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bdso-simple.obo
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format-version: 1.2
data-version: pcl/releases/2023-03-01/bdso-simple.owl
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
subsetdef: ro-eco ""
ontology: pcl/bdso-simple
property_value: dc-title "Brain Data Standards Cell Ontology" xsd:string
property_value: dcterms-license http://creativecommons.org/licenses/by/4.0/
property_value: owl:versionInfo "2023-03-01" xsd:string
[Typedef]
id: RO:0002100
name: has soma location
def: "Relation between a neuron and an anatomical structure that its soma is part of." []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
property_value: RO:0001900 RO:0001901
transitive_over: part_of ! part_of
expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" []
[Typedef]
id: RO:0002292
name: expresses
def: "Inverse of 'expressed in'" []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
[Typedef]
id: RO:0015001
name: has exemplar data
def: "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." []
property_value: IAO:0000112 "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" xsd:string
property_value: IAO:0000116 "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315
property_value: IAO:0000232 "This relation is not meant to capture the relation between occurrents and data." xsd:string
inverse_of: RO:0015002 ! exemplar data of
transitive_over: RO:0015003 ! subcluster of
[Typedef]
id: RO:0015002
name: exemplar data of
property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315
[Typedef]
id: RO:0015003
name: subcluster of
def: "A relation between a group and another group it is part of but does not fully constitute." []
property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596
property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string
is_transitive: true
is_a: part_of ! part_of
[Typedef]
id: RO:0015004
name: has characterizing marker set
def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." []
synonym: "has marker gene combination" EXACT []
synonym: "has marker signature set" EXACT []
property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-7258-9596
property_value: IAO:0000112 "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1')." xsd:string
property_value: IAO:0000112 "transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3." xsd:string
property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string
property_value: IAO:0000232 "This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context." xsd:string
[Typedef]
id: RO:HOM0000007
name: in historical homology relationship with
def: "Homology that is defined by common descent." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://purl.obolibrary.org/obo/HOM_0000007, ISBN:0123195837]
synonym: "cladistic homology" EXACT []
synonym: "historical homologous to" EXACT []
synonym: "homology" BROAD []
synonym: "phylogenetic homology" EXACT []
synonym: "taxic homology" EXACT []
synonym: "true homology" RELATED []
xref: ECO:0000080
xref: RO_proposed_relation:homologous_to
xref: SO:0000330
xref: SO:0000853
xref: SO:0000857
xref: SO:homologous_to
xref: TAO:homologous_to
property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch
property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127
property_value: seeAlso HOM:0000007
is_symmetric: true
[Typedef]
id: bearer_of
name: bearer of
name: has characteristic
namespace: external
def: "Inverse of characteristic_of" []
xref: RO:0000053
property_value: IAO:0000111 "bearer of" xsd:string
property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string
property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000118 "bearer_of" xsd:string
property_value: IAO:0000118 "is bearer of" xsd:string
property_value: RO:0001900 RO:0001901
is_inverse_functional: true
[Typedef]
id: capable_of
name: capable of
namespace: external
namespace: uberon
def: "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. " []
subset: ro-eco
xref: RO:0002215
property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string
property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "has function realized in" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450
property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string
[Typedef]
id: dc-description
name: description
namespace: uberon
xref: http://purl.org/dc/elements/1.1/description
is_metadata_tag: true
[Typedef]
id: dc-title
name: title
namespace: uberon
xref: http://purl.org/dc/elements/1.1/title
is_metadata_tag: true
[Typedef]
id: dcterms-license
name: license
namespace: uberon
xref: http://purl.org/dc/terms/license
is_metadata_tag: true
[Typedef]
id: has_part
name: has part
name: has_part
namespace: external
namespace: quality
namespace: uberon
def: "a core relation that holds between a whole and its part" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
xref: BFO:0000051
property_value: IAO:0000111 "has part" xsd:string
property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string
property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string
property_value: IAO:0000118 "has_part" xsd:string
property_value: RO:0001900 RO:0001901
is_transitive: true
[Typedef]
id: in_taxon
name: in taxon
namespace: uberon
def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." []
comment: Connects a biological entity to its taxon of origin.
subset: ro-eco
xref: RO:0002162
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints
holds_over_chain: capable_of in_taxon
holds_over_chain: has_part in_taxon
holds_over_chain: part_of in_taxon
[Typedef]
id: part_of
name: part of
name: part_of
namespace: external
namespace: quality
namespace: uberon
def: "a core relation that holds between a part and its whole" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
xref: BFO:0000050
property_value: IAO:0000111 "is part of" xsd:string
property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string
property_value: IAO:0000118 "part_of" xsd:string
property_value: RO:0001900 RO:0001901
property_value: RO:0040042 BFO:0000002
property_value: RO:0040042 BFO:0000003
property_value: RO:0040042 BFO:0000004
property_value: RO:0040042 BFO:0000017
property_value: RO:0040042 BFO:0000019
property_value: RO:0040042 BFO:0000020
property_value: RO:0040042 BFO:0000031
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string
is_transitive: true
inverse_of: has_part ! has part