
annotated target: protein
is inferred: true

immunoglobulin gamma Fc receptor II/III/IV
type: Class
subclass of: protein
definition: A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III.
imported from: cl.owl

Axiom
annotated source: immunoglobulin gamma Fc receptor II/III/IV
annotated property: subClassOf
annotated target: protein
is inferred: true

ADP-ribosyl cyclase 1
type: Class
subclass of: ADP-ribosyl cyclase
definition: An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD38
has exact synonym: I-19
has exact synonym: NIM-R5 antigen
has exact synonym: T10
has exact synonym: cADPr hydrolase 1
has exact synonym: cyclic ADP-ribose hydrolase 1

Axiom
annotated source: ADP-ribosyl cyclase 1
annotated property: subClassOf
annotated target: ADP-ribosyl cyclase
is inferred: true

cadherin-5
type: Class
subclass of: cadherin
definition: A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: 7B4 antigen
has exact synonym: CD144
has exact synonym: CDH5
has exact synonym: VE-cadherin
has exact synonym: vascular endothelial cadherin

Axiom
annotated source: cadherin-5
annotated property: subClassOf
annotated target: cadherin
is inferred: true

low affinity immunoglobulin gamma Fc region receptor III
type: Class
subclass of: immunoglobulin gamma Fc receptor II/III/IV
definition: An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD16
has exact synonym: Fc-gamma RIII
has exact synonym: FcRIII
has exact synonym: Fcgr3
has exact synonym: IgG Fc receptor III

Axiom
annotated source: low affinity immunoglobulin gamma Fc region receptor III
annotated property: subClassOf
annotated target: immunoglobulin gamma Fc receptor II/III/IV
is inferred: true

prominin
type: Class
subclass of: protein
definition: A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain.
imported from: cl.owl

Axiom
annotated source: prominin
annotated property: subClassOf
annotated target: protein
is inferred: true

prominin-1
type: Class
subclass of: prominin
definition: A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD133
has exact synonym: PROM1
has exact synonym: antigen AC133
has exact synonym: antigen AC133 homolog
has exact synonym: prominin-like protein 1
has_related_synonym: PROML1
has_related_synonym: Prom

Axiom
annotated source: prominin-1
annotated property: subClassOf
annotated target: prominin
is inferred: true

5'-nucleotidase
type: Class
subclass of: protein
definition: A protein that is a translation product of the human NT5E gene or a 1:1 ortholog thereof.
imported from: cl.owl
imported from: clo.owl
has exact synonym: 5'-NT
has exact synonym: CD73
has exact synonym: NT5E
has exact synonym: ecto-5'-nucleotidase
has_related_synonym: NT5
has_related_synonym: NTE

Axiom
annotated source: 5'-nucleotidase
annotated property: subClassOf
annotated target: protein
is inferred: true

CD59-like glycoprotein
type: Class
subclass of: protein
definition: A protein that is a translation product of the CD59 or closely related gene. This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (Pfam:PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues.
imported from: cl.owl

Axiom
annotated source: CD59-like glycoprotein
annotated property: subClassOf
annotated target: protein
is inferred: true

CSF-1/PDGF receptor-type tyrosine-protein kinase
type: Class
subclass of: protein
definition: A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (Pfam:PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. Pfam:PF00047 is most common, but other members of the Ig domain clan, Pfam:PF07679 and Pfam:PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines.
imported from: cl.owl

Axiom
annotated source: CSF-1/PDGF receptor-type tyrosine-protein kinase
annotated property: subClassOf
annotated target: protein
is inferred: true

SLAM family member 1
type: Class
subclass of: protein
definition: A protein that is a translation product of the human SLAMF1 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD150
has exact synonym: CDw150
has exact synonym: IPO-3
has exact synonym: SLAMF1
has_related_synonym: SLAM

Axiom
annotated source: SLAM family member 1
annotated property: subClassOf
annotated target: protein
is inferred: true

T-cell surface glycoprotein CD5
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD5
has exact synonym: Lyt-1
has exact synonym: ly-1
has exact synonym: lymphocyte antigen 1
has exact synonym: lymphocyte antigen T1/Leu-1
has_related_synonym: LEU1

Axiom
annotated source: T-cell surface glycoprotein CD5
annotated property: subClassOf
annotated target: protein
is inferred: true

Thy-1 membrane glycoprotein
type: Class
subclass of: protein
definition: A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof.
imported from: cl.owl
imported from: clo.owl
has exact synonym: CD90
has exact synonym: CDw90
has exact synonym: THY1
has exact synonym: Thy-1 antigen
has_related_synonym: Thy-1

Axiom
annotated source: Thy-1 membrane glycoprotein
annotated property: subClassOf
annotated target: protein
is inferred: true

interleukin-7 receptor subunit alpha
type: Class
subclass of: protein
definition: A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD127
has exact synonym: CDw127
has exact synonym: IL-7 receptor subunit alpha
has exact synonym: IL-7R subunit alpha
has exact synonym: IL-7R-alpha
has exact synonym: IL-7RA
has exact synonym: IL7R

Axiom
annotated source: interleukin-7 receptor subunit alpha
annotated property: subClassOf
annotated target: protein
is inferred: true

KLRB1-like protein
type: Class
subclass of: protein
definition: A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat.
imported from: cl.owl

Axiom
annotated source: KLRB1-like protein
annotated property: subClassOf
annotated target: protein
is inferred: true

CD14 molecule
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD14
has exact synonym: monocyte differentiation antigen CD14
has exact synonym: myeloid cell-specific leucine-rich glycoprotein

Axiom
annotated source: CD14 molecule
annotated property: subClassOf
annotated target: protein
is inferred: true

CD33 molecule
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD33
has exact synonym: gp67
has exact synonym: myeloid cell surface antigen CD33
has exact synonym: sialic acid-binding Ig-like lectin 3
has exact synonym: siglec-3
has_related_synonym: SIGLEC3

Axiom
annotated source: CD33 molecule
annotated property: subClassOf
annotated target: protein
is inferred: true

natural killer cell receptor 2B4
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD244 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD244
has exact synonym: NAIL
has exact synonym: NK cell activation-inducing ligand
has exact synonym: NK cell type I receptor protein 2B4
has exact synonym: NKR2B4
has exact synonym: non-MHC restricted killing associated
has_related_synonym: 2B4
has_related_synonym: Nmrk

Axiom
annotated source: natural killer cell receptor 2B4
annotated property: subClassOf
annotated target: protein
is inferred: true

signal transducer CD24
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD24
has exact synonym: HSA
has exact synonym: M1/69-J11D heat stable antigen
has exact synonym: R13-Ag
has exact synonym: X62 heat stable antigen
has exact synonym: ly-52
has exact synonym: lymphocyte antigen 52
has exact synonym: nectadrin
has exact synonym: small cell lung carcinoma cluster 4 antigen
has_related_synonym: CD24A

Axiom
annotated source: signal transducer CD24
annotated property: subClassOf
annotated target: protein
is inferred: true

thrombomodulin-like receptor
type: Class
subclass of: protein
definition: A protein with core architecture consisting of a signal sequence, a Lectin C-type domain (Pfam:PF00059), 5 or 6 EGF-like domains (Pfam:PF00008, Pfam:PF09064, or Pfam:PF07645), a transmembrane region, and a small cytoplasmic region (36-51 amino acids).
imported from: cl.owl

Axiom
annotated source: thrombomodulin-like receptor
annotated property: subClassOf
annotated target: protein
is inferred: true

transferrin receptor protein 1
type: Class
subclass of: protein
definition: A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof.
imported from: cl.owl
has_broad_synonym: p90
has exact synonym: CD71
has exact synonym: T9
has exact synonym: TFRC
has exact synonym: TfR
has exact synonym: TfR1
has exact synonym: Trfr
has_related_synonym: TR

Axiom
annotated source: transferrin receptor protein 1
annotated property: subClassOf
annotated target: protein
is inferred: true

vascular endothelial growth factor receptor
type: Class
subclass of: protein
definition: A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain.
imported from: cl.owl

Axiom
annotated source: vascular endothelial growth factor receptor
annotated property: subClassOf
annotated target: protein
is inferred: true

receptor-type tyrosine-protein kinase FLT3
type: Class
subclass of: CSF-1/PDGF receptor-type tyrosine-protein kinase
definition: A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human FLT3 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD135
has exact synonym: FLK-2
has exact synonym: FLT-3
has exact synonym: FLT3
has exact synonym: Fms-like tyrosine kinase 3
has exact synonym: fetal liver kinase 2
has exact synonym: stem cell tyrosine kinase 1
has exact synonym: tyrosine-protein kinase FLT3
has exact synonym: tyrosine-protein kinase receptor FLT3
has exact synonym: tyrosine-protein kinase receptor flk-2
has_related_synonym: STK-1
has_related_synonym: STK1

Axiom
annotated source: receptor-type tyrosine-protein kinase FLT3
annotated property: subClassOf
annotated target: CSF-1/PDGF receptor-type tyrosine-protein kinase
is inferred: true

complement component C1q receptor
type: Class
subclass of: thrombomodulin-like receptor
definition: A thrombomodulin-like receptor that is a translation product of the human CD93 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: C1q/MBL/SPA receptor
has exact synonym: C1qR
has exact synonym: C1qR(p)
has exact synonym: C1qRp
has exact synonym: CD93
has exact synonym: CDw93
has exact synonym: cell surface antigen AA4
has exact synonym: complement component 1 q subcomponent receptor 1
has exact synonym: ly-68
has exact synonym: lymphocyte antigen 68
has exact synonym: matrix-remodeling-associated protein 4
has_related_synonym: Aa4
has_related_synonym: C1QR1
has_related_synonym: Ly68
has_related_synonym: MXRA4

Axiom
annotated source: complement component C1q receptor
annotated property: subClassOf
annotated target: thrombomodulin-like receptor
is inferred: true

mast/stem cell growth factor receptor
type: Class
subclass of: CSF-1/PDGF receptor-type tyrosine-protein kinase
definition: A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD117
has exact synonym: KIT
has exact synonym: SCFR
has exact synonym: proto-oncogene c-Kit
has exact synonym: tyrosine-protein kinase Kit
has_related_synonym: Sl

Axiom
annotated source: mast/stem cell growth factor receptor
annotated property: subClassOf
annotated target: CSF-1/PDGF receptor-type tyrosine-protein kinase
is inferred: true

vascular endothelial growth factor receptor 2
type: Class
subclass of: vascular endothelial growth factor receptor
definition: A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD309
has exact synonym: FLK-1
has exact synonym: KDR
has exact synonym: VEGFR-2
has exact synonym: fetal liver kinase 1
has exact synonym: kinase NYK
has exact synonym: kinase insert domain receptor
has exact synonym: protein-tyrosine kinase receptor flk-1
has_related_synonym: FLK1

Axiom
annotated source: vascular endothelial growth factor receptor 2
annotated property: subClassOf
annotated target: vascular endothelial growth factor receptor
is inferred: true

ly-6-like protein
type: Class
subclass of: protein
definition: A protein that is the translation product of any of the LY6 genes (LY6A-LY6I).
imported from: cl.owl

Axiom
annotated source: ly-6-like protein
annotated property: subClassOf
annotated target: protein
is inferred: true

killer cell lectin-like receptor subfamily B member 1C
type: Class
subclass of: KLRB1-like protein
definition: A KLRB1-like protein that is a translation product of the mouse Klrb1c gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: CD161 antigen-like family member C
has exact synonym: CD161c
has exact synonym: Klrb1c
has exact synonym: NK1.1
has exact synonym: NKR-P1 40
has exact synonym: NKR-P1.9
has exact synonym: NKR-P1C
has exact synonym: ly-55c
has exact synonym: lymphocyte antigen 55c
has exact synonym: natural killer cell surface protein P1-40
has_related_synonym: Ly55c
has_related_synonym: Nkrp1c

Axiom
annotated source: killer cell lectin-like receptor subfamily B member 1C
annotated property: subClassOf
annotated target: KLRB1-like protein
is inferred: true

lymphocyte antigen 6G
type: Class
subclass of: ly-6-like protein
definition: A ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: Ly6g
has exact synonym: ly-6G
has exact synonym: ly-6G.1

Axiom
annotated source: lymphocyte antigen 6G
annotated property: subClassOf
annotated target: ly-6-like protein
is inferred: true

lymphocyte antigen 6A-2/6E-1
type: Class
subclass of: ly-6-like protein
definition: A ly-6-like protein that is a translation product of the mouse Ly6a gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: Ly6a
has exact synonym: T-cell-activating protein
has exact synonym: ly-6A.2/Ly-6E.1
has exact synonym: stem cell antigen 1
has_related_synonym: Ly6
has_related_synonym: SCA-1
has_related_synonym: TAP

Axiom
annotated source: lymphocyte antigen 6A-2/6E-1
annotated property: subClassOf
annotated target: ly-6-like protein
is inferred: true

lymphocyte antigen 76
type: Class
subclass of: protein
definition: A protein that is a translation product of the mouse Ly76 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: Ly76
has exact synonym: ter-119
has exact synonym: ter119

Axiom
annotated source: lymphocyte antigen 76
annotated property: subClassOf
annotated target: protein
is inferred: true

T-cell acute lymphocytic leukemia protein 1
type: Class
subclass of: protein
definition: A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof.
imported from: cl.owl
has exact synonym: T-cell leukemia/lymphoma protein 5
has exact synonym: TAL-1
has exact synonym: TAL1
has exact synonym: bHLHa17
has exact synonym: class A basic helix-loop-helix protein 17
has exact synonym: stem cell protein
has_related_synonym: SCL
has_related_synonym: TCL5

Axiom
annotated source: T-cell acute lymphocytic leukemia protein 1
annotated property: subClassOf
annotated target: protein
is inferred: true

amino acid chain
type: Class
subclass of: material entity
definition: An organic amino compound that is a polymer of amino acid chain components (unmodified amino-acid residues and/or modified amino-acid residues linked by peptide bonds or derivatives of such bonds.
imported from: cl.owl
imported from: clo.owl
has_narrow_synonym: peptide
has_narrow_synonym: polypeptide

Axiom
annotated source: amino acid chain
annotated property: subClassOf
annotated target: material entity
is inferred: true

integrin alpha
type: Class
subclass of: protein
definition: A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif.
imported from: cl.owl

Axiom
annotated source: integrin alpha
annotated property: subClassOf
annotated target: protein
is inferred: true

region
type: Class
subclass of: generically dependent continuant
editor preferred label: region
definition: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
alternative term: primary structure of sequence macromolecule
alternative term: sequence
imported from: obi.owl
imported from: so.owl

Axiom
annotated source: region
annotated property: subClassOf
annotated target: generically dependent continuant
is inferred: true

supercontig
type: Class
subclass of: sequence_assembly
editor preferred label: supercontig
definition: One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
imported from: obi.owl
imported from: so.owl

Axiom
annotated source: supercontig
annotated property: subClassOf
annotated target: sequence_assembly
is inferred: true

contig
type: Class
subclass of: sequence_assembly
editor preferred label: contig
definition: A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
imported from: obi.owl
imported from: so.owl

Axiom
annotated source: contig
annotated property: subClassOf
annotated target: sequence_assembly
is inferred: true

sequence_assembly
type: Class
subclass of: assembly
editor preferred label: sequence_assembly
definition: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
imported from: obi.owl
imported from: so.owl

Axiom
annotated source: sequence_assembly
annotated property: subClassOf
annotated target: assembly
is inferred: true

assembly
type: Class
subclass of: region
editor preferred label: assembly
definition: A region of the genome of known length that is composed by ordering and aligning two or more different regions.
imported from: obi.owl
imported from: so.owl

Axiom
annotated source: assembly
annotated property: subClassOf
annotated target: region
is inferred: true

zone of skin
type: Class
subclass of: ectoderm-derived structure
subclass of: UBERON_0034944
subclass of: Restriction
  on property: part_of
  some values from: skin of body
subclass of: Restriction
  on property: has part
  some values from: skin epidermis
subclass of: Restriction
  on property: has part
  some values from: dermis
definition: Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
imported from: cl.owl
has exact synonym: portion of skin
has exact synonym: region of skin
has exact synonym: skin
has exact synonym: skin region
has exact synonym: skin zone

Axiom
annotated source: zone of skin
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

Axiom
annotated source: zone of skin
annotated property: subClassOf
annotated target: UBERON_0034944
is inferred: true

tube
type: Class
subclass of: anatomical conduit
subclass of: Restriction
  on property: has part
  some values from: subdivision of tube
definition: Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
imported from: cl.owl
has exact synonym: anatomical tube
has_narrow_synonym: duct

Axiom
annotated source: tube
annotated property: subClassOf
annotated target: anatomical conduit
is inferred: true

appendage
type: Class
subclass of: organism subdivision
definition: Major subdivision of an organism that protrudes from the body[DOS, CARO].
imported from: cl.owl
has_related_synonym: appendages
has_related_synonym: extremitaet
has_related_synonym: extremity
has_related_synonym: limbs/digits/tail

Axiom
annotated source: appendage
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

lamina propria
type: Class
subclass of: organ component layer
subclass of: Restriction
  on property: part_of
  some values from: mucosa
subclass of: Restriction
  on property: has part
  some values from: loose connective tissue
definition: A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions.
imported from: cl.owl
has exact synonym: lamina propria mucosa
has exact synonym: lamina propria mucosae
has_related_synonym: tunica propria

Axiom
annotated source: lamina propria
annotated property: subClassOf
annotated target: organ component layer
is inferred: true

head
type: Class
subclass of: subdivision of organism along main body axis
subclass of: Restriction
  on property: part_of
  some values from: craniocervical region
definition: The head is the anterior-most division of the body [GO].
imported from: cl.owl
has exact synonym: head (volume)
has_narrow_synonym: adult head
has_related_synonym: cephalic area

Axiom
annotated source: head
annotated property: subClassOf
annotated target: subdivision of organism along main body axis
is inferred: true

vessel
type: Class
subclass of: anatomical conduit
definition: A tubular structure that contains, conveys body fluid, such as blood or lymph.
imported from: cl.owl

Axiom
annotated source: vessel
annotated property: subClassOf
annotated target: anatomical conduit
is inferred: true

duct
type: Class
subclass of: organ subunit
subclass of: Restriction
  on property: has part
  some values from: UBERON_0034969
definition: A tubular structure that transports secreted or excreted substances.
imported from: cl.owl
has exact synonym: anatomical duct
has_narrow_synonym: exocrine duct
has_narrow_synonym: exocrine gland duct
has_related_synonym: ducts

Axiom
annotated source: duct
annotated property: subClassOf
annotated target: organ subunit
is inferred: true

anatomical wall
type: Class
subclass of: organ part
subclass of: Restriction
  on property: has part
  some values from: organ component layer
definition: Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
imported from: cl.owl
has_broad_synonym: wall
has exact synonym: wall of organ
has_related_synonym: organ wall

Axiom
annotated source: anatomical wall
annotated property: subClassOf
annotated target: organ part
is inferred: true

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
has db xref: AnatomicalStructure
has db xref: http://www.snomedbrowser.com/Codes/Details/362889002
has db xref: AAO:0010825
has db xref: AEO:0000003
has db xref: BILA:0000003
has db xref: CARO:0000003
has db xref: EHDAA2:0003003
has db xref: EMAPA:0
has db xref: FBbt:00007001
has db xref: FMA:305751
has db xref: FMA:67135
has db xref: GAID:781
has db xref: HAO:0000003
has db xref: MA:0003000
has db xref: MESH:D000825
has db xref: TAO:0000037
has db xref: TGMA:0001823
has db xref: VHOG:0001759
has db xref: WBbt:0000100
has db xref: XAO:0003000
has db xref: ZFA:0000037
has exact synonym: biological structure
has exact synonym: connected biological structure
has OBO namespace: uberon
id: UBERON:0000061
in subset: upper level

Axiom
annotated source: anatomical structure
annotated property: subClassOf
annotated target: material anatomical entity
is inferred: true

organ
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: anatomical system
definition: Anatomical structure that performs a specific function or group of functions [WP].
imported from: cl.owl
has_related_synonym: anatomical unit
has_related_synonym: body organ
has_related_synonym: element

Axiom
annotated source: organ
annotated property: subClassOf
annotated target: multicellular anatomical structure
is inferred: true

organ subunit
type: Class
subclass of: organ part
definition: A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
imported from: cl.owl
has_related_synonym: organ region with fixed fiat boundary
has_related_synonym: organ segment
has_related_synonym: segment of organ

Axiom
annotated source: organ subunit
annotated property: subClassOf
annotated target: organ part
is inferred: true

organ part
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: organ
definition: A multicellular structure that is a part of an organ.
imported from: cl.owl
has exact synonym: cardinal organ part
has_related_synonym: regional part of organ

Axiom
annotated source: organ part
annotated property: subClassOf
annotated target: multicellular anatomical structure
is inferred: true

respiratory tract
type: Class
subclass of: respiratory airway
subclass of: endoderm-derived structure
subclass of: Restriction
  on property: develops from
  some values from: presumptive gut
subclass of: Restriction
  on property: develops from
  some values from: respiratory primordium
definition: Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts
imported from: cl.owl

Axiom
annotated source: respiratory tract
annotated property: subClassOf
annotated target: respiratory airway
is inferred: true

Axiom
annotated source: respiratory tract
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

proximo-distal subdivision of respiratory tract
type: Class
equivalent class: Class
  intersection of: subdivision of tube
  intersection of: Restriction
    on property: part_of
    some values from: respiratory tract
subclass of: endoderm-derived structure
subclass of: subdivision of tube
subclass of: Restriction
  on property: part_of
  some values from: respiratory tract
definition: An section of a respiratory tract.
imported from: cl.owl
has_related_synonym: respiratory tract
has_related_synonym: subdivision of respiratory tract

Axiom
annotated source: proximo-distal subdivision of respiratory tract
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

Axiom
annotated source: proximo-distal subdivision of respiratory tract
annotated property: subClassOf
annotated target: subdivision of tube
is inferred: true

regional part of nervous system
type: Class
equivalent class: Class
  intersection of: multi-tissue structure
  intersection of: Restriction
    on property: part_of
    some values from: nervous system
subclass of: multi-tissue structure
subclass of: Restriction
  on property: part_of
  some values from: nervous system
definition: Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
imported from: cl.owl
has exact synonym: part of nervous system

Axiom
annotated source: regional part of nervous system
annotated property: subClassOf
annotated target: multi-tissue structure
is inferred: true

subdivision of skeletal system
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part_of
  some values from: skeletal system
subclass of: Restriction
  on property: has part
  some values from: skeletal element
definition: Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
imported from: cl.owl
has exact synonym: skeletal system subdivision
has_related_synonym: skeletal system part

Axiom
annotated source: subdivision of skeletal system
annotated property: subClassOf
annotated target: organ system subdivision
is inferred: true

external ectoderm
type: Class
subclass of: unilaminar epithelium
subclass of: embryonic tissue
subclass of: Restriction
  on property: part_of
  some values from: ectoderm
definition: The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
imported from: cl.owl
has exact synonym: surface (external) ectoderm
has exact synonym: surface ectoderm

Axiom
annotated source: external ectoderm
annotated property: subClassOf
annotated target: unilaminar epithelium
is inferred: true

Axiom
annotated source: external ectoderm
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

mixed endoderm/mesoderm-derived structure
type: Class
equivalent class: Class
  intersection of: anatomical structure
  intersection of: Restriction
    on property: develops from
    some values from: endoderm
  intersection of: Restriction
    on property: develops from
    some values from: mesoderm
subclass of: endoderm-derived structure
subclass of: mesoderm-derived structure
definition: An anatomical structure that develops from the endoderm and the mesoderm.
imported from: cl.owl

Axiom
annotated source: mixed endoderm/mesoderm-derived structure
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

Axiom
annotated source: mixed endoderm/mesoderm-derived structure
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

male reproductive system
type: Class
equivalent class: Class
  intersection of: reproductive system
  intersection of: Restriction
    on property: part_of
    some values from: male organism
subclass of: reproductive system
subclass of: Restriction
  on property: part_of
  some values from: male organism
definition: The organs associated with producing offspring in the gender that produces spermatozoa.
imported from: cl.owl
has exact synonym: genitalia of male organism
has exact synonym: male genital system
has exact synonym: male genitalia
has exact synonym: male genitals
has exact synonym: male organism genitalia
has exact synonym: male organism reproductive system
has exact synonym: reproductive system of male organism
has_related_synonym: male genital organ
has_related_synonym: male genital tract
has_related_synonym: male reproductive tract
has_related_synonym: systema genitale masculinum

Axiom
annotated source: male reproductive system
annotated property: subClassOf
annotated target: reproductive system
is inferred: true

morula
type: Class
subclass of: embryo
subclass of: Restriction
  on property: part_of
  some values from: conceptus
definition: A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum.
imported from: cl.owl
has_related_synonym: morula (2-16 cells)

Axiom
annotated source: morula
annotated property: subClassOf
annotated target: embryo
is inferred: true

inner cell mass
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part_of
  some values from: embryo
subclass of: Restriction
  on property: develops from
  some values from: morula
subclass of: Restriction
  on property: develops from
  some values from: blastocyst
definition: A mass of cells that develop into the body of the embryo and some extraembryonic tissues
imported from: cl.owl
has_related_synonym: ICM
has_related_synonym: early embryoblast
has_related_synonym: embryoblast
has_related_synonym: embryoblastus; massa cellularis interna; pluriblastus senior
has_related_synonym: pluriblast

Axiom
annotated source: inner cell mass
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

trophoblast
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part_of
  some values from: blastocyst
subclass of: Restriction
  on property: develops from
  some values from: trophectoderm
definition: the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta
imported from: cl.owl
has exact synonym: trophoblast layer
has_related_synonym: massa cellularis externa
has_related_synonym: trophoblastus
has_related_synonym: trophoderm

Axiom
annotated source: trophoblast
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

bilaminar disc
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: develops from
  some values from: inner cell mass
definition: A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc.
imported from: cl.owl
has_broad_synonym: embryonic disc
has_broad_synonym: embryonic shield
has_broad_synonym: germinal disc
has_broad_synonym: germinal disk
has exact synonym: bilaminary embryonic disc
has exact synonym: bilaminary germ disc
has_related_synonym: bilaminar disk

Axiom
annotated source: bilaminar disc
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

cardiac neural crest
type: Class
subclass of: anatomical structure
subclass of: ectoderm-derived structure
subclass of: embryonic tissue
subclass of: Restriction
  on property: part_of
  some values from: neural crest
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: vagal neural crest
definition: portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]
imported from: cl.owl
has_related_synonym: cardiac neural crest complex
has_related_synonym: complexus cristae neuralis cardiacus

Axiom
annotated source: cardiac neural crest
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: cardiac neural crest
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

Axiom
annotated source: cardiac neural crest
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

lung epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: lung
subclass of: lower respiratory tract epithelium
subclass of: Restriction
  on property: part_of
  some values from: lung
definition: The epithelial layer of the lung.
imported from: cl.owl
has exact synonym: epithelial tissue of lung
has exact synonym: epithelium of lung
has exact synonym: lung epithelial tissue
has_related_synonym: pulmonary epithelium

Axiom
annotated source: lung epithelium
annotated property: subClassOf
annotated target: lower respiratory tract epithelium
is inferred: true

respiratory tube
type: Class
equivalent class: Class
  intersection of: tube
  intersection of: Restriction
    on property: part_of
    some values from: respiratory tract
subclass of: tube
subclass of: endoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: respiratory tract
subclass of: Restriction
  on property: has part
  some values from: epithelium
definition: A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
imported from: cl.owl
has exact synonym: segment of tracheobronchial tree
has_narrow_synonym: respiratory conducting tube
has_narrow_synonym: segment of tracheobronchial tree
has_narrow_synonym: tracheobronchial tree segment

Axiom
annotated source: respiratory tube
annotated property: subClassOf
annotated target: tube
is inferred: true

Axiom
annotated source: respiratory tube
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

lung bud
type: Class
subclass of: epithelial bud
subclass of: endo-epithelium
subclass of: Restriction
  on property: develops from
  some values from: lung primordium
subclass of: Restriction
  on property: develops from
  some values from: respiratory primordium
definition: Structure derived from foregut that becomes a lung[GO].
imported from: cl.owl
has_related_synonym: gemma pulmonalis
has_related_synonym: gemma respiratoria
has_related_synonym: lung bud
has_related_synonym: primary lung bud
has_related_synonym: respiratory diverticulum

Axiom
annotated source: lung bud
annotated property: subClassOf
annotated target: epithelial bud
is inferred: true

Axiom
annotated source: lung bud
annotated property: subClassOf
annotated target: endo-epithelium
is inferred: true

anterior region of body
type: Class
subclass of: organism subdivision
imported from: cl.owl

Axiom
annotated source: anterior region of body
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

posterior region of body
type: Class
subclass of: organism subdivision
imported from: cl.owl

Axiom
annotated source: posterior region of body
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

membranous layer
type: Class
subclass of: organ component layer
subclass of: Restriction
  on property: part_of
  some values from: organ part
imported from: cl.owl
has_broad_synonym: membrane
has exact synonym: membranous organ component

Axiom
annotated source: membranous layer
annotated property: subClassOf
annotated target: organ component layer
is inferred: true

intestine
type: Class
subclass of: subdivision of digestive tract
subclass of: Restriction
  on property: part_of
  some values from: alimentary part of gastrointestinal system
definition: Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
imported from: cl.owl
has exact synonym: bowel
has_related_synonym: intestinal tract

Axiom
annotated source: intestine
annotated property: subClassOf
annotated target: subdivision of digestive tract
is inferred: true

cloaca
type: Class
subclass of: mesoderm-derived structure
subclass of: subdivision of tube
subclass of: Restriction
  on property: part_of
  some values from: digestive tract
subclass of: Restriction
  on property: part_of
  some values from: genitourinary system
definition: Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures
imported from: cl.owl
has_related_synonym: cloacal chamber
has_related_synonym: vent

Axiom
annotated source: cloaca
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: cloaca
annotated property: subClassOf
annotated target: subdivision of tube
is inferred: true

embryonic cloaca
type: Class
subclass of: cloaca
subclass of: Restriction
  on property: part_of
  some values from: embryo
subclass of: Restriction
  on property: part_of
  some values from: renal system
subclass of: Restriction
  on property: part_of
  some values from: internal anal region
definition: endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].
imported from: cl.owl
has_related_synonym: cloaca

Axiom
annotated source: embryonic cloaca
annotated property: subClassOf
annotated target: cloaca
is inferred: true

primitive urogenital sinus
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part_of
  some values from: embryonic cloaca
subclass of: Restriction
  on property: part_of
  some values from: renal system
definition: the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females
imported from: cl.owl
has_broad_synonym: urogenital sinus
has exact synonym: UGS
has exact synonym: fetal UGS
has exact synonym: sinus urogenitalis

Axiom
annotated source: primitive urogenital sinus
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

pair of lungs
type: Class
subclass of: UBERON_0034925
subclass of: Restriction
  on property: part_of
  some values from: lower respiratory tract
subclass of: Restriction
  on property: has part
  some values from: right lung
subclass of: Restriction
  on property: has part
  some values from: left lung
definition: The pair of anatomical structures comprised of a left lung and right lung.
imported from: cl.owl
has exact synonym: lungs
has exact synonym: lungs pair
has exact synonym: pulmones
has exact synonym: set of lungs

Axiom
annotated source: pair of lungs
annotated property: subClassOf
annotated target: UBERON_0034925
is inferred: true

respiration organ
type: Class
subclass of: organ
subclass of: Restriction
  on property: part_of
  some values from: respiratory system
definition: Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
imported from: cl.owl
has exact synonym: apparatus respiratorius organ
has exact synonym: breathing organ
has exact synonym: organ of apparatus respiratorius
has exact synonym: organ of respiratory system
has exact synonym: respiratory organ
has exact synonym: respiratory system organ
has_related_synonym: gas exchange organ

Axiom
annotated source: respiration organ
annotated property: subClassOf
annotated target: organ
is inferred: true

amniotic fluid
type: Class
subclass of: organism substance
definition: Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
imported from: cl.owl
has_related_synonym: acqua amnii
has_related_synonym: liquor amnii

Axiom
annotated source: amniotic fluid
annotated property: subClassOf
annotated target: organism substance
is inferred: true

blood
type: Class
subclass of: anatomical structure
subclass of: haemolymphatic fluid
subclass of: Restriction
  on property: part_of
  some values from: hematopoietic system
subclass of: Restriction
  on property: has part
  some values from: blood plasma
subclass of: Restriction
  on property: develops from
  some values from: presumptive blood
definition: A fluid that is composed of blood plasma and erythrocytes.
imported from: cl.owl
has exact synonym: portion of blood
has exact synonym: vertebrate blood
has_related_synonym: whole blood

Axiom
annotated source: blood
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: blood
annotated property: subClassOf
annotated target: haemolymphatic fluid
is inferred: true

haemolymphatic fluid
type: Class
equivalent class: Class
  intersection of: organism substance
  intersection of: Restriction
    on property: part_of
    some values from: hemolymphoid system
subclass of: bodily fluid
subclass of: Restriction
  on property: part_of
  some values from: hemolymphoid system
definition: Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
imported from: cl.owl
has_related_synonym: blood or blood analog
has_related_synonym: circulating fluid

Axiom
annotated source: haemolymphatic fluid
annotated property: subClassOf
annotated target: bodily fluid
is inferred: true

amnion
type: Class
subclass of: anatomical structure
subclass of: mesoderm-derived structure
subclass of: extraembryonic membrane
subclass of: Restriction
  on property: has part
  some values from: amniotic ectoderm
subclass of: Restriction
  on property: has part
  some values from: amniotic mesoderm
subclass of: Restriction
  on property: develops from
  some values from: amniotic fold
definition: the thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected
imported from: cl.owl
has exact synonym: amnios

Axiom
annotated source: amnion
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: amnion
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: amnion
annotated property: subClassOf
annotated target: extraembryonic membrane
is inferred: true

blastula
type: Class
subclass of: embryo
subclass of: Restriction
  on property: develops from
  some values from: cleaving embryo
definition: Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
imported from: cl.owl
has exact synonym: blastula embryo
has_related_synonym: blastosphere

Axiom
annotated source: blastula
annotated property: subClassOf
annotated target: embryo
is inferred: true

late embryo
type: Class
subclass of: embryo
definition: An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
imported from: cl.owl
has_narrow_synonym: fetus
has_related_synonym: embryo late growth stage
has_related_synonym: embryo late stage

Axiom
annotated source: late embryo
annotated property: subClassOf
annotated target: embryo
is inferred: true

gastric gland
type: Class
subclass of: exocrine gland
subclass of: gland of foregut
subclass of: Restriction
  on property: part_of
  some values from: stomach glandular epithelium
definition: The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
imported from: cl.owl

Axiom
annotated source: gastric gland
annotated property: subClassOf
annotated target: exocrine gland
is inferred: true

Axiom
annotated source: gastric gland
annotated property: subClassOf
annotated target: gland of foregut
is inferred: true

gut wall
type: Class
equivalent class: Class
  intersection of: anatomical wall
  intersection of: Restriction
    on property: part_of
    some values from: digestive tract
subclass of: anatomical wall
subclass of: Restriction
  on property: part_of
  some values from: digestive tract
definition: The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
imported from: cl.owl
has exact synonym: digestive tract wall
has exact synonym: wall of digestive tract
has exact synonym: wall of gut
has_related_synonym: wall of alimentary tract

Axiom
annotated source: gut wall
annotated property: subClassOf
annotated target: anatomical wall
is inferred: true

intestinal gland
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part_of
    some values from: intestinal mucosa
subclass of: gland of digestive tract
subclass of: Restriction
  on property: part_of
  some values from: intestinal mucosa
definition: A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm].
imported from: cl.owl
has exact synonym: bowel mucosa gland
has exact synonym: bowel mucosa of organ gland
has exact synonym: bowel mucous membrane gland
has exact synonym: bowel organ mucosa gland
has exact synonym: gland of bowel mucosa
has exact synonym: gland of bowel mucosa of organ
has exact synonym: gland of bowel mucous membrane
has exact synonym: gland of bowel organ mucosa
has exact synonym: gland of intestinal mucosa
has exact synonym: gland of intestine mucosa
has exact synonym: gland of intestine mucosa of organ
has exact synonym: gland of intestine mucous membrane
has exact synonym: gland of intestine organ mucosa
has exact synonym: gland of mucosa of bowel
has exact synonym: gland of mucosa of intestine
has exact synonym: gland of mucosa of organ of bowel
has exact synonym: gland of mucosa of organ of intestine
has exact synonym: gland of mucous membrane of bowel
has exact synonym: gland of mucous membrane of intestine
has exact synonym: gland of organ mucosa of bowel
has exact synonym: gland of organ mucosa of intestine
has exact synonym: glandula intestinalis
has exact synonym: intestinal mucosa gland
has exact synonym: intestine mucosa gland
has exact synonym: intestine mucosa of organ gland
has exact synonym: intestine mucous membrane gland
has exact synonym: intestine organ mucosa gland
has exact synonym: mucosa of bowel gland
has exact synonym: mucosa of intestine gland
has exact synonym: mucosa of organ of bowel gland
has exact synonym: mucosa of organ of intestine gland
has exact synonym: mucous membrane of bowel gland
has exact synonym: mucous membrane of intestine gland
has exact synonym: organ mucosa of bowel gland
has exact synonym: organ mucosa of intestine gland
has_related_synonym: glandulae intestinales

Axiom
annotated source: intestinal gland
annotated property: subClassOf
annotated target: gland of digestive tract
is inferred: true

mucosa
type: Class
subclass of: organ component layer
subclass of: Restriction
  on property: has part
  some values from: epithelium
subclass of: Restriction
  on property: has part
  some values from: connective tissue
definition: A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]
imported from: cl.owl
has exact synonym: mucosa of organ
has exact synonym: mucosa of organ part
has exact synonym: mucosal region
has exact synonym: mucous membrane
has exact synonym: organ mucosa
has_related_synonym: region of mucosa
has_related_synonym: tunica mucosa

Axiom
annotated source: mucosa
annotated property: subClassOf
annotated target: organ component layer
is inferred: true

parenchyma
type: Class
subclass of: organ part
definition: functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.
imported from: cl.owl

Axiom
annotated source: parenchyma
annotated property: subClassOf
annotated target: organ part
is inferred: true

blastocyst
type: Class
subclass of: anatomical structure
subclass of: embryonic structure
subclass of: Restriction
  on property: part_of
  some values from: blastula
subclass of: Restriction
  on property: has part
  some values from: inner cell mass
subclass of: Restriction
  on property: has part
  some values from: trophoblast
subclass of: Restriction
  on property: develops from
  some values from: morula
definition: The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO].
imported from: cl.owl
has_related_synonym: blastocystis
has_related_synonym: blastula

Axiom
annotated source: blastocyst
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: blastocyst
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

urothelium
type: Class
subclass of: multilaminar epithelium
subclass of: endo-epithelium
subclass of: Restriction
  on property: part_of
  some values from: renal system
definition: An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra.
imported from: cl.owl
has_broad_synonym: transitional epithelium
has exact synonym: epithelium transitionale
has exact synonym: transitional epithelium
has exact synonym: uroepithelium

Axiom
annotated source: urothelium
annotated property: subClassOf
annotated target: multilaminar epithelium
is inferred: true

Axiom
annotated source: urothelium
annotated property: subClassOf
annotated target: endo-epithelium
is inferred: true

hindlimb stylopod
type: Class
equivalent class: Class
  intersection of: stylopod
  intersection of: Restriction
    on property: part_of
    some values from: hindlimb
subclass of: stylopod
subclass of: lower limb segment
subclass of: Restriction
  on property: part_of
  some values from: leg
subclass of: Restriction
  on property: has part
  some values from: femur endochondral element
definition: The part of the hindlimb between pelvis and the knee, corresponding to the femur.
imported from: cl.owl
has exact synonym: hind limb stylopod
has exact synonym: hind limb stylopodium
has exact synonym: hind propodium
has exact synonym: hindlimb propodium
has exact synonym: hindlimb stylopod
has exact synonym: hindlimb stylopodium
has exact synonym: proximal segment of free lower limb
has exact synonym: stylopod of hind limb
has exact synonym: stylopod of hindlimb
has exact synonym: stylopod of lower limb
has exact synonym: thigh
has exact synonym: upper leg
has_related_synonym: femur

Axiom
annotated source: hindlimb stylopod
annotated property: subClassOf
annotated target: stylopod
is inferred: true

Axiom
annotated source: hindlimb stylopod
annotated property: subClassOf
annotated target: lower limb segment
is inferred: true

tracheal mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: part_of
    some values from: respiratory airway
subclass of: respiratory system mucosa
subclass of: Restriction
  on property: part_of
  some values from: respiratory airway
definition: A mucosa that is part of a respiratory airway.
imported from: cl.owl
has exact synonym: mucosa of organ of trachea
has exact synonym: mucosa of organ of windpipe
has exact synonym: mucosa of trachea
has exact synonym: mucosa of windpipe
has exact synonym: mucous membrane of trachea
has exact synonym: mucous membrane of windpipe
has exact synonym: organ mucosa of trachea
has exact synonym: organ mucosa of windpipe
has exact synonym: trachea mucosa
has exact synonym: trachea mucosa of organ
has exact synonym: trachea mucous membrane
has exact synonym: trachea organ mucosa
has exact synonym: tracheal mucous membrane
has exact synonym: tunica mucosa (tracheae)
has exact synonym: tunica mucosa tracheae
has exact synonym: windpipe mucosa
has exact synonym: windpipe mucosa of organ
has exact synonym: windpipe mucous membrane
has exact synonym: windpipe organ mucosa

Axiom
annotated source: tracheal mucosa
annotated property: subClassOf
annotated target: respiratory system mucosa
is inferred: true

musculature of body
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part_of
  some values from: musculoskeletal system
subclass of: Restriction
  on property: has part
  some values from: musculature
definition: The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
imported from: cl.owl
has exact synonym: muscle system
has exact synonym: muscle system of body
has exact synonym: muscular system
has exact synonym: musculature system
has exact synonym: set of all muscles
has exact synonym: set of muscles of body
has exact synonym: vertebrate muscular system
has_related_synonym: muskelsystem

Axiom
annotated source: musculature of body
annotated property: subClassOf
annotated target: organ system subdivision
is inferred: true

scalp
type: Class
subclass of: anatomical structure
subclass of: UBERON_0034921
subclass of: Restriction
  on property: part_of
  some values from: head
subclass of: Restriction
  on property: has part
  some values from: zone of skin
subclass of: Restriction
  on property: has part
  some values from: periosteum
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: skin of head
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: epicranial aponeurosis
definition: The outer covering of the calvaria. It is composed of several layers: SKIN; subcutaneous connective tissue; the occipitofrontal muscle which includes the tendonous galea aponeurotica; Loose connective tissue; and the pericranium (the PERIOSTEUM of the SKULL).
imported from: cl.owl
has_related_synonym: scalpus

Axiom
annotated source: scalp
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: scalp
annotated property: subClassOf
annotated target: UBERON_0034921
is inferred: true

bronchial mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: part_of
    some values from: bronchus
subclass of: tracheal mucosa
subclass of: endoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: bronchus
definition: A mucosa that is part of a bronchus [Automatically generated definition].
imported from: cl.owl
has exact synonym: bronchi mucosa
has exact synonym: bronchi mucosa of organ
has exact synonym: bronchi mucous membrane
has exact synonym: bronchi organ mucosa
has exact synonym: bronchial trunk mucosa
has exact synonym: bronchial trunk mucosa of organ
has exact synonym: bronchial trunk mucous membrane
has exact synonym: bronchial trunk organ mucosa
has exact synonym: bronchus mucosa
has exact synonym: bronchus mucosa of organ
has exact synonym: bronchus mucous membrane
has exact synonym: bronchus organ mucosa
has exact synonym: mucosa of bronchi
has exact synonym: mucosa of bronchial trunk
has exact synonym: mucosa of bronchus
has exact synonym: mucosa of organ of bronchi
has exact synonym: mucosa of organ of bronchial trunk
has exact synonym: mucosa of organ of bronchus
has exact synonym: mucous membrane of bronchi
has exact synonym: mucous membrane of bronchial trunk
has exact synonym: mucous membrane of bronchus
has exact synonym: organ mucosa of bronchi
has exact synonym: organ mucosa of bronchial trunk
has exact synonym: organ mucosa of bronchus
has exact synonym: tunica mucosa bronchi

Axiom
annotated source: bronchial mucosa
annotated property: subClassOf
annotated target: tracheal mucosa
is inferred: true

Axiom
annotated source: bronchial mucosa
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

dermal papilla
type: Class
subclass of: tissue
subclass of: ectoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: papillary layer of dermis
definition: A mesodermal signaling center of the hair follicle consisting of closely packed specialized mesenchymal fibroblasts. Framed by the enlarged bulb matrix in anagen.
imported from: cl.owl
has exact synonym: dermal papillae
has exact synonym: follicular papilla
has_related_synonym: dermal papilla cell
has_related_synonym: hair follicle dermal papilla
has_related_synonym: hair papilla
has_related_synonym: papilla corii
has_related_synonym: papilla dermatis
has_related_synonym: papilla dermis
has_related_synonym: papilla of corium
has_related_synonym: papillae dermis
has_related_synonym: skin papilla

Axiom
annotated source: dermal papilla
annotated property: subClassOf
annotated target: tissue
is inferred: true

Axiom
annotated source: dermal papilla
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

organism substance
type: Class
subclass of: material anatomical entity
subclass of: Restriction
  on property: part_of
  some values from: multicellular organism
definition: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
imported from: cl.owl
has exact synonym: body fluid or substance
has exact synonym: body substance
has exact synonym: organism substance
has exact synonym: portion of body substance
has exact synonym: portion of organism substance

Axiom
annotated source: organism substance
annotated property: subClassOf
annotated target: material anatomical entity
is inferred: true

anatomical space
type: Class
subclass of: immaterial anatomical entity
definition: Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
imported from: cl.owl
has_broad_synonym: lumen
has_broad_synonym: space
has exact synonym: lumen space
has_related_synonym: anatomical spaces

Axiom
annotated source: anatomical space
annotated property: subClassOf
annotated target: immaterial anatomical entity
is inferred: true

material anatomical entity
type: Class
subclass of: anatomical entity
definition: Anatomical entity that has mass.
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
has db xref: AAO:0010264
has db xref: AEO:0000006
has db xref: BILA:0000006
has db xref: CARO:0000006
has db xref: EHDAA2:0003006
has db xref: FBbt:00007016
has db xref: FMA:67165
has db xref: HAO:0000006
has db xref: TAO:0001836
has db xref: TGMA:0001826
has db xref: VHOG:0001721
has OBO namespace: uberon
id: UBERON:0000465
in subset: upper level

Axiom
annotated source: material anatomical entity
annotated property: subClassOf
annotated target: anatomical entity
is inferred: true

immaterial anatomical entity
type: Class
subclass of: anatomical entity
definition: Anatomical entity that has no mass.
imported from: cl.owl
has exact synonym: immaterial physical anatomical entity

Axiom
annotated source: immaterial anatomical entity
annotated property: subClassOf
annotated target: anatomical entity
is inferred: true

anatomical system
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: multicellular organism
subclass of: Restriction
  on property: has part
  some values from: organ
definition: Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
imported from: cl.owl
has_broad_synonym: system
has exact synonym: body system
has exact synonym: connected anatomical system
has exact synonym: organ system
has_related_synonym: anatomical systems

Axiom
annotated source: anatomical system
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

multicellular organism
type: Class
subclass of: multicellular anatomical structure
definition: Anatomical structure that is an individual member of a species and consists of more than one cell.
editor note: TODO - split body and mc organism? body continues after death stage
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
has_relational_adjective: organismal
has db xref: Multi-cellular organism
has db xref: C13041
has db xref: birnlex 18
has db xref: http://www.snomedbrowser.com/Codes/Details/243928005
has db xref: AAO:0010026
has db xref: AEO:0000191
has db xref: BILA:0000012
has db xref: BSA:0000038
has db xref: BTO:0000042
has db xref: CARO:0000012
has db xref: EFO:0002906
has db xref: EHDAA2:0003103
has db xref: EHDAA2:0003191
has db xref: EHDAA:1
has db xref: EHDAA:9178
has db xref: EMAPA:25765
has db xref: EV:0100016
has db xref: FBbt:00000001
has db xref: FMA:256135
has db xref: HAO:0000012
has db xref: TADS:0000001
has db xref: TAO:0001094
has db xref: TGMA:0001832
has db xref: VHOG:0000671
has db xref: WBbt:0007833
has db xref: XAO:0003004
has db xref: ZFA:0001094
has db xref: galen:Organism
has db xref: ncithesaurus:Whole_Organism
has exact synonym: multi-cellular organism
has exact synonym: organism
has exact synonym: whole organism
has narrow synonym: animal
has OBO namespace: uberon
has related synonym: Koerper
has related synonym: body
has related synonym: whole body
id: UBERON:0000468
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: upper level
has_broad_synonym: organism
has_related_synonym: whole organism

Axiom
annotated source: multicellular organism
annotated property: subClassOf
annotated target: multicellular anatomical structure
is inferred: true

female reproductive system
type: Class
equivalent class: Class
  intersection of: reproductive system
  intersection of: Restriction
    on property: part_of
    some values from: female organism
subclass of: reproductive system
subclass of: Restriction
  on property: part_of
  some values from: female organism
definition: The organs and associated structures associated with bearing offspring in a female animal.
imported from: cl.owl
has exact synonym: female organism genitalia
has exact synonym: female organism reproductive system
has exact synonym: genitalia of female organism
has exact synonym: reproductive system of female organism
has_related_synonym: female genital system
has_related_synonym: female genital tract
has_related_synonym: female genitalia
has_related_synonym: female genitals
has_related_synonym: female reproductive tract
has_related_synonym: gynaecological tissue
has_related_synonym: systema genitale femininum

Axiom
annotated source: female reproductive system
annotated property: subClassOf
annotated target: reproductive system
is inferred: true

organism subdivision
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: multicellular organism
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: circulatory system
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: musculature
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: nervous system
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: skeletal system
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: integumental system
definition: Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
imported from: cl.owl
has exact synonym: anatomic region
has_related_synonym: body part
has_related_synonym: body region
has_related_synonym: cardinal body part

Axiom
annotated source: organism subdivision
annotated property: subClassOf
annotated target: multicellular anatomical structure
is inferred: true

acellular anatomical structure
type: Class
subclass of: anatomical structure
definition: Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
imported from: cl.owl
has_related_synonym: acellular anatomical structures

Axiom
annotated source: acellular anatomical structure
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

anatomical cluster
type: Class
subclass of: anatomical entity
definition: Anatomical group that has its parts adjacent to one another.
imported from: cl.owl

Axiom
annotated source: anatomical cluster
annotated property: subClassOf
annotated target: anatomical entity
is inferred: true

extraembryonic structure
type: Class
equivalent class: Class
  intersection of: developing anatomical structure
  intersection of: Restriction
    on property: part_of
    some values from: UBERON_0016887
subclass of: developing anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: UBERON_0016887
definition: A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
imported from: cl.owl
has exact synonym: extra-embryonic structure
has_related_synonym: extraembryonic structures
has_related_synonym: extraembryonic tissue

Axiom
annotated source: extraembryonic structure
annotated property: subClassOf
annotated target: developing anatomical structure
is inferred: true

tissue
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: multicellular organism
definition: Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
editor note: changed label and definition to reflect CARO2
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
has db xref: http://linkedlifedata.com/resource/umls/id/C0040300
has db xref: C12801
has db xref: birnlex 19
has db xref: AAO:0000607
has db xref: AAO:0010054
has db xref: AEO:0000043
has db xref: BILA:0000043
has db xref: CALOHA:TS-2090
has db xref: CARO:0000043
has db xref: EHDAA2:0003043
has db xref: EMAPA:35868
has db xref: FBbt:00007003
has db xref: FMA:9637
has db xref: HAO:0000043
has db xref: MA:0003002
has db xref: MESH:D014024
has db xref: TAO:0001477
has db xref: TGMA:0001844
has db xref: UMLS:C0040300
has db xref: VHOG:0001757
has db xref: WBbt:0005729
has db xref: XAO:0003040
has db xref: ZFA:0001477
has db xref: galen:Tissue
has exact synonym: portion of tissue
has exact synonym: tissue portion
has narrow synonym: simple tissue
has OBO namespace: uberon
id: UBERON:0000479
in subset: pheno slim
in subset: upper level

Axiom
annotated source: tissue
annotated property: subClassOf
annotated target: multicellular anatomical structure
is inferred: true

multi-tissue structure
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: has part
  some values from: tissue
definition: Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
imported from: cl.owl
has_related_synonym: multi-tissue structures

Axiom
annotated source: multi-tissue structure
annotated property: subClassOf
annotated target: multicellular anatomical structure
is inferred: true

epithelium
type: Class
equivalent class: Class
  union of: multilaminar epithelium
  union of: unilaminar epithelium
subclass of: tissue
subclass of: Restriction
  on property: has part
  some values from: basement membrane of epithelium
definition: Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
imported from: cl.owl
has exact synonym: epithelial tissue
has exact synonym: portion of epithelium

Axiom
annotated source: epithelium
annotated property: subClassOf
annotated target: tissue
is inferred: true

simple columnar epithelium
type: Class
subclass of: unilaminar epithelium
subclass of: columnar epithelium
definition: Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]
imported from: cl.owl
has_broad_synonym: columnar epithelium
has_broad_synonym: columnar epithlium
has exact synonym: epithelium simplex columnare
has exact synonym: simple columnar epithelium
has_related_synonym: simple columnar epithelia

Axiom
annotated source: simple columnar epithelium
annotated property: subClassOf
annotated target: unilaminar epithelium
is inferred: true

Axiom
annotated source: simple columnar epithelium
annotated property: subClassOf
annotated target: columnar epithelium
is inferred: true

multilaminar epithelium
type: Class
subclass of: epithelium
definition: Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]
imported from: cl.owl
has exact synonym: stratified epithelium
has_related_synonym: laminated epithelium

Axiom
annotated source: multilaminar epithelium
annotated property: subClassOf
annotated target: epithelium
is inferred: true

unilaminar epithelium
type: Class
subclass of: epithelium
definition: Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
imported from: cl.owl
has exact synonym: simple epithelium
has_related_synonym: unilaminar epithelia

Axiom
annotated source: unilaminar epithelium
annotated property: subClassOf
annotated target: epithelium
is inferred: true

interstitial fluid
type: Class
subclass of: organism substance
subclass of: Restriction
  on property: part_of
  some values from: tissue
definition: Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.
imported from: cl.owl
has exact synonym: intercellular fluid
has exact synonym: tissue fluid

Axiom
annotated source: interstitial fluid
annotated property: subClassOf
annotated target: organism substance
is inferred: true

thoracic segment of trunk
type: Class
subclass of: subdivision of trunk
subclass of: subdivision of organism along main body axis
subclass of: Restriction
  on property: has part
  some values from: thoracic skeleton
definition: Subdivision of trunk that lies between the head and the abdomen.
imported from: cl.owl
has exact synonym: thorax
has_related_synonym: anterior subdivision of trunk
has_related_synonym: upper body
has_related_synonym: upper trunk

Axiom
annotated source: thoracic segment of trunk
annotated property: subClassOf
annotated target: subdivision of trunk
is inferred: true

Axiom
annotated source: thoracic segment of trunk
annotated property: subClassOf
annotated target: subdivision of organism along main body axis
is inferred: true

abdomen
type: Class
subclass of: subdivision of trunk
subclass of: Restriction
  on property: part_of
  some values from: abdominal segment of trunk
definition: The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
imported from: cl.owl
has exact synonym: abdominopelvic region
has exact synonym: abdominopelvis
has_related_synonym: adult abdomen
has_related_synonym: belly
has_related_synonym: celiac region

Axiom
annotated source: abdomen
annotated property: subClassOf
annotated target: subdivision of trunk
is inferred: true

embryo
type: Class
subclass of: multicellular organism
definition: Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
imported from: cl.owl
has exact synonym: embryonic organism
has_related_synonym: developing organism
has_related_synonym: developmental tissue

Axiom
annotated source: embryo
annotated property: subClassOf
annotated target: multicellular organism
is inferred: true

germ layer
type: Class
subclass of: germ layer / neural crest
definition: A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
imported from: cl.owl
has_broad_synonym: embryonic tissue
has exact synonym: germinal layer
has_narrow_synonym: primary germ layer
has_related_synonym: embryonic germ layer
has_related_synonym: embryonic germ layers

Axiom
annotated source: germ layer
annotated property: subClassOf
annotated target: germ layer / neural crest
is inferred: true

ectoderm
type: Class
subclass of: germ layer
subclass of: Restriction
  on property: develops from
  some values from: presumptive ectoderm
definition: Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
imported from: cl.owl
has exact synonym: embryonic ectoderm

Axiom
annotated source: ectoderm
annotated property: subClassOf
annotated target: germ layer
is inferred: true

endoderm
type: Class
subclass of: germ layer
subclass of: Restriction
  on property: develops from
  some values from: presumptive endoderm
definition: Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
imported from: cl.owl
has_related_synonym: entoderm

Axiom
annotated source: endoderm
annotated property: subClassOf
annotated target: germ layer
is inferred: true

mesoderm
type: Class
subclass of: germ layer
subclass of: Restriction
  on property: develops from
  some values from: presumptive mesoderm
definition: The middle germ layer of the embryo, between the endoderm and ectoderm.
imported from: cl.owl
has_related_synonym: embryonic mesoderm
has_related_synonym: entire mesoderm
has_related_synonym: mesodermal mantle

Axiom
annotated source: mesoderm
annotated property: subClassOf
annotated target: germ layer
is inferred: true

stomach
type: Class
subclass of: subdivision of digestive tract
subclass of: food storage organ
subclass of: Restriction
  on property: part_of
  some values from: foregut
definition: An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
imported from: cl.owl
has_narrow_synonym: stomach chamber
has_related_synonym: anterior intestine
has_related_synonym: gaster
has_related_synonym: mesenteron
has_related_synonym: ventriculus

Axiom
annotated source: stomach
annotated property: subClassOf
annotated target: subdivision of digestive tract
is inferred: true

Axiom
annotated source: stomach
annotated property: subClassOf
annotated target: food storage organ
is inferred: true

heart
type: Class
equivalent class: Class
  intersection of: primary circulatory organ
  intersection of: Restriction
    on property: has part
    some values from: cardiac chamber
subclass of: anatomical structure
subclass of: mesoderm-derived structure
subclass of: thoracic segment organ
subclass of: primary circulatory organ
subclass of: structure with developmental contribution from neural crest
subclass of: Restriction
  on property: part_of
  some values from: UBERON_0015410
subclass of: Restriction
  on property: has part
  some values from: cardiac chamber
subclass of: Restriction
  on property: develops from
  some values from: heart tube
definition: A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
imported from: cl.owl
has exact synonym: chambered heart
has exact synonym: vertebrate heart
has_narrow_synonym: branchial heart
has_related_synonym: Herz@de
has_related_synonym: cardium

Axiom
annotated source: heart
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: heart
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: heart
annotated property: subClassOf
annotated target: thoracic segment organ
is inferred: true

Axiom
annotated source: heart
annotated property: subClassOf
annotated target: primary circulatory organ
is inferred: true

Axiom
annotated source: heart
annotated property: subClassOf
annotated target: structure with developmental contribution from neural crest
is inferred: true

endocrine system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: has part
  some values from: endocrine gland
definition: Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
imported from: cl.owl
has exact synonym: endocrine glandular system
has exact synonym: endocrine system
has exact synonym: systema endocrinum

Axiom
annotated source: endocrine system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

brain
type: Class
subclass of: organ
subclass of: ectoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: multicellular organism
subclass of: Restriction
  on property: part_of
  some values from: central nervous system
subclass of: Restriction
  on property: develops from
  some values from: future brain
definition: The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
imported from: cl.owl
has_related_synonym: encephalon
has_related_synonym: suprasegmental levels of nervous system
has_related_synonym: suprasegmental structures
has_related_synonym: synganglion
has_related_synonym: the brain

Axiom
annotated source: brain
annotated property: subClassOf
annotated target: organ
is inferred: true

Axiom
annotated source: brain
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

leg
type: Class
subclass of: multi-limb segment region
subclass of: lower limb segment
definition: The portion of the hindlimb that contains both the stylopod and zeugopod.
imported from: cl.owl
has exact synonym: tetrapod leg
has_related_synonym: lower extremity

Axiom
annotated source: leg
annotated property: subClassOf
annotated target: multi-limb segment region
is inferred: true

Axiom
annotated source: leg
annotated property: subClassOf
annotated target: lower limb segment
is inferred: true

femur
type: Class
subclass of: hindlimb long bone
subclass of: upper leg bone
subclass of: bone of hip region
subclass of: femur endochondral element
subclass of: Restriction
  on property: part_of
  some values from: hindlimb stylopod
subclass of: Restriction
  on property: part_of
  some values from: hindlimb skeleton
subclass of: Restriction
  on property: develops from
  some values from: femur cartilage element
definition: Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified].
imported from: cl.owl
has exact synonym: thigh bone
has_related_synonym: femoral bone
has_related_synonym: mesomere 1 of pevlic appendage
has_related_synonym: os femorale
has_related_synonym: os femoris
has_related_synonym: os longissimum
has_related_synonym: proximal metapterygial mesomere of pelvic appendage
has_related_synonym: proximal metapterygial mesomere of pelvic fin

Axiom
annotated source: femur
annotated property: subClassOf
annotated target: hindlimb long bone
is inferred: true

Axiom
annotated source: femur
annotated property: subClassOf
annotated target: upper leg bone
is inferred: true

Axiom
annotated source: femur
annotated property: subClassOf
annotated target: bone of hip region
is inferred: true

Axiom
annotated source: femur
annotated property: subClassOf
annotated target: femur endochondral element
is inferred: true

skeletal joint
type: Class
equivalent class: Class
  union of: synovial joint
  union of: nonsynovial joint
subclass of: articulation
definition: Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
imported from: cl.owl
has_broad_synonym: articulation
has_broad_synonym: joint
has_related_synonym: articular joint
has_related_synonym: joints

Axiom
annotated source: skeletal joint
annotated property: subClassOf
annotated target: articulation
is inferred: true

reproductive system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: has part
  some values from: gonad
definition: Anatomical system that has as its parts the organs concerned with reproduction.
imported from: cl.owl
has_related_synonym: Geschlechtsorgan
has_related_synonym: animal reproductive system
has_related_synonym: genital system
has_related_synonym: genital tract
has_related_synonym: genitalia
has_related_synonym: organa genitalia
has_related_synonym: reproductive tissue
has_related_synonym: reproductive tract
has_related_synonym: systemata genitalia

Axiom
annotated source: reproductive system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

gonad
type: Class
subclass of: reproductive organ
subclass of: Restriction
  on property: develops from
  some values from: gonad primordium
definition: Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
imported from: cl.owl
has exact synonym: gonada
has_related_synonym: gonads

Axiom
annotated source: gonad
annotated property: subClassOf
annotated target: reproductive organ
is inferred: true

oviduct
type: Class
subclass of: tube
subclass of: reproductive structure
subclass of: Restriction
  on property: part_of
  some values from: female reproductive system
definition: A tube or collection of tubes in an animal from the ovaries to the outside of the body.
imported from: cl.owl
has exact synonym: ovarian duct
has exact synonym: ovarian tube
has exact synonym: uterine tube
has_related_synonym: female reproductive tracts
has_related_synonym: oviducts
has_related_synonym: tuba uterina
has_related_synonym: tuba uterinae
has_related_synonym: tubular parts of female reproductive system

Axiom
annotated source: oviduct
annotated property: subClassOf
annotated target: tube
is inferred: true

Axiom
annotated source: oviduct
annotated property: subClassOf
annotated target: reproductive structure
is inferred: true

uterus
type: Class
subclass of: subdivision of oviduct
subclass of: Restriction
  on property: part_of
  some values from: internal genitalia
subclass of: Restriction
  on property: develops from
  some values from: embryonic uterus
definition: the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth
imported from: cl.owl

Axiom
annotated source: uterus
annotated property: subClassOf
annotated target: subdivision of oviduct
is inferred: true

skin epidermis
type: Class
equivalent class: Class
  intersection of: outer epithelium
  intersection of: Restriction
    on property: part_of
    some values from: skin of body
subclass of: outer epithelium
subclass of: UBERON_3000961
subclass of: Restriction
  on property: part_of
  some values from: skin of body
definition: The outer epithelial layer of the skin that is superficial to the dermis.
imported from: cl.owl
has_broad_synonym: epidermis
has_broad_synonym: skin
has exact synonym: vertebrate epidermis

Axiom
annotated source: skin epidermis
annotated property: subClassOf
annotated target: outer epithelium
is inferred: true

Axiom
annotated source: skin epidermis
annotated property: subClassOf
annotated target: UBERON_3000961
is inferred: true

respiratory system
type: Class
subclass of: anatomical system
definition: Functional system which consists of structures involved in respiration.
imported from: cl.owl
has exact synonym: apparatus respiratorius
has exact synonym: respiratory system
has_related_synonym: Atmungssystem
has_related_synonym: apparatus respiratorius
has_related_synonym: systema respiratorium

Axiom
annotated source: respiratory system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

respiratory airway
type: Class
subclass of: compound organ
subclass of: Restriction
  on property: part_of
  some values from: respiratory system
definition: An airway through which respiratory air passes in organisms.
imported from: cl.owl
has_broad_synonym: airway
has_broad_synonym: airways

Axiom
annotated source: respiratory airway
annotated property: subClassOf
annotated target: compound organ
is inferred: true

digestive system
type: Class
subclass of: anatomical system
definition: Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
imported from: cl.owl
has_related_synonym: alimentary system
has_related_synonym: alimentary tract
has_related_synonym: gastrointestinal system
has_related_synonym: gut

Axiom
annotated source: digestive system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

renal system
type: Class
subclass of: anatomical system
definition: The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products..
imported from: cl.owl
has exact synonym: excretory system
has exact synonym: renal system
has exact synonym: systema urinaria
has exact synonym: systema urinarium
has exact synonym: urinary system
has exact synonym: urinary tract
has_related_synonym: renal or urinary system
has_related_synonym: renal/urinary system

Axiom
annotated source: renal system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

circulatory system
type: Class
subclass of: anatomical system
definition: organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
imported from: cl.owl
has_related_synonym: systema cardiovasculare

Axiom
annotated source: circulatory system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

adipose tissue
type: Class
subclass of: dense irregular connective tissue
definition: Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
imported from: cl.owl
has exact synonym: fat
has exact synonym: fat tissue
has exact synonym: fatty tissue
has_related_synonym: adipose
has_related_synonym: bodyfat
has_related_synonym: fatty depot

Axiom
annotated source: adipose tissue
annotated property: subClassOf
annotated target: dense irregular connective tissue
is inferred: true

musculature
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part_of
  some values from: musculature of body
subclass of: Restriction
  on property: has part
  some values from: muscle organ
definition: A subdivision of the muscular system corresponding to a subdisivision of an organism.
imported from: cl.owl
has exact synonym: muscle group
has exact synonym: muscles set
has exact synonym: musculature
has exact synonym: musculi
has exact synonym: set of muscles
has exact synonym: set of skeletal muscles
has_related_synonym: muscle system
has_related_synonym: muscles
has_related_synonym: musculature system

Axiom
annotated source: musculature
annotated property: subClassOf
annotated target: organ system subdivision
is inferred: true

nervous system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: develops from
  some values from: UBERON_0016880
definition: The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
imported from: cl.owl
has exact synonym: neurological system
has_narrow_synonym: nerve net
has_related_synonym: systema nervosum

Axiom
annotated source: nervous system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

central nervous system
type: Class
subclass of: ectoderm-derived structure
subclass of: organ system subdivision
subclass of: Restriction
  on property: part_of
  some values from: nervous system
subclass of: Restriction
  on property: develops from
  some values from: UBERON_0016879
definition: The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
imported from: cl.owl
has exact synonym: CNS
has exact synonym: systema nervosum centrale
has_narrow_synonym: cerebrospinal axis
has_related_synonym: neuraxis

Axiom
annotated source: central nervous system
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

Axiom
annotated source: central nervous system
annotated property: subClassOf
annotated target: organ system subdivision
is inferred: true

yolk sac
type: Class
subclass of: extraembryonic tissue
subclass of: extraembryonic membrane
subclass of: epithelial sac
definition: A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP].
imported from: cl.owl
has_related_synonym: saccus vitellinus
has_related_synonym: vesicula umbilicalis

Axiom
annotated source: yolk sac
annotated property: subClassOf
annotated target: extraembryonic tissue
is inferred: true

Axiom
annotated source: yolk sac
annotated property: subClassOf
annotated target: extraembryonic membrane
is inferred: true

Axiom
annotated source: yolk sac
annotated property: subClassOf
annotated target: epithelial sac
is inferred: true

foregut
type: Class
subclass of: subdivision of digestive tract
definition: Anterior subdivision of a digestive tract.
imported from: cl.owl
has_related_synonym: praeenteron
has_related_synonym: proenteron

Axiom
annotated source: foregut
annotated property: subClassOf
annotated target: subdivision of digestive tract
is inferred: true

esophagus
type: Class
subclass of: subdivision of digestive tract
subclass of: thoracic cavity element
subclass of: digestive system element
subclass of: Restriction
  on property: part_of
  some values from: upper digestive tract
definition: Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
imported from: cl.owl
has exact synonym: gullet
has exact synonym: oesophagus

Axiom
annotated source: esophagus
annotated property: subClassOf
annotated target: subdivision of digestive tract
is inferred: true

Axiom
annotated source: esophagus
annotated property: subClassOf
annotated target: thoracic cavity element
is inferred: true

Axiom
annotated source: esophagus
annotated property: subClassOf
annotated target: digestive system element
is inferred: true

midgut
type: Class
subclass of: subdivision of digestive tract
definition: Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
imported from: cl.owl
has_related_synonym: mesenteron

Axiom
annotated source: midgut
annotated property: subClassOf
annotated target: subdivision of digestive tract
is inferred: true

hindgut
type: Class
subclass of: subdivision of digestive tract
subclass of: Restriction
  on property: develops from
  some values from: mesenchyme
definition: The caudalmost subdivision of a digestive tract.
imported from: cl.owl
has_related_synonym: metenteron

Axiom
annotated source: hindgut
annotated property: subClassOf
annotated target: subdivision of digestive tract
is inferred: true

primordium
type: Class
subclass of: developing anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: multicellular organism
definition: Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
imported from: cl.owl
has_related_synonym: bud
has_related_synonym: future organ
has_related_synonym: placode
has_related_synonym: primordia
has_related_synonym: rudiment

Axiom
annotated source: primordium
annotated property: subClassOf
annotated target: developing anatomical structure
is inferred: true

neural tube
type: Class
subclass of: epithelial tube
subclass of: embryonic tissue
subclass of: ecto-epithelium
subclass of: UBERON_0016879
subclass of: Restriction
  on property: develops from
  some values from: neural rod
definition: In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
imported from: cl.owl
has_related_synonym: neural primordium
has_related_synonym: presumptive central nervous system
has_related_synonym: tubus neuralis

Axiom
annotated source: neural tube
annotated property: subClassOf
annotated target: epithelial tube
is inferred: true

Axiom
annotated source: neural tube
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: neural tube
annotated property: subClassOf
annotated target: ecto-epithelium
is inferred: true

Axiom
annotated source: neural tube
annotated property: subClassOf
annotated target: UBERON_0016879
is inferred: true

anatomical entity
type: Class
subclass of: independent continuant
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
has db xref: http://linkedlifedata.com/resource/umls/id/C1515976
has db xref: C12219
has db xref: birnlex 6
has db xref: AAO:0010841
has db xref: AEO:0000000
has db xref: BILA:0000000
has db xref: CARO:0000000
has db xref: EHDAA2:0002229
has db xref: FBbt:10000000
has db xref: FBbt_root:00000000
has db xref: FMA:62955
has db xref: HAO:0000000
has db xref: MA:0000001
has db xref: TAO:0100000
has db xref: TGMA:0001822
has db xref: UMLS:C1515976
has db xref: XAO:0000000
has db xref: ZFA:0100000
has OBO namespace: uberon
id: UBERON:0001062
in subset: upper level

Axiom
annotated source: anatomical entity
annotated property: subClassOf
annotated target: independent continuant
is inferred: true

skin of head
type: Class
equivalent class: Class
  intersection of: zone of skin
  intersection of: Restriction
    on property: part_of
    some values from: head
subclass of: head or neck skin
subclass of: Restriction
  on property: part_of
  some values from: head
definition: A zone of skin that is part of a head [Automatically generated definition].
imported from: cl.owl
has exact synonym: adult head zone of skin
has exact synonym: head skin
has exact synonym: head zone of skin
has exact synonym: zone of skin of adult head
has exact synonym: zone of skin of head

Axiom
annotated source: skin of head
annotated property: subClassOf
annotated target: head or neck skin
is inferred: true

wall of esophagus
type: Class
equivalent class: Class
  intersection of: anatomical wall
  intersection of: Restriction
    on property: part_of
    some values from: esophagus
subclass of: gut wall
subclass of: Restriction
  on property: part_of
  some values from: esophagus
definition: An anatomical wall that is part of a esophagus [Automatically generated definition].
imported from: cl.owl
has exact synonym: anatomical wall of esophagus
has exact synonym: anatomical wall of gullet
has exact synonym: anatomical wall of oesophagus
has exact synonym: esophageal wall
has exact synonym: esophagus anatomical wall
has exact synonym: esophagus wall
has exact synonym: gullet anatomical wall
has exact synonym: gullet wall
has exact synonym: oesophagus anatomical wall
has exact synonym: oesophagus wall
has exact synonym: wall of gullet
has exact synonym: wall of oesophagus

Axiom
annotated source: wall of esophagus
annotated property: subClassOf
annotated target: gut wall
is inferred: true

vertebral column
type: Class
subclass of: subdivision of skeletal system
subclass of: Restriction
  on property: part_of
  some values from: postcranial axial skeletal system
subclass of: Restriction
  on property: has part
  some values from: vertebral element
definition: Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO].
imported from: cl.owl
has_broad_synonym: spine
has_narrow_synonym: backbone
has_narrow_synonym: vertebral column skeleton
has_related_synonym: columna vertebralis
has_related_synonym: dorsal spine
has_related_synonym: spinal column
has_related_synonym: vertebral region

Axiom
annotated source: vertebral column
annotated property: subClassOf
annotated target: subdivision of skeletal system
is inferred: true

skeletal muscle tissue
type: Class
subclass of: striated muscle tissue
subclass of: Restriction
  on property: part_of
  some values from: skeletal muscle organ
definition: Muscle tissue that consists primarily of skeletal muscle fibers.
imported from: cl.owl
has_broad_synonym: skeletal muscle
has_related_synonym: skeletal muscle system
has_related_synonym: somatic muscle

Axiom
annotated source: skeletal muscle tissue
annotated property: subClassOf
annotated target: striated muscle tissue
is inferred: true

wall of stomach
type: Class
equivalent class: Class
  intersection of: anatomical wall
  intersection of: Restriction
    on property: part_of
    some values from: stomach
subclass of: gut wall
subclass of: Restriction
  on property: part_of
  some values from: stomach
definition: the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between
imported from: cl.owl
has exact synonym: anatomical wall of stomach
has exact synonym: anatomical wall of ventriculus
has exact synonym: gastric wall
has exact synonym: stomach anatomical wall
has exact synonym: stomach wall
has exact synonym: ventriculus anatomical wall
has exact synonym: ventriculus wall
has exact synonym: wall of ventriculus

Axiom
annotated source: wall of stomach
annotated property: subClassOf
annotated target: gut wall
is inferred: true

portal lobule
type: Class
subclass of: endoderm-derived structure
subclass of: lobule
subclass of: Restriction
  on property: part_of
  some values from: liver parenchyma
definition: The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel.
imported from: cl.owl

Axiom
annotated source: portal lobule
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

Axiom
annotated source: portal lobule
annotated property: subClassOf
annotated target: lobule
is inferred: true

hepatic acinus
type: Class
subclass of: endoderm-derived structure
subclass of: acinus of exocrine gland
subclass of: Restriction
  on property: part_of
  some values from: liver parenchyma
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: portal lobule
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: liver lobule
definition: The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids.
imported from: cl.owl
has exact synonym: liver acinus
has exact synonym: portal acinus

Axiom
annotated source: hepatic acinus
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

Axiom
annotated source: hepatic acinus
annotated property: subClassOf
annotated target: acinus of exocrine gland
is inferred: true

biliary tree
type: Class
subclass of: endoderm-derived structure
subclass of: digestive system element
subclass of: Restriction
  on property: part_of
  some values from: biliary system
subclass of: Restriction
  on property: has part
  some values from: interlobular bile duct
subclass of: Restriction
  on property: has part
  some values from: intralobular bile duct
subclass of: Restriction
  on property: has part
  some values from: bile duct
subclass of: Restriction
  on property: has part
  some values from: extrahepatic bile duct
subclass of: Restriction
  on property: develops from
  some values from: biliary bud
definition: A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder.
imported from: cl.owl
has_related_synonym: biliary tract

Axiom
annotated source: biliary tree
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

Axiom
annotated source: biliary tree
annotated property: subClassOf
annotated target: digestive system element
is inferred: true

hepatic artery
type: Class
subclass of: artery
definition: An artery that supplies the liver.
imported from: cl.owl
has exact synonym: arteria hepatica propria
has_related_synonym: arteria hepatica

Axiom
annotated source: hepatic artery
annotated property: subClassOf
annotated target: artery
is inferred: true

mucosa of stomach
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: part_of
    some values from: stomach
subclass of: gastrointestinal system mucosa
subclass of: Restriction
  on property: part_of
  some values from: wall of stomach
definition: The mucosal layer that lines the stomach.
imported from: cl.owl
has exact synonym: gastric mucosa
has exact synonym: gastric mucous membrane
has exact synonym: mucosa of organ of stomach
has exact synonym: mucosa of organ of ventriculus
has exact synonym: mucosa of ventriculus
has exact synonym: mucous membrane of stomach
has exact synonym: mucous membrane of ventriculus
has exact synonym: organ mucosa of stomach
has exact synonym: organ mucosa of ventriculus
has exact synonym: stomach mucosa
has exact synonym: stomach mucosa of organ
has exact synonym: stomach mucous membrane
has exact synonym: stomach organ mucosa
has exact synonym: tunica mucosa (gaster)
has exact synonym: tunica mucosa gastricae
has exact synonym: ventriculus mucosa
has exact synonym: ventriculus mucosa of organ
has exact synonym: ventriculus mucous membrane
has exact synonym: ventriculus organ mucosa
has_related_synonym: Magenschleimhaut
has_related_synonym: tunica mucosa gastris

Axiom
annotated source: mucosa of stomach
annotated property: subClassOf
annotated target: gastrointestinal system mucosa
is inferred: true

intestinal mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: part_of
    some values from: intestine
subclass of: gastrointestinal system mucosa
subclass of: Restriction
  on property: part_of
  some values from: wall of intestine
definition: Mucosal layer that lines the intestine.
imported from: cl.owl
has exact synonym: bowel mucosa
has exact synonym: bowel mucosa of organ
has exact synonym: bowel mucous membrane
has exact synonym: bowel organ mucosa
has exact synonym: intestine mucosa
has exact synonym: intestine mucosa of organ
has exact synonym: intestine mucous membrane
has exact synonym: intestine organ mucosa
has exact synonym: mucosa of bowel
has exact synonym: mucosa of intestine
has exact synonym: mucosa of organ of bowel
has exact synonym: mucosa of organ of intestine
has exact synonym: mucous membrane of bowel
has exact synonym: mucous membrane of intestine
has exact synonym: organ mucosa of bowel
has exact synonym: organ mucosa of intestine
has exact synonym: tunica mucosa intestini

Axiom
annotated source: intestinal mucosa
annotated property: subClassOf
annotated target: gastrointestinal system mucosa
is inferred: true

interlobular bile duct
type: Class
subclass of: intrahepatic bile duct
subclass of: Restriction
  on property: part_of
  some values from: portal triad
definition: The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad.
imported from: cl.owl
has exact synonym: interlobular ductule

Axiom
annotated source: interlobular bile duct
annotated property: subClassOf
annotated target: intrahepatic bile duct
is inferred: true

wall of intestine
type: Class
equivalent class: Class
  intersection of: anatomical wall
  intersection of: Restriction
    on property: part_of
    some values from: intestine
subclass of: gut wall
subclass of: Restriction
  on property: part_of
  some values from: intestine
definition: An anatomical wall that is part of a intestine [Automatically generated definition].
imported from: cl.owl
has exact synonym: anatomical wall of bowel
has exact synonym: anatomical wall of intestine
has exact synonym: bowel anatomical wall
has exact synonym: bowel wall
has exact synonym: intestinal wall
has exact synonym: intestine anatomical wall
has exact synonym: intestine wall
has exact synonym: wall of bowel
has_related_synonym: bowel wall

Axiom
annotated source: wall of intestine
annotated property: subClassOf
annotated target: gut wall
is inferred: true

pelvic girdle region
type: Class
equivalent class: Class
  intersection of: appendage girdle region
  intersection of: Restriction
    on property: part_of
    some values from: pelvic complex
subclass of: appendage girdle region
subclass of: UBERON_0015212
subclass of: Restriction
  on property: part_of
  some values from: pelvic region of trunk
subclass of: Restriction
  on property: part_of
  some values from: pelvic complex
subclass of: Restriction
  on property: has part
  some values from: pelvic girdle skeleton
definition: The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions.
imported from: cl.owl
has_related_synonym: girdle - pelvic
has_related_synonym: pelvic girdle

Axiom
annotated source: pelvic girdle region
annotated property: subClassOf
annotated target: appendage girdle region
is inferred: true

Axiom
annotated source: pelvic girdle region
annotated property: subClassOf
annotated target: UBERON_0015212
is inferred: true

epithelium of stomach
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: stomach
subclass of: simple columnar epithelium
subclass of: epithelium of mucosa
subclass of: gastrointestinal system epithelium
subclass of: UBERON_0015833
subclass of: Restriction
  on property: part_of
  some values from: mucosa of stomach
definition: The epithelial layer of the stomach .
imported from: cl.owl
has exact synonym: epithelial tissue of stomach
has exact synonym: epithelial tissue of ventriculus
has exact synonym: epithelium of ventriculus
has exact synonym: stomach epithelial tissue
has exact synonym: stomach epithelium
has exact synonym: ventriculus epithelial tissue
has exact synonym: ventriculus epithelium
has_related_synonym: gastric epithelium

Axiom
annotated source: epithelium of stomach
annotated property: subClassOf
annotated target: simple columnar epithelium
is inferred: true

Axiom
annotated source: epithelium of stomach
annotated property: subClassOf
annotated target: epithelium of mucosa
is inferred: true

Axiom
annotated source: epithelium of stomach
annotated property: subClassOf
annotated target: gastrointestinal system epithelium
is inferred: true

Axiom
annotated source: epithelium of stomach
annotated property: subClassOf
annotated target: UBERON_0015833
is inferred: true

intestinal epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: intestine
subclass of: simple columnar epithelium
subclass of: epithelium of mucosa
subclass of: digestive tract epithelium
subclass of: gastrointestinal system epithelium
subclass of: Restriction
  on property: part_of
  some values from: intestinal mucosa
definition: Epithelial layer that lines the intestine.
imported from: cl.owl
has exact synonym: bowel epithelial tissue
has exact synonym: bowel epithelium
has exact synonym: epithelial tissue of bowel
has exact synonym: epithelial tissue of intestine
has exact synonym: epithelium of bowel
has exact synonym: epithelium of intestine
has exact synonym: intestine epithelial tissue
has_narrow_synonym: villous epithelium
has_related_synonym: intestine epithelium

Axiom
annotated source: intestinal epithelium
annotated property: subClassOf
annotated target: simple columnar epithelium
is inferred: true

Axiom
annotated source: intestinal epithelium
annotated property: subClassOf
annotated target: epithelium of mucosa
is inferred: true

Axiom
annotated source: intestinal epithelium
annotated property: subClassOf
annotated target: digestive tract epithelium
is inferred: true

Axiom
annotated source: intestinal epithelium
annotated property: subClassOf
annotated target: gastrointestinal system epithelium
is inferred: true

portal triad
type: Class
subclass of: endoderm-derived structure
subclass of: UBERON_0034921
subclass of: Restriction
  on property: part_of
  some values from: hepatic acinus
subclass of: Restriction
  on property: has part
  some values from: hepatic artery
subclass of: Restriction
  on property: has part
  some values from: portal vein
subclass of: Restriction
  on property: has part
  some values from: intrahepatic bile duct
definition: A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel
imported from: cl.owl
has exact synonym: trias hepatica
has_related_synonym: trias hepatica

Axiom
annotated source: portal triad
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

Axiom
annotated source: portal triad
annotated property: subClassOf
annotated target: UBERON_0034921
is inferred: true

liver parenchyma
type: Class
equivalent class: Class
  intersection of: parenchyma
  intersection of: Restriction
    on property: part_of
    some values from: liver
subclass of: parenchyma
subclass of: endoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: liver
subclass of: Restriction
  on property: develops from
  some values from: hepatic diverticulum
definition: The functional units of the liver including the lobules.
imported from: cl.owl
has exact synonym: hepatic parenchyma
has exact synonym: liver parenchyme
has exact synonym: parenchyma of liver
has_related_synonym: hepatic parenchyme

Axiom
annotated source: liver parenchyma
annotated property: subClassOf
annotated target: parenchyma
is inferred: true

Axiom
annotated source: liver parenchyma
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

intralobular bile duct
type: Class
subclass of: intrahepatic bile duct
subclass of: interlobular duct
subclass of: Restriction
  on property: part_of
  some values from: hepatic acinus
subclass of: Restriction
  on property: part_of
  some values from: liver lobule
definition: the tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule
imported from: cl.owl
has exact synonym: canal of Herring
has exact synonym: cholangiole
has exact synonym: ductus interlobularis bilifer
has_related_synonym: canal of Hering
has_related_synonym: canals of Hering
has_related_synonym: duct of Herring
has_related_synonym: intrahepatic bile ductule

Axiom
annotated source: intralobular bile duct
annotated property: subClassOf
annotated target: intrahepatic bile duct
is inferred: true

Axiom
annotated source: intralobular bile duct
annotated property: subClassOf
annotated target: interlobular duct
is inferred: true

anal region
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: terminal part of digestive tract
definition: The anus and surrounding regions. Encompasses both internal and external regions, where present
imported from: cl.owl
has_related_synonym: posterior
has_related_synonym: posterior end of organism

Axiom
annotated source: anal region
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

skeletal system
type: Class
equivalent class: Class
  intersection of: organ system subdivision
  intersection of: Restriction
    on property: has part
    some values from: skeleton
  intersection of: Restriction
    on property: has part
    some values from: articular system
subclass of: organ system subdivision
subclass of: Restriction
  on property: part_of
  some values from: musculoskeletal system
subclass of: Restriction
  on property: has part
  some values from: skeleton
subclass of: Restriction
  on property: has part
  some values from: articular system
definition: Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
imported from: cl.owl
has exact synonym: skeleton system
has_narrow_synonym: set of all bones and joints
has_related_synonym: Skelettsystem

Axiom
annotated source: skeletal system
annotated property: subClassOf
annotated target: organ system subdivision
is inferred: true

hindlimb skeleton
type: Class
subclass of: skeleton of limb
subclass of: pelvic appendage skeleton
subclass of: Restriction
  on property: part_of
  some values from: hindlimb
subclass of: Restriction
  on property: part_of
  some values from: skeleton of pelvic complex
definition: Subdivision of skeleton consisting of all skeletal elements in an hindlimb region.
imported from: cl.owl
has exact synonym: bones of lower limb
has exact synonym: free lower limb skeleton
has exact synonym: hind limb skeleton
has exact synonym: hind-limb skeleton
has exact synonym: hindlimb skeleton
has exact synonym: lower limb skeleton
has exact synonym: ossa membri inferioris
has exact synonym: set of bones of lower limb
has exact synonym: skeleton of free lower limb
has exact synonym: skeleton of lower limb

Axiom
annotated source: hindlimb skeleton
annotated property: subClassOf
annotated target: skeleton of limb
is inferred: true

Axiom
annotated source: hindlimb skeleton
annotated property: subClassOf
annotated target: pelvic appendage skeleton
is inferred: true

hip
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: part_of
  some values from: pelvic complex
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: pelvic girdle region
definition: The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified].
imported from: cl.owl
has exact synonym: hip region
has exact synonym: regio coxae
has_related_synonym: coxa

Axiom
annotated source: hip
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

bone element
type: Class
subclass of: skeletal element
subclass of: Restriction
  on property: has part
  some values from: bone tissue
definition: Skeletal element that is composed of bone tissue.
imported from: cl.owl
has exact synonym: bone organ
has_related_synonym: bone
has_related_synonym: bones

Axiom
annotated source: bone element
annotated property: subClassOf
annotated target: skeletal element
is inferred: true

digestive tract
type: Class
subclass of: tube
subclass of: Restriction
  on property: part_of
  some values from: digestive system
subclass of: Restriction
  on property: develops from
  some values from: presumptive gut
definition: A tube extending from the mouth to the anus.
imported from: cl.owl
has_broad_synonym: gut
has exact synonym: digestive tube
has exact synonym: enteric tract
has_narrow_synonym: alimentary canal
has_narrow_synonym: alimentary tract
has_related_synonym: digestive canal
has_related_synonym: gut tube

Axiom
annotated source: digestive tract
annotated property: subClassOf
annotated target: tube
is inferred: true

lower respiratory tract
type: Class
subclass of: anatomical structure
subclass of: proximo-distal subdivision of respiratory tract
subclass of: Restriction
  on property: has part
  some values from: pair of lungs
definition: The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]
imported from: cl.owl

Axiom
annotated source: lower respiratory tract
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: lower respiratory tract
annotated property: subClassOf
annotated target: proximo-distal subdivision of respiratory tract
is inferred: true

muscle organ
type: Class
subclass of: anatomical structure
subclass of: organ
subclass of: muscle structure
subclass of: Restriction
  on property: part_of
  some values from: musculature
subclass of: Restriction
  on property: has part
  some values from: muscle tissue
definition: Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
imported from: cl.owl
has_broad_synonym: muscle

Axiom
annotated source: muscle organ
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: muscle organ
annotated property: subClassOf
annotated target: organ
is inferred: true

Axiom
annotated source: muscle organ
annotated property: subClassOf
annotated target: muscle structure
is inferred: true

artery
type: Class
subclass of: arterial blood vessel
definition: An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
imported from: cl.owl
has exact synonym: arterial subtree
has exact synonym: arterial tree organ part
has exact synonym: arteries
has_related_synonym: arterial system
has_related_synonym: arterial vessel

Axiom
annotated source: artery
annotated property: subClassOf
annotated target: arterial blood vessel
is inferred: true

vein
type: Class
subclass of: venous blood vessel
definition: Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
imported from: cl.owl
has_broad_synonym: venous subtree
has_broad_synonym: venous vessel
has exact synonym: venous tree organ part
has_related_synonym: vascular element
has_related_synonym: vena
has_related_synonym: venae

Axiom
annotated source: vein
annotated property: subClassOf
annotated target: venous blood vessel
is inferred: true

forebrain
type: Class
subclass of: regional part of brain
subclass of: Restriction
  on property: develops from
  some values from: anterior neural tube
subclass of: Restriction
  on property: develops from
  some values from: future forebrain
definition: The most anterior region the brain including both the telencephalon and diencephalon.
imported from: cl.owl
has_broad_synonym: FB
has_related_synonym: prosencephalon

Axiom
annotated source: forebrain
annotated property: subClassOf
annotated target: regional part of brain
is inferred: true

epithelium of trachea
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: trachea
subclass of: lower respiratory tract epithelium
subclass of: Restriction
  on property: part_of
  some values from: trachea
definition: the epithelial lining of the trachea which contains numerous ciliated cells
imported from: cl.owl
has exact synonym: epithelial tissue of trachea
has exact synonym: epithelial tissue of windpipe
has exact synonym: epithelium of windpipe
has exact synonym: trachea epithelial tissue
has exact synonym: trachea epithelium
has exact synonym: tracheal epithelium
has exact synonym: windpipe epithelial tissue
has exact synonym: windpipe epithelium

Axiom
annotated source: epithelium of trachea
annotated property: subClassOf
annotated target: lower respiratory tract epithelium
is inferred: true

epithelium of respiratory bronchiole
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: respiratory bronchiole
subclass of: epithelium of bronchiole
subclass of: Restriction
  on property: part_of
  some values from: respiratory bronchiole
definition: An epithelium that is part of a respiratory bronchiole [Automatically generated definition].
imported from: cl.owl
has exact synonym: bronchiolus respiratorius epithelial tissue
has exact synonym: bronchiolus respiratorius epithelium
has exact synonym: epithelial tissue of bronchiolus respiratorius
has exact synonym: epithelial tissue of respiratory bronchiole
has exact synonym: epithelium of bronchiolus respiratorius
has exact synonym: respiratory bronchiole epithelial tissue
has exact synonym: respiratory bronchiole epithelium

Axiom
annotated source: epithelium of respiratory bronchiole
annotated property: subClassOf
annotated target: epithelium of bronchiole
is inferred: true

terminal bronchiole epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: terminal bronchiole
subclass of: epithelium of bronchiole
subclass of: Restriction
  on property: part_of
  some values from: terminal bronchiole
definition: An epithelium that lines a terminal bronchiole.
imported from: cl.owl
has exact synonym: bronchiolus terminalis epithelial tissue
has exact synonym: bronchiolus terminalis epithelium
has exact synonym: epithelial tissue of bronchiolus terminalis
has exact synonym: epithelial tissue of terminal bronchiole
has exact synonym: epithelium of bronchiolus terminalis
has exact synonym: epithelium of terminal bronchiole
has exact synonym: terminal bronchiole epithelial tissue
has exact synonym: terminal bronchiole epithelium

Axiom
annotated source: terminal bronchiole epithelium
annotated property: subClassOf
annotated target: epithelium of bronchiole
is inferred: true

blood plasma
type: Class
subclass of: haemolymphatic fluid
subclass of: Restriction
  on property: part_of
  some values from: blood
definition: The liquid component of blood, in which erythrocytes are suspended.
imported from: cl.owl
has_broad_synonym: plasma
has_broad_synonym: portion of plasma
has exact synonym: blood plasm
has exact synonym: portion of blood plasma

Axiom
annotated source: blood plasma
annotated property: subClassOf
annotated target: haemolymphatic fluid
is inferred: true

epithelium of esophagus
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: esophagus
subclass of: epithelium of mucosa
subclass of: digestive tract epithelium
subclass of: Restriction
  on property: part_of
  some values from: esophagus mucosa
definition: the epithelial layer that lines the luminal space of the esophagus
imported from: cl.owl
has exact synonym: epithelial tissue of esophagus
has exact synonym: epithelial tissue of gullet
has exact synonym: epithelial tissue of oesophagus
has exact synonym: epithelium of gullet
has exact synonym: epithelium of oesophagus
has exact synonym: esophageal epithelium
has exact synonym: esophagus epithelial tissue
has exact synonym: esophagus epithelium
has exact synonym: gullet epithelial tissue
has exact synonym: gullet epithelium
has exact synonym: oesophagus epithelial tissue
has_related_synonym: oesophagus epithelium

Axiom
annotated source: epithelium of esophagus
annotated property: subClassOf
annotated target: epithelium of mucosa
is inferred: true

Axiom
annotated source: epithelium of esophagus
annotated property: subClassOf
annotated target: digestive tract epithelium
is inferred: true

blood vessel
type: Class
subclass of: vessel
subclass of: mesoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: blood vasculature
subclass of: Restriction
  on property: has part
  some values from: epithelial tube open at both ends
subclass of: Restriction
  on property: develops from
  some values from: splanchnic layer of lateral plate mesoderm
subclass of: Restriction
  on property: develops from
  some values from: vascular cord
definition: A vessel through which blood circulates in the body.
imported from: cl.owl
has_broad_synonym: vascular element
has exact synonym: region of vascular tree organ
has exact synonym: vascular tree organ region
has_related_synonym: vas sanguineum

Axiom
annotated source: blood vessel
annotated property: subClassOf
annotated target: vessel
is inferred: true

Axiom
annotated source: blood vessel
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

crypt of Lieberkuhn
type: Class
subclass of: intestinal gland
definition: the tubular intestinal glands found in the mucosal membranes
imported from: cl.owl
has_broad_synonym: intestinal gland
has exact synonym: Lieberkuhn crypt
has exact synonym: Lieberkuhn gland
has exact synonym: Lieberkuhn's gland
has exact synonym: Lieberkuhn's glands
has exact synonym: crypt of Lieberkuhn
has exact synonym: crypt of Lieberkühn
has exact synonym: crypts of Lieberkühn
has exact synonym: follicles of lieberkuhn
has exact synonym: intestinal crypt
has exact synonym: intestinal crypts
has exact synonym: lieberkuhn crypt
has_related_synonym: intestinal gland of Lieberkuhn

Axiom
annotated source: crypt of Lieberkuhn
annotated property: subClassOf
annotated target: intestinal gland
is inferred: true

placenta
type: Class
subclass of: organ
subclass of: mesoderm-derived structure
subclass of: reproductive structure
subclass of: Restriction
  on property: part_of
  some values from: female reproductive system
subclass of: Restriction
  on property: part_of
  some values from: UBERON_0016887
subclass of: Restriction
  on property: develops from
  some values from: uterus
subclass of: Restriction
  on property: develops from
  some values from: chorion
subclass of: Restriction
  on property: develops from
  some values from: allantois
definition: organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
imported from: cl.owl
has exact synonym: allantoic placenta
has exact synonym: eutherian placenta

Axiom
annotated source: placenta
annotated property: subClassOf
annotated target: organ
is inferred: true

Axiom
annotated source: placenta
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: placenta
annotated property: subClassOf
annotated target: reproductive structure
is inferred: true

papillary layer of dermis
type: Class
subclass of: ectoderm-derived structure
subclass of: integumentary system layer
subclass of: Restriction
  on property: part_of
  some values from: dermis
subclass of: Restriction
  on property: has part
  some values from: areolar connective tissue
subclass of: Restriction
  on property: has part
  some values from: dense irregular connective tissue
definition: The upper layer of the dermis beneath the epidermis, composed of dense irregular connective tissue[ncit,modified].
imported from: cl.owl
has exact synonym: corpus papillary
has exact synonym: dermis papillary layer
has exact synonym: papillary dermis
has exact synonym: papillary layer
has exact synonym: papillary layer of dermis
has exact synonym: stratum papillare
has exact synonym: stratum papillare (dermis)
has exact synonym: stratum papillare corii
has exact synonym: stratum papillare dermis
has exact synonym: superficial dermis
has_related_synonym: dermal papillary layer
has_related_synonym: stratum papillare

Axiom
annotated source: papillary layer of dermis
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

Axiom
annotated source: papillary layer of dermis
annotated property: subClassOf
annotated target: integumentary system layer
is inferred: true

portal vein
type: Class
subclass of: vein
subclass of: Restriction
  on property: part_of
  some values from: portal system
definition: A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO].
imported from: cl.owl
has exact synonym: portal venous tree organ part

Axiom
annotated source: portal vein
annotated property: subClassOf
annotated target: vein
is inferred: true

stratum basale of epidermis
type: Class
subclass of: ectoderm-derived structure
subclass of: structure with developmental contribution from neural crest
subclass of: integumentary system layer
subclass of: Restriction
  on property: part_of
  some values from: skin epidermis
definition: the deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells
imported from: cl.owl
has_broad_synonym: Malpighian layer
has_broad_synonym: rete Malphighii
has_broad_synonym: rete Malpighii
has_broad_synonym: stratum Malpighi
has_broad_synonym: stratum basale
has_broad_synonym: stratum germinosum
has exact synonym: basal cell layer of epidermis
has exact synonym: basal epidermal layer
has exact synonym: epidermal basal stratum
has exact synonym: epidermis stratum basale
has exact synonym: stratum basalis of epidermis
has exact synonym: stratum germinativum
has exact synonym: stratum germinosum of epidermis
has_related_synonym: basal cell layer of skin
has_related_synonym: basal layer of epidermis
has_related_synonym: epidermis basal layer
has_related_synonym: epidermis sensorial layer
has_related_synonym: epidermis stratum germinativum

Axiom
annotated source: stratum basale of epidermis
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

Axiom
annotated source: stratum basale of epidermis
annotated property: subClassOf
annotated target: structure with developmental contribution from neural crest
is inferred: true

Axiom
annotated source: stratum basale of epidermis
annotated property: subClassOf
annotated target: integumentary system layer
is inferred: true

epithelium of bronchus
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: bronchus
subclass of: lower respiratory tract epithelium
subclass of: Restriction
  on property: part_of
  some values from: bronchus
definition: An epithelium that is part of a bronchus [Automatically generated definition].
imported from: cl.owl
has exact synonym: bronchi epithelial tissue
has exact synonym: bronchi epithelium
has exact synonym: bronchial epithelium
has exact synonym: bronchial trunk epithelial tissue
has exact synonym: bronchial trunk epithelium
has exact synonym: bronchus epithelial tissue
has exact synonym: bronchus epithelium
has exact synonym: epithelial tissue of bronchi
has exact synonym: epithelial tissue of bronchial trunk
has exact synonym: epithelial tissue of bronchus
has exact synonym: epithelium of bronchi
has exact synonym: epithelium of bronchial trunk

Axiom
annotated source: epithelium of bronchus
annotated property: subClassOf
annotated target: lower respiratory tract epithelium
is inferred: true

striated muscle tissue
type: Class
subclass of: muscle tissue
definition: Muscle tissue that contains fibers that are divided by transverse bands into striations.
imported from: cl.owl
has exact synonym: striated muscle

Axiom
annotated source: striated muscle tissue
annotated property: subClassOf
annotated target: muscle tissue
is inferred: true

lung
type: Class
subclass of: respiration organ
subclass of: endoderm-derived structure
subclass of: thoracic cavity element
subclass of: UBERON_0015212
subclass of: Restriction
  on property: part_of
  some values from: pair of lungs
subclass of: Restriction
  on property: develops from
  some values from: lung bud
definition: Respiration organ that develops as an oupocketing of the esophagus.
imported from: cl.owl
has exact synonym: pulmo

Axiom
annotated source: lung
annotated property: subClassOf
annotated target: respiration organ
is inferred: true

Axiom
annotated source: lung
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

Axiom
annotated source: lung
annotated property: subClassOf
annotated target: thoracic cavity element
is inferred: true

Axiom
annotated source: lung
annotated property: subClassOf
annotated target: UBERON_0015212
is inferred: true

vasculature
type: Class
subclass of: anatomical cluster
subclass of: Restriction
  on property: part_of
  some values from: vascular system
subclass of: Restriction
  on property: has part
  some values from: vessel
subclass of: Restriction
  on property: has part
  some values from: haemolymphatic fluid
definition: An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
imported from: cl.owl
has exact synonym: vascular network

Axiom
annotated source: vasculature
annotated property: subClassOf
annotated target: anatomical cluster
is inferred: true

embryonic structure
type: Class
equivalent class: Class
  intersection of: developing anatomical structure
  intersection of: Restriction
    on property: part_of
    some values from: embryo
subclass of: developing anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: embryo
definition: Anatomical structure that is part of an embryo.
imported from: cl.owl
has exact synonym: developing embryonic structure
has exact synonym: embryonic anatomical structure
has_related_synonym: developing structure
has_related_synonym: embryonale Struktur
has_related_synonym: embryonic structures

Axiom
annotated source: embryonic structure
annotated property: subClassOf
annotated target: developing anatomical structure
is inferred: true

epithelium of bronchiole
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: bronchiole
subclass of: lung epithelium
subclass of: epithelium of bronchus
subclass of: epithelium of mucosa
subclass of: Restriction
  on property: part_of
  some values from: mucosa of bronchiole
definition: An epithelium that is part of a bronchiole [Automatically generated definition].
imported from: cl.owl
has exact synonym: bronchiolar epithelium
has exact synonym: bronchiole epithelial tissue
has exact synonym: bronchiole epithelium
has exact synonym: epithelial tissue of bronchiole
has exact synonym: epithelial tissue of lobular bronchiole
has exact synonym: epithelium of lobular bronchiole
has exact synonym: lobular bronchiole epithelial tissue
has exact synonym: lobular bronchiole epithelium

Axiom
annotated source: epithelium of bronchiole
annotated property: subClassOf
annotated target: lung epithelium
is inferred: true

Axiom
annotated source: epithelium of bronchiole
annotated property: subClassOf
annotated target: epithelium of bronchus
is inferred: true

Axiom
annotated source: epithelium of bronchiole
annotated property: subClassOf
annotated target: epithelium of mucosa
is inferred: true

dermis
type: Class
subclass of: ectoderm-derived structure
subclass of: structure with developmental contribution from neural crest
subclass of: integumentary system layer
subclass of: Restriction
  on property: part_of
  some values from: skin of body
subclass of: Restriction
  on property: has part
  some values from: connective tissue
subclass of: Restriction
  on property: has part
  some values from: collection of collagen fibrils
subclass of: Restriction
  on property: develops from
  some values from: future dermis
definition: The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
imported from: cl.owl
has exact synonym: vertebrate dermis
has_related_synonym: corium
has_related_synonym: cutis

Axiom
annotated source: dermis
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

Axiom
annotated source: dermis
annotated property: subClassOf
annotated target: structure with developmental contribution from neural crest
is inferred: true

Axiom
annotated source: dermis
annotated property: subClassOf
annotated target: integumentary system layer
is inferred: true

hypodermis
type: Class
subclass of: mesoderm-derived structure
subclass of: integumentary system layer
subclass of: Restriction
  on property: part_of
  some values from: integument
subclass of: Restriction
  on property: has part
  some values from: adipose tissue
subclass of: Restriction
  on property: has part
  some values from: loose connective tissue
definition: Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
imported from: cl.owl
has exact synonym: hypoderm
has exact synonym: vertebrate hypodermis
has_related_synonym: sub-tegumental tissue
has_related_synonym: subcutaneous tissue
has_related_synonym: subcutis
has_related_synonym: subtegumental tissue
has_related_synonym: superficial fascia
has_related_synonym: tela subcutanea

Axiom
annotated source: hypodermis
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: hypodermis
annotated property: subClassOf
annotated target: integumentary system layer
is inferred: true

postcranial axial skeleton
type: Class
subclass of: subdivision of skeleton
subclass of: Restriction
  on property: part_of
  some values from: axial skeleton plus cranial skeleton
subclass of: Restriction
  on property: part_of
  some values from: postcranial axial skeletal system
definition: The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
imported from: cl.owl
has_broad_synonym: axial skeleton
has exact synonym: post-cranial axial skeleton

Axiom
annotated source: postcranial axial skeleton
annotated property: subClassOf
annotated target: subdivision of skeleton
is inferred: true

appendicular skeleton
type: Class
subclass of: subdivision of skeleton
subclass of: Restriction
  on property: part_of
  some values from: appendicular skeletal system
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: appendage
definition: Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
imported from: cl.owl
has exact synonym: appendicular skeleton
has exact synonym: entire appendicular skeleton
has_narrow_synonym: paired fin skeleton
has_related_synonym: skeleton appendiculare

Axiom
annotated source: appendicular skeleton
annotated property: subClassOf
annotated target: subdivision of skeleton
is inferred: true

skin of body
type: Class
subclass of: anatomical structure
subclass of: organ
subclass of: ectoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: integument
subclass of: Restriction
  on property: has part
  some values from: zone of skin
subclass of: Restriction
  on property: develops from
  some values from: embryonic skin basal layer
definition: The organ covering the body that consists of the dermis and epidermis.
imported from: cl.owl
has exact synonym: entire skin
has exact synonym: skin organ
has_related_synonym: entire integument
has_related_synonym: integument
has_related_synonym: integumental organ
has_related_synonym: pelt
has_related_synonym: skin

Axiom
annotated source: skin of body
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: skin of body
annotated property: subClassOf
annotated target: organ
is inferred: true

Axiom
annotated source: skin of body
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

trunk
type: Class
subclass of: subdivision of organism along main body axis
subclass of: Restriction
  on property: part_of
  some values from: body proper
definition: Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
imported from: cl.owl
has exact synonym: thoracolumbar region
has exact synonym: torso
has exact synonym: trunk region
has_related_synonym: Rumpf

Axiom
annotated source: trunk
annotated property: subClassOf
annotated target: subdivision of organism along main body axis
is inferred: true

limb
type: Class
subclass of: paired limb/fin
subclass of: Restriction
  on property: has part
  some values from: skeleton of limb
subclass of: Restriction
  on property: develops from
  some values from: limb bud
definition: A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts.
imported from: cl.owl
has exact synonym: free limb
has exact synonym: limb sensu Vertebrata
has exact synonym: pentadactyl limb
has exact synonym: tetrapod limb
has_narrow_synonym: flipper
has_related_synonym: extremities
has_related_synonym: extremity

Axiom
annotated source: limb
annotated property: subClassOf
annotated target: paired limb/fin
is inferred: true

hindlimb
type: Class
equivalent class: Class
  intersection of: limb
  intersection of: Restriction
    on property: part_of
    some values from: pelvic complex
subclass of: limb
subclass of: pelvic appendage
subclass of: Restriction
  on property: part_of
  some values from: posterior region of body
subclass of: Restriction
  on property: has part
  some values from: hindlimb skeleton
subclass of: Restriction
  on property: develops from
  some values from: hindlimb bud
definition: A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts.
imported from: cl.owl
has exact synonym: free lower limb
has exact synonym: hind limb
has exact synonym: hind-limb
has exact synonym: hindlimb
has exact synonym: inferior member
has exact synonym: lower limb
has exact synonym: membrum inferius
has_related_synonym: free part of lower limb
has_related_synonym: lower extremity
has_related_synonym: membrum inferius
has_related_synonym: pelvic appendage

Axiom
annotated source: hindlimb
annotated property: subClassOf
annotated target: limb
is inferred: true

Axiom
annotated source: hindlimb
annotated property: subClassOf
annotated target: pelvic appendage
is inferred: true

liver
type: Class
subclass of: anatomical structure
subclass of: exocrine gland
subclass of: endoderm-derived structure
subclass of: abdomen element
subclass of: digestive system gland
subclass of: Restriction
  on property: part_of
  some values from: abdomen
subclass of: Restriction
  on property: part_of
  some values from: endocrine system
subclass of: Restriction
  on property: part_of
  some values from: digestive system
subclass of: Restriction
  on property: part_of
  some values from: exocrine system
subclass of: Restriction
  on property: part_of
  some values from: hepatobiliary system
subclass of: Restriction
  on property: has part
  some values from: liver lobule
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: immune system
subclass of: Restriction
  on property: develops from
  some values from: liver primordium
subclass of: Restriction
  on property: develops from
  some values from: septum transversum
subclass of: Restriction
  on property: develops from
  some values from: liver bud
definition: An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
imported from: cl.owl
has_related_synonym: iecur
has_related_synonym: jecur

Axiom
annotated source: liver
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: liver
annotated property: subClassOf
annotated target: exocrine gland
is inferred: true

Axiom
annotated source: liver
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

Axiom
annotated source: liver
annotated property: subClassOf
annotated target: abdomen element
is inferred: true

Axiom
annotated source: liver
annotated property: subClassOf
annotated target: digestive system gland
is inferred: true

right lung
type: Class
subclass of: lung
subclass of: Restriction
  on property: part_of
  some values from: pair of lungs
definition: Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
imported from: cl.owl

Axiom
annotated source: right lung
annotated property: subClassOf
annotated target: lung
is inferred: true

left lung
type: Class
subclass of: lung
subclass of: Restriction
  on property: part_of
  some values from: pair of lungs
definition: Lung which consists of the left upper lobe and left lower lobe.[FMA]
imported from: cl.owl

Axiom
annotated source: left lung
annotated property: subClassOf
annotated target: lung
is inferred: true

bronchus
type: Class
subclass of: respiratory tube
subclass of: Restriction
  on property: part_of
  some values from: tracheobronchial tree
definition: the upper conducting airways of the lung; these airways arise from the terminus of the trachea
imported from: cl.owl
has exact synonym: bronchi
has exact synonym: bronchial trunk
has_related_synonym: bronchial tissue

Axiom
annotated source: bronchus
annotated property: subClassOf
annotated target: respiratory tube
is inferred: true

bronchiole
type: Class
subclass of: respiratory tube
subclass of: Restriction
  on property: part_of
  some values from: lung
subclass of: Restriction
  on property: part_of
  some values from: bronchus
subclass of: Restriction
  on property: part_of
  some values from: tracheobronchial tree
subclass of: Restriction
  on property: part_of
  some values from: pulmonary lobule
definition: the conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching
imported from: cl.owl
has exact synonym: lobular bronchiole
has_related_synonym: bronchioli
has_related_synonym: bronchiolus

Axiom
annotated source: bronchiole
annotated property: subClassOf
annotated target: respiratory tube
is inferred: true

terminal bronchiole
type: Class
subclass of: bronchiole
definition: the last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls
imported from: cl.owl
has exact synonym: bronchiolus terminalis
has_related_synonym: bronchioli terminalis
has_related_synonym: terminal bronchiole tube

Axiom
annotated source: terminal bronchiole
annotated property: subClassOf
annotated target: bronchiole
is inferred: true

respiratory bronchiole
type: Class
subclass of: bronchiole
subclass of: Restriction
  on property: part_of
  some values from: pulmonary acinus
definition: A bronchiole that is the first segment of the respiratory zone.
imported from: cl.owl
has exact synonym: bronchiolus respiratorii
has exact synonym: bronchiolus respiratorius

Axiom
annotated source: respiratory bronchiole
annotated property: subClassOf
annotated target: bronchiole
is inferred: true

hemolymphoid system
type: Class
subclass of: anatomical system
definition: Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
imported from: cl.owl
has exact synonym: hematolymphoid system
has exact synonym: lymphomyeloid complex
has_related_synonym: haemolymphoid system

Axiom
annotated source: hemolymphoid system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

integument
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part_of
  some values from: multicellular organism
subclass of: Restriction
  on property: part_of
  some values from: integumental system
subclass of: Restriction
  on property: has part
  some values from: hypodermis
subclass of: Restriction
  on property: has part
  some values from: skin of body
definition: The dermis, epidermis and hypodermis.
imported from: cl.owl
has exact synonym: dermis plus epidermis plus hypodermis
has exact synonym: integumentum commune
has exact synonym: skin and subcutaneous tissue
has exact synonym: skin plus hypodermis
has exact synonym: the integument
has_related_synonym: Hautsystem@de
has_related_synonym: dermal system
has_related_synonym: dermoid system
has_related_synonym: skin
has_related_synonym: tegument
has_related_synonym: vertebrate integument

Axiom
annotated source: integument
annotated property: subClassOf
annotated target: organ system subdivision
is inferred: true

musculoskeletal system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: has part
  some values from: musculature of body
subclass of: Restriction
  on property: has part
  some values from: skeletal system
definition: Anatomical system that consists of the muscular and skeletal systems.
imported from: cl.owl
has exact synonym: musculo-skeletal system

Axiom
annotated source: musculoskeletal system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

synovial joint
type: Class
subclass of: skeletal joint
definition: Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
imported from: cl.owl
has exact synonym: articulatio synoviale
has exact synonym: diarthroses
has exact synonym: diarthrosis
has exact synonym: diarthrosis joint
has_related_synonym: diarthrodial joints

Axiom
annotated source: synovial joint
annotated property: subClassOf
annotated target: skeletal joint
is inferred: true

biliary system
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part_of
  some values from: hepatobiliary system
subclass of: Restriction
  on property: has part
  some values from: biliary tree
definition: Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree).
imported from: cl.owl
has exact synonym: biliary apparatus
has_related_synonym: biliary tract

Axiom
annotated source: biliary system
annotated property: subClassOf
annotated target: organ system subdivision
is inferred: true

somite
type: Class
subclass of: developing anatomical structure
subclass of: epithelial vesicle
subclass of: Restriction
  on property: develops from
  some values from: presomitic mesoderm
definition: Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
imported from: cl.owl
has_broad_synonym: mesodermal cluster
has_related_synonym: epimere
has_related_synonym: epimere mesoderm
has_related_synonym: epithelial somite
has_related_synonym: somites
has_related_synonym: somitic mesoderm
has_related_synonym: somitus

Axiom
annotated source: somite
annotated property: subClassOf
annotated target: developing anatomical structure
is inferred: true

Axiom
annotated source: somite
annotated property: subClassOf
annotated target: epithelial vesicle
is inferred: true

exocrine system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: has part
  some values from: exocrine gland
definition: Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
imported from: cl.owl
has exact synonym: exocrine glandular system

Axiom
annotated source: exocrine system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

umbilical cord
type: Class
subclass of: extraembryonic structure
subclass of: Restriction
  on property: develops from
  some values from: connecting stalk
definition: The connecting cord from the developing embryo to the placenta.
imported from: cl.owl
has exact synonym: chorda umbilicalis
has exact synonym: funiculus umbilicalis
has_related_synonym: birth cord
has_related_synonym: connecting stalk
has_related_synonym: funiculus umbilicalis
has_related_synonym: yolk stalk

Axiom
annotated source: umbilical cord
annotated property: subClassOf
annotated target: extraembryonic structure
is inferred: true

neural crest
type: Class
subclass of: ectoderm-derived structure
subclass of: structure with developmental contribution from neural crest
subclass of: germ layer / neural crest
subclass of: Restriction
  on property: part_of
  some values from: neurectoderm
subclass of: Restriction
  on property: develops from
  some values from: neural plate
subclass of: Restriction
  on property: develops from
  some values from: neural fold
definition: A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
imported from: cl.owl
has exact synonym: NC
has_related_synonym: crista neuralis
has_related_synonym: neural crest material

Axiom
annotated source: neural crest
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

Axiom
annotated source: neural crest
annotated property: subClassOf
annotated target: structure with developmental contribution from neural crest
is inferred: true

Axiom
annotated source: neural crest
annotated property: subClassOf
annotated target: germ layer / neural crest
is inferred: true

neurectoderm
type: Class
subclass of: germ layer
subclass of: ectoderm-derived structure
subclass of: Restriction
  on property: develops from
  some values from: ectoderm
definition: Embryonic ectoderm that gives rise to nervous tissue.
imported from: cl.owl
has exact synonym: neural ectoderm
has exact synonym: neuroectoderm
has_related_synonym: epithelium tubi neuralis; neuroectoderma
has_related_synonym: neuaral ectoderm
has_related_synonym: presumptive central nervous system
has_related_synonym: ventral neurogenic region

Axiom
annotated source: neurectoderm
annotated property: subClassOf
annotated target: germ layer
is inferred: true

Axiom
annotated source: neurectoderm
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

pelvic region of trunk
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: part_of
  some values from: abdominal segment of trunk
subclass of: Restriction
  on property: has part
  some values from: pelvic girdle skeleton
definition: The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.
imported from: cl.owl
has exact synonym: lesser pelvis
has exact synonym: pelvic region
has exact synonym: pelvis
has exact synonym: pelvis region
has exact synonym: true pelvis

Axiom
annotated source: pelvic region of trunk
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

exocrine gland
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part_of
    some values from: exocrine system
subclass of: gland
subclass of: Restriction
  on property: part_of
  some values from: exocrine system
subclass of: Restriction
  on property: has part
  some values from: duct
definition: A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
imported from: cl.owl
has exact synonym: ducted gland
has exact synonym: glandula exocrina

Axiom
annotated source: exocrine gland
annotated property: subClassOf
annotated target: gland
is inferred: true

prostate gland
type: Class
subclass of: mixed endoderm/mesoderm-derived structure
subclass of: male accessory sex gland
subclass of: Restriction
  on property: develops from
  some values from: prostate bud
definition: The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
imported from: cl.owl
has exact synonym: male prostate
has exact synonym: prostate
has_related_synonym: prostata

Axiom
annotated source: prostate gland
annotated property: subClassOf
annotated target: mixed endoderm/mesoderm-derived structure
is inferred: true

Axiom
annotated source: prostate gland
annotated property: subClassOf
annotated target: male accessory sex gland
is inferred: true

endocrine gland
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part_of
    some values from: endocrine system
subclass of: gland
subclass of: Restriction
  on property: part_of
  some values from: endocrine system
definition: Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
imported from: cl.owl
has exact synonym: ductless gland
has exact synonym: glandula endocrina
has_related_synonym: ductless gland
has_related_synonym: glandulae endocrinae

Axiom
annotated source: endocrine gland
annotated property: subClassOf
annotated target: gland
is inferred: true

bone marrow
type: Class
equivalent class: Class
  intersection of: tissue
  intersection of: Restriction
    on property: part_of
    some values from: bone element
  intersection of: Restriction
    on property: has part
    some values from: hematopoietic tissue
subclass of: anatomical structure
subclass of: tissue
subclass of: mesoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: bone element
subclass of: Restriction
  on property: part_of
  some values from: hematopoietic system
subclass of: Restriction
  on property: part_of
  some values from: immune system
subclass of: Restriction
  on property: has part
  some values from: hematopoietic tissue
definition: the soft tissue that fills the cavities of bones
imported from: cl.owl
has exact synonym: medulla ossea
has exact synonym: medulla ossium
has_related_synonym: medulla of bone
has_related_synonym: medullary bone

Axiom
annotated source: bone marrow
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: bone marrow
annotated property: subClassOf
annotated target: tissue
is inferred: true

Axiom
annotated source: bone marrow
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

connective tissue
type: Class
subclass of: tissue
definition: Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
external_definition: One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
external_definition: Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
external_definition: Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
external_ontology_notes: MA also has set of connective tissues
has db xref: http://linkedlifedata.com/resource/umls/id/C0009780
has db xref: C12374
has db xref: http://www.snomedbrowser.com/Codes/Details/361919005
has db xref: AAO:0000098
has db xref: BTO:0000421
has db xref: CALOHA:TS-2009
has db xref: EFO:0000952
has db xref: EMAPA:35251
has db xref: FMA:9640
has db xref: GAID:100
has db xref: MA:0000011
has db xref: MAT:0000301
has db xref: MESH:D003238
has db xref: MIAA:0000301
has db xref: OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA
has db xref: TAO:0001641
has db xref: UMLS:C0009780
has db xref: VSAO:0000017
has db xref: XAO:0001017
has db xref: ZFA:0001632
has db xref: galen:ConnectiveTissue
has exact synonym: portion of connective tissue
has exact synonym: textus connectivus
has OBO namespace: uberon
has related synonym: Bindegewebe
id: UBERON:0002384
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
Contributor: cmungall
Contributor: wdahdul

Axiom
annotated source: connective tissue
annotated property: subClassOf
annotated target: tissue
is inferred: true

muscle tissue
type: Class
subclass of: tissue
subclass of: mesoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: musculature
definition: Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
imported from: cl.owl
has exact synonym: muscular tissue
has exact synonym: portion of muscle tissue
has exact synonym: textus muscularis

Axiom
annotated source: muscle tissue
annotated property: subClassOf
annotated target: tissue
is inferred: true

Axiom
annotated source: muscle tissue
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

hematopoietic system
type: Class
subclass of: anatomical system
subclass of: mesoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: hemolymphoid system
subclass of: Restriction
  on property: develops from
  some values from: blood island
definition: Anatomical system that is involved in the production of hematopoietic cells.
imported from: cl.owl
has exact synonym: haematological system
has exact synonym: haemopoietic system
has exact synonym: organa haemopoietica
has_related_synonym: Blutbildungssystem
has_related_synonym: haematopoietic system
has_related_synonym: hematological system
has_related_synonym: hematolymphoid system
has_related_synonym: hemopoietic system

Axiom
annotated source: hematopoietic system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

Axiom
annotated source: hematopoietic system
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

lymph
type: Class
subclass of: haemolymphatic fluid
subclass of: Restriction
  on property: part_of
  some values from: lymphatic part of lymphoid system
subclass of: Restriction
  on property: develops from
  some values from: interstitial fluid
definition: Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
imported from: cl.owl
has_related_synonym: lympha

Axiom
annotated source: lymph
annotated property: subClassOf
annotated target: haemolymphatic fluid
is inferred: true

bile duct
type: Class
equivalent class: Class
  intersection of: duct
  intersection of: Restriction
    on property: part_of
    some values from: biliary tree
subclass of: digestive system duct
subclass of: endoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: biliary tree
subclass of: Restriction
  on property: develops from
  some values from: hepatic diverticulum
definition: Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine.
imported from: cl.owl
has_related_synonym: bile tube
has_related_synonym: biliary duct
has_related_synonym: gall duct
has_related_synonym: hepatic duct

Axiom
annotated source: bile duct
annotated property: subClassOf
annotated target: digestive system duct
is inferred: true

Axiom
annotated source: bile duct
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

immune system
type: Class
subclass of: anatomical system
definition: Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
imported from: cl.owl

Axiom
annotated source: immune system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

vertebra
type: Class
subclass of: endochondral bone
subclass of: irregular bone
subclass of: vertebral element
subclass of: Restriction
  on property: develops from
  some values from: vertebra cartilage element
definition: The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
imported from: cl.owl
has exact synonym: vertebra bone
has exact synonym: vertebrae

Axiom
annotated source: vertebra
annotated property: subClassOf
annotated target: endochondral bone
is inferred: true

Axiom
annotated source: vertebra
annotated property: subClassOf
annotated target: irregular bone
is inferred: true

Axiom
annotated source: vertebra
annotated property: subClassOf
annotated target: vertebral element
is inferred: true

integumental system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part_of
  some values from: multicellular organism
subclass of: Restriction
  on property: has part
  some values from: outer epithelium
definition: Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
imported from: cl.owl
has exact synonym: integumentary system
has_related_synonym: body surface
has_related_synonym: dermal system
has_related_synonym: external covering of organism
has_related_synonym: integumentum commune
has_related_synonym: organism surface
has_related_synonym: surface

Axiom
annotated source: integumental system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

abdominal segment of trunk
type: Class
subclass of: subdivision of trunk
subclass of: subdivision of organism along main body axis
definition: The abdominal segment of the torso.
imported from: cl.owl
has_related_synonym: abdomen/pelvis/perineum
has_related_synonym: lower body
has_related_synonym: lower trunk
has_related_synonym: lumbar region

Axiom
annotated source: abdominal segment of trunk
annotated property: subClassOf
annotated target: subdivision of trunk
is inferred: true

Axiom
annotated source: abdominal segment of trunk
annotated property: subClassOf
annotated target: subdivision of organism along main body axis
is inferred: true

cartilage tissue
type: Class
subclass of: skeletal tissue
definition: Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
imported from: cl.owl
has exact synonym: cartilage tissue
has exact synonym: cartilaginous tissue
has exact synonym: chondrogenic tissue
has_related_synonym: cartilage
has_related_synonym: cartilages
has_related_synonym: portion of cartilage tissue

Axiom
annotated source: cartilage tissue
annotated property: subClassOf
annotated target: skeletal tissue
is inferred: true

hepatobiliary system
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part_of
  some values from: digestive system
subclass of: Restriction
  on property: has part
  some values from: liver
subclass of: Restriction
  on property: has part
  some values from: biliary system
definition: The part of the digestive system that contains the liver and the biliary system
imported from: cl.owl
has exact synonym: hepaticobiliary system
has exact synonym: liver and biliary system
has_related_synonym: liver/biliary system

Axiom
annotated source: hepatobiliary system
annotated property: subClassOf
annotated target: organ system subdivision
is inferred: true

limb bone
type: Class
equivalent class: Class
  intersection of: bone element
  intersection of: Restriction
    on property: part_of
    some values from: limb
subclass of: endochondral bone
subclass of: bone of free limb or fin
subclass of: limb endochondral element
subclass of: Restriction
  on property: develops from
  some values from: limb cartilage element
definition: A bone that is part of a limb [Automatically generated definition].
imported from: cl.owl
has exact synonym: bone of extremity
has exact synonym: bone of limb
has exact synonym: free limb bone

Axiom
annotated source: limb bone
annotated property: subClassOf
annotated target: endochondral bone
is inferred: true

Axiom
annotated source: limb bone
annotated property: subClassOf
annotated target: bone of free limb or fin
is inferred: true

Axiom
annotated source: limb bone
annotated property: subClassOf
annotated target: limb endochondral element
is inferred: true

lymphoid system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part_of
  some values from: hemolymphoid system
subclass of: Restriction
  on property: part_of
  some values from: immune system
definition: The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP].
imported from: cl.owl
has_narrow_synonym: lymphatic system
has_related_synonym: lymphatic circulatory system
has_related_synonym: lymphatic drainage system
has_related_synonym: systema lymphoideum

Axiom
annotated source: lymphoid system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

esophagus mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: part_of
    some values from: esophagus
subclass of: mucosa
subclass of: Restriction
  on property: part_of
  some values from: wall of esophagus
definition: A mucosa that is part of a esophagus [Automatically generated definition].
imported from: cl.owl
has exact synonym: esophageal mucosa
has exact synonym: esophageal mucous membrane
has exact synonym: esophagus mucosa
has exact synonym: esophagus mucous membrane
has exact synonym: lamina muscularis mucosae oesophageae
has exact synonym: mucosa of esophagus
has exact synonym: mucosa of oesophagus
has exact synonym: mucous membrane of esophagus
has exact synonym: mucous membrane of oesophagus
has exact synonym: oesophageal mucosa
has exact synonym: oesophagus mucosa
has exact synonym: oesophagus mucous membrane
has exact synonym: tunica mucosa esophagi
has exact synonym: tunica mucosa oesophageae
has exact synonym: tunica mucosa oesophagi
has_related_synonym: muscularis mucosae of oesophagus
has_related_synonym: tunica mucosa oesophagi

Axiom
annotated source: esophagus mucosa
annotated property: subClassOf
annotated target: mucosa
is inferred: true

stylopod
type: Class
subclass of: limb segment
subclass of: Restriction
  on property: has part
  some values from: stylopodial skeleton
definition: The proximal free limb segment. Includes as parts the stylopod skeleton.
imported from: cl.owl
has_broad_synonym: proximal part of limb
has exact synonym: propodium
has exact synonym: proximal free limb segment
has exact synonym: stylopodial limb segment
has exact synonym: stylopodium
has_related_synonym: proximal segment of free limb

Axiom
annotated source: stylopod
annotated property: subClassOf
annotated target: limb segment
is inferred: true

bone tissue
type: Class
subclass of: skeletal tissue
subclass of: Restriction
  on property: part_of
  some values from: bone element
definition: Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
imported from: cl.owl
has exact synonym: calcium tissue
has exact synonym: osseous tissue
has exact synonym: osteogenic tissue
has_narrow_synonym: mineralized bone tissue
has_related_synonym: bone
has_related_synonym: portion of bone tissue

Axiom
annotated source: bone tissue
annotated property: subClassOf
annotated target: skeletal tissue
is inferred: true

long bone
type: Class
subclass of: bone element
subclass of: Restriction
  on property: part_of
  some values from: appendicular skeleton
definition: Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd].
imported from: cl.owl
has_related_synonym: os longum

Axiom
annotated source: long bone
annotated property: subClassOf
annotated target: bone element
is inferred: true

endochondral bone
type: Class
equivalent class: Class
  intersection of: bone element
  intersection of: Restriction
    on property: develops from
    some values from: cartilaginous condensation
subclass of: bone element
subclass of: endochondral element
subclass of: Restriction
  on property: develops from
  some values from: cartilage element
definition: Replacement bone that forms within cartilage.
imported from: cl.owl
has exact synonym: ossified chondrogenic bone
has_related_synonym: cartilaginous bone
has_related_synonym: endochondral bones

Axiom
annotated source: endochondral bone
annotated property: subClassOf
annotated target: bone element
is inferred: true

Axiom
annotated source: endochondral bone
annotated property: subClassOf
annotated target: endochondral element
is inferred: true

periosteum
type: Class
subclass of: membranous layer
subclass of: Restriction
  on property: part_of
  some values from: bone element
subclass of: Restriction
  on property: has part
  some values from: dense irregular connective tissue
definition: the thick fibrous membrane that closely invests the entire surface of a bone except the articular cartilage at synovial joints
imported from: cl.owl

Axiom
annotated source: periosteum
annotated property: subClassOf
annotated target: membranous layer
is inferred: true

limb segment
type: Class
equivalent class: Class
  intersection of: subdivision of organism along appendicular axis
  intersection of: Restriction
    on property: part_of
    some values from: limb
subclass of: paired limb/fin segment
subclass of: Restriction
  on property: part_of
  some values from: limb
subclass of: Restriction
  on property: has part
  some values from: skeletal muscle organ
definition: A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
imported from: cl.owl
has exact synonym: free limb segment
has exact synonym: segment of limb
has exact synonym: subdivision of limb
has_related_synonym: extremity part
has_related_synonym: limb region
has_related_synonym: region of limb

Axiom
annotated source: limb segment
annotated property: subClassOf
annotated target: paired limb/fin segment
is inferred: true

gland
type: Class
subclass of: organ
definition: an organ that functions as a secretory or excretory organ
imported from: cl.owl
has exact synonym: glandular organ
has_related_synonym: Druese
has_related_synonym: glandula

Axiom
annotated source: gland
annotated property: subClassOf
annotated target: organ
is inferred: true

epiblast (generic)
type: Class
subclass of: embryonic structure
definition: In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
imported from: cl.owl
has exact synonym: epiblast
has_related_synonym: blastocyst
has_related_synonym: ectoblast
has_related_synonym: epiblastus
has_related_synonym: primitive ectoderm

Axiom
annotated source: epiblast (generic)
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

regional part of brain
type: Class
equivalent class: Class
  intersection of: multi-tissue structure
  intersection of: Restriction
    on property: part_of
    some values from: brain
subclass of: regional part of nervous system
subclass of: ectoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: brain
subclass of: Restriction
  on property: has part
  some values from: neural tissue
definition: Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.
imported from: cl.owl
has exact synonym: anatomical structure of brain
has exact synonym: biological structure of brain
has exact synonym: brain anatomical structure
has exact synonym: brain biological structure
has exact synonym: brain part
has exact synonym: neuraxis segment
has exact synonym: neuroanatomical region
has exact synonym: segment of brain

Axiom
annotated source: regional part of brain
annotated property: subClassOf
annotated target: regional part of nervous system
is inferred: true

Axiom
annotated source: regional part of brain
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

pre-chordal neural plate
type: Class
subclass of: ectoderm-derived structure
subclass of: embryonic tissue
subclass of: Restriction
  on property: part_of
  some values from: neural plate
definition: The portion of neural plate anterior to the mid-hindbrain junction.
imported from: cl.owl
has_related_synonym: anterior neural plate

Axiom
annotated source: pre-chordal neural plate
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

Axiom
annotated source: pre-chordal neural plate
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

presomitic mesoderm
type: Class
subclass of: presumptive structure
subclass of: Restriction
  on property: part_of
  some values from: paraxial mesoderm
subclass of: Restriction
  on property: develops from
  some values from: presumptive segmental plate
definition: Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
imported from: cl.owl
has exact synonym: segmental plate
has exact synonym: unsegmented paraxial mesoderm
has_related_synonym: PSM
has_related_synonym: presumptive somite mesoderm
has_related_synonym: somitogenic mesoderm
has_related_synonym: somitomeric mesoderm
has_related_synonym: unsegmented mesenchyme

Axiom
annotated source: presomitic mesoderm
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

blood island
type: Class
subclass of: presumptive structure
subclass of: Restriction
  on property: develops from
  some values from: lateral plate mesoderm
definition: Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
imported from: cl.owl
has_broad_synonym: ventral lateral plate mesoderm
has exact synonym: blood islands
has_related_synonym: VBI
has_related_synonym: caudal hematopoietic tissue
has_related_synonym: posterior ICM
has_related_synonym: posterior blood island
has_related_synonym: ventral blood island

Axiom
annotated source: blood island
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

intermediate mesoderm
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part_of
  some values from: mesoderm
subclass of: Restriction
  on property: part_of
  some values from: trunk mesenchyme
subclass of: Restriction
  on property: develops from
  some values from: mesoderm
definition: The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
imported from: cl.owl
has_related_synonym: IM
has_related_synonym: intermediate mesenchyme
has_related_synonym: intermediate plate
has_related_synonym: intermediate plate mesoderm
has_related_synonym: mesenchyma intermedium

Axiom
annotated source: intermediate mesoderm
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

neural plate
type: Class
subclass of: embryonic tissue
subclass of: ecto-epithelium
subclass of: UBERON_0016879
subclass of: Restriction
  on property: develops from
  some values from: presumptive neural plate
definition: A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]
imported from: cl.owl
has_related_synonym: lamina neuralis
has_related_synonym: presumptive central nervous system

Axiom
annotated source: neural plate
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: neural plate
annotated property: subClassOf
annotated target: ecto-epithelium
is inferred: true

Axiom
annotated source: neural plate
annotated property: subClassOf
annotated target: UBERON_0016879
is inferred: true

paraxial mesoderm
type: Class
subclass of: embryonic tissue
subclass of: dense mesenchyme tissue
subclass of: UBERON_0015212
subclass of: Restriction
  on property: part_of
  some values from: embryo
subclass of: Restriction
  on property: develops from
  some values from: presumptive paraxial mesoderm
definition: The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
imported from: cl.owl
has exact synonym: paraxial mesenchyme
has exact synonym: somitic mesoderm
has_related_synonym: mesoderma paraxiale

Axiom
annotated source: paraxial mesoderm
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: paraxial mesoderm
annotated property: subClassOf
annotated target: dense mesenchyme tissue
is inferred: true

Axiom
annotated source: paraxial mesoderm
annotated property: subClassOf
annotated target: UBERON_0015212
is inferred: true

anterior neural tube
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part_of
  some values from: neural tube
subclass of: Restriction
  on property: develops from
  some values from: pre-chordal neural plate
imported from: cl.owl

Axiom
annotated source: anterior neural tube
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

lateral plate mesoderm
type: Class
subclass of: embryonic structure
subclass of: mesoderm-derived structure
subclass of: embryonic tissue
subclass of: dense mesenchyme tissue
subclass of: Restriction
  on property: part_of
  some values from: mesoderm
subclass of: Restriction
  on property: develops from
  some values from: mesoderm
definition: Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
imported from: cl.owl
has exact synonym: LPM
has exact synonym: lateral mesoderm
has_related_synonym: lateral plate
has_related_synonym: lateral plate mesenchyme
has_related_synonym: mesoderma laminae lateralis

Axiom
annotated source: lateral plate mesoderm
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

Axiom
annotated source: lateral plate mesoderm
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: lateral plate mesoderm
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: lateral plate mesoderm
annotated property: subClassOf
annotated target: dense mesenchyme tissue
is inferred: true

myotome
type: Class
subclass of: UBERON_0017650
subclass of: Restriction
  on property: develops from
  some values from: somite
subclass of: Restriction
  on property: develops from
  some values from: dermomyotome
definition: A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
imported from: cl.owl
has exact synonym: myomeres
has_related_synonym: muscle plate
has_related_synonym: myomere
has_related_synonym: myotome region
has_related_synonym: myotomes
has_related_synonym: myotomus

Axiom
annotated source: myotome
annotated property: subClassOf
annotated target: UBERON_0017650
is inferred: true

heart primordium
type: Class
subclass of: primordium
subclass of: Restriction
  on property: part_of
  some values from: cardiovascular system
subclass of: Restriction
  on property: develops from
  some values from: lateral plate mesoderm
subclass of: Restriction
  on property: develops from
  some values from: cardiogenic splanchnic mesoderm
definition: Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
imported from: cl.owl
has_related_synonym: cardiac field
has_related_synonym: fused heart primordium

Axiom
annotated source: heart primordium
annotated property: subClassOf
annotated target: primordium
is inferred: true

sclerotome
type: Class
subclass of: developing mesenchymal condensation
subclass of: migrating mesenchyme population
subclass of: Restriction
  on property: develops from
  some values from: somite
definition: Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
imported from: cl.owl
has exact synonym: sclerotomes
has_related_synonym: sclerotomus

Axiom
annotated source: sclerotome
annotated property: subClassOf
annotated target: developing mesenchymal condensation
is inferred: true

Axiom
annotated source: sclerotome
annotated property: subClassOf
annotated target: migrating mesenchyme population
is inferred: true

female organism
type: Class
subclass of: multicellular organism
definition: Gonochoristic organism that can produce female gametes.
imported from: cl.owl
has_narrow_synonym: female human body
has_related_synonym: female

Axiom
annotated source: female organism
annotated property: subClassOf
annotated target: multicellular organism
is inferred: true

male organism
type: Class
subclass of: multicellular organism
definition: Gonochoristic organism that can produce male gametes.
imported from: cl.owl
has_narrow_synonym: male human body
has_related_synonym: male

Axiom
annotated source: male organism
annotated property: subClassOf
annotated target: multicellular organism
is inferred: true

surface structure
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: integumental system
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: outer epithelium
definition: Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
imported from: cl.owl
has exact synonym: anatomical surface feature
has_related_synonym: surface feature
has_related_synonym: surface region
has_related_synonym: surface structures

Axiom
annotated source: surface structure
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

compound organ
type: Class
subclass of: organ
definition: Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
imported from: cl.owl
has_related_synonym: organ

Axiom
annotated source: compound organ
annotated property: subClassOf
annotated target: organ
is inferred: true

mesenchyme
type: Class
subclass of: tissue
definition: Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO].
imported from: cl.owl
has exact synonym: mesenchymal tissue
has exact synonym: mesenchyme tissue
has exact synonym: portion of mesenchymal tissue
has exact synonym: portion of mesenchyme tissue
has_related_synonym: mesenchyma

Axiom
annotated source: mesenchyme
annotated property: subClassOf
annotated target: tissue
is inferred: true

chorion
type: Class
subclass of: anatomical structure
subclass of: mesoderm-derived structure
subclass of: extraembryonic membrane
subclass of: Restriction
  on property: has part
  some values from: chorionic mesenchyme
subclass of: Restriction
  on property: has part
  some values from: chorionic ectoderm
subclass of: Restriction
  on property: develops from
  some values from: amniotic fold
definition: the outermost extraembryonic membrane
imported from: cl.owl
has exact synonym: chorion (vertebrates)
has exact synonym: embryonic chorion
has exact synonym: fetal chorion
has exact synonym: uterine chorion
has_related_synonym: chorion frondosum
has_related_synonym: chorionic sac

Axiom
annotated source: chorion
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: chorion
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: chorion
annotated property: subClassOf
annotated target: extraembryonic membrane
is inferred: true

trachea
type: Class
subclass of: respiratory tube
subclass of: Restriction
  on property: part_of
  some values from: tracheobronchial tree
subclass of: Restriction
  on property: develops from
  some values from: respiratory primordium
definition: The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
imported from: cl.owl
has exact synonym: cartilaginous trachea
has exact synonym: vertebrate trachea
has exact synonym: windpipe
has_related_synonym: tracheal tubule

Axiom
annotated source: trachea
annotated property: subClassOf
annotated target: respiratory tube
is inferred: true

reproductive organ
type: Class
subclass of: organ
subclass of: reproductive structure
definition: An organ involved in reproduction
imported from: cl.owl
has exact synonym: genital organ
has exact synonym: reproductive system organ
has exact synonym: sex organ
has_related_synonym: genitalia

Axiom
annotated source: reproductive organ
annotated property: subClassOf
annotated target: organ
is inferred: true

Axiom
annotated source: reproductive organ
annotated property: subClassOf
annotated target: reproductive structure
is inferred: true

amniotic ectoderm
type: Class
subclass of: extraembryonic structure
subclass of: unilaminar epithelium
subclass of: extraembryonic tissue
subclass of: meso-epithelium
subclass of: Restriction
  on property: part_of
  some values from: amnion
subclass of: Restriction
  on property: develops from
  some values from: epiblast (generic)
imported from: cl.owl
has exact synonym: amnion ectoderm
has exact synonym: amnionic ectoderm
has_related_synonym: amnion epithelium

Axiom
annotated source: amniotic ectoderm
annotated property: subClassOf
annotated target: extraembryonic structure
is inferred: true

Axiom
annotated source: amniotic ectoderm
annotated property: subClassOf
annotated target: unilaminar epithelium
is inferred: true

Axiom
annotated source: amniotic ectoderm
annotated property: subClassOf
annotated target: extraembryonic tissue
is inferred: true

Axiom
annotated source: amniotic ectoderm
annotated property: subClassOf
annotated target: meso-epithelium
is inferred: true

endoderm of foregut
type: Class
equivalent class: Class
  intersection of: unilaminar epithelium
  intersection of: Restriction
    on property: part_of
    some values from: foregut
  intersection of: Restriction
    on property: develops from
    some values from: endoderm
subclass of: unilaminar epithelium
subclass of: endo-epithelium
subclass of: UBERON_0015833
definition: An endoderm that is part of a foregut [Automatically generated definition].
imported from: cl.owl
has exact synonym: foregut endoderm

Axiom
annotated source: endoderm of foregut
annotated property: subClassOf
annotated target: unilaminar epithelium
is inferred: true

Axiom
annotated source: endoderm of foregut
annotated property: subClassOf
annotated target: endo-epithelium
is inferred: true

Axiom
annotated source: endoderm of foregut
annotated property: subClassOf
annotated target: UBERON_0015833
is inferred: true

amniotic mesoderm
type: Class
equivalent class: Class
  intersection of: mesenchyme
  intersection of: Restriction
    on property: part_of
    some values from: amnion
subclass of: extraembryonic structure
subclass of: dense mesenchyme tissue
subclass of: extraembryonic membrane mesenchyme
subclass of: Restriction
  on property: part_of
  some values from: amnion
subclass of: Restriction
  on property: develops from
  some values from: extraembryonic mesoderm
definition: A mesenchyme that is part of a amnion.
imported from: cl.owl
has exact synonym: amnion mesenchyme
has exact synonym: amnion mesoderm
has exact synonym: amnionic mesoderm
has exact synonym: mesenchyme of amnion
has_related_synonym: amnionic mesenchyme
has_related_synonym: amnionic mesoderm

Axiom
annotated source: amniotic mesoderm
annotated property: subClassOf
annotated target: extraembryonic structure
is inferred: true

Axiom
annotated source: amniotic mesoderm
annotated property: subClassOf
annotated target: dense mesenchyme tissue
is inferred: true

Axiom
annotated source: amniotic mesoderm
annotated property: subClassOf
annotated target: extraembryonic membrane mesenchyme
is inferred: true

chorionic mesenchyme
type: Class
equivalent class: Class
  intersection of: mesenchyme
  intersection of: Restriction
    on property: part_of
    some values from: chorion
subclass of: extraembryonic structure
subclass of: dense mesenchyme tissue
subclass of: extraembryonic membrane mesenchyme
subclass of: Restriction
  on property: part_of
  some values from: chorion
subclass of: Restriction
  on property: develops from
  some values from: somatic layer of lateral plate mesoderm
subclass of: Restriction
  on property: develops from
  some values from: extraembryonic mesoderm
definition: A mesenchyme that is part of a chorion.
imported from: cl.owl
has exact synonym: chorion mesenchyme
has exact synonym: chorion mesoderm
has exact synonym: chorionic mesenchyme
has exact synonym: mesenchyme of chorion
has exact synonym: mesenchyme of chorion (vertebrates)

Axiom
annotated source: chorionic mesenchyme
annotated property: subClassOf
annotated target: extraembryonic structure
is inferred: true

Axiom
annotated source: chorionic mesenchyme
annotated property: subClassOf
annotated target: dense mesenchyme tissue
is inferred: true

Axiom
annotated source: chorionic mesenchyme
annotated property: subClassOf
annotated target: extraembryonic membrane mesenchyme
is inferred: true

gland of foregut
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part_of
    some values from: foregut
subclass of: gland of digestive tract
subclass of: Restriction
  on property: part_of
  some values from: foregut
definition: A gland that is part of a foregut [Automatically generated definition].
imported from: cl.owl
has exact synonym: foregut gland

Axiom
annotated source: gland of foregut
annotated property: subClassOf
annotated target: gland of digestive tract
is inferred: true

epithelium of mucosa
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: mucosa
subclass of: epithelium
subclass of: Restriction
  on property: part_of
  some values from: mucosa
definition: A layer of epithelial cells on the surface of the mucosa.
imported from: cl.owl
has_related_synonym: lamina epithelialis mucosa
has_related_synonym: lamina epithelialis mucosae

Axiom
annotated source: epithelium of mucosa
annotated property: subClassOf
annotated target: epithelium
is inferred: true

epithelium of hindgut
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: hindgut
subclass of: digestive tract epithelium
subclass of: Restriction
  on property: part_of
  some values from: hindgut
definition: An epithelium that is part of a hindgut [Automatically generated definition].
imported from: cl.owl
has exact synonym: epithelial tissue of hindgut
has exact synonym: hindgut epithelial tissue
has exact synonym: hindgut epithelium

Axiom
annotated source: epithelium of hindgut
annotated property: subClassOf
annotated target: digestive tract epithelium
is inferred: true

chorionic ectoderm
type: Class
equivalent class: Class
  intersection of: extraembryonic structure
  intersection of: Restriction
    on property: part_of
    some values from: chorion
  intersection of: Restriction
    on property: develops from
    some values from: ectoderm
subclass of: extraembryonic structure
subclass of: Restriction
  on property: part_of
  some values from: chorion
subclass of: Restriction
  on property: develops from
  some values from: ectoderm
definition: A extraembryonic structure that develops_from a ectoderm and is part of a chorion.
imported from: cl.owl
has exact synonym: chorion ectoderm
has_related_synonym: chorion epithelium
has_related_synonym: chorionic epithelium

Axiom
annotated source: chorionic ectoderm
annotated property: subClassOf
annotated target: extraembryonic structure
is inferred: true

gland of digestive tract
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part_of
    some values from: digestive tract
subclass of: gland
subclass of: digestive system element
subclass of: Restriction
  on property: part_of
  some values from: digestive tract
definition: A gland that is part of a digestive tract [Automatically generated definition].
imported from: cl.owl
has exact synonym: digestive tract gland
has exact synonym: gland of digestive tract
has exact synonym: gland of lower gastrointestinal tract
has exact synonym: gut gland
has exact synonym: lower gastrointestinal tract gland

Axiom
annotated source: gland of digestive tract
annotated property: subClassOf
annotated target: gland
is inferred: true

Axiom
annotated source: gland of digestive tract
annotated property: subClassOf
annotated target: digestive system element
is inferred: true

mesenchyme of umbilical cord
type: Class
equivalent class: Class
  intersection of: mesenchyme
  intersection of: Restriction
    on property: part_of
    some values from: umbilical cord
subclass of: mesenchyme
subclass of: mesoderm-derived structure
subclass of: extraembryonic tissue
subclass of: Restriction
  on property: part_of
  some values from: umbilical cord
definition: A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP]
imported from: cl.owl
has exact synonym: Wharton's jelly
has exact synonym: umbilical cord mesenchyme

Axiom
annotated source: mesenchyme of umbilical cord
annotated property: subClassOf
annotated target: mesenchyme
is inferred: true

Axiom
annotated source: mesenchyme of umbilical cord
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: mesenchyme of umbilical cord
annotated property: subClassOf
annotated target: extraembryonic tissue
is inferred: true

hindlimb bone
type: Class
equivalent class: Class
  intersection of: bone element
  intersection of: Restriction
    on property: part_of
    some values from: hindlimb
subclass of: limb bone
subclass of: bone of pelvic complex
subclass of: hindlimb endochondral element
subclass of: Restriction
  on property: develops from
  some values from: hindlimb cartilage element
definition: A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle)
imported from: cl.owl
has exact synonym: bone of hind limb
has exact synonym: bone of hindlimb
has exact synonym: bone of inferior member
has exact synonym: bone of lower extremity
has exact synonym: bone organ of hind limb
has exact synonym: bone organ of hindlimb
has exact synonym: bone organ of lower extremity
has exact synonym: hind limb bone
has exact synonym: hind limb bone organ
has exact synonym: hindlimb bone organ

Axiom
annotated source: hindlimb bone
annotated property: subClassOf
annotated target: limb bone
is inferred: true

Axiom
annotated source: hindlimb bone
annotated property: subClassOf
annotated target: bone of pelvic complex
is inferred: true

Axiom
annotated source: hindlimb bone
annotated property: subClassOf
annotated target: hindlimb endochondral element
is inferred: true

arterial blood vessel
type: Class
equivalent class: Class
  intersection of: blood vessel
  intersection of: Restriction
    on property: part_of
    some values from: arterial system
subclass of: blood vessel
subclass of: Restriction
  on property: part_of
  some values from: arterial system
definition: A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
imported from: cl.owl

Axiom
annotated source: arterial blood vessel
annotated property: subClassOf
annotated target: blood vessel
is inferred: true

limb long bone
type: Class
equivalent class: Class
  intersection of: long bone
  intersection of: Restriction
    on property: part_of
    some values from: limb
subclass of: limb bone
subclass of: long bone
definition: A long bone that is part of a limb [Automatically generated definition].
imported from: cl.owl
has exact synonym: long bone of limb

Axiom
annotated source: limb long bone
annotated property: subClassOf
annotated target: limb bone
is inferred: true

Axiom
annotated source: limb long bone
annotated property: subClassOf
annotated target: long bone
is inferred: true

hindlimb long bone
type: Class
equivalent class: Class
  intersection of: long bone
  intersection of: Restriction
    on property: part_of
    some values from: hindlimb
subclass of: hindlimb bone
subclass of: limb long bone
definition: A long bone that is part of a hindlimb [Automatically generated definition].
imported from: cl.owl
has exact synonym: hind limb long bone
has exact synonym: inferior member long bone
has exact synonym: long bone of hind limb
has exact synonym: long bone of hindlimb
has exact synonym: long bone of inferior member
has exact synonym: long bone of lower extremity
has exact synonym: lower extremity long bone

Axiom
annotated source: hindlimb long bone
annotated property: subClassOf
annotated target: hindlimb bone
is inferred: true

Axiom
annotated source: hindlimb long bone
annotated property: subClassOf
annotated target: limb long bone
is inferred: true

extrahepatic bile duct
type: Class
subclass of: bile duct
definition: Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct.
imported from: cl.owl
has_related_synonym: bile duct extrahepatic part
has_related_synonym: extrahepatic biliary system

Axiom
annotated source: extrahepatic bile duct
annotated property: subClassOf
annotated target: bile duct
is inferred: true

intrahepatic bile duct
type: Class
equivalent class: Class
  intersection of: bile duct
  intersection of: Restriction
    on property: part_of
    some values from: liver
subclass of: bile duct
subclass of: Restriction
  on property: part_of
  some values from: liver
definition: Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct.
imported from: cl.owl
has exact synonym: bile duct intrahepatic part
has_related_synonym: intrahepatic biliary system

Axiom
annotated source: intrahepatic bile duct
annotated property: subClassOf
annotated target: bile duct
is inferred: true

neural tissue
type: Class
subclass of: tissue
subclass of: Restriction
  on property: part_of
  some values from: nervous system
definition: Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
imported from: cl.owl
has exact synonym: nerve tissue
has exact synonym: nervous tissue
has exact synonym: portion of neural tissue

Axiom
annotated source: neural tissue
annotated property: subClassOf
annotated target: tissue
is inferred: true

prostate bud
type: Class
subclass of: urogenital sinus epithelium
subclass of: epithelial bud
subclass of: Restriction
  on property: develops from
  some values from: prostate field
definition: A region of the fetal urogenital sinus epithelium destined to become the prostate[GO].
imported from: cl.owl
has exact synonym: prostate ductal progenitor
has exact synonym: prostatic bud
has_related_synonym: prostate gland bud
has_related_synonym: prostate primordium

Axiom
annotated source: prostate bud
annotated property: subClassOf
annotated target: urogenital sinus epithelium
is inferred: true

Axiom
annotated source: prostate bud
annotated property: subClassOf
annotated target: epithelial bud
is inferred: true

upper leg bone
type: Class
equivalent class: Class
  intersection of: bone element
  intersection of: Restriction
    on property: part_of
    some values from: hindlimb stylopod
subclass of: leg bone
subclass of: Restriction
  on property: part_of
  some values from: hindlimb stylopod
definition: A bone that is part of a hindlimb stylopod [Automatically generated definition].
imported from: cl.owl
has_related_synonym: femur

Axiom
annotated source: upper leg bone
annotated property: subClassOf
annotated target: leg bone
is inferred: true

hindlimb mesenchyme
type: Class
equivalent class: Class
  intersection of: mesenchyme
  intersection of: Restriction
    on property: part_of
    some values from: hindlimb
subclass of: limb mesenchyme
subclass of: Restriction
  on property: part_of
  some values from: hindlimb
definition: Mesenchyme that is part of a developing hindlimb [Automatically generated definition].
imported from: cl.owl
has exact synonym: hind limb mesenchyme
has exact synonym: inferior member mesenchyme
has exact synonym: lower extremity mesenchyme
has exact synonym: mesenchyme of hind limb
has exact synonym: mesenchyme of hindlimb
has exact synonym: mesenchyme of inferior member
has exact synonym: mesenchyme of lower extremity

Axiom
annotated source: hindlimb mesenchyme
annotated property: subClassOf
annotated target: limb mesenchyme
is inferred: true

liver primordium
type: Class
subclass of: simple columnar epithelium
subclass of: primordium
subclass of: embryonic tissue
subclass of: presumptive structure
subclass of: epithelium of foregut-midgut junction
subclass of: Restriction
  on property: part_of
  some values from: endoderm of foregut-midgut junction
subclass of: Restriction
  on property: develops from
  some values from: foregut
definition: A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum.
imported from: cl.owl
has exact synonym: embryological hepatic plate
has exact synonym: primordium of the liver
has_related_synonym: hepatic plate
has_related_synonym: liver bud
has_related_synonym: liver endoderm

Axiom
annotated source: liver primordium
annotated property: subClassOf
annotated target: simple columnar epithelium
is inferred: true

Axiom
annotated source: liver primordium
annotated property: subClassOf
annotated target: primordium
is inferred: true

Axiom
annotated source: liver primordium
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: liver primordium
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

Axiom
annotated source: liver primordium
annotated property: subClassOf
annotated target: epithelium of foregut-midgut junction
is inferred: true

epithelial tube
type: Class
subclass of: tube
subclass of: epithelium
definition: Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
imported from: cl.owl
has exact synonym: epithelial or endothelial tube

Axiom
annotated source: epithelial tube
annotated property: subClassOf
annotated target: tube
is inferred: true

Axiom
annotated source: epithelial tube
annotated property: subClassOf
annotated target: epithelium
is inferred: true

venous blood vessel
type: Class
equivalent class: Class
  intersection of: blood vessel
  intersection of: Restriction
    on property: part_of
    some values from: venous system
subclass of: blood vessel
subclass of: Restriction
  on property: part_of
  some values from: venous system
definition: A blood vessel that carries blood from the capillaries toward the heart
imported from: cl.owl
has exact synonym: segment of venous tree organ
has exact synonym: venous tree organ segment

Axiom
annotated source: venous blood vessel
annotated property: subClassOf
annotated target: blood vessel
is inferred: true

digestive system duct
type: Class
equivalent class: Class
  intersection of: duct
  intersection of: Restriction
    on property: part_of
    some values from: digestive system
subclass of: duct
subclass of: Restriction
  on property: part_of
  some values from: digestive system
definition: A duct that is part of a digestive system [Automatically generated definition].
imported from: cl.owl
has exact synonym: duct of digestive system
has exact synonym: duct of gastrointestinal system
has exact synonym: gastrointestinal system duct

Axiom
annotated source: digestive system duct
annotated property: subClassOf
annotated target: duct
is inferred: true

digestive tract epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: digestive tract
subclass of: epithelium
subclass of: Restriction
  on property: part_of
  some values from: digestive tract
definition: An epithelium that lines the lumen of the digestive tract.
imported from: cl.owl
has exact synonym: digestive tract epithelial tissue
has exact synonym: epithelial tissue of digestive tract
has exact synonym: epithelial tissue of gut
has exact synonym: epithelium of digestive tract
has exact synonym: epithelium of gut
has exact synonym: gastrodermis
has exact synonym: gut epithelial tissue
has exact synonym: gut epithelium
has_related_synonym: alimentary tract epithelium

Axiom
annotated source: digestive tract epithelium
annotated property: subClassOf
annotated target: epithelium
is inferred: true

reproductive gland
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part_of
    some values from: reproductive system
subclass of: gland
subclass of: reproductive structure
definition: Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
imported from: cl.owl
has exact synonym: genitalia gland
has exact synonym: gland of genitalia
has exact synonym: gland of reproductive system
has exact synonym: reproductive gland
has exact synonym: reproductive system gland
has exact synonym: sex gland

Axiom
annotated source: reproductive gland
annotated property: subClassOf
annotated target: gland
is inferred: true

Axiom
annotated source: reproductive gland
annotated property: subClassOf
annotated target: reproductive structure
is inferred: true

dermatome
type: Class
subclass of: UBERON_0017650
subclass of: Restriction
  on property: develops from
  some values from: somite
subclass of: Restriction
  on property: develops from
  some values from: dermomyotome
definition: A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
imported from: cl.owl
has exact synonym: cutis plate
has exact synonym: dermatomal mesenchyme
has_related_synonym: epimere mesoderm
has_related_synonym: mesenchyma dermatomiale

Axiom
annotated source: dermatome
annotated property: subClassOf
annotated target: UBERON_0017650
is inferred: true

anatomical conduit
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: has part
  some values from: anatomical conduit space
definition: Any tube, opening or passage that connects two distinct anatomical spaces.
imported from: cl.owl
has_narrow_synonym: foramen
has_narrow_synonym: foramina
has_related_synonym: opening
has_related_synonym: ostia
has_related_synonym: ostium

Axiom
annotated source: anatomical conduit
annotated property: subClassOf
annotated target: multicellular anatomical structure
is inferred: true

endoderm-derived structure
type: Class
equivalent class: Class
  intersection of: anatomical structure
  intersection of: Restriction
    on property: develops from
    some values from: endoderm
subclass of: anatomical structure
subclass of: Restriction
  on property: develops from
  some values from: endoderm
definition: An anatomical structure that develops (entirely or partially) from the endoderm.
imported from: cl.owl

Axiom
annotated source: endoderm-derived structure
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

mesoderm-derived structure
type: Class
equivalent class: Class
  intersection of: anatomical structure
  intersection of: Restriction
    on property: develops from
    some values from: mesoderm
subclass of: anatomical structure
subclass of: Restriction
  on property: develops from
  some values from: mesoderm
definition: An anatomical structure that develops (entirely or partially) from the mesoderm.
imported from: cl.owl
has exact synonym: mesodermal derivative

Axiom
annotated source: mesoderm-derived structure
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

ectoderm-derived structure
type: Class
equivalent class: Class
  intersection of: anatomical structure
  intersection of: Restriction
    on property: develops from
    some values from: ectoderm
subclass of: anatomical structure
subclass of: Restriction
  on property: develops from
  some values from: ectoderm
definition: An anatomical structure that develops (entirely or partially) from the ectoderm.
imported from: cl.owl
has exact synonym: ectodermal deriviative

Axiom
annotated source: ectoderm-derived structure
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

genitourinary system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: has part
    some values from: reproductive system
  intersection of: Restriction
    on property: has part
    some values from: renal system
subclass of: anatomical system
subclass of: mesoderm-derived structure
subclass of: Restriction
  on property: has part
  some values from: reproductive system
subclass of: Restriction
  on property: has part
  some values from: renal system
subclass of: Restriction
  on property: develops from
  some values from: intermediate mesoderm
definition: Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.
imported from: cl.owl
has exact synonym: urogenital system
has_related_synonym: GU tract
has_related_synonym: UG tract
has_related_synonym: Urogenitalsystem
has_related_synonym: genito-urinary system
has_related_synonym: genitourinary tract
has_related_synonym: urogenital tract

Axiom
annotated source: genitourinary system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

Axiom
annotated source: genitourinary system
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

cardiogenic plate
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: develops from
  some values from: heart primordium
definition: The first recognizable structure derived from the heart field
imported from: cl.owl
has exact synonym: myocardial plate
has_related_synonym: cardiac crescent
has_related_synonym: cardiogenic crescent
has_related_synonym: heart rudiment

Axiom
annotated source: cardiogenic plate
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

primary heart field
type: Class
subclass of: embryonic structure
subclass of: mesoderm-derived structure
subclass of: embryonic tissue
subclass of: anlage
subclass of: Restriction
  on property: part_of
  some values from: lateral plate mesoderm
subclass of: Restriction
  on property: part_of
  some values from: UBERON_0036146
definition: A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
imported from: cl.owl
has exact synonym: first heart field
has exact synonym: primary heart field
has_related_synonym: FHF
has_related_synonym: PHF
has_related_synonym: heart field

Axiom
annotated source: primary heart field
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

Axiom
annotated source: primary heart field
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: primary heart field
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: primary heart field
annotated property: subClassOf
annotated target: anlage
is inferred: true

heart tube
type: Class
subclass of: epithelial tube
subclass of: embryonic tissue
subclass of: meso-epithelium
subclass of: Restriction
  on property: develops from
  some values from: primitive heart tube
definition: An epithelial tube that will give rise to the mature heart.
imported from: cl.owl
has exact synonym: embryonic heart tube
has exact synonym: endocardial heart tube
has exact synonym: endocardial tube

Axiom
annotated source: heart tube
annotated property: subClassOf
annotated target: epithelial tube
is inferred: true

Axiom
annotated source: heart tube
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: heart tube
annotated property: subClassOf
annotated target: meso-epithelium
is inferred: true

cardiac chamber
type: Class
subclass of: organ part
subclass of: mesoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: heart
definition: A cardiac chamber surrounds an enclosed cavity within the heart
imported from: cl.owl
has exact synonym: chamber of heart
has exact synonym: heart chamber

Axiom
annotated source: cardiac chamber
annotated property: subClassOf
annotated target: organ part
is inferred: true

Axiom
annotated source: cardiac chamber
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

septum transversum
type: Class
subclass of: mesenchyme
subclass of: Restriction
  on property: part_of
  some values from: trunk
definition: A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG].
imported from: cl.owl
has exact synonym: transverse septum

Axiom
annotated source: septum transversum
annotated property: subClassOf
annotated target: mesenchyme
is inferred: true

internal genitalia
type: Class
subclass of: reproductive organ
definition: The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals
imported from: cl.owl
has exact synonym: internal genitalia
has exact synonym: internal genitals
has_related_synonym: internal reproductive organ
has_related_synonym: internal sex organ

Axiom
annotated source: internal genitalia
annotated property: subClassOf
annotated target: reproductive organ
is inferred: true

endodermal part of digestive tract
type: Class
equivalent class: Class
  intersection of: subdivision of digestive tract
  intersection of: Restriction
    on property: part_of
    some values from: digestive tract
  intersection of: Restriction
    on property: develops from
    some values from: endoderm
subclass of: endoderm-derived structure
subclass of: subdivision of digestive tract
definition: A portions of the gut that is derived from endoderm.
imported from: cl.owl
has exact synonym: endodermal gut
has exact synonym: gut endoderm

Axiom
annotated source: endodermal part of digestive tract
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

Axiom
annotated source: endodermal part of digestive tract
annotated property: subClassOf
annotated target: subdivision of digestive tract
is inferred: true

skeleton
type: Class
subclass of: UBERON_0034925
subclass of: Restriction
  on property: part_of
  some values from: skeletal system
subclass of: Restriction
  on property: has part
  some values from: skeletal element
definition: Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
imported from: cl.owl
has exact synonym: set of all bones
has exact synonym: set of bones of body

Axiom
annotated source: skeleton
annotated property: subClassOf
annotated target: UBERON_0034925
is inferred: true

dermomyotome
type: Class
subclass of: multilaminar epithelium
subclass of: UBERON_0016888
subclass of: Restriction
  on property: develops from
  some values from: somite
definition: The bilaminar epithelium formed from the myotome and dermatome.
imported from: cl.owl
has_related_synonym: dermamyotome
has_related_synonym: dermomyotomes

Axiom
annotated source: dermomyotome
annotated property: subClassOf
annotated target: multilaminar epithelium
is inferred: true

Axiom
annotated source: dermomyotome
annotated property: subClassOf
annotated target: UBERON_0016888
is inferred: true

heart rudiment
type: Class
subclass of: meso-epithelium
subclass of: Restriction
  on property: develops from
  some values from: heart primordium
subclass of: Restriction
  on property: develops from
  some values from: cardiogenic plate
definition: A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
imported from: cl.owl
has exact synonym: heart cone
has exact synonym: rudimentary heart

Axiom
annotated source: heart rudiment
annotated property: subClassOf
annotated target: meso-epithelium
is inferred: true

allantois
type: Class
subclass of: mesoderm-derived structure
subclass of: extraembryonic membrane
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: renal system
subclass of: Restriction
  on property: develops from
  some values from: cloaca
definition: A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG].
imported from: cl.owl
has_related_synonym: allantoic bud

Axiom
annotated source: allantois
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: allantois
annotated property: subClassOf
annotated target: extraembryonic membrane
is inferred: true

trophectoderm
type: Class
subclass of: unilaminar epithelium
subclass of: extraembryonic tissue
subclass of: Restriction
  on property: part_of
  some values from: extraembryonic membrane
subclass of: Restriction
  on property: develops from
  some values from: morula
definition: outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition
imported from: cl.owl

Axiom
annotated source: trophectoderm
annotated property: subClassOf
annotated target: unilaminar epithelium
is inferred: true

Axiom
annotated source: trophectoderm
annotated property: subClassOf
annotated target: extraembryonic tissue
is inferred: true

limb bud
type: Class
subclass of: paired limb/fin bud
definition: An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
imported from: cl.owl
has exact synonym: limb buds
has exact synonym: limbbud
has_related_synonym: gemmae membrorum

Axiom
annotated source: limb bud
annotated property: subClassOf
annotated target: paired limb/fin bud
is inferred: true

apical ectodermal ridge
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part_of
  some values from: ectoderm
subclass of: Restriction
  on property: part_of
  some values from: paired limb/fin bud
definition: multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP].
imported from: cl.owl
has exact synonym: apical epidermal ridge
has_related_synonym: AER
has_related_synonym: crista ectodermalis apicalis

Axiom
annotated source: apical ectodermal ridge
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

paired limb/fin bud
type: Class
subclass of: surface structure
subclass of: presumptive structure
subclass of: Restriction
  on property: has part
  some values from: apical ectodermal ridge
definition: An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
imported from: cl.owl
has exact synonym: limb - fin bud
has exact synonym: paired appendage bud
has exact synonym: paired limb/fin bud

Axiom
annotated source: paired limb/fin bud
annotated property: subClassOf
annotated target: surface structure
is inferred: true

Axiom
annotated source: paired limb/fin bud
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

bone of free limb or fin
type: Class
equivalent class: Class
  intersection of: bone element
  intersection of: Restriction
    on property: part_of
    some values from: paired limb/fin
subclass of: mesoderm-derived structure
subclass of: bone of appendage girdle complex
subclass of: Restriction
  on property: part_of
  some values from: paired limb/fin skeleton
definition: A bone that is part of an appendage [Automatically generated definition].
imported from: cl.owl
has exact synonym: appendage bone
has exact synonym: bone of appendage
has exact synonym: bone of free segment of appendicular skeleton

Axiom
annotated source: bone of free limb or fin
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: bone of free limb or fin
annotated property: subClassOf
annotated target: bone of appendage girdle complex
is inferred: true

skeleton of limb
type: Class
subclass of: limb skeleton subdivision
subclass of: paired limb/fin skeleton
subclass of: Restriction
  on property: part_of
  some values from: limb
definition: The collection of all skeletal elements in an individual limb.
imported from: cl.owl
has exact synonym: free limb skeleton
has exact synonym: limb skeleton
has exact synonym: set of bones of limb

Axiom
annotated source: skeleton of limb
annotated property: subClassOf
annotated target: limb skeleton subdivision
is inferred: true

Axiom
annotated source: skeleton of limb
annotated property: subClassOf
annotated target: paired limb/fin skeleton
is inferred: true

cardiovascular system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: part_of
    some values from: circulatory system
  intersection of: Restriction
    on property: has part
    some values from: heart
  intersection of: Restriction
    on property: has part
    some values from: blood vessel
subclass of: anatomical system
subclass of: Restriction
  on property: part_of
  some values from: circulatory system
subclass of: Restriction
  on property: has part
  some values from: heart
subclass of: Restriction
  on property: has part
  some values from: blood vessel
definition: Anatomical system that has as its parts the heart and blood vessels.
imported from: cl.owl
has_related_synonym: CV system
has_related_synonym: Herz und Gefaesssystem

Axiom
annotated source: cardiovascular system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

lymph vasculature
type: Class
equivalent class: Class
  intersection of: vasculature
  intersection of: Restriction
    on property: has part
    some values from: lymph
subclass of: anatomical structure
subclass of: vasculature
subclass of: Restriction
  on property: part_of
  some values from: lymphatic part of lymphoid system
subclass of: Restriction
  on property: has part
  some values from: lymph
definition: A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.
imported from: cl.owl
has exact synonym: lymphatic trunks and ducts
has exact synonym: lymphatic vasculature
has exact synonym: lymphatic vessel network
has exact synonym: lymphatic vessels set
has exact synonym: set of lymphatic vessels
has exact synonym: trunci et ductus lymphatici
has_related_synonym: lymph vessels

Axiom
annotated source: lymph vasculature
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: lymph vasculature
annotated property: subClassOf
annotated target: vasculature
is inferred: true

blood vasculature
type: Class
subclass of: vasculature
subclass of: Restriction
  on property: has part
  some values from: blood vessel
definition: A vascular network consisting of blood vessels.
imported from: cl.owl
has exact synonym: blood vascular network
has exact synonym: set of blood vessels
has_related_synonym: blood system
has_related_synonym: blood vessel system
has_related_synonym: blood vessels

Axiom
annotated source: blood vasculature
annotated property: subClassOf
annotated target: vasculature
is inferred: true

arterial system
type: Class
subclass of: vascular system
subclass of: Restriction
  on property: part_of
  some values from: cardiovascular system
subclass of: Restriction
  on property: has part
  some values from: artery
definition: The part of the cardiovascular system consisting of all arteries.
imported from: cl.owl

Axiom
annotated source: arterial system
annotated property: subClassOf
annotated target: vascular system
is inferred: true

venous system
type: Class
subclass of: vascular system
subclass of: Restriction
  on property: has part
  some values from: vein
definition: The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
imported from: cl.owl
has exact synonym: vein system

Axiom
annotated source: venous system
annotated property: subClassOf
annotated target: vascular system
is inferred: true

liver lobule
type: Class
subclass of: organ part
subclass of: endoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: liver parenchyma
definition: the polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein
imported from: cl.owl
has exact synonym: hepatic lobule
has exact synonym: lobuli hepatici
has exact synonym: lobulus hepaticus
has_related_synonym: lobules of liver
has_related_synonym: lobuli hepatis

Axiom
annotated source: liver lobule
annotated property: subClassOf
annotated target: organ part
is inferred: true

Axiom
annotated source: liver lobule
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

paired limb/fin
type: Class
equivalent class: Class
  intersection of: appendage
  intersection of: Restriction
    on property: part_of
    some values from: appendage girdle complex
subclass of: appendage
subclass of: Restriction
  on property: part_of
  some values from: appendage girdle complex
subclass of: Restriction
  on property: has part
  some values from: zone of skin
subclass of: Restriction
  on property: has part
  some values from: musculature
subclass of: Restriction
  on property: has part
  some values from: vasculature
subclass of: Restriction
  on property: has part
  some values from: paired limb/fin skeleton
subclass of: Restriction
  on property: develops from
  some values from: paired limb/fin bud
definition: An appendage that is part of an appendage girdle complex.
imported from: cl.owl
has exact synonym: girdle-associated appendage
has exact synonym: limb or fin
has exact synonym: limb/fin
has exact synonym: pectoral or pelvic appendage
has exact synonym: pelvic/pectoral appendage
has_narrow_synonym: jointed paired lateral appendage
has_narrow_synonym: paired appendage

Axiom
annotated source: paired limb/fin
annotated property: subClassOf
annotated target: appendage
is inferred: true

pelvic appendage
type: Class
equivalent class: Class
  intersection of: paired limb/fin
  intersection of: Restriction
    on property: part_of
    some values from: pelvic complex
subclass of: paired limb/fin
subclass of: Restriction
  on property: part_of
  some values from: pelvic complex
subclass of: Restriction
  on property: has part
  some values from: pelvic appendage skeleton
subclass of: Restriction
  on property: develops from
  some values from: pelvic appendage bud
definition: Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues.
imported from: cl.owl
has_broad_synonym: posterior appendage
has exact synonym: hindlimb/pelvic fin
has exact synonym: pelvic appendage
has exact synonym: pelvic limb/fin
has exact synonym: posterior limb/fin
has exact synonym: posterior paired appendage

Axiom
annotated source: pelvic appendage
annotated property: subClassOf
annotated target: paired limb/fin
is inferred: true

conceptus
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: has part
  some values from: embryonic structure
subclass of: Restriction
  on property: has part
  some values from: UBERON_0016887
definition: The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
imported from: cl.owl
has exact synonym: embryo plus adnexa

Axiom
annotated source: conceptus
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

gastrula
type: Class
subclass of: embryo
subclass of: Restriction
  on property: develops from
  some values from: blastula
definition: Organism at the gastrula stage.
imported from: cl.owl
has exact synonym: gastrula embryo
has_related_synonym: blastocystis trilaminaris
has_related_synonym: tri-laminar disc
has_related_synonym: tri-laminar disk
has_related_synonym: trilaminar blastocyst
has_related_synonym: trilaminar blastoderm
has_related_synonym: trilaminar disc
has_related_synonym: trilaminar disk
has_related_synonym: trilaminar germ

Axiom
annotated source: gastrula
annotated property: subClassOf
annotated target: embryo
is inferred: true

skeletal tissue
type: Class
subclass of: connective tissue
subclass of: Restriction
  on property: part_of
  some values from: skeletal element
definition: A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
imported from: cl.owl

Axiom
annotated source: skeletal tissue
annotated property: subClassOf
annotated target: connective tissue
is inferred: true

skeletal element
type: Class
subclass of: organ
subclass of: Restriction
  on property: part_of
  some values from: skeletal system
definition: Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
imported from: cl.owl

Axiom
annotated source: skeletal element
annotated property: subClassOf
annotated target: organ
is inferred: true

articular system
type: Class
subclass of: UBERON_0034925
subclass of: Restriction
  on property: part_of
  some values from: skeletal system
subclass of: Restriction
  on property: has part
  some values from: skeletal joint
definition: Anatomical system that consists of all the joints of the body.
imported from: cl.owl
has exact synonym: joint system
has exact synonym: set of all joints of body
has_related_synonym: set of all joints
has_related_synonym: set of joints of body

Axiom
annotated source: articular system
annotated property: subClassOf
annotated target: UBERON_0034925
is inferred: true

respiratory system mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: part_of
    some values from: respiratory system
subclass of: mucosa
subclass of: Restriction
  on property: part_of
  some values from: respiratory system
definition: the mucous membrane lining the respiratory tract
imported from: cl.owl
has exact synonym: apparatus respiratorius mucosa
has exact synonym: apparatus respiratorius mucosa of organ
has exact synonym: apparatus respiratorius mucous membrane
has exact synonym: mucosa of apparatus respiratorius
has exact synonym: mucosa of organ of apparatus respiratorius
has exact synonym: mucosa of organ of respiratory system
has exact synonym: mucosa of respiratory system
has exact synonym: mucous membrane of apparatus respiratorius
has exact synonym: mucous membrane of respiratory system
has exact synonym: respiratory system mucosa of organ
has exact synonym: respiratory system mucous membrane
has_related_synonym: laryngeal mucous membrane
has_related_synonym: respiratory mucosa
has_related_synonym: respiratory tract mucosa

Axiom
annotated source: respiratory system mucosa
annotated property: subClassOf
annotated target: mucosa
is inferred: true

gastrointestinal system mucosa
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: part_of
    some values from: alimentary part of gastrointestinal system
subclass of: mucosa
subclass of: Restriction
  on property: part_of
  some values from: digestive tract
subclass of: Restriction
  on property: part_of
  some values from: alimentary part of gastrointestinal system
definition: A mucosa that is part of a gastrointestinal system.
imported from: cl.owl
has exact synonym: digestive tract mucosa
has exact synonym: gut mucosa
has exact synonym: gut mucuous membrane
has exact synonym: mucosa of gut

Axiom
annotated source: gastrointestinal system mucosa
annotated property: subClassOf
annotated target: mucosa
is inferred: true

respiratory tract epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: respiratory tract
subclass of: respiratory system epithelium
subclass of: endo-epithelium
subclass of: pseudostratified ciliated columnar epithelium
subclass of: Restriction
  on property: part_of
  some values from: proximo-distal subdivision of respiratory tract
definition: the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi
imported from: cl.owl
has exact synonym: epithelial tissue of respiratory tract
has exact synonym: epithelium of respiratory tract
has exact synonym: respiratory tract epithelial tissue
has_related_synonym: airway epithelium
has_related_synonym: respiratory epithelium

Axiom
annotated source: respiratory tract epithelium
annotated property: subClassOf
annotated target: respiratory system epithelium
is inferred: true

Axiom
annotated source: respiratory tract epithelium
annotated property: subClassOf
annotated target: endo-epithelium
is inferred: true

Axiom
annotated source: respiratory tract epithelium
annotated property: subClassOf
annotated target: pseudostratified ciliated columnar epithelium
is inferred: true

respiratory system epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: respiratory system
subclass of: epithelium
subclass of: Restriction
  on property: part_of
  some values from: respiratory system
definition: An epithelium that is part of a respiratory system [Automatically generated definition].
imported from: cl.owl
has exact synonym: apparatus respiratorius epithelial tissue
has exact synonym: apparatus respiratorius epithelium
has exact synonym: epithelial tissue of apparatus respiratorius
has exact synonym: epithelial tissue of respiratory system
has exact synonym: epithelium of apparatus respiratorius
has exact synonym: epithelium of respiratory system
has exact synonym: respiratory system epithelial tissue

Axiom
annotated source: respiratory system epithelium
annotated property: subClassOf
annotated target: epithelium
is inferred: true

gastrointestinal system epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: alimentary part of gastrointestinal system
subclass of: epithelium
subclass of: Restriction
  on property: part_of
  some values from: alimentary part of gastrointestinal system
definition: An epithelium that is part of a digestive system [Automatically generated definition].
imported from: cl.owl
has exact synonym: digestive system epithelial tissue
has exact synonym: digestive system epithelium
has exact synonym: epithelial tissue of digestive system
has exact synonym: epithelial tissue of gastrointestinal system
has exact synonym: epithelium of digestive system
has exact synonym: epithelium of gastrointestinal system
has exact synonym: gastrointestinal system epithelial tissue

Axiom
annotated source: gastrointestinal system epithelium
annotated property: subClassOf
annotated target: epithelium
is inferred: true

lower respiratory tract epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: lower respiratory tract
subclass of: respiratory tract epithelium
subclass of: Restriction
  on property: part_of
  some values from: lower respiratory tract
definition: An epithelium that is part of a lower respiratory tract [Automatically generated definition].
imported from: cl.owl
has exact synonym: epithelial tissue of lower respiratory tract
has exact synonym: epithelium of lower respiratory tract
has exact synonym: lower respiratory tract epithelial tissue

Axiom
annotated source: lower respiratory tract epithelium
annotated property: subClassOf
annotated target: respiratory tract epithelium
is inferred: true

somatic layer of lateral plate mesoderm
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part_of
  some values from: lateral plate mesoderm
definition: Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP].
imported from: cl.owl
has exact synonym: outer layer of lateral plate mesoderm
has_related_synonym: parietal mesoderm
has_related_synonym: somatic mesoderm

Axiom
annotated source: somatic layer of lateral plate mesoderm
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

splanchnic layer of lateral plate mesoderm
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part_of
  some values from: lateral plate mesoderm
definition: Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
imported from: cl.owl
has_broad_synonym: visceral mesoderm
has exact synonym: inner layer of lateral plate mesoderm
has_related_synonym: splanchnic mesoderm

Axiom
annotated source: splanchnic layer of lateral plate mesoderm
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

somatopleure
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part_of
  some values from: lateral plate mesoderm
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: ectoderm
definition: A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP].
imported from: cl.owl

Axiom
annotated source: somatopleure
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

urogenital sinus epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: primitive urogenital sinus
subclass of: embryonic cloacal epithelium
subclass of: Restriction
  on property: part_of
  some values from: primitive urogenital sinus
subclass of: Restriction
  on property: develops from
  some values from: embryonic cloacal epithelium
definition: The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra
imported from: cl.owl
has exact synonym: UGE
has exact synonym: epithelium of urogenital sinus

Axiom
annotated source: urogenital sinus epithelium
annotated property: subClassOf
annotated target: embryonic cloacal epithelium
is inferred: true

articulation
type: Class
subclass of: UBERON_0034921
subclass of: Restriction
  on property: part_of
  some values from: articular system
definition: Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
imported from: cl.owl
has_narrow_synonym: joint

Axiom
annotated source: articulation
annotated property: subClassOf
annotated target: UBERON_0034921
is inferred: true

upper digestive tract
type: Class
subclass of: subdivision of digestive tract
subclass of: Restriction
  on property: develops from
  some values from: foregut
definition: The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum.
imported from: cl.owl
has exact synonym: upper GI tract
has exact synonym: upper gastrointestinal tract

Axiom
annotated source: upper digestive tract
annotated property: subClassOf
annotated target: subdivision of digestive tract
is inferred: true

biliary bud
type: Class
subclass of: endodermal part of digestive tract
subclass of: epithelial sac
subclass of: epithelium of foregut-midgut junction
subclass of: digestive tract diverticulum
subclass of: Restriction
  on property: part_of
  some values from: hepatobiliary system
subclass of: Restriction
  on property: part_of
  some values from: foregut-midgut junction
subclass of: Restriction
  on property: develops from
  some values from: septum transversum
imported from: cl.owl
has_related_synonym: hepatic diverticulum

Axiom
annotated source: biliary bud
annotated property: subClassOf
annotated target: endodermal part of digestive tract
is inferred: true

Axiom
annotated source: biliary bud
annotated property: subClassOf
annotated target: epithelial sac
is inferred: true

Axiom
annotated source: biliary bud
annotated property: subClassOf
annotated target: epithelium of foregut-midgut junction
is inferred: true

Axiom
annotated source: biliary bud
annotated property: subClassOf
annotated target: digestive tract diverticulum
is inferred: true

subdivision of digestive tract
type: Class
subclass of: subdivision of tube
subclass of: Restriction
  on property: part_of
  some values from: digestive tract
definition: A proximal-distal subdivision of the digestive tract.
imported from: cl.owl
has_related_synonym: alimentary system subdivision
has_related_synonym: intestinal tract
has_related_synonym: segment of intestinal tract
has_related_synonym: subdivision of alimentary system

Axiom
annotated source: subdivision of digestive tract
annotated property: subClassOf
annotated target: subdivision of tube
is inferred: true

organ component layer
type: Class
subclass of: organ part
subclass of: Restriction
  on property: part_of
  some values from: anatomical wall
definition: A part of a wall of an organ that forms a layer.
imported from: cl.owl

Axiom
annotated source: organ component layer
annotated property: subClassOf
annotated target: organ part
is inferred: true

mucosa of bronchiole
type: Class
equivalent class: Class
  intersection of: mucosa
  intersection of: Restriction
    on property: part_of
    some values from: bronchiole
subclass of: bronchial mucosa
subclass of: Restriction
  on property: part_of
  some values from: bronchiole
definition: A mucosa that is part of a bronchiole [Automatically generated definition].
imported from: cl.owl
has exact synonym: bronchiole mucosa
has exact synonym: bronchiole mucosa of organ
has exact synonym: bronchiole mucous membrane
has exact synonym: bronchiole organ mucosa
has exact synonym: lobular bronchiole mucosa
has exact synonym: lobular bronchiole mucosa of organ
has exact synonym: lobular bronchiole mucous membrane
has exact synonym: lobular bronchiole organ mucosa
has exact synonym: mucosa of lobular bronchiole
has exact synonym: mucosa of organ of bronchiole
has exact synonym: mucosa of organ of lobular bronchiole
has exact synonym: mucous membrane of bronchiole
has exact synonym: mucous membrane of lobular bronchiole
has exact synonym: organ mucosa of bronchiole
has exact synonym: organ mucosa of lobular bronchiole

Axiom
annotated source: mucosa of bronchiole
annotated property: subClassOf
annotated target: bronchial mucosa
is inferred: true

neural groove
type: Class
subclass of: embryonic structure
subclass of: Restriction
  on property: part_of
  some values from: neural plate
definition: The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
imported from: cl.owl

Axiom
annotated source: neural groove
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

neural fold
type: Class
subclass of: embryonic structure
subclass of: epithelial fold
subclass of: embryonic tissue
subclass of: ecto-epithelium
subclass of: UBERON_0015212
subclass of: Restriction
  on property: part_of
  some values from: neural groove
definition: One of the two elevated edges of the neural groove[GO,MP].
imported from: cl.owl
has exact synonym: medullary fold

Axiom
annotated source: neural fold
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

Axiom
annotated source: neural fold
annotated property: subClassOf
annotated target: epithelial fold
is inferred: true

Axiom
annotated source: neural fold
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: neural fold
annotated property: subClassOf
annotated target: ecto-epithelium
is inferred: true

Axiom
annotated source: neural fold
annotated property: subClassOf
annotated target: UBERON_0015212
is inferred: true

neural rod
type: Class
subclass of: UBERON_0016879
subclass of: Restriction
  on property: develops from
  some values from: neural keel
definition: A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
imported from: cl.owl
has_related_synonym: neural tube rod

Axiom
annotated source: neural rod
annotated property: subClassOf
annotated target: UBERON_0016879
is inferred: true

muscle structure
type: Class
subclass of: anatomical structure
definition: Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
imported from: cl.owl
has exact synonym: musculus
has_related_synonym: muscle
has_related_synonym: muscle element

Axiom
annotated source: muscle structure
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

epithelial bud
type: Class
subclass of: epithelial fold
definition: A bud is a protrusion that forms from an epithelial sheet by localized folding.
imported from: cl.owl

Axiom
annotated source: epithelial bud
annotated property: subClassOf
annotated target: epithelial fold
is inferred: true

reproductive structure
type: Class
equivalent class: Class
  intersection of: multicellular anatomical structure
  intersection of: Restriction
    on property: part_of
    some values from: reproductive system
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: reproductive system
definition: Any anatomical structure that is part of the reproductive system.
imported from: cl.owl
has exact synonym: reproductive system element
has exact synonym: reproductive system structure

Axiom
annotated source: reproductive structure
annotated property: subClassOf
annotated target: multicellular anatomical structure
is inferred: true

epithelial fold
type: Class
subclass of: epithelium
definition: An epithelial sheet bent on a linear axis.
imported from: cl.owl

Axiom
annotated source: epithelial fold
annotated property: subClassOf
annotated target: epithelium
is inferred: true

abdomen element
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: part_of
    some values from: abdomen
subclass of: abdominal segment element
subclass of: Restriction
  on property: part_of
  some values from: abdomen
definition: An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
imported from: cl.owl
has exact synonym: abdomen organ

Axiom
annotated source: abdomen element
annotated property: subClassOf
annotated target: abdominal segment element
is inferred: true

abdominal segment element
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: part_of
    some values from: abdominal segment of trunk
subclass of: trunk region element
subclass of: Restriction
  on property: part_of
  some values from: abdominal segment of trunk
definition: An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
imported from: cl.owl
has exact synonym: abdominal segment organ

Axiom
annotated source: abdominal segment element
annotated property: subClassOf
annotated target: trunk region element
is inferred: true

trunk region element
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: part_of
    some values from: trunk
subclass of: organ
subclass of: Restriction
  on property: part_of
  some values from: trunk
definition: An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
imported from: cl.owl
has exact synonym: trunk organ

Axiom
annotated source: trunk region element
annotated property: subClassOf
annotated target: organ
is inferred: true

thoracic cavity element
type: Class
subclass of: thoracic segment organ
definition: An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
imported from: cl.owl
has exact synonym: thoracic cavity organ

Axiom
annotated source: thoracic cavity element
annotated property: subClassOf
annotated target: thoracic segment organ
is inferred: true

thoracic segment organ
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: part_of
    some values from: thoracic segment of trunk
subclass of: trunk region element
subclass of: Restriction
  on property: part_of
  some values from: thoracic segment of trunk
definition: An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
imported from: cl.owl
has_related_synonym: upper body organ

Axiom
annotated source: thoracic segment organ
annotated property: subClassOf
annotated target: trunk region element
is inferred: true

upper leg mesenchyme
type: Class
equivalent class: Class
  intersection of: mesenchyme
  intersection of: Restriction
    on property: part_of
    some values from: hindlimb stylopod
subclass of: hindlimb mesenchyme
subclass of: Restriction
  on property: part_of
  some values from: hindlimb stylopod
definition: Mesenchyme that is part of a developing hindlimb stylopod [Automatically generated definition].
imported from: cl.owl

Axiom
annotated source: upper leg mesenchyme
annotated property: subClassOf
annotated target: hindlimb mesenchyme
is inferred: true

trunk mesenchyme
type: Class
equivalent class: Class
  intersection of: mesenchyme
  intersection of: Restriction
    on property: part_of
    some values from: embryo
  intersection of: Restriction
    on property: part_of
    some values from: trunk
subclass of: mesenchyme
subclass of: embryonic tissue
subclass of: Restriction
  on property: part_of
  some values from: trunk
subclass of: Restriction
  on property: part_of
  some values from: entire embryonic mesenchyme
definition: Mesenchyme that is part of a developing trunk.
imported from: cl.owl
has_related_synonym: trunk and cervical mesenchyme

Axiom
annotated source: trunk mesenchyme
annotated property: subClassOf
annotated target: mesenchyme
is inferred: true

Axiom
annotated source: trunk mesenchyme
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

embryonic tissue
type: Class
equivalent class: Class
  intersection of: tissue
  intersection of: Restriction
    on property: part_of
    some values from: embryo
subclass of: tissue
subclass of: Restriction
  on property: part_of
  some values from: embryonic structure
definition: A portion of tissue that is part of an embryo.
imported from: cl.owl
has exact synonym: portion of embryonic tissue
has_related_synonym: developing tissue

Axiom
annotated source: embryonic tissue
annotated property: subClassOf
annotated target: tissue
is inferred: true

extraembryonic tissue
type: Class
equivalent class: Class
  intersection of: tissue
  intersection of: Restriction
    on property: part_of
    some values from: UBERON_0016887
subclass of: tissue
subclass of: Restriction
  on property: part_of
  some values from: UBERON_0016887
definition: Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
imported from: cl.owl
has exact synonym: extra-embryonic tissue

Axiom
annotated source: extraembryonic tissue
annotated property: subClassOf
annotated target: tissue
is inferred: true

male reproductive gland
type: Class
equivalent class: Class
  intersection of: reproductive gland
  intersection of: Restriction
    on property: part_of
    some values from: male reproductive system
subclass of: reproductive gland
subclass of: Restriction
  on property: part_of
  some values from: male reproductive system
definition: A sex gland that is part of a male reproductive system.
imported from: cl.owl
has_related_synonym: accessory sex gland

Axiom
annotated source: male reproductive gland
annotated property: subClassOf
annotated target: reproductive gland
is inferred: true

alimentary part of gastrointestinal system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part_of
  some values from: digestive system
definition: The part of the digestive system that excludes the hepatobiliary system.
imported from: cl.owl
has_related_synonym: GI tract
has_related_synonym: alimentary system
has_related_synonym: alimentary tract
has_related_synonym: gastro-intestinal system
has_related_synonym: gastrointestinal (GI) tract
has_related_synonym: gastrointestinal system
has_related_synonym: gastrointestinal tract

Axiom
annotated source: alimentary part of gastrointestinal system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

hindlimb bud
type: Class
subclass of: limb bud
subclass of: pelvic appendage bud
definition: A limb bud that develops into a hindlimb.
imported from: cl.owl
has exact synonym: hind limb bud
has exact synonym: posterior limb bud
has_related_synonym: leg bud
has_related_synonym: limb bud - hindlimb

Axiom
annotated source: hindlimb bud
annotated property: subClassOf
annotated target: limb bud
is inferred: true

Axiom
annotated source: hindlimb bud
annotated property: subClassOf
annotated target: pelvic appendage bud
is inferred: true

pelvic appendage bud
type: Class
subclass of: paired limb/fin bud
subclass of: Restriction
  on property: part_of
  some values from: posterior region of body
definition: A limb bud that develops into a hindlimb or pelvic fin.
imported from: cl.owl
has exact synonym: hindlimb/pelvic fin bud
has_related_synonym: pelvic fin bud
has_related_synonym: pelvic fin buds

Axiom
annotated source: pelvic appendage bud
annotated property: subClassOf
annotated target: paired limb/fin bud
is inferred: true

developing anatomical structure
type: Class
subclass of: material anatomical entity
imported from: cl.owl
has_related_synonym: developing structure
has_related_synonym: developmental structure
has_related_synonym: developmental tissue

Axiom
annotated source: developing anatomical structure
annotated property: subClassOf
annotated target: material anatomical entity
is inferred: true

vagal neural crest
type: Class
subclass of: ectoderm-derived structure
subclass of: embryonic tissue
subclass of: Restriction
  on property: part_of
  some values from: neural crest
definition: Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA].
imported from: cl.owl
has exact synonym: VNC
has_related_synonym: enteric neural crest
has_related_synonym: post-otic neural crest

Axiom
annotated source: vagal neural crest
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

Axiom
annotated source: vagal neural crest
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

primitive heart tube
type: Class
subclass of: multi-tissue structure
subclass of: mesoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: embryo
subclass of: Restriction
  on property: develops from
  some values from: heart rudiment
definition: Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
imported from: cl.owl
has exact synonym: primitive heart tube
has_narrow_synonym: early primitive heart tube

Axiom
annotated source: primitive heart tube
annotated property: subClassOf
annotated target: multi-tissue structure
is inferred: true

Axiom
annotated source: primitive heart tube
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

gonad primordium
type: Class
subclass of: primordium
subclass of: Restriction
  on property: part_of
  some values from: reproductive system
definition: Portion of tissue that gives rise to the immature gonad.
imported from: cl.owl
has exact synonym: future gonad
has exact synonym: gonadal primordium
has exact synonym: primitive gonad
has exact synonym: undifferentiated gonad
has_related_synonym: immature gonad

Axiom
annotated source: gonad primordium
annotated property: subClassOf
annotated target: primordium
is inferred: true

lung primordium
type: Class
subclass of: primordium
subclass of: Restriction
  on property: part_of
  some values from: respiratory primordium
subclass of: Restriction
  on property: develops from
  some values from: foregut
definition: A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
imported from: cl.owl
has_related_synonym: lateral diverticula
has_related_synonym: lung diverticulum
has_related_synonym: lung endoderm

Axiom
annotated source: lung primordium
annotated property: subClassOf
annotated target: primordium
is inferred: true

extraembryonic membrane
type: Class
subclass of: membranous layer
subclass of: Restriction
  on property: part_of
  some values from: UBERON_0016887
definition: Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo.
imported from: cl.owl

Axiom
annotated source: extraembryonic membrane
annotated property: subClassOf
annotated target: membranous layer
is inferred: true

extraembryonic mesoderm
type: Class
subclass of: mesoderm-derived structure
subclass of: extraembryonic tissue
subclass of: dense mesenchyme tissue
subclass of: Restriction
  on property: develops from
  some values from: lateral plate mesoderm
subclass of: Restriction
  on property: develops from
  some values from: inner cell mass derived epiblast
definition: .
imported from: cl.owl
has exact synonym: extra-embryonic mesoderm
has exact synonym: extraembryonic mesenchyme

Axiom
annotated source: extraembryonic mesoderm
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: extraembryonic mesoderm
annotated property: subClassOf
annotated target: extraembryonic tissue
is inferred: true

Axiom
annotated source: extraembryonic mesoderm
annotated property: subClassOf
annotated target: dense mesenchyme tissue
is inferred: true

acellular membrane
type: Class
subclass of: acellular anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: anatomical structure
definition: A acellular anatomical structure that is the bounding layer of a anatomical structure.
imported from: cl.owl

Axiom
annotated source: acellular membrane
annotated property: subClassOf
annotated target: acellular anatomical structure
is inferred: true

basement membrane of epithelium
type: Class
subclass of: acellular membrane
subclass of: Restriction
  on property: part_of
  some values from: epithelium
definition: An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
imported from: cl.owl
has exact synonym: basement membrane of connective tissue
has exact synonym: membrana basalis
has_related_synonym: basement membrane

Axiom
annotated source: basement membrane of epithelium
annotated property: subClassOf
annotated target: acellular membrane
is inferred: true

embryonic uterus
type: Class
subclass of: presumptive structure
imported from: cl.owl
has exact synonym: fetal uterus

Axiom
annotated source: embryonic uterus
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

portal system
type: Class
subclass of: vasculature
definition: In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP].
imported from: cl.owl
has exact synonym: portal venous system

Axiom
annotated source: portal system
annotated property: subClassOf
annotated target: vasculature
is inferred: true

developing mesenchymal condensation
type: Class
subclass of: dense mesenchyme tissue
subclass of: cell condensation
definition: A delimited region of dense mesenchyme within looser mesenchyme.
imported from: cl.owl
has exact synonym: mesenchyme condensation

Axiom
annotated source: developing mesenchymal condensation
annotated property: subClassOf
annotated target: dense mesenchyme tissue
is inferred: true

Axiom
annotated source: developing mesenchymal condensation
annotated property: subClassOf
annotated target: cell condensation
is inferred: true

cartilaginous condensation
type: Class
subclass of: developing mesenchymal condensation
subclass of: Restriction
  on property: part_of
  some values from: skeleton
subclass of: Restriction
  on property: develops from
  some values from: pre-cartilage condensation
definition: Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
imported from: cl.owl
has exact synonym: cartilage condensation
has exact synonym: cartilagenous condensation
has exact synonym: chondrogenic condensation

Axiom
annotated source: cartilaginous condensation
annotated property: subClassOf
annotated target: developing mesenchymal condensation
is inferred: true

pre-cartilage condensation
type: Class
subclass of: embryonic tissue
subclass of: developing mesenchymal condensation
subclass of: Restriction
  on property: part_of
  some values from: skeleton
definition: A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
imported from: cl.owl
has exact synonym: pre-chondrogenic condensation
has exact synonym: precartilage condensation
has exact synonym: precartilagenous condensation
has exact synonym: prechondrogenic condensation

Axiom
annotated source: pre-cartilage condensation
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: pre-cartilage condensation
annotated property: subClassOf
annotated target: developing mesenchymal condensation
is inferred: true

leg bone
type: Class
equivalent class: Class
  intersection of: bone element
  intersection of: Restriction
    on property: part_of
    some values from: leg
subclass of: hindlimb bone
subclass of: Restriction
  on property: part_of
  some values from: leg
definition: A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx
imported from: cl.owl

Axiom
annotated source: leg bone
annotated property: subClassOf
annotated target: hindlimb bone
is inferred: true

endo-epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: develops from
    some values from: endoderm
subclass of: epithelium
subclass of: endoderm-derived structure
definition: Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
imported from: cl.owl
has exact synonym: endoderm-derived epithelium
has exact synonym: endoepithelium

Axiom
annotated source: endo-epithelium
annotated property: subClassOf
annotated target: epithelium
is inferred: true

Axiom
annotated source: endo-epithelium
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

axial skeleton plus cranial skeleton
type: Class
subclass of: subdivision of skeleton
subclass of: Restriction
  on property: part_of
  some values from: axial skeletal system
subclass of: Restriction
  on property: develops from
  some values from: sclerotome
definition: Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
imported from: cl.owl
has_related_synonym: skeleton axiale

Axiom
annotated source: axial skeleton plus cranial skeleton
annotated property: subClassOf
annotated target: subdivision of skeleton
is inferred: true

amniotic fold
type: Class
subclass of: extraembryonic structure
subclass of: Restriction
  on property: develops from
  some values from: somatopleure
definition: A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong].
imported from: cl.owl
has exact synonym: amnionic fold

Axiom
annotated source: amniotic fold
annotated property: subClassOf
annotated target: extraembryonic structure
is inferred: true

multi-limb segment region
type: Class
subclass of: subdivision of organism along appendicular axis
subclass of: Restriction
  on property: has part
  some values from: limb segment
definition: A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions).
imported from: cl.owl

Axiom
annotated source: multi-limb segment region
annotated property: subClassOf
annotated target: subdivision of organism along appendicular axis
is inferred: true

femur pre-cartilage condensation
type: Class
subclass of: upper leg mesenchyme
subclass of: pre-cartilage condensation
subclass of: hindlimb pre-cartilage condensation
subclass of: femur endochondral element
definition: A femur endochondral element that is composed primarily of a pre-cartilage condensation.
imported from: cl.owl
has_related_synonym: femoral pre-cartilage condensation

Axiom
annotated source: femur pre-cartilage condensation
annotated property: subClassOf
annotated target: upper leg mesenchyme
is inferred: true

Axiom
annotated source: femur pre-cartilage condensation
annotated property: subClassOf
annotated target: pre-cartilage condensation
is inferred: true

Axiom
annotated source: femur pre-cartilage condensation
annotated property: subClassOf
annotated target: hindlimb pre-cartilage condensation
is inferred: true

Axiom
annotated source: femur pre-cartilage condensation
annotated property: subClassOf
annotated target: femur endochondral element
is inferred: true

foregut-midgut junction
type: Class
equivalent class: Class
  intersection of: anatomical junction
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: part_of
      some values from: foregut
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: part_of
      some values from: midgut
subclass of: anatomical junction
subclass of: Restriction
  on property: part_of
  some values from: digestive tract
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: foregut
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: midgut
definition: An anatomical junctions that overlaps the foregut and midgut.
imported from: cl.owl

Axiom
annotated source: foregut-midgut junction
annotated property: subClassOf
annotated target: anatomical junction
is inferred: true

future brain
type: Class
subclass of: presumptive structure
subclass of: Restriction
  on property: part_of
  some values from: neurectoderm
definition: The embryonic precursor of the brain.
imported from: cl.owl
has exact synonym: brain rudiment
has exact synonym: presumptive brain
has_narrow_synonym: encephalon
has_related_synonym: embryonic brain

Axiom
annotated source: future brain
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

future forebrain
type: Class
subclass of: presumptive structure
subclass of: Restriction
  on property: part_of
  some values from: future brain
definition: A presumptive structure that has the potential to develop into a forebrain.
imported from: cl.owl
has exact synonym: future prosencephalon
has exact synonym: presumptive forebrain
has exact synonym: presumptive prosencephalon
has_related_synonym: prosencephalon

Axiom
annotated source: future forebrain
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

bodily fluid
type: Class
subclass of: organism substance
definition: Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
imported from: cl.owl
has_broad_synonym: fluid
has exact synonym: body fluid

Axiom
annotated source: bodily fluid
annotated property: subClassOf
annotated target: organism substance
is inferred: true

lymphatic part of lymphoid system
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part_of
  some values from: circulatory system
subclass of: Restriction
  on property: part_of
  some values from: lymphoid system
definition: An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system.
imported from: cl.owl
has exact synonym: lymphatic system
has exact synonym: lymphatic tree system
has_related_synonym: lymporeticular system

Axiom
annotated source: lymphatic part of lymphoid system
annotated property: subClassOf
annotated target: organ system subdivision
is inferred: true

pharynx
type: Class
subclass of: subdivision of digestive tract
definition: The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
imported from: cl.owl
has_related_synonym: anterior part of foregut
has_related_synonym: pharyngeal tube

Axiom
annotated source: pharynx
annotated property: subClassOf
annotated target: subdivision of digestive tract
is inferred: true

presumptive endoderm
type: Class
subclass of: presumptive structure
subclass of: Restriction
  on property: part_of
  some values from: blastula
definition: Presumptive structure of the blastula that will develop into endoderm.
imported from: cl.owl

Axiom
annotated source: presumptive endoderm
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

presumptive blood
type: Class
subclass of: presumptive structure
imported from: cl.owl
has exact synonym: future blood

Axiom
annotated source: presumptive blood
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

presumptive structure
type: Class
subclass of: embryonic structure
definition: Portion of embryonic tissue determined by fate mapping to become a structure.
imported from: cl.owl
has exact synonym: future structure
has exact synonym: presumptive structures

Axiom
annotated source: presumptive structure
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

presumptive ectoderm
type: Class
subclass of: presumptive structure
subclass of: Restriction
  on property: part_of
  some values from: blastula
definition: Presumptive structure of the blastula that will develop into ectoderm.
imported from: cl.owl
has_related_synonym: presumptive epidermis

Axiom
annotated source: presumptive ectoderm
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

presumptive mesoderm
type: Class
subclass of: presumptive structure
subclass of: Restriction
  on property: part_of
  some values from: blastula
definition: Presumptive structure of the blastula that will develop into mesoderm.
imported from: cl.owl

Axiom
annotated source: presumptive mesoderm
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

aponeurosis
type: Class
subclass of: membranous layer
subclass of: Restriction
  on property: part_of
  some values from: muscle organ
definition: A sheet of extracellular matrix.
imported from: cl.owl
has_related_synonym: aponeuroses
has_related_synonym: aponeurotic

Axiom
annotated source: aponeurosis
annotated property: subClassOf
annotated target: membranous layer
is inferred: true

epicranial aponeurosis
type: Class
subclass of: aponeurosis
subclass of: Restriction
  on property: part_of
  some values from: scalp
definition: The galea aponeurotica (epicranial aponeurosis, aponeurosis epicranialis) is a tough layer of dense fibrous tissue which covers the upper part of the cranium; behind, it is attached, in the interval between its union with the Occipitales, to the external occipital protuberance and highest nuchal lines of the occipital bone; in front, it forms a short and narrow prolongation between its union with the Frontales. On either side it gives origin to the Auriculares anterior and superior; in this situation it loses its aponeurotic character, and is continued over the temporal fascia to the zygomatic arch as a layer of laminated areolar tissue. It is closely connected to the integument by the firm, dense, fibro-fatty layer which forms the superficial fascia of the scalp: it is attached to the pericranium by loose cellular tissue, which allows the aponeurosis, carrying with it the integument to move through a considerable distance.
imported from: cl.owl
has exact synonym: aponeurosis epicranialis
has exact synonym: aponeurosis of epicranius
has exact synonym: epicranial aponeurosis
has exact synonym: epicranius aponeurosis
has exact synonym: galea aponeurotica
has_related_synonym: cranial aponeurosis
has_related_synonym: epicranial aponeurosis
has_related_synonym: galea aponeurosis
has_related_synonym: galea aponeurotica; aponeurosis epicranialis
has_related_synonym: galeal aponeurosis

Axiom
annotated source: epicranial aponeurosis
annotated property: subClassOf
annotated target: aponeurosis
is inferred: true

glandular epithelium
type: Class
subclass of: epithelium
definition: An epithelium that is composed primarily of secretory cells.
imported from: cl.owl

Axiom
annotated source: glandular epithelium
annotated property: subClassOf
annotated target: epithelium
is inferred: true

areolar connective tissue
type: Class
subclass of: loose connective tissue
subclass of: Restriction
  on property: part_of
  some values from: lamina propria
definition: Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand.
imported from: cl.owl
has exact synonym: loose areolar connective tissue
has_related_synonym: areolar tissue
has_related_synonym: loose connective tissue

Axiom
annotated source: areolar connective tissue
annotated property: subClassOf
annotated target: loose connective tissue
is inferred: true

terminal part of digestive tract
type: Class
subclass of: subdivision of digestive tract
subclass of: Restriction
  on property: develops from
  some values from: hindgut
definition: The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus.
imported from: cl.owl
has_narrow_synonym: rectum
has_related_synonym: rectal part of digestive tract
has_related_synonym: terminal section of digestive tract

Axiom
annotated source: terminal part of digestive tract
annotated property: subClassOf
annotated target: subdivision of digestive tract
is inferred: true

stomach glandular epithelium
type: Class
equivalent class: Class
  intersection of: glandular epithelium
  intersection of: Restriction
    on property: part_of
    some values from: stomach
subclass of: epithelium of stomach
subclass of: glandular columnar epithelium
subclass of: Restriction
  on property: part_of
  some values from: stomach glandular region mucosa
subclass of: Restriction
  on property: has part
  some values from: gastric gland
definition: A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands.
imported from: cl.owl
has_narrow_synonym: epithelium of gastric gland
has_related_synonym: gastric gland epithelium

Axiom
annotated source: stomach glandular epithelium
annotated property: subClassOf
annotated target: epithelium of stomach
is inferred: true

Axiom
annotated source: stomach glandular epithelium
annotated property: subClassOf
annotated target: glandular columnar epithelium
is inferred: true

digestive system gland
type: Class
equivalent class: Class
  intersection of: endocrine gland
  intersection of: Restriction
    on property: part_of
    some values from: digestive system
subclass of: endocrine gland
subclass of: digestive system element
definition: Any gland that is part of the digestive system.
imported from: cl.owl
has_related_synonym: digestive gland

Axiom
annotated source: digestive system gland
annotated property: subClassOf
annotated target: endocrine gland
is inferred: true

Axiom
annotated source: digestive system gland
annotated property: subClassOf
annotated target: digestive system element
is inferred: true

glandular columnar epithelium
type: Class
subclass of: simple columnar epithelium
subclass of: glandular epithelium
definition: Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]
imported from: cl.owl

Axiom
annotated source: glandular columnar epithelium
annotated property: subClassOf
annotated target: simple columnar epithelium
is inferred: true

Axiom
annotated source: glandular columnar epithelium
annotated property: subClassOf
annotated target: glandular epithelium
is inferred: true

stomach glandular region mucosa
type: Class
equivalent class: Class
  intersection of: mucosa of stomach
  intersection of: Restriction
    on property: part_of
    some values from: stomach glandular region
subclass of: mucosa of stomach
subclass of: Restriction
  on property: part_of
  some values from: stomach glandular region
definition: stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region.
imported from: cl.owl
has exact synonym: stomach glandular region glandular mucous membrane

Axiom
annotated source: stomach glandular region mucosa
annotated property: subClassOf
annotated target: mucosa of stomach
is inferred: true

vascular cord
type: Class
subclass of: developing anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: primordial vasculature
definition: The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
imported from: cl.owl

Axiom
annotated source: vascular cord
annotated property: subClassOf
annotated target: developing anatomical structure
is inferred: true

cardiogenic splanchnic mesoderm
type: Class
subclass of: mesoderm-derived structure
subclass of: embryonic tissue
subclass of: Restriction
  on property: part_of
  some values from: primary heart field
subclass of: Restriction
  on property: part_of
  some values from: anterior lateral plate mesoderm
subclass of: Restriction
  on property: develops from
  some values from: splanchnic layer of lateral plate mesoderm
definition: The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
imported from: cl.owl
has exact synonym: cardiogenic splanchnopleure
has_related_synonym: cardiac mesoderm
has_related_synonym: cardiogenic mesoderm
has_related_synonym: cardiogenic region
has_related_synonym: heart primordia

Axiom
annotated source: cardiogenic splanchnic mesoderm
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: cardiogenic splanchnic mesoderm
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

cleaving embryo
type: Class
subclass of: embryo
definition: Organism at the cleavage stage.
imported from: cl.owl

Axiom
annotated source: cleaving embryo
annotated property: subClassOf
annotated target: embryo
is inferred: true

presumptive gut
type: Class
subclass of: presumptive structure
imported from: cl.owl
has exact synonym: future digestive tract
has exact synonym: future digestive tube
has exact synonym: future gut
has exact synonym: primitive gut
has_related_synonym: embryonic digestive tube
has_related_synonym: primordial digestive tube
has_related_synonym: primordial gut

Axiom
annotated source: presumptive gut
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

primary circulatory organ
type: Class
subclass of: UBERON_0015228
definition: A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
imported from: cl.owl
has_narrow_synonym: dorsal tube
has_narrow_synonym: heart
has_related_synonym: adult heart

Axiom
annotated source: primary circulatory organ
annotated property: subClassOf
annotated target: UBERON_0015228
is inferred: true

neural keel
type: Class
subclass of: UBERON_0016879
subclass of: Restriction
  on property: develops from
  some values from: neural plate
definition: An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
imported from: cl.owl
has_related_synonym: presumptive central nervous system

Axiom
annotated source: neural keel
annotated property: subClassOf
annotated target: UBERON_0016879
is inferred: true

tracheobronchial tree
type: Class
subclass of: anatomical structure
subclass of: organ
subclass of: endoderm-derived structure
subclass of: Restriction
  on property: part_of
  some values from: lower respiratory tract
subclass of: Restriction
  on property: has part
  some values from: bronchus
subclass of: Restriction
  on property: has part
  some values from: trachea
subclass of: Restriction
  on property: has part
  some values from: ciliated columnar epithelium
definition: The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells.
imported from: cl.owl
has exact synonym: arbor tracheobronchialis
has_related_synonym: tracheobronchial system

Axiom
annotated source: tracheobronchial tree
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

Axiom
annotated source: tracheobronchial tree
annotated property: subClassOf
annotated target: organ
is inferred: true

Axiom
annotated source: tracheobronchial tree
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

pelvic appendage skeleton
type: Class
subclass of: paired limb/fin skeleton
subclass of: Restriction
  on property: part_of
  some values from: pelvic appendage
definition: The collection of all skeletal elements in a pelvic appendage region.
imported from: cl.owl

Axiom
annotated source: pelvic appendage skeleton
annotated property: subClassOf
annotated target: paired limb/fin skeleton
is inferred: true

presumptive segmental plate
type: Class
subclass of: presumptive structure
subclass of: Restriction
  on property: develops from
  some values from: trunk paraxial mesoderm
definition: A presumptive structure that has the potential to develop into a presomitic mesoderm.
imported from: cl.owl
has_related_synonym: presumptive segmental plates

Axiom
annotated source: presumptive segmental plate
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

presumptive neural plate
type: Class
subclass of: UBERON_0016879
subclass of: Restriction
  on property: part_of
  some values from: gastrula
subclass of: Restriction
  on property: develops from
  some values from: neurectoderm
definition: A presumptive structure that has the potential to develop into a neural plate.
imported from: cl.owl
has exact synonym: prospective neuroectoderm
has exact synonym: prospective vegetal ectoderm

Axiom
annotated source: presumptive neural plate
annotated property: subClassOf
annotated target: UBERON_0016879
is inferred: true

presumptive paraxial mesoderm
type: Class
subclass of: presumptive structure
subclass of: Restriction
  on property: part_of
  some values from: blastula
definition: The part of the blastula that has the potential to develop into a paraxial mesoderm.
imported from: cl.owl
has exact synonym: future paraxial mesenchyme
has exact synonym: future paraxial mesoderm

Axiom
annotated source: presumptive paraxial mesoderm
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

outer epithelium
type: Class
subclass of: surface structure
subclass of: ecto-epithelium
subclass of: Restriction
  on property: part_of
  some values from: multicellular organism
subclass of: Restriction
  on property: develops from
  some values from: enveloping layer of ectoderm
definition: The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
imported from: cl.owl
has exact synonym: epidermis
has exact synonym: epidermis (sensu Metazoa)
has exact synonym: outer epidermal layer
has exact synonym: outer epithelial layer
has_related_synonym: hypoderm
has_related_synonym: hypodermis

Axiom
annotated source: outer epithelium
annotated property: subClassOf
annotated target: surface structure
is inferred: true

Axiom
annotated source: outer epithelium
annotated property: subClassOf
annotated target: ecto-epithelium
is inferred: true

enveloping layer of ectoderm
type: Class
subclass of: unilaminar epithelium
subclass of: embryonic tissue
subclass of: ecto-epithelium
subclass of: Restriction
  on property: part_of
  some values from: embryo
subclass of: Restriction
  on property: develops from
  some values from: external ectoderm
definition: Outermost layer of cells surrounding the embryo.
imported from: cl.owl
has exact synonym: EVL
has exact synonym: enveloping layer

Axiom
annotated source: enveloping layer of ectoderm
annotated property: subClassOf
annotated target: unilaminar epithelium
is inferred: true

Axiom
annotated source: enveloping layer of ectoderm
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: enveloping layer of ectoderm
annotated property: subClassOf
annotated target: ecto-epithelium
is inferred: true

epithelial sac
type: Class
subclass of: epithelial tube
subclass of: sac
definition: An epithelial tube that is open at one end only.
imported from: cl.owl

Axiom
annotated source: epithelial sac
annotated property: subClassOf
annotated target: epithelial tube
is inferred: true

Axiom
annotated source: epithelial sac
annotated property: subClassOf
annotated target: sac
is inferred: true

epithelial tube open at both ends
type: Class
subclass of: epithelial tube
definition: An epithelial tube open at both ends that allows fluid flow.
imported from: cl.owl

Axiom
annotated source: epithelial tube open at both ends
annotated property: subClassOf
annotated target: epithelial tube
is inferred: true

epithelial vesicle
type: Class
subclass of: epithelium
definition: A closed epithelium with a lumen.
imported from: cl.owl

Axiom
annotated source: epithelial vesicle
annotated property: subClassOf
annotated target: epithelium
is inferred: true

dense mesenchyme tissue
type: Class
subclass of: mesenchyme
definition: Mesenchyme with little extracellular matrix.
imported from: cl.owl

Axiom
annotated source: dense mesenchyme tissue
annotated property: subClassOf
annotated target: mesenchyme
is inferred: true

migrating mesenchyme population
type: Class
subclass of: mesenchyme
definition: Mesenchymal cells that are migrating.
imported from: cl.owl

Axiom
annotated source: migrating mesenchyme population
annotated property: subClassOf
annotated target: mesenchyme
is inferred: true

ciliated columnar epithelium
type: Class
subclass of: simple columnar epithelium
subclass of: ciliated epithelium
definition: Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]
imported from: cl.owl

Axiom
annotated source: ciliated columnar epithelium
annotated property: subClassOf
annotated target: simple columnar epithelium
is inferred: true

Axiom
annotated source: ciliated columnar epithelium
annotated property: subClassOf
annotated target: ciliated epithelium
is inferred: true

ciliated epithelium
type: Class
subclass of: epithelium
definition: Epithelium bearing vibratile cilia on the free surface.
imported from: cl.owl

Axiom
annotated source: ciliated epithelium
annotated property: subClassOf
annotated target: epithelium
is inferred: true

anatomical junction
type: Class
subclass of: anatomical structure
definition: An anatomical structure that connects two structures
imported from: cl.owl
has_broad_synonym: junction
has exact synonym: anatomical junction

Axiom
annotated source: anatomical junction
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

anlage
type: Class
subclass of: tissue
subclass of: developing anatomical structure
definition: Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
imported from: cl.owl
has_broad_synonym: field
has exact synonym: developmental field
has_related_synonym: future organ
has_related_synonym: organ field

Axiom
annotated source: anlage
annotated property: subClassOf
annotated target: tissue
is inferred: true

Axiom
annotated source: anlage
annotated property: subClassOf
annotated target: developing anatomical structure
is inferred: true

vascular system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: part_of
  some values from: cardiovascular system
definition: Anatomical system that consists of all blood and lymph vessels.
imported from: cl.owl
has_related_synonym: Gefaesssystem@de

Axiom
annotated source: vascular system
annotated property: subClassOf
annotated target: anatomical system
is inferred: true

connecting stalk
type: Class
subclass of: extraembryonic structure
subclass of: Restriction
  on property: develops from
  some values from: extraembryonic mesoderm
definition: A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord.
imported from: cl.owl

Axiom
annotated source: connecting stalk
annotated property: subClassOf
annotated target: extraembryonic structure
is inferred: true

craniocervical region
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: part_of
  some values from: anterior region of body
subclass of: Restriction
  on property: part_of
  some values from: body proper
subclass of: Restriction
  on property: has part
  some values from: head
subclass of: Restriction
  on property: has part
  some values from: pharynx
definition: The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
imported from: cl.owl
has_related_synonym: cephalic area
has_related_synonym: cephalic part of animal
has_related_synonym: cephalic region
has_related_synonym: head and neck
has_related_synonym: head or neck

Axiom
annotated source: craniocervical region
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

appendage girdle region
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: part_of
  some values from: appendage girdle complex
subclass of: Restriction
  on property: has part
  some values from: girdle skeleton
definition: An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
imported from: cl.owl
has_broad_synonym: girdle
has_broad_synonym: girdle region
has_related_synonym: fin girdle
has_related_synonym: fin girdle region
has_related_synonym: limb girdle
has_related_synonym: limb girdle region

Axiom
annotated source: appendage girdle region
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

pelvic girdle skeleton
type: Class
subclass of: mesoderm-derived structure
subclass of: girdle skeleton
subclass of: Restriction
  on property: part_of
  some values from: pelvic girdle region
subclass of: Restriction
  on property: part_of
  some values from: skeleton of pelvic complex
subclass of: Restriction
  on property: develops from
  some values from: mesenchyme from somatopleure
definition: Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.
imported from: cl.owl
has exact synonym: pelvic girdle skeleton
has exact synonym: skeletal parts of pelvic girdle
has exact synonym: skeleton of pelvic girdle
has_related_synonym: pelvic girdle

Axiom
annotated source: pelvic girdle skeleton
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: pelvic girdle skeleton
annotated property: subClassOf
annotated target: girdle skeleton
is inferred: true

cartilage element
type: Class
subclass of: skeletal element
subclass of: Restriction
  on property: has part
  some values from: cartilage tissue
subclass of: Restriction
  on property: develops from
  some values from: cartilaginous condensation
definition: Skeletal element that is composed of cartilage tissue and may be permanent or transient.
imported from: cl.owl
has exact synonym: cartilage organ
has exact synonym: cartilaginous element
has exact synonym: chondrogenic element
has_related_synonym: cartilage

Axiom
annotated source: cartilage element
annotated property: subClassOf
annotated target: skeletal element
is inferred: true

irregular bone
type: Class
subclass of: bone element
definition: The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid.
imported from: cl.owl
has exact synonym: os irregulare
has_related_synonym: os irregulare

Axiom
annotated source: irregular bone
annotated property: subClassOf
annotated target: bone element
is inferred: true

bone of hip region
type: Class
subclass of: bone element
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: part_of
    some values from: hip
imported from: cl.owl

Axiom
annotated source: bone of hip region
annotated property: subClassOf
annotated target: bone element
is inferred: true

inner cell mass derived epiblast
type: Class
equivalent class: Class
  intersection of: epiblast (generic)
  intersection of: Restriction
    on property: develops from
    some values from: inner cell mass
subclass of: epiblast (generic)
subclass of: Restriction
  on property: part_of
  some values from: bilaminar disc
subclass of: Restriction
  on property: develops from
  some values from: inner cell mass
definition: An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers
imported from: cl.owl
has_related_synonym: embryonic epiblast

Axiom
annotated source: inner cell mass derived epiblast
annotated property: subClassOf
annotated target: epiblast (generic)
is inferred: true

lower limb segment
type: Class
equivalent class: Class
  intersection of: limb segment
  intersection of: Restriction
    on property: part_of
    some values from: hindlimb
subclass of: limb segment
subclass of: Restriction
  on property: part_of
  some values from: hindlimb
definition: A limb segment that is part of a hindlimb.
imported from: cl.owl
has exact synonym: free lower limb segment
has exact synonym: free lower limb subdivision
has exact synonym: segment of free lower limb
has exact synonym: subdivision of free lower limb

Axiom
annotated source: lower limb segment
annotated property: subClassOf
annotated target: limb segment
is inferred: true

hepatic diverticulum
type: Class
subclass of: endodermal part of digestive tract
subclass of: embryonic tissue
subclass of: epithelial sac
subclass of: epithelium of foregut-midgut junction
subclass of: digestive tract diverticulum
subclass of: Restriction
  on property: part_of
  some values from: septum transversum
subclass of: Restriction
  on property: part_of
  some values from: foregut-midgut junction
subclass of: Restriction
  on property: develops from
  some values from: liver primordium
definition: An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts.
imported from: cl.owl
has exact synonym: liver diverticulum
has_related_synonym: diverticulum hepaticum

Axiom
annotated source: hepatic diverticulum
annotated property: subClassOf
annotated target: endodermal part of digestive tract
is inferred: true

Axiom
annotated source: hepatic diverticulum
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: hepatic diverticulum
annotated property: subClassOf
annotated target: epithelial sac
is inferred: true

Axiom
annotated source: hepatic diverticulum
annotated property: subClassOf
annotated target: epithelium of foregut-midgut junction
is inferred: true

Axiom
annotated source: hepatic diverticulum
annotated property: subClassOf
annotated target: digestive tract diverticulum
is inferred: true

liver bud
type: Class
subclass of: endodermal part of digestive tract
subclass of: epithelial sac
subclass of: epithelium of foregut-midgut junction
subclass of: digestive tract diverticulum
subclass of: Restriction
  on property: part_of
  some values from: foregut-midgut junction
subclass of: Restriction
  on property: develops from
  some values from: hepatic diverticulum
imported from: cl.owl

Axiom
annotated source: liver bud
annotated property: subClassOf
annotated target: endodermal part of digestive tract
is inferred: true

Axiom
annotated source: liver bud
annotated property: subClassOf
annotated target: epithelial sac
is inferred: true

Axiom
annotated source: liver bud
annotated property: subClassOf
annotated target: epithelium of foregut-midgut junction
is inferred: true

Axiom
annotated source: liver bud
annotated property: subClassOf
annotated target: digestive tract diverticulum
is inferred: true

pulmonary acinus
type: Class
subclass of: pulmonary lobule
definition: The part of the airway consisting of a respiratory bronchiole and all of its branches
imported from: cl.owl
has exact synonym: acinus pulmonaris
has exact synonym: arbor alveolaris
has exact synonym: lobulus pulmonis primarius
has exact synonym: primary pulmonary lobule
has exact synonym: respiratory lobule

Axiom
annotated source: pulmonary acinus
annotated property: subClassOf
annotated target: pulmonary lobule
is inferred: true

respiratory primordium
type: Class
subclass of: primordium
subclass of: Restriction
  on property: part_of
  some values from: endoderm of foregut
imported from: cl.owl

Axiom
annotated source: respiratory primordium
annotated property: subClassOf
annotated target: primordium
is inferred: true

entire embryonic mesenchyme
type: Class
subclass of: anatomical cluster
subclass of: Restriction
  on property: part_of
  some values from: embryo
subclass of: Restriction
  on property: has part
  some values from: mesenchyme
definition: Sum total of mesenchyme in the embryo.
imported from: cl.owl

Axiom
annotated source: entire embryonic mesenchyme
annotated property: subClassOf
annotated target: anatomical cluster
is inferred: true

epithelium of foregut-midgut junction
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: foregut-midgut junction
subclass of: unilaminar epithelium
subclass of: digestive tract epithelium
subclass of: endo-epithelium
subclass of: Restriction
  on property: part_of
  some values from: digestive tract epithelium
subclass of: Restriction
  on property: part_of
  some values from: foregut-midgut junction
subclass of: Restriction
  on property: develops from
  some values from: endoderm of foregut-midgut junction
definition: An epithelium that is part of a foregut-midgut junction.
imported from: cl.owl

Axiom
annotated source: epithelium of foregut-midgut junction
annotated property: subClassOf
annotated target: unilaminar epithelium
is inferred: true

Axiom
annotated source: epithelium of foregut-midgut junction
annotated property: subClassOf
annotated target: digestive tract epithelium
is inferred: true

Axiom
annotated source: epithelium of foregut-midgut junction
annotated property: subClassOf
annotated target: endo-epithelium
is inferred: true

anal membrane endodermal component
type: Class
equivalent class: Class
  intersection of: unilaminar epithelium
  intersection of: Restriction
    on property: part_of
    some values from: anal region
  intersection of: Restriction
    on property: develops from
    some values from: endoderm
subclass of: unilaminar epithelium
subclass of: endo-epithelium
subclass of: Restriction
  on property: part_of
  some values from: anal region
definition: An endoderm that is part of a anal region.
imported from: cl.owl

Axiom
annotated source: anal membrane endodermal component
annotated property: subClassOf
annotated target: unilaminar epithelium
is inferred: true

Axiom
annotated source: anal membrane endodermal component
annotated property: subClassOf
annotated target: endo-epithelium
is inferred: true

endoderm of foregut-midgut junction
type: Class
equivalent class: Class
  intersection of: endoderm
  intersection of: Restriction
    on property: part_of
    some values from: foregut-midgut junction
subclass of: endoderm
subclass of: Restriction
  on property: part_of
  some values from: foregut-midgut junction
definition: An endoderm that is part of a foregut-midgut junction.
imported from: cl.owl

Axiom
annotated source: endoderm of foregut-midgut junction
annotated property: subClassOf
annotated target: endoderm
is inferred: true

subdivision of trunk
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: part_of
  some values from: trunk
imported from: cl.owl
has exact synonym: region of trunk
has exact synonym: trunk subdivision

Axiom
annotated source: subdivision of trunk
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

trunk paraxial mesoderm
type: Class
subclass of: trunk mesenchyme
subclass of: Restriction
  on property: part_of
  some values from: paraxial mesoderm
subclass of: Restriction
  on property: part_of
  some values from: trunk mesenchyme
imported from: cl.owl
has exact synonym: trunk and cervical paraxial mesenchyme
has_related_synonym: trunk paraxial mesenchyme

Axiom
annotated source: trunk paraxial mesoderm
annotated property: subClassOf
annotated target: trunk mesenchyme
is inferred: true

limb mesenchyme
type: Class
equivalent class: Class
  intersection of: mesenchyme
  intersection of: Restriction
    on property: part_of
    some values from: limb
subclass of: mesenchyme
subclass of: Restriction
  on property: part_of
  some values from: limb
definition: The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells.
imported from: cl.owl
has_related_synonym: limb mesoderm

Axiom
annotated source: limb mesenchyme
annotated property: subClassOf
annotated target: mesenchyme
is inferred: true

glandular acinus
type: Class
subclass of: UBERON_0034922
subclass of: Restriction
  on property: part_of
  some values from: gland
definition: The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
imported from: cl.owl
has_broad_synonym: acinus
has_related_synonym: acini

Axiom
annotated source: glandular acinus
annotated property: subClassOf
annotated target: UBERON_0034922
is inferred: true

embryonic cloacal epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: embryonic cloaca
subclass of: embryonic tissue
subclass of: anal membrane endodermal component
subclass of: cloacal epithelium
subclass of: Restriction
  on property: part_of
  some values from: embryonic cloaca
subclass of: Restriction
  on property: part_of
  some values from: digestive tract epithelium
subclass of: Restriction
  on property: develops from
  some values from: epithelium of hindgut
definition: An epithelium that is part of a embryonic cloaca.
imported from: cl.owl
has_broad_synonym: cloacal epithelium

Axiom
annotated source: embryonic cloacal epithelium
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: embryonic cloacal epithelium
annotated property: subClassOf
annotated target: anal membrane endodermal component
is inferred: true

Axiom
annotated source: embryonic cloacal epithelium
annotated property: subClassOf
annotated target: cloacal epithelium
is inferred: true

prostate field
type: Class
subclass of: mixed endoderm/mesoderm-derived structure
subclass of: embryonic tissue
subclass of: presumptive structure
subclass of: anlage
subclass of: Restriction
  on property: part_of
  some values from: urogenital sinus epithelium
definition: A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop.
imported from: cl.owl
has_related_synonym: prostate primordium

Axiom
annotated source: prostate field
annotated property: subClassOf
annotated target: mixed endoderm/mesoderm-derived structure
is inferred: true

Axiom
annotated source: prostate field
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: prostate field
annotated property: subClassOf
annotated target: presumptive structure
is inferred: true

Axiom
annotated source: prostate field
annotated property: subClassOf
annotated target: anlage
is inferred: true

digestive tract diverticulum
type: Class
equivalent class: Class
  intersection of: sac
  intersection of: Restriction
    on property: part_of
    some values from: digestive tract
subclass of: subdivision of digestive tract
subclass of: sac
definition: Branch or outpocketing of the digestive tract.
imported from: cl.owl
has_related_synonym: diverticulum of gut
has_related_synonym: intestinal pouch

Axiom
annotated source: digestive tract diverticulum
annotated property: subClassOf
annotated target: subdivision of digestive tract
is inferred: true

Axiom
annotated source: digestive tract diverticulum
annotated property: subClassOf
annotated target: sac
is inferred: true

sac
type: Class
subclass of: anatomical structure
imported from: cl.owl
has exact synonym: pouch
has_related_synonym: diverticulum

Axiom
annotated source: sac
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

zone of stomach
type: Class
equivalent class: Class
  intersection of: UBERON_0034944
  intersection of: Restriction
    on property: part_of
    some values from: stomach
subclass of: UBERON_0034944
subclass of: Restriction
  on property: part_of
  some values from: stomach
definition: A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland.
imported from: cl.owl
has exact synonym: gastric zone
has exact synonym: region of stomach
has exact synonym: section of stomach

Axiom
annotated source: zone of stomach
annotated property: subClassOf
annotated target: UBERON_0034944
is inferred: true

anterior lateral plate mesoderm
type: Class
subclass of: mesoderm-derived structure
subclass of: embryonic tissue
subclass of: Restriction
  on property: part_of
  some values from: lateral plate mesoderm
imported from: cl.owl
has exact synonym: ALPM

Axiom
annotated source: anterior lateral plate mesoderm
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: anterior lateral plate mesoderm
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

lobule
type: Class
subclass of: organ subunit
imported from: cl.owl
has exact synonym: lobulus

Axiom
annotated source: lobule
annotated property: subClassOf
annotated target: organ subunit
is inferred: true

multicellular anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has more than one cell as a part.
imported from: cl.owl
imported from: clo.owl
imported from: uberon.owl
has db xref: CARO:0010000
has db xref: FBbt:00100313
has exact synonym: multicellular structure
has OBO namespace: uberon
id: UBERON:0010000
in subset: upper level

Axiom
annotated source: multicellular anatomical structure
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

food storage organ
type: Class
subclass of: digestive system element
subclass of: Restriction
  on property: part_of
  some values from: digestive tract
subclass of: Restriction
  on property: part_of
  some values from: alimentary part of gastrointestinal system
definition: An organ of the digestive tract that is capable of retaining and storing food
imported from: cl.owl

Axiom
annotated source: food storage organ
annotated property: subClassOf
annotated target: digestive system element
is inferred: true

future dermis
type: Class
subclass of: mesenchyme
subclass of: Restriction
  on property: part_of
  some values from: integument
subclass of: Restriction
  on property: develops from
  some values from: sclerotome
subclass of: Restriction
  on property: develops from
  some values from: dermatome
definition: Mesenchyme that has the potential to develop into a dermis.
imported from: cl.owl

Axiom
annotated source: future dermis
annotated property: subClassOf
annotated target: mesenchyme
is inferred: true

femur cartilage element
type: Class
subclass of: upper leg mesenchyme
subclass of: cartilaginous condensation
subclass of: hindlimb cartilage element
subclass of: femur endochondral element
subclass of: Restriction
  on property: part_of
  some values from: upper leg mesenchyme
subclass of: Restriction
  on property: develops from
  some values from: femur pre-cartilage condensation
definition: A femur endochondral element that is composed primarily of cartilage tissue.
imported from: cl.owl
has exact synonym: femoral cartilage condensation

Axiom
annotated source: femur cartilage element
annotated property: subClassOf
annotated target: upper leg mesenchyme
is inferred: true

Axiom
annotated source: femur cartilage element
annotated property: subClassOf
annotated target: cartilaginous condensation
is inferred: true

Axiom
annotated source: femur cartilage element
annotated property: subClassOf
annotated target: hindlimb cartilage element
is inferred: true

Axiom
annotated source: femur cartilage element
annotated property: subClassOf
annotated target: femur endochondral element
is inferred: true

male accessory sex gland
type: Class
subclass of: male reproductive gland
definition: Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male.
imported from: cl.owl
has_related_synonym: male accessory gland
has_related_synonym: male accessory reproductive gland

Axiom
annotated source: male accessory sex gland
annotated property: subClassOf
annotated target: male reproductive gland
is inferred: true

structure with developmental contribution from neural crest
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has some part that develops from the neural crest.
imported from: cl.owl

Axiom
annotated source: structure with developmental contribution from neural crest
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

germ layer / neural crest
type: Class
subclass of: embryonic structure
subclass of: embryonic tissue
subclass of: Restriction
  on property: develops from
  some values from: epiblast (generic)
imported from: cl.owl

Axiom
annotated source: germ layer / neural crest
annotated property: subClassOf
annotated target: embryonic structure
is inferred: true

Axiom
annotated source: germ layer / neural crest
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

extraembryonic membrane mesenchyme
type: Class
equivalent class: Class
  intersection of: mesenchyme
  intersection of: Restriction
    on property: part_of
    some values from: extraembryonic membrane
subclass of: mesenchyme
subclass of: mesoderm-derived structure
subclass of: extraembryonic tissue
subclass of: Restriction
  on property: part_of
  some values from: extraembryonic membrane
subclass of: Restriction
  on property: develops from
  some values from: extraembryonic mesoderm
definition: Mesenchyme that is part of a extraembryonic membrane.
imported from: cl.owl

Axiom
annotated source: extraembryonic membrane mesenchyme
annotated property: subClassOf
annotated target: mesenchyme
is inferred: true

Axiom
annotated source: extraembryonic membrane mesenchyme
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: extraembryonic membrane mesenchyme
annotated property: subClassOf
annotated target: extraembryonic tissue
is inferred: true

endochondral element
type: Class
subclass of: skeletal element
definition: A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
imported from: cl.owl
has exact synonym: endochondral replacement element

Axiom
annotated source: endochondral element
annotated property: subClassOf
annotated target: skeletal element
is inferred: true

pulmonary lobule
type: Class
equivalent class: Class
  intersection of: lobule
  intersection of: Restriction
    on property: part_of
    some values from: lung
subclass of: endoderm-derived structure
subclass of: lobule
subclass of: Restriction
  on property: part_of
  some values from: lung
subclass of: Restriction
  on property: has part
  some values from: terminal bronchiole
definition: The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa.
imported from: cl.owl
has exact synonym: lobulus pulmonis

Axiom
annotated source: pulmonary lobule
annotated property: subClassOf
annotated target: endoderm-derived structure
is inferred: true

Axiom
annotated source: pulmonary lobule
annotated property: subClassOf
annotated target: lobule
is inferred: true

ecto-epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: develops from
    some values from: ectoderm
subclass of: epithelium
subclass of: ectoderm-derived structure
definition: Epithelium composed of cells that develops from the ectoderm[FMA,modified].
imported from: cl.owl
has exact synonym: ectoderm-derived epithelium

Axiom
annotated source: ecto-epithelium
annotated property: subClassOf
annotated target: epithelium
is inferred: true

Axiom
annotated source: ecto-epithelium
annotated property: subClassOf
annotated target: ectoderm-derived structure
is inferred: true

mesenchyme from somatopleure
type: Class
equivalent class: Class
  intersection of: mesenchyme
  intersection of: Restriction
    on property: part_of
    some values from: embryo
  intersection of: Restriction
    on property: develops from
    some values from: somatopleure
subclass of: mesoderm-derived structure
subclass of: embryonic tissue
subclass of: dense mesenchyme tissue
subclass of: Restriction
  on property: part_of
  some values from: entire embryonic mesenchyme
subclass of: Restriction
  on property: develops from
  some values from: somatopleure
definition: Mesenchyme that develops_from a somatopleure.
imported from: cl.owl

Axiom
annotated source: mesenchyme from somatopleure
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: mesenchyme from somatopleure
annotated property: subClassOf
annotated target: embryonic tissue
is inferred: true

Axiom
annotated source: mesenchyme from somatopleure
annotated property: subClassOf
annotated target: dense mesenchyme tissue
is inferred: true

pseudostratified columnar epithelium
type: Class
subclass of: simple columnar epithelium
definition: A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
imported from: cl.owl

Axiom
annotated source: pseudostratified columnar epithelium
annotated property: subClassOf
annotated target: simple columnar epithelium
is inferred: true

pseudostratified ciliated columnar epithelium
type: Class
subclass of: ciliated columnar epithelium
subclass of: pseudostratified columnar epithelium
definition: Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
imported from: cl.owl
has exact synonym: epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)

Axiom
annotated source: pseudostratified ciliated columnar epithelium
annotated property: subClassOf
annotated target: ciliated columnar epithelium
is inferred: true

Axiom
annotated source: pseudostratified ciliated columnar epithelium
annotated property: subClassOf
annotated target: pseudostratified columnar epithelium
is inferred: true

paired limb/fin segment
type: Class
equivalent class: Class
  intersection of: subdivision of organism along appendicular axis
  intersection of: Restriction
    on property: part_of
    some values from: paired limb/fin
subclass of: subdivision of organism along appendicular axis
subclass of: Restriction
  on property: part_of
  some values from: paired limb/fin
definition: An appendage segment that is part of a limb/fin.
imported from: cl.owl
has exact synonym: limb/fin segment

Axiom
annotated source: paired limb/fin segment
annotated property: subClassOf
annotated target: subdivision of organism along appendicular axis
is inferred: true

appendage girdle complex
type: Class
subclass of: organism subdivision
subclass of: UBERON_0015212
subclass of: Restriction
  on property: part_of
  some values from: multicellular organism
definition: An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
imported from: cl.owl
has exact synonym: appendage complex
has exact synonym: appendage-girdle complex
has exact synonym: appendage/girdle complex
has exact synonym: girdle plus limb or fin
has_related_synonym: limb

Axiom
annotated source: appendage girdle complex
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

Axiom
annotated source: appendage girdle complex
annotated property: subClassOf
annotated target: UBERON_0015212
is inferred: true

pelvic complex
type: Class
equivalent class: Class
  intersection of: appendage girdle complex
  intersection of: Restriction
    on property: has part
    some values from: pelvic girdle region
subclass of: appendage girdle complex
subclass of: Restriction
  on property: has part
  some values from: pelvic girdle region
subclass of: Restriction
  on property: has part
  some values from: skeleton of pelvic complex
definition: Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.
imported from: cl.owl
has exact synonym: pelvic appendage/girdle complex
has exact synonym: pelvic girdle plus pelvic limb or fin
has exact synonym: pelvic girdle plus posterior limb or fin
has_related_synonym: lower limb
has_related_synonym: lower limb and pelvic girdle
has_related_synonym: lower limb and pelvis

Axiom
annotated source: pelvic complex
annotated property: subClassOf
annotated target: appendage girdle complex
is inferred: true

limb skeleton subdivision
type: Class
equivalent class: Class
  intersection of: subdivision of skeleton
  intersection of: Restriction
    on property: part_of
    some values from: limb
subclass of: subdivision of skeleton
subclass of: Restriction
  on property: part_of
  some values from: appendicular skeleton
subclass of: Restriction
  on property: part_of
  some values from: limb
definition: Skeletal subdivision that is a segment of the limb skeleton.
imported from: cl.owl

Axiom
annotated source: limb skeleton subdivision
annotated property: subClassOf
annotated target: subdivision of skeleton
is inferred: true

girdle skeleton
type: Class
subclass of: subdivision of skeleton
subclass of: Restriction
  on property: part_of
  some values from: appendicular skeleton
subclass of: Restriction
  on property: part_of
  some values from: appendage girdle region
definition: The subdivision of the skeleton of either the pectoral or pelvic girdle.
imported from: cl.owl
has exact synonym: skeleton of girdle

Axiom
annotated source: girdle skeleton
annotated property: subClassOf
annotated target: subdivision of skeleton
is inferred: true

bone of appendage girdle complex
type: Class
equivalent class: Class
  intersection of: bone element
  intersection of: Restriction
    on property: part_of
    some values from: appendage girdle complex
subclass of: bone element
subclass of: Restriction
  on property: part_of
  some values from: appendicular skeleton
subclass of: Restriction
  on property: part_of
  some values from: appendage girdle complex
definition: A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle).
imported from: cl.owl
has_related_synonym: bone of extended limb/fin region
has_related_synonym: limb bone

Axiom
annotated source: bone of appendage girdle complex
annotated property: subClassOf
annotated target: bone element
is inferred: true

bone of pelvic complex
type: Class
equivalent class: Class
  intersection of: bone element
  intersection of: Restriction
    on property: part_of
    some values from: pelvic complex
subclass of: bone of appendage girdle complex
subclass of: Restriction
  on property: part_of
  some values from: pelvic complex
definition: A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle.
imported from: cl.owl
has_related_synonym: hindlimb bone

Axiom
annotated source: bone of pelvic complex
annotated property: subClassOf
annotated target: bone of appendage girdle complex
is inferred: true

subdivision of organism along appendicular axis
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: part_of
  some values from: appendage
definition: A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
imported from: cl.owl
has exact synonym: appendage segment
has exact synonym: appendicular segment

Axiom
annotated source: subdivision of organism along appendicular axis
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

limb cartilage element
type: Class
subclass of: cartilage element
subclass of: limb endochondral element
subclass of: Restriction
  on property: develops from
  some values from: limb bone pre-cartilage condensation
definition: A skeletal element that is part of a limb and composed of cartilage tissue.
imported from: cl.owl

Axiom
annotated source: limb cartilage element
annotated property: subClassOf
annotated target: cartilage element
is inferred: true

Axiom
annotated source: limb cartilage element
annotated property: subClassOf
annotated target: limb endochondral element
is inferred: true

limb bone pre-cartilage condensation
type: Class
subclass of: limb endochondral element
subclass of: Restriction
  on property: has part
  some values from: pre-cartilage condensation
definition: A skeletal element that is part of a limb and composed of pre-cartilage tissue.
imported from: cl.owl

Axiom
annotated source: limb bone pre-cartilage condensation
annotated property: subClassOf
annotated target: limb endochondral element
is inferred: true

hindlimb cartilage element
type: Class
subclass of: limb cartilage element
subclass of: hindlimb endochondral element
subclass of: Restriction
  on property: develops from
  some values from: hindlimb pre-cartilage condensation
definition: A cartilaginous condensation that has the potential to develop into a hindlimb bone.
imported from: cl.owl
has exact synonym: hindlimb cartilage condensation

Axiom
annotated source: hindlimb cartilage element
annotated property: subClassOf
annotated target: limb cartilage element
is inferred: true

Axiom
annotated source: hindlimb cartilage element
annotated property: subClassOf
annotated target: hindlimb endochondral element
is inferred: true

hindlimb pre-cartilage condensation
type: Class
subclass of: limb bone pre-cartilage condensation
subclass of: hindlimb endochondral element
definition: A pre-cartilage condensation that has the potential to develop into a hindlimb bone.
imported from: cl.owl
has exact synonym: hindlimb pre-cartilage condensation

Axiom
annotated source: hindlimb pre-cartilage condensation
annotated property: subClassOf
annotated target: limb bone pre-cartilage condensation
is inferred: true

Axiom
annotated source: hindlimb pre-cartilage condensation
annotated property: subClassOf
annotated target: hindlimb endochondral element
is inferred: true

subdivision of skeleton
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part_of
  some values from: subdivision of skeletal system
subclass of: Restriction
  on property: part_of
  some values from: skeleton
definition: Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
imported from: cl.owl
has exact synonym: skeletal subdivision
has_related_synonym: subdivision of skeleton (in vivo)

Axiom
annotated source: subdivision of skeleton
annotated property: subClassOf
annotated target: organ system subdivision
is inferred: true

vertebral element
type: Class
subclass of: skeletal element
subclass of: Restriction
  on property: part_of
  some values from: vertebral column
subclass of: Restriction
  on property: develops from
  some values from: sclerotome
definition: Skeletal element that forms around the notochord and is part of the vertebral column.
imported from: cl.owl
has_broad_synonym: vertebra skeletal element
has exact synonym: vertebra element
has_narrow_synonym: vertebra endochondral element
has_narrow_synonym: vertebral endochondral element

Axiom
annotated source: vertebral element
annotated property: subClassOf
annotated target: skeletal element
is inferred: true

vertebra cartilage element
type: Class
subclass of: cartilage element
subclass of: vertebral element
subclass of: Restriction
  on property: develops from
  some values from: vertebra pre-cartilage condensation
definition: The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
imported from: cl.owl
has exact synonym: vertebral cartilage condensation

Axiom
annotated source: vertebra cartilage element
annotated property: subClassOf
annotated target: cartilage element
is inferred: true

Axiom
annotated source: vertebra cartilage element
annotated property: subClassOf
annotated target: vertebral element
is inferred: true

vertebra pre-cartilage condensation
type: Class
subclass of: vertebral element
subclass of: Restriction
  on property: has part
  some values from: pre-cartilage condensation
subclass of: Restriction
  on property: develops from
  some values from: sclerotome
definition: The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column.
imported from: cl.owl
has exact synonym: vertebral pre-cartilage condensation

Axiom
annotated source: vertebra pre-cartilage condensation
annotated property: subClassOf
annotated target: vertebral element
is inferred: true

nonsynovial joint
type: Class
subclass of: skeletal joint
definition: Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
imported from: cl.owl
has exact synonym: solid joint

Axiom
annotated source: nonsynovial joint
annotated property: subClassOf
annotated target: skeletal joint
is inferred: true

axial skeletal system
type: Class
subclass of: subdivision of skeletal system
subclass of: Restriction
  on property: has part
  some values from: skeletal joint
subclass of: Restriction
  on property: has part
  some values from: axial skeleton plus cranial skeleton
definition: Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
imported from: cl.owl

Axiom
annotated source: axial skeletal system
annotated property: subClassOf
annotated target: subdivision of skeletal system
is inferred: true

postcranial axial skeletal system
type: Class
subclass of: subdivision of skeletal system
subclass of: Restriction
  on property: develops from
  some values from: sclerotome
definition: Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
imported from: cl.owl
has_broad_synonym: axial skeletal system
has exact synonym: post-cranial axial skeletal system

Axiom
annotated source: postcranial axial skeletal system
annotated property: subClassOf
annotated target: subdivision of skeletal system
is inferred: true

organ system subdivision
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part_of
  some values from: anatomical system
definition: A subdivision of an anatomical system.
imported from: cl.owl

Axiom
annotated source: organ system subdivision
annotated property: subClassOf
annotated target: multicellular anatomical structure
is inferred: true

appendicular skeletal system
type: Class
subclass of: subdivision of skeletal system
subclass of: Restriction
  on property: has part
  some values from: skeletal joint
subclass of: Restriction
  on property: has part
  some values from: appendicular skeleton
definition: Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
imported from: cl.owl

Axiom
annotated source: appendicular skeletal system
annotated property: subClassOf
annotated target: subdivision of skeletal system
is inferred: true

embryonic skin basal layer
type: Class
subclass of: unilaminar epithelium
subclass of: ecto-epithelium
subclass of: Restriction
  on property: part_of
  some values from: integument
subclass of: Restriction
  on property: develops from
  some values from: external ectoderm
imported from: cl.owl
has_related_synonym: basal cell layer of skin
has_related_synonym: outer epithelium of body

Axiom
annotated source: embryonic skin basal layer
annotated property: subClassOf
annotated target: unilaminar epithelium
is inferred: true

Axiom
annotated source: embryonic skin basal layer
annotated property: subClassOf
annotated target: ecto-epithelium
is inferred: true

paired limb/fin skeleton
type: Class
subclass of: mesoderm-derived structure
subclass of: subdivision of skeleton
subclass of: Restriction
  on property: part_of
  some values from: appendicular skeleton
subclass of: Restriction
  on property: part_of
  some values from: paired limb/fin
subclass of: Restriction
  on property: develops from
  some values from: lateral plate mesoderm
definition: The collection of all skeletal elements in an individual limb or fin.
imported from: cl.owl
has exact synonym: limb/fin skeleton
has exact synonym: skeletal parts of limb/fin
has exact synonym: skeleton of limb/fin

Axiom
annotated source: paired limb/fin skeleton
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: paired limb/fin skeleton
annotated property: subClassOf
annotated target: subdivision of skeleton
is inferred: true

stylopodial skeleton
type: Class
subclass of: mesoderm-derived structure
subclass of: limb skeleton subdivision
subclass of: Restriction
  on property: part_of
  some values from: stylopod
subclass of: Restriction
  on property: part_of
  some values from: skeleton of limb
definition: Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified].
imported from: cl.owl
has exact synonym: stylopodium skeleton
has_related_synonym: mesomere 1
has_related_synonym: propodial skeleton
has_related_synonym: propodium
has_related_synonym: proximal metapterygial mesomere
has_related_synonym: stylopod
has_related_synonym: stylopodium

Axiom
annotated source: stylopodial skeleton
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: stylopodial skeleton
annotated property: subClassOf
annotated target: limb skeleton subdivision
is inferred: true

cell condensation
type: Class
subclass of: anatomical structure
definition: Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
imported from: cl.owl

Axiom
annotated source: cell condensation
annotated property: subClassOf
annotated target: anatomical structure
is inferred: true

subdivision of organism along main body axis
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: part_of
  some values from: main body axis
definition: A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
imported from: cl.owl
has exact synonym: axial subdivision of organism
has_related_synonym: body segment
has_related_synonym: main body segment

Axiom
annotated source: subdivision of organism along main body axis
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

embryonic cardiovascular system
type: Class
equivalent class: Class
  intersection of: cardiovascular system
  intersection of: Restriction
    on property: part_of
    some values from: conceptus
subclass of: cardiovascular system
subclass of: Restriction
  on property: part_of
  some values from: conceptus
definition: A cardiovascular system that is part of a conceptus.
imported from: cl.owl
has exact synonym: conceptus cardiovascular system
has_related_synonym: embryonic circulatory system
has_related_synonym: fetal circulatory system

Axiom
annotated source: embryonic cardiovascular system
annotated property: subClassOf
annotated target: cardiovascular system
is inferred: true

irregular connective tissue
type: Class
subclass of: connective tissue
definition: Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
imported from: cl.owl

Axiom
annotated source: irregular connective tissue
annotated property: subClassOf
annotated target: connective tissue
is inferred: true

dense irregular connective tissue
type: Class
subclass of: irregular connective tissue
subclass of: dense connective tissue
definition: Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
imported from: cl.owl
has exact synonym: irregular dense connective tissue
has exact synonym: typus irregularis (textus connectivus collagenosus compactus)

Axiom
annotated source: dense irregular connective tissue
annotated property: subClassOf
annotated target: irregular connective tissue
is inferred: true

Axiom
annotated source: dense irregular connective tissue
annotated property: subClassOf
annotated target: dense connective tissue
is inferred: true

dense connective tissue
type: Class
subclass of: connective tissue
subclass of: Restriction
  on property: has part
  some values from: collection of collagen fibrils
definition: Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets
imported from: cl.owl

Axiom
annotated source: dense connective tissue
annotated property: subClassOf
annotated target: connective tissue
is inferred: true

loose connective tissue
type: Class
subclass of: irregular connective tissue
definition: Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
imported from: cl.owl
has exact synonym: textus connectivus collagenosus laxus
has exact synonym: textus connectivus laxus

Axiom
annotated source: loose connective tissue
annotated property: subClassOf
annotated target: irregular connective tissue
is inferred: true

acinus of exocrine gland
type: Class
equivalent class: Class
  intersection of: glandular acinus
  intersection of: Restriction
    on property: part_of
    some values from: exocrine gland
subclass of: glandular acinus
subclass of: Restriction
  on property: part_of
  some values from: exocrine gland
definition: An acinus that is part of a exocrine gland.
imported from: cl.owl
has exact synonym: exocrine gland acinus

Axiom
annotated source: acinus of exocrine gland
annotated property: subClassOf
annotated target: glandular acinus
is inferred: true

collection of collagen fibrils
type: Class
subclass of: acellular anatomical structure
imported from: cl.owl

Axiom
annotated source: collection of collagen fibrils
annotated property: subClassOf
annotated target: acellular anatomical structure
is inferred: true

stomach glandular region
type: Class
equivalent class: Class
  intersection of: zone of stomach
  intersection of: Restriction
    on property: has part
    some values from: stomach glandular epithelium
subclass of: zone of stomach
subclass of: Restriction
  on property: has part
  some values from: stomach glandular epithelium
definition: A region of the stomach that is lined with glandular epithelium.
imported from: cl.owl
has_related_synonym: glandular stomach

Axiom
annotated source: stomach glandular region
annotated property: subClassOf
annotated target: zone of stomach
is inferred: true

umbilical cord blood
type: Class
subclass of: blood
subclass of: Restriction
  on property: part_of
  some values from: late embryo
definition: blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
imported from: cl.owl
has_related_synonym: cord blood
has_related_synonym: fetal blood
has_related_synonym: umbilical cord blood

Axiom
annotated source: umbilical cord blood
annotated property: subClassOf
annotated target: blood
is inferred: true

head or neck skin
type: Class
equivalent class: Class
  intersection of: zone of skin
  intersection of: Restriction
    on property: part_of
    some values from: craniocervical region
subclass of: zone of skin
subclass of: Restriction
  on property: part_of
  some values from: craniocervical region
definition: A zone of skin that is part of a craniocervical region.
imported from: cl.owl

Axiom
annotated source: head or neck skin
annotated property: subClassOf
annotated target: zone of skin
is inferred: true

columnar epithelium
type: Class
subclass of: epithelium
definition: An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]
imported from: cl.owl

Axiom
annotated source: columnar epithelium
annotated property: subClassOf
annotated target: epithelium
is inferred: true

meso-epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: develops from
    some values from: mesoderm
subclass of: epithelium
subclass of: mesoderm-derived structure
definition: Epithelium that derives from the mesoderm. [Automatically generated definition].
imported from: cl.owl
has exact synonym: mesoderm-derived epithelium
has exact synonym: mesoepithelium

Axiom
annotated source: meso-epithelium
annotated property: subClassOf
annotated target: epithelium
is inferred: true

Axiom
annotated source: meso-epithelium
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

internal anal region
type: Class
subclass of: multi-tissue structure
subclass of: Restriction
  on property: part_of
  some values from: anal region
imported from: cl.owl

Axiom
annotated source: internal anal region
annotated property: subClassOf
annotated target: multi-tissue structure
is inferred: true

hematopoietic tissue
type: Class
subclass of: mesoderm-derived structure
subclass of: UBERON_0034769
subclass of: Restriction
  on property: part_of
  some values from: hematopoietic system
definition: Blood-forming tissue, consisting of reticular fibers and cells.
imported from: cl.owl
has exact synonym: haemopoietic tissue
has exact synonym: hematopoietic tissue
has exact synonym: hemopoietic tissue
has exact synonym: textus haemopoieticus
has_narrow_synonym: bone marrow tissue

Axiom
annotated source: hematopoietic tissue
annotated property: subClassOf
annotated target: mesoderm-derived structure
is inferred: true

Axiom
annotated source: hematopoietic tissue
annotated property: subClassOf
annotated target: UBERON_0034769
is inferred: true

skeleton of pelvic complex
type: Class
subclass of: subdivision of skeleton
subclass of: Restriction
  on property: part_of
  some values from: appendicular skeleton
subclass of: Restriction
  on property: part_of
  some values from: pelvic complex
definition: The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.
imported from: cl.owl
has_related_synonym: bones of lower limb
has_related_synonym: lower limb skeleton
has_related_synonym: ossa membri inferioris
has_related_synonym: pelvic complex skeleton
has_related_synonym: set of bones of lower limb
has_related_synonym: skeleton of posterior limb/fin and girdle

Axiom
annotated source: skeleton of pelvic complex
annotated property: subClassOf
annotated target: subdivision of skeleton
is inferred: true

cloacal epithelium
type: Class
equivalent class: Class
  intersection of: epithelium
  intersection of: Restriction
    on property: part_of
    some values from: cloaca
subclass of: mixed endoderm/mesoderm-derived structure
subclass of: digestive tract epithelium
subclass of: endo-epithelium
subclass of: meso-epithelium
subclass of: Restriction
  on property: part_of
  some values from: cloaca
definition: An epithelium that is part of a cloaca.
imported from: cl.owl
has_related_synonym: cloacal endoderm

Axiom
annotated source: cloacal epithelium
annotated property: subClassOf
annotated target: mixed endoderm/mesoderm-derived structure
is inferred: true

Axiom
annotated source: cloacal epithelium
annotated property: subClassOf
annotated target: digestive tract epithelium
is inferred: true

Axiom
annotated source: cloacal epithelium
annotated property: subClassOf
annotated target: endo-epithelium
is inferred: true

Axiom
annotated source: cloacal epithelium
annotated property: subClassOf
annotated target: meso-epithelium
is inferred: true

subdivision of oviduct
type: Class
subclass of: reproductive structure
subclass of: subdivision of tube
subclass of: Restriction
  on property: part_of
  some values from: oviduct
definition: A section through the tube or network of tubes that connects the ovaries to the outside of the body.
imported from: cl.owl
has exact synonym: subdivision of oviduct
has exact synonym: subdivision of uterine tube
has exact synonym: uterine tube zone
has exact synonym: zone of uterine tube
has_narrow_synonym: subdivision of fallopian tube

Axiom
annotated source: subdivision of oviduct
annotated property: subClassOf
annotated target: reproductive structure
is inferred: true

Axiom
annotated source: subdivision of oviduct
annotated property: subClassOf
annotated target: subdivision of tube
is inferred: true

subdivision of tube
type: Class
subclass of: organ part
subclass of: Restriction
  on property: part_of
  some values from: tube
subclass of: Restriction
  on property: has part
  some values from: anatomical wall
subclass of: Restriction
  on property: has part
  some values from: anatomical space
imported from: cl.owl

Axiom
annotated source: subdivision of tube
annotated property: subClassOf
annotated target: organ part
is inferred: true

anatomical conduit space
type: Class
subclass of: anatomical space
subclass of: Restriction
  on property: part_of
  some values from: anatomical conduit
definition: An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
imported from: cl.owl
has_narrow_synonym: foramen space

Axiom
annotated source: anatomical conduit space
annotated property: subClassOf
annotated target: anatomical space
is inferred: true

main body axis
type: Class
subclass of: organism subdivision
definition: A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
imported from: cl.owl

Axiom
annotated source: main body axis
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

body proper
type: Class
subclass of: organism subdivision
subclass of: Restriction
  on property: part_of
  some values from: main body axis
definition: The region of the organism associated with the visceral organs.
imported from: cl.owl
has_related_synonym: body
has_related_synonym: whole body

Axiom
annotated source: body proper
annotated property: subClassOf
annotated target: organism subdivision
is inferred: true

integumentary system layer
type: Class
equivalent class: Class
  intersection of: organ component layer
  intersection of: Restriction
    on property: part_of
    some values from: integumental system
subclass of: organ component layer
subclass of: Restriction
  on property: part_of
  some values from: integumental system
definition: A organ component layer that is part of a integumental system.
imported from: cl.owl
has_narrow_synonym: layer of skin
has_narrow_synonym: skin layer

Axiom
annotated source: integumentary system layer
annotated property: subClassOf
annotated target: organ component layer
is inferred: true

digestive system element
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: part_of
    some values from: digestive system
subclass of: organ
subclass of: Restriction
  on property: part_of
  some values from: digestive system
definition: Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
imported from: cl.owl
has exact synonym: digestive organ
has exact synonym: digestive system organ

Axiom
annotated source: digestive system element
annotated property: subClassOf
annotated target: organ
is inferred: true

thoracic skeleton
type: Class
subclass of: subdivision of skeleton
subclass of: Restriction
  on property: part_of
  some values from: thoracic segment of trunk
subclass of: Restriction
  on property: part_of
  some values from: postcranial axial skeleton
definition: Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
imported from: cl.owl
has exact synonym: skeleton of thorax
has exact synonym: thoracic part of axial skeleton
has exact synonym: thoracic skeleton

Axiom
annotated source: thoracic skeleton
annotated property: subClassOf
annotated target: subdivision of skeleton
is inferred: true

interlobular duct
type: Class
subclass of: UBERON_0035050
subclass of: Restriction
  on property: part_of
  some values from: connective tissue
definition: A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory.
imported from: cl.owl

Axiom
annotated source: interlobular duct
annotated property: subClassOf
annotated target: UBERON_0035050
is inferred: true

skeletal muscle organ
type: Class
subclass of: muscle organ
subclass of: Restriction
  on property: part_of
  some values from: UBERON_0018254
subclass of: Restriction
  on property: has part
  some values from: skeletal muscle tissue
subclass of: Restriction
  on property: develops from
  some values from: myotome
definition: A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).
imported from: cl.owl
has_broad_synonym: skeletal muscle

Axiom
annotated source: skeletal muscle organ
annotated property: subClassOf
annotated target: muscle organ
is inferred: true

primordial vasculature
type: Class
subclass of: primordium
subclass of: Restriction
  on property: part_of
  some values from: embryonic cardiovascular system
definition: A portion of tissue that will develop into vasculature.
imported from: cl.owl

Axiom
annotated source: primordial vasculature
annotated property: subClassOf
annotated target: primordium
is inferred: true

hindlimb endochondral element
type: Class
equivalent class: Class
  intersection of: endochondral element
  intersection of: Restriction
    on property: part_of
    some values from: hindlimb
equivalent class: Class
  union of: hindlimb bone
  union of: hindlimb cartilage element
  union of: hindlimb pre-cartilage condensation
subclass of: limb endochondral element
subclass of: Restriction
  on property: part_of
  some values from: hindlimb skeleton
definition: A hindlimb bone or its cartilage or pre-cartilage precursor.
imported from: cl.owl
has_broad_synonym: hindlimb bone skeletal element

Axiom
annotated source: hindlimb endochondral element
annotated property: subClassOf
annotated target: limb endochondral element
is inferred: true

femur endochondral element
type: Class
equivalent class: Class
  union of: femur
  union of: femur pre-cartilage condensation
  union of: femur cartilage element
subclass of: hindlimb endochondral element
subclass of: Restriction
  on property: part_of
  some values from: hindlimb stylopod
definition: A femur bone or its cartilage or pre-cartilage precursor.
imported from: cl.owl
has_broad_synonym: femur skeletal element
has exact synonym: femur element

Axiom
annotated source: femur endochondral element
annotated property: subClassOf
annotated target: hindlimb endochondral element
is inferred: true

limb endochondral element
type: Class
equivalent class: Class
  intersection of: endochondral element
  intersection of: Restriction
    on property: part_of
    some values from: limb
equivalent class: Class
  union of: limb bone
  union of: limb cartilage element
  union of: limb bone pre-cartilage condensation
subclass of: mesoderm-derived structure
subclass of: endochondral element
subclass of: Restriction
  on property: part_of
  some values from: skeleton of limb
definition: A limb bone or its cartilage or pre-cartilage precursor.
imported from: cl.owl
has_broad_synonym: limb bone skeletal element
has exact synonym: limb bone endochondral element