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uberonfovt.obo
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uberonfovt.obo
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format-version: 1.2
data-version: releases/2021-01-12
subsetdef: goslim_aspergillus ""
subsetdef: goslim_candida ""
subsetdef: goslim_chembl ""
subsetdef: goslim_generic ""
subsetdef: goslim_metagenomics ""
subsetdef: goslim_pir ""
subsetdef: goslim_plant ""
subsetdef: goslim_pombe ""
subsetdef: goslim_yeast ""
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 ""
subsetdef: RO:0002259 ""
subsetdef: upper_level ""
ontology: uberonfovt
property_value: http://purl.org/dc/elements/1.1/description "None" xsd:string
property_value: http://purl.org/dc/elements/1.1/title "UBERON FOVT module" xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
property_value: owl:versionInfo "2021-01-12" xsd:string
[Term]
id: BFO:0000002
name: continuant
def: "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." []
disjoint_from: BFO:0000003 ! occurrent
relationship: part_of BFO:0000002 ! continuant
[Term]
id: BFO:0000003
name: occurrent
def: "An entity that has temporal parts and that happens, unfolds or develops through time." []
relationship: part_of BFO:0000003 ! occurrent
[Term]
id: BFO:0000004
name: independent continuant
def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." []
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant
relationship: part_of BFO:0000004 ! independent continuant
[Term]
id: BFO:0000015
name: process
def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." []
is_a: BFO:0000003 ! occurrent
[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "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." []
is_a: BFO:0000002 ! continuant
relationship: part_of BFO:0000020 ! specifically dependent continuant
[Term]
id: BFO:0000040
name: material entity
def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." []
is_a: BFO:0000004 ! independent continuant
[Term]
id: BSPO:0000000
name: left side
namespace: spatial
def: "The side of an organism that is left of the sagittal plane." [BSPO:cjm]
synonym: "left" EXACT []
is_a: BSPO:0000054 ! anatomical side
relationship: left_of BSPO:0000007 ! right side
relationship: starts_axis BSPO:0000017 ! left-right axis
[Term]
id: BSPO:0000001
name: upper side
namespace: spatial
comment: Consider merging with superior side.
synonym: "upper" EXACT []
is_a: BSPO:0000054 ! anatomical side
relationship: starts_axis BSPO:0000011 ! upper-lower axis
[Term]
id: BSPO:0000002
name: lower side
namespace: spatial
comment: Consider merging with inferior side.
synonym: "lower" EXACT []
is_a: BSPO:0000054 ! anatomical side
relationship: finishes_axis BSPO:0000011 ! upper-lower axis
[Term]
id: BSPO:0000007
name: right side
namespace: spatial
def: "The side of an organism that is right of the sagittal plane." [BSPO:cjm, BSPO:wd]
synonym: "right" EXACT []
is_a: BSPO:0000054 ! anatomical side
relationship: finishes_axis BSPO:0000017 ! left-right axis
[Term]
id: BSPO:0000010
name: anatomical axis
namespace: spatial
def: "A straight line through space, intersecting an anatomical entity." [BSPO:cjm]
comment: Axis directions are defined in terms of axes.
xref: http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG
is_a: CARO:0000008 ! anatomical line
relationship: passes_through CARO:0000000 ! anatomical entity
[Term]
id: BSPO:0000011
name: upper-lower axis
namespace: spatial
def: "An anatomical axis determined by gravity." [BSPO:cjm]
synonym: "superior-inferior axis" RELATED []
is_a: BSPO:0000010 ! anatomical axis
[Term]
id: BSPO:0000013
name: anterior-posterior axis
namespace: spatial
def: "An axis that extends through an organism from head end to opposite end of body or tail." [BSPO:cjm]
comment: In sponges, AP is used to indicate the direction of movement [in larval stage] (as it is in other metazoans that move, e.g., the basal bilaterians). [PM]
synonym: "A-P axis" EXACT []
synonym: "anteroposterior axis" EXACT []
synonym: "AP axis" EXACT []
synonym: "cephalocaudal axis" NARROW [http://en.wikipedia.org/wiki/Anatomical_terms_of_location]
synonym: "craniocaudal axis" NARROW vertebrate []
synonym: "longitudinal axis" RELATED []
synonym: "rostral/caudal" NARROW vertebrate []
synonym: "rostrocaudal axis" NARROW vertebrate []
is_a: BSPO:0000010 ! anatomical axis
intersection_of: BSPO:0000010 ! anatomical axis
intersection_of: orthogonal_to BSPO:0000018 ! transverse plane
relationship: approximately_perpendicular_to BSPO:0000016 ! dorsal-ventral axis
relationship: orthogonal_to BSPO:0000018 ! transverse plane
[Term]
id: BSPO:0000016
name: dorsal-ventral axis
namespace: spatial
def: "An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body." [BSPO:curators]
synonym: "anterior-posterior axis" NARROW human []
synonym: "D-V axis" EXACT []
synonym: "dorsoventral axis" EXACT []
synonym: "DV axis" EXACT []
is_a: BSPO:0000010 ! anatomical axis
intersection_of: BSPO:0000010 ! anatomical axis
intersection_of: orthogonal_to BSPO:0000019 ! horizontal plane
relationship: orthogonal_to BSPO:0000019 ! horizontal plane
[Term]
id: BSPO:0000017
name: left-right axis
namespace: spatial
def: "An axis that bisects an organism from left to right sides of body, through a sagittal plane." [BSPO:cjm]
synonym: "dextro-sinister axis" EXACT []
synonym: "L-R axis" EXACT []
synonym: "left to right axis" EXACT []
synonym: "LR axis" EXACT []
synonym: "R-L axis" EXACT []
synonym: "right to left axis" EXACT []
synonym: "right-left axis" EXACT []
synonym: "RL axis" EXACT []
is_a: BSPO:0000010 ! anatomical axis
intersection_of: BSPO:0000010 ! anatomical axis
intersection_of: orthogonal_to BSPO:0000417 ! sagittal plane
relationship: orthogonal_to BSPO:0000417 ! sagittal plane
[Term]
id: BSPO:0000018
name: transverse plane
namespace: spatial
def: "Anatomical plane that divides body into anterior and posterior parts." [BSPO:mah]
synonym: "axial plane" EXACT []
synonym: "axial section" EXACT []
synonym: "cross-section" RELATED []
synonym: "transverse section" EXACT []
xref: FMA:12247
is_a: BSPO:0000400 ! anatomical plane
[Term]
id: BSPO:0000019
name: horizontal plane
namespace: spatial
def: "Anatomical plane that divides bilateral body into dorsal and ventral parts." [BSPO:mah]
synonym: "coronal section" RELATED []
synonym: "frontal plane" EXACT []
synonym: "frontal section" RELATED []
synonym: "horizontal anatomical plane" EXACT [FMA:52810]
synonym: "horizontal section" EXACT []
xref: FMA:52810
is_a: BSPO:0000400 ! anatomical plane
[Term]
id: BSPO:0000054
name: anatomical side
namespace: spatial
def: "An anatomical region bounded by a plane perpendicular to an axis through the middle." [BSPO:cjm]
xref: FBql:00005841
is_a: BSPO:0000070 ! anatomical region
[Term]
id: BSPO:0000070
name: anatomical region
namespace: spatial
def: "A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm." [BSPO:cjm]
comment: to be merged into CARO
xref: FBql:00005841
is_a: CARO:0000003 ! anatomical structure
[Term]
id: BSPO:0000400
name: anatomical plane
namespace: spatial
def: "A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions." [BSPO:cjm]
comment: These anatomical sections are applicable to most bilaterally symmetrical animals, but bipedal animals such as humans have more complex usage of these terms. For example, in post-embryonic humans a coronal plane is vertical and a transverse plane is horizontal, but for embryos and quadrupeds a coronal plane is horizontal and a transverse plane is vertical.
synonym: "anatomical cross-section" EXACT []
synonym: "anatomical section" EXACT []
synonym: "cross-section" RELATED []
synonym: "plane" EXACT []
synonym: "section" EXACT []
xref: FMA:242982
is_a: CARO:0000010 ! anatomical boundary
[Term]
id: BSPO:0000417
name: sagittal plane
namespace: spatial
def: "Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size." [BSPO:cjm, BSPO:DOS, BSPO:mah]
synonym: "left/right plane" EXACT []
synonym: "median plane" EXACT []
synonym: "sagittal section" EXACT []
xref: FMA:11361
is_a: BSPO:0000010 ! anatomical axis
is_a: BSPO:0000400 ! anatomical plane
intersection_of: BSPO:0000400 ! anatomical plane
intersection_of: orthogonal_to BSPO:0000017 ! left-right axis
intersection_of: parallel_to BSPO:0000013 ! anterior-posterior axis
intersection_of: parallel_to BSPO:0000016 ! dorsal-ventral axis
relationship: orthogonal_to BSPO:0000017 ! left-right axis
relationship: parallel_to BSPO:0000013 ! anterior-posterior axis
relationship: parallel_to BSPO:0000016 ! dorsal-ventral axis
[Term]
id: CARO:0000000
name: anatomical entity
namespace: spatial
def: "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." [CARO:MAH]
is_a: CARO:0030000 ! biological entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl
[Term]
id: CARO:0000003
name: anatomical structure
namespace: spatial
def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CC:DOS]
is_a: CARO:0000006 ! material anatomical entity
[Term]
id: CARO:0000006
name: material anatomical entity
namespace: spatial
def: "An anatomical entity that has mass." [CC:DOS]
is_a: CARO:0000000 ! anatomical entity
[Term]
id: CARO:0000007
name: immaterial anatomical entity
namespace: spatial
def: "An anatomical entity that has no mass." [CC:DOS]
is_a: CARO:0000000 ! anatomical entity
[Term]
id: CARO:0000008
name: anatomical line
namespace: spatial
def: "A one dimensional, immaterial anatomical entity." [CC:DOS]
is_a: CARO:0000007 ! immaterial anatomical entity
[Term]
id: CARO:0000010
name: anatomical boundary
namespace: spatial
def: "A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures." [CC:DOS]
is_a: CARO:0000007 ! immaterial anatomical entity
[Term]
id: CARO:0030000
name: biological entity
is_a: BFO:0000004 ! independent continuant
[Term]
id: GO:0003674
name: molecular_function
is_a: BFO:0000015 ! process
property_value: IAO:0000589 "molecular process" xsd:string
[Term]
id: GO:0003824
name: catalytic activity
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
alt_id: GO:0000004
alt_id: GO:0007582
alt_id: GO:0044699
def: "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." [GOC:pdt]
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. 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 'no data' (ND), is used to indicate this.
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
synonym: "biological process" EXACT []
synonym: "physiological process" EXACT []
synonym: "single organism process" RELATED []
synonym: "single-organism process" RELATED []
xref: Wikipedia:Biological_process
is_a: BFO:0000015 ! process
created_by: jl
creation_date: 2012-09-19T15:05:24Z
[Term]
id: GO:0016301
name: kinase activity
is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups
[Term]
id: GO:0016740
name: transferase activity
is_a: GO:0003824 ! catalytic activity
[Term]
id: GO:0016772
name: transferase activity, transferring phosphorus-containing groups
is_a: GO:0016740 ! transferase activity
[Term]
id: PATO:0000001
name: quality
namespace: quality
alt_id: PATO:0000072
def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG]
is_a: BFO:0000020 ! specifically dependent continuant
property_value: IAO:0000589 "quality (PATO)" xsd:string
[Term]
id: UBERON:0001062
name: anatomical entity
namespace: uberon
def: "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." [FMA:62955, http://orcid.org/0000-0001-9114-8737]
subset: upper_level
xref: AAO:0010841
xref: AEO:0000000
xref: BILA:0000000
xref: BIRNLEX:6
xref: CARO:0000000
xref: EHDAA2:0002229
xref: FBbt:10000000
xref: FBbt_root:00000000
xref: FMA:62955
xref: HAO:0000000
xref: http://linkedlifedata.com/resource/umls/id/C1515976
xref: MA:0000001
xref: NCIT:C12219
xref: TAO:0100000
xref: TGMA:0001822
xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"}
xref: WBbt:0000100
xref: XAO:0000000
xref: ZFA:0100000
[Term]
id: UBERONFOVT:00000000
name: root node
[Typedef]
id: BFO:0000062
name: preceded by
def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string
property_value: IAO:0000111 "preceded by" xsd:string
property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string
property_value: IAO:0000118 "is preceded by" xsd:string
property_value: IAO:0000118 "preceded_by" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
holds_over_chain: part_of BFO:0000062
is_transitive: true
is_a: RO:0002086 ! ends after
inverse_of: BFO:0000063 ! precedes
[Typedef]
id: BFO:0000063
name: precedes
def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: IAO:0000111 "precedes" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
holds_over_chain: part_of BFO:0000063
is_transitive: true
is_a: RO:0002222 ! temporally related to
[Typedef]
id: BFO:0000066
name: occurs in
def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
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
property_value: IAO:0000111 "occurs in" xsd:string
property_value: IAO:0000118 "occurs_in" xsd:string
property_value: IAO:0000118 "unfolds in" xsd:string
property_value: IAO:0000118 "unfolds_in" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000003 ! occurrent
range: BFO:0000004 ! independent continuant
holds_over_chain: part_of BFO:0000066
inverse_of: BFO:0000067 ! contains process
transitive_over: part_of ! part_of
[Typedef]
id: BFO:0000067
name: contains process
def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
property_value: IAO:0000111 "site of" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Typedef]
id: RO:0000056
name: participates in
def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" []
property_value: IAO:0000111 "participates in" xsd:string
property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string
property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string
property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string
property_value: IAO:0000118 "participates_in" xsd:string
domain: BFO:0000002 ! continuant
range: BFO:0000003 ! occurrent
inverse_of: RO:0000057 ! has participant
[Typedef]
id: RO:0000057
name: has participant
def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string
property_value: IAO:0000111 "has participant" xsd:string
property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string
property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string
property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000118 "has_participant" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000002 ! continuant
holds_over_chain: has_part RO:0000057
[Typedef]
id: RO:0002013
name: has regulatory component activity
def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." []
is_a: RO:0002017 ! has component activity
is_a: RO:0002334 ! regulated by
created_by: dos
creation_date: 2017-05-24T09:30:46Z
[Typedef]
id: RO:0002014
name: has negative regulatory component activity
def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." []
comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
is_a: RO:0002013 ! has regulatory component activity
is_a: RO:0002335 ! negatively regulated by
created_by: dos
creation_date: 2017-05-24T09:31:01Z
[Typedef]
id: RO:0002015
name: has positive regulatory component activity
def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." []
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
is_a: RO:0002013 ! has regulatory component activity
is_a: RO:0002336 ! positively regulated by
created_by: dos
creation_date: 2017-05-24T09:31:17Z
[Typedef]
id: RO:0002017
name: has component activity
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
is_a: RO:0002018 ! has component process
created_by: dos
creation_date: 2017-05-24T09:44:33Z
[Typedef]
id: RO:0002018
name: has component process
def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
is_a: RO:0002180 ! has component
created_by: dos
creation_date: 2017-05-24T09:49:21Z
[Typedef]
id: RO:0002022
name: directly regulated by
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"}
is_a: RO:0002334 ! regulated by
inverse_of: RO:0002578 ! directly regulates
created_by: dos
creation_date: 2017-09-17T13:52:24Z
[Typedef]
id: RO:0002023
name: directly negatively regulated by
def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos]
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002630 ! directly negatively regulates
created_by: dos
creation_date: 2017-09-17T13:52:38Z
[Typedef]
id: RO:0002024
name: directly positively regulated by
def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos]
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002629 ! directly positively regulates
created_by: dos
creation_date: 2017-09-17T13:52:47Z
[Typedef]
id: RO:0002025
name: has effector activity
def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos]
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
is_functional: true
is_a: RO:0002017 ! has component activity
is_a: RO:0002211 ! regulates
created_by: dos
creation_date: 2017-09-22T14:14:36Z
[Typedef]
id: RO:0002086
name: ends after
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_transitive: true
is_a: RO:0002222 ! temporally related to
[Typedef]
id: RO:0002087
name: immediately preceded by
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "starts_at_end_of" xsd:string
is_a: BFO:0000062 ! preceded by
inverse_of: RO:0002090 ! immediately precedes
[Typedef]
id: RO:0002090
name: immediately precedes
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "ends_at_start_of" xsd:string
property_value: IAO:0000118 "meets" xsd:string
property_value: RO:0002575 BFO:0000063
is_a: BFO:0000063 ! precedes
[Typedef]
id: RO:0002131
name: overlaps
def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: RO:0001900 RO:0001901
holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"}
holds_over_chain: has_part RO:0002131
holds_over_chain: part_of part_of
is_a: RO:0002323 ! mereotopologically related to
transitive_over: part_of ! part_of
expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []
[Typedef]
id: RO:0002180
name: has component
def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string
property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency
is_a: has_part ! has part
[Typedef]
id: RO:0002202
name: develops from
def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" []
comment: This is the transitive form of the develops from relation
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000117 "Melissa Haendel" xsd:string
property_value: IAO:0000117 "Terry Meehan" xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000004 ! independent continuant
is_transitive: true
is_a: RO:0002258 ! developmentally preceded by
inverse_of: RO:0002203 ! develops into
[Typedef]
id: RO:0002203
name: develops into
def: "inverse of develops from" []
subset: RO:0002259
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000117 "Terry Meehan" xsd:string
is_transitive: true
is_a: RO:0002286 ! developmentally succeeded by
is_a: RO:0002387 ! has potential to develop into
is_a: RO:0002388 ! has potential to directly develop into
[Typedef]
id: RO:0002211
name: regulates
def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." []
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
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Hill" xsd:string
property_value: IAO:0000117 "Tanya Berardini" xsd:string
property_value: IAO:0000119 "GO" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string
property_value: IAO:0000589 "regulates (processual)" xsd:string
property_value: IAO:0000600 "false" xsd:boolean
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
holds_over_chain: RO:0002578 RO:0002578
is_transitive: true
is_a: RO:0002411 ! causally upstream of
inverse_of: RO:0002334 ! regulated by
transitive_over: RO:0002025 ! has effector activity
[Typedef]
id: RO:0002212
name: negatively regulates
def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." []
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
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string
property_value: RO:0004050 RO:0002211
is_a: RO:0002211 ! regulates
is_a: RO:0002305 ! causally upstream of, negative effect
inverse_of: RO:0002335 ! negatively regulated by
[Typedef]
id: RO:0002213
name: positively regulates
def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." []
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
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "positively regulates (process to process)" xsd:string
property_value: RO:0004049 RO:0002211
holds_over_chain: RO:0002212 RO:0002212
is_transitive: true
is_a: RO:0002211 ! regulates
is_a: RO:0002304 ! causally upstream of, positive effect
inverse_of: RO:0002336 ! positively regulated by
[Typedef]
id: RO:0002215
name: capable of
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
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 "Chris Mungall" xsd:string
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
domain: BFO:0000004 ! independent continuant
range: BFO:0000015 ! process
is_a: RO:0002216 ! capable of part of
expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" []
[Typedef]
id: RO:0002216
name: capable of part of
def: "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." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function in" xsd:string
property_value: seeAlso "defining-property-chains-involving-reflexivity"
holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process
expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" []
[Typedef]
id: RO:0002222
name: temporally related to
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
subset: ro-eco
property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
[Typedef]
id: RO:0002233
name: has input
def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." []
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
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "consumes" xsd:string
domain: BFO:0000015 ! process
range: BFO:0000040 ! material entity
is_a: RO:0000057 ! has participant
inverse_of: RO:0002352 ! input of
[Typedef]
id: RO:0002254
name: has developmental contribution from
def: "x has developmental contribution from y iff x has some part z such that z develops from y" []
property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: CARO:0000000 ! anatomical entity
range: CARO:0000000 ! anatomical entity
holds_over_chain: has_part RO:0002202
is_a: RO:0002258 ! developmentally preceded by
inverse_of: RO:0002255 ! developmentally contributes to
[Typedef]
id: RO:0002255
name: developmentally contributes to
def: "inverse of has developmental contribution from" []
subset: RO:0002259
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: RO:0002203 part_of
is_a: RO:0002286 ! developmentally succeeded by
is_a: RO:0002385 ! has potential to developmentally contribute to
[Typedef]
id: RO:0002258
name: developmentally preceded by
def: "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" []
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "false" xsd:boolean
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string
domain: BFO:0000002 ! continuant
range: BFO:0000002 ! continuant
is_a: RO:0002324 ! developmentally related to
inverse_of: RO:0002286 ! developmentally succeeded by
[Typedef]
id: RO:0002263
name: acts upstream of
def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
holds_over_chain: RO:0002327 RO:0002411
is_a: RO:0002264 ! acts upstream of or within
[Typedef]
id: RO:0002264
name: acts upstream of or within
def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
synonym: "affects" RELATED []
property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within
holds_over_chain: RO:0002327 RO:0002418
is_a: RO:0002500 ! causal agent in process
[Typedef]
id: RO:0002286
name: developmentally succeeded by
def: "Inverse of developmentally preceded by" []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002384 ! has developmental potential involving
[Typedef]
id: RO:0002304
name: causally upstream of, positive effect
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: http://purl.org/dc/terms/creator "cjm" xsd:string
property_value: RO:0004049 RO:0002411
is_a: RO:0002411 ! causally upstream of
is_a: RO:0004047 ! causally upstream of or within, positive effect
[Typedef]
id: RO:0002305
name: causally upstream of, negative effect
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
property_value: http://purl.org/dc/terms/creator "cjm" xsd:string
property_value: RO:0004050 RO:0002411
is_a: RO:0002411 ! causally upstream of
is_a: RO:0004046 ! causally upstream of or within, negative effect
[Typedef]
id: RO:0002323
name: mereotopologically related to
def: "A mereological relationship or a topological relationship" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string
property_value: RO:0001900 RO:0001901
[Typedef]
id: RO:0002324
name: developmentally related to
def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string
[Typedef]
id: RO:0002327
name: enables
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "catalyzes" xsd:string
property_value: IAO:0000118 "executes" xsd:string
property_value: IAO:0000118 "has" xsd:string
property_value: IAO:0000118 "is catalyzing" xsd:string
property_value: IAO:0000118 "is executing" xsd:string
property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string
property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string
is_a: RO:0002215 ! capable of
inverse_of: RO:0002333 ! enabled by
transitive_over: has_part ! has part
transitive_over: RO:0002017 ! has component activity
[Typedef]
id: RO:0002328
name: functionally related to
def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string
[Typedef]
id: RO:0002329
name: part of structure that is capable of
def: "this relation holds between c and p when c is part of some c', and c' is capable of p." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "false" xsd:boolean
holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"}
is_a: RO:0002328 ! functionally related to
[Typedef]
id: RO:0002331
name: involved in
def: "c involved_in p if and only if c enables some process p', and p' is part of p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "actively involved in" xsd:string
property_value: IAO:0000118 "enables part of" xsd:string
property_value: seeAlso Involved:in
holds_over_chain: RO:0002327 part_of
is_a: RO:0000056 ! participates in
is_a: RO:0002431 ! involved in or involved in regulation of
transitive_over: part_of ! part_of
[Typedef]
id: RO:0002333
name: enabled by
def: "inverse of enables" []
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0000057 ! has participant
is_a: RO:0002328 ! functionally related to
[Typedef]
id: RO:0002334
name: regulated by
def: "inverse of regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000589 "regulated by (processual)" xsd:string
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
is_transitive: true
is_a: RO:0002427 ! causally downstream of or within
[Typedef]
id: RO:0002335
name: negatively regulated by
def: "inverse of negatively regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002334 ! regulated by
[Typedef]
id: RO:0002336
name: positively regulated by
def: "inverse of positively regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002334 ! regulated by
[Typedef]
id: RO:0002352
name: input of
def: "inverse of has input" []
subset: ro-eco
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0000056 ! participates in
is_a: RO:0002328 ! functionally related to
[Typedef]
id: RO:0002384
name: has developmental potential involving
def: "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)." []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: CARO:0000000 ! anatomical entity
range: CARO:0000000 ! anatomical entity
is_a: RO:0002324 ! developmentally related to
[Typedef]
id: RO:0002385
name: has potential to developmentally contribute to
def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002384 ! has developmental potential involving
[Typedef]
id: RO:0002387
name: has potential to develop into
def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002384 ! has developmental potential involving
[Typedef]
id: RO:0002388
name: has potential to directly develop into
def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002387 ! has potential to develop into
[Typedef]
id: RO:0002404
name: causally downstream of
def: "inverse of upstream of" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: BFO:0000062 ! preceded by
is_a: RO:0002427 ! causally downstream of or within
inverse_of: RO:0002411 ! causally upstream of