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ro-full.obo
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format-version: 1.2
data-version: ro/releases/2024-04-24/ro-full.owl
subsetdef: common_anatomy ""
subsetdef: efo_slim ""
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: human_reference_atlas ""
subsetdef: pheno_slim ""
subsetdef: ro-eco ""
subsetdef: RO:0002259 ""
subsetdef: uberon_slim ""
subsetdef: upper_level ""
subsetdef: vertebrate_core ""
ontology: ro/ro-full
property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/
property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string
property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI
property_value: owl:versionInfo "2024-04-24" 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: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant
relationship: RO:0002214 BFO:0000002 {all_only="true"} ! has prototype continuant
relationship: RO:HOM0000000 BFO:0000002 {all_only="true"} ! continuant
[Term]
id: BFO:0000003
name: occurrent
def: "An entity that has temporal parts and that happens, unfolds or develops through time." []
relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent
relationship: RO:HOM0000000 BFO:0000003 {all_only="true"} ! occurrent
[Term]
id: BFO:0000004
name: independent continuant
def: "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])" []
comment: 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 ! characteristic
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant
[Term]
id: BFO:0000006
name: spatial region
is_a: BFO:0000141 ! immaterial entity
[Term]
id: BFO:0000015
name: process
def: "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])" []
comment: 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
relationship: RO:0002214 BFO:0000015 {all_only="true"} ! has prototype process
[Term]
id: BFO:0000016
name: disposition
is_a: BFO:0000017 ! realizable entity
disjoint_from: BFO:0000023 ! role
[Term]
id: BFO:0000017
name: realizable
name: realizable entity
def: "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." []
is_a: BFO:0000020 ! characteristic
disjoint_from: BFO:0000019 ! quality
relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity
[Term]
id: BFO:0000019
name: quality
is_a: BFO:0000020 ! characteristic
relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality
[Term]
id: BFO:0000020
name: characteristic
name: specifically dependent continuant
def: "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])" []
comment: 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
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of characteristic
property_value: seeAlso "https://github.com/OBOFoundry/COB/issues/65" xsd:string
property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string
[Term]
id: BFO:0000023
name: role
def: "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." []
is_a: BFO:0000017 ! realizable entity
[Term]
id: BFO:0000031
name: generically dependent continuant
def: "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])" []
comment: 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.
is_a: BFO:0000002 ! continuant
relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant
[Term]
id: BFO:0000034
name: function
is_a: BFO:0000016 ! disposition
[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
disjoint_from: BFO:0000141 ! immaterial entity
[Term]
id: BFO:0000141
name: immaterial entity
is_a: BFO:0000004 ! independent continuant
[Term]
id: CHEBI:50906
is_a: PATO:0000001 ! quality
[Term]
id: CL:0000000
name: cell
def: "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." [CARO:mah]
def: "A material entity that has a plasma membrane and results from cellular division." []
comment: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
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).
comment: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.
xref: CALOHA:TS-2035
xref: FBbt:00007002
xref: FMA:68646
xref: GO:0005623
xref: KUPO:0000002
xref: MESH:D002477
xref: VHOG:0001533
xref: WBbt:0004017
xref: XAO:0003012
is_a: UBERON:0000061 ! anatomical structure
[Term]
id: CL:0000101
name: sensory neuron
def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544]
xref: BTO:0001037
xref: FBbt:00005124
xref: FMA:84649
xref: MESH:D011984
xref: WBbt:0005759
is_a: CL:0000540 ! neuron
[Term]
id: CL:0000540
name: neuron
def: "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." [http://en.wikipedia.org/wiki/Neuron, MESH:D009474]
comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.
synonym: "nerve cell" EXACT []
xref: BTO:0000938
xref: CALOHA:TS-0683
xref: FBbt:00005106
xref: FMA:54527
xref: VHOG:0001483
xref: WBbt:0003679
is_a: CL:0000000 ! cell
property_value: RO:0002175 NCBITaxon:9606
[Term]
id: COB:0000121
name: measurement datum
[Term]
id: COB:0001000
name: exposure of organism
def: "A process during which an organism comes into contact with another entity." []
is_a: BFO:0000015 ! process
[Term]
id: ENVO:01000254
name: environmental system
def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43]
comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
synonym: "environment" EXACT []
xref: EcoLexicon:environment
is_a: RO:0002577 ! system
creation_date: 2013-09-23T16:04:08Z
[Term]
id: ENVO:01000739
name: habitat
def: "An environmental system which can sustain and allow the growth of an ecological population." [EnvO:EnvO]
comment: A habitat's specificity to an ecological population differentiates it from other environment classes.
xref: EcoLexicon:habitat
xref: https://en.wikipedia.org/wiki/Habitat
xref: LTER:238
xref: SWEETRealm:Habitat
is_a: ENVO:01000254 ! environmental system
[Term]
id: GO:0003674
name: gene product or complex activity
name: molecular_function
def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt]
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
comment: This is the same as GO molecular function
synonym: "molecular function" EXACT []
is_a: BFO:0000015 ! process
disjoint_from: GO:0008150 ! biological_process
[Term]
id: GO:0004842
name: ubiquitin-protein transferase activity
def: "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages." [GOC:BioGRID, GOC:jh2, PMID:9635407]
synonym: "E2" BROAD []
synonym: "E3" BROAD []
synonym: "ubiquitin conjugating enzyme activity" NARROW []
synonym: "ubiquitin ligase activity" NARROW []
synonym: "ubiquitin protein ligase activity" NARROW []
synonym: "ubiquitin protein-ligase activity" NARROW []
synonym: "ubiquitin-conjugating enzyme activity" NARROW []
xref: KEGG_REACTION:R03876
xref: Reactome:R-HSA-1169394 "ISGylation of IRF3"
xref: Reactome:R-HSA-1169395 "ISGylation of viral protein NS1"
xref: Reactome:R-HSA-1169397 "Activation of ISG15 by UBA7 E1 ligase"
xref: Reactome:R-HSA-1169398 "ISGylation of host protein filamin B"
xref: Reactome:R-HSA-1169402 "ISGylation of E2 conjugating enzymes"
xref: Reactome:R-HSA-1169405 "ISGylation of protein phosphatase 1 beta (PP2CB)"
xref: Reactome:R-HSA-1169406 "ISGylation of host proteins"
xref: Reactome:R-HSA-1234163 "Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha"
xref: Reactome:R-HSA-1234172 "Nuclear VBC complex ubiquitinylates HIF-alpha"
xref: Reactome:R-HSA-1253282 "ERBB4 ubiquitination by WWP1/ITCH"
xref: Reactome:R-HSA-1358789 "Self-ubiquitination of RNF41"
xref: Reactome:R-HSA-1358790 "RNF41 ubiquitinates ERBB3"
xref: Reactome:R-HSA-1358792 "RNF41 ubiquitinates activated ERBB3"
xref: Reactome:R-HSA-1363331 "Ubiquitination of p130 (RBL2) by SCF (Skp2)"
xref: Reactome:R-HSA-168915 "K63-linked ubiquitination of RIP1 bound to the activated TLR complex"
xref: Reactome:R-HSA-173542 "SMURF2 ubiquitinates SMAD2"
xref: Reactome:R-HSA-173545 "Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling"
xref: Reactome:R-HSA-174057 "Multiubiquitination of APC/C-associated Cdh1"
xref: Reactome:R-HSA-174104 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex"
xref: Reactome:R-HSA-174144 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex"
xref: Reactome:R-HSA-174159 "Ubiquitination of Emi1 by SCF-beta-TrCP"
xref: Reactome:R-HSA-174195 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex"
xref: Reactome:R-HSA-174227 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex"
xref: Reactome:R-HSA-179417 "Multiubiquitination of Nek2A"
xref: Reactome:R-HSA-180540 "Multi-ubiquitination of APOBEC3G"
xref: Reactome:R-HSA-180597 "Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex"
xref: Reactome:R-HSA-182986 "CBL-mediated ubiquitination of CIN85"
xref: Reactome:R-HSA-182993 "Ubiquitination of stimulated EGFR (CBL)"
xref: Reactome:R-HSA-183036 "Ubiquitination of stimulated EGFR (CBL:GRB2)"
xref: Reactome:R-HSA-183051 "CBL ubiquitinates Sprouty"
xref: Reactome:R-HSA-183084 "CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix"
xref: Reactome:R-HSA-183089 "CBL binds and ubiquitinates phosphorylated Sprouty"
xref: Reactome:R-HSA-1852623 "Ubiquitination of NICD1 by FBWX7"
xref: Reactome:R-HSA-187575 "Ubiquitination of phospho-p27/p21"
xref: Reactome:R-HSA-1912357 "ITCH ubiquitinates DTX"
xref: Reactome:R-HSA-1912386 "Ubiquitination of NOTCH1 by ITCH in the absence of ligand"
xref: Reactome:R-HSA-1918092 "CHIP (STUB1) mediates ubiquitination of ERBB2"
xref: Reactome:R-HSA-1918095 "CUL5 mediates ubiquitination of ERBB2"
xref: Reactome:R-HSA-1977296 "NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer"
xref: Reactome:R-HSA-1980074 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1"
xref: Reactome:R-HSA-1980118 "ARRB mediates NOTCH1 ubiquitination"
xref: Reactome:R-HSA-201425 "Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling"
xref: Reactome:R-HSA-202453 "Auto-ubiquitination of TRAF6"
xref: Reactome:R-HSA-202534 "Ubiquitination of NEMO by TRAF6"
xref: Reactome:R-HSA-205118 "TRAF6 polyubiquitinates NRIF"
xref: Reactome:R-HSA-209063 "Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex"
xref: Reactome:R-HSA-211734 "Ubiquitination of PAK-2p34"
xref: Reactome:R-HSA-2169050 "SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7"
xref: Reactome:R-HSA-2172172 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH2"
xref: Reactome:R-HSA-2179276 "SMURF2 monoubiquitinates SMAD3"
xref: Reactome:R-HSA-2186747 "Ubiquitination of SKI/SKIL by RNF111/SMURF2"
xref: Reactome:R-HSA-2186785 "RNF111 ubiquitinates SMAD7"
xref: Reactome:R-HSA-2187368 "STUB1 (CHIP) ubiquitinates SMAD3"
xref: Reactome:R-HSA-2213017 "Auto-ubiquitination of TRAF3"
xref: Reactome:R-HSA-264444 "Autoubiquitination of phospho-COP1(Ser-387 )"
xref: Reactome:R-HSA-2682349 "RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels"
xref: Reactome:R-HSA-2730904 "Auto-ubiquitination of TRAF6"
xref: Reactome:R-HSA-2737728 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants"
xref: Reactome:R-HSA-2769007 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants"
xref: Reactome:R-HSA-2900765 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants"
xref: Reactome:R-HSA-3000335 "SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA"
xref: Reactome:R-HSA-3134804 "STING ubiquitination by TRIM32 or TRIM56"
xref: Reactome:R-HSA-3134946 "DDX41 ubiquitination by TRIM21"
xref: Reactome:R-HSA-3249386 "DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1"
xref: Reactome:R-HSA-3780995 "NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2"
xref: Reactome:R-HSA-3781009 "NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1"
xref: Reactome:R-HSA-3788724 "Cdh1:APC/C ubiquitinates EHMT1 and EHMT2"
xref: Reactome:R-HSA-3797226 "Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease)"
xref: Reactome:R-HSA-400267 "BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins"
xref: Reactome:R-HSA-4332236 "CBL neddylates TGFBR2"
xref: Reactome:R-HSA-446877 "TRAF6 is K63 poly-ubiquitinated"
xref: Reactome:R-HSA-450358 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation"
xref: Reactome:R-HSA-451418 "Pellino ubiquitinates IRAK1"
xref: Reactome:R-HSA-5205682 "Parkin promotes the ubiquitination of mitochondrial substrates"
xref: Reactome:R-HSA-5357757 "BIRC(cIAP1/2) ubiquitinates RIPK1"
xref: Reactome:R-HSA-5362412 "SYVN1 ubiquitinates Hh C-terminal fragments"
xref: Reactome:R-HSA-5483238 "Hh processing variants are ubiquitinated"
xref: Reactome:R-HSA-5607725 "SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP"
xref: Reactome:R-HSA-5607728 "beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex"
xref: Reactome:R-HSA-5607756 "TRAF6 oligomer autoubiquitinates"
xref: Reactome:R-HSA-5607757 "K63polyUb-TRAF6 ubiquitinates TAK1"
xref: Reactome:R-HSA-5610742 "SCF(beta-TrCP) ubiquitinates p-GLI1"
xref: Reactome:R-HSA-5610745 "SCF(beta-TrCP) ubiquitinates p-GLI2"
xref: Reactome:R-HSA-5610746 "SCF(beta-TrCP) ubiquitinates p-GLI3"
xref: Reactome:R-HSA-5652009 "RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA"
xref: Reactome:R-HSA-5655170 "RCHY1 monoubiquitinates POLH"
xref: Reactome:R-HSA-5660753 "SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA"
xref: Reactome:R-HSA-5667107 "SIAH1, SIAH2 ubiquitinate SNCAIP"
xref: Reactome:R-HSA-5667111 "PARK2 K63-Ubiquitinates SNCAIP"
xref: Reactome:R-HSA-5668454 "K63polyUb-cIAP1,2 ubiquitinates TRAF3"
xref: Reactome:R-HSA-5668534 "cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK"
xref: Reactome:R-HSA-5675470 "BIRC2/3 (cIAP1/2) is autoubiquitinated"
xref: Reactome:R-HSA-5684250 "SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2"
xref: Reactome:R-HSA-5691108 "SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2"
xref: Reactome:R-HSA-5693108 "TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains"
xref: Reactome:R-HSA-68712 "The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1"
xref: Reactome:R-HSA-69598 "Ubiquitination of phosphorylated Cdc25A"
xref: Reactome:R-HSA-741386 "RIP2 induces K63-linked ubiquitination of NEMO"
xref: Reactome:R-HSA-75824 "Ubiquitination of Cyclin D1"
xref: Reactome:R-HSA-870449 "TRIM33 monoubiquitinates SMAD4"
xref: Reactome:R-HSA-8948709 "DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3"
xref: Reactome:R-HSA-8956106 "VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha"
xref: Reactome:R-HSA-9013069 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH3"
xref: Reactome:R-HSA-9013974 "Auto-ubiquitination of TRAF3 within activated TLR3 complex"
xref: Reactome:R-HSA-9014342 "K63-linked ubiquitination of RIP1 bound to the activated TLR complex"
xref: Reactome:R-HSA-918224 "DDX58 is K63 polyubiquitinated"
xref: Reactome:R-HSA-936412 "RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS"
xref: Reactome:R-HSA-936942 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2"
xref: Reactome:R-HSA-936986 "Activated TRAF6 synthesizes unanchored polyubiquitin chains"
xref: Reactome:R-HSA-9628444 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation"
xref: Reactome:R-HSA-9645394 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation"
xref: Reactome:R-HSA-9645414 "Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer"
xref: Reactome:R-HSA-9688831 "STUB1 ubiquitinates RIPK3 at K55, K363"
xref: Reactome:R-HSA-9701000 "BRCA1:BARD1 heterodimer autoubiquitinates"
xref: Reactome:R-HSA-9750946 "TRAF2,6 ubiquitinates NLRC5"
xref: Reactome:R-HSA-975118 "TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex"
xref: Reactome:R-HSA-975147 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane"
xref: Reactome:R-HSA-9758604 "Ubiquitination of IKBKG by TRAF6"
xref: Reactome:R-HSA-9793444 "ITCH polyubiquitinates MLKL at K50"
xref: Reactome:R-HSA-9793485 "PRKN polyubiquitinates RIPK3"
xref: Reactome:R-HSA-9793679 "LUBAC ubiquitinates RIPK1 at K627"
xref: Reactome:R-HSA-9796346 "MIB2 ubiquitinates RIPK1 at K377, K604, K634"
xref: Reactome:R-HSA-9796387 "STUB1 ubiquitinates RIPK1 at K571, K604, K627"
xref: Reactome:R-HSA-9796626 "MIB2 ubiquitinates CFLAR"
xref: Reactome:R-HSA-9815507 "MIB2 ubiquitinates CYLD at K338, K530"
xref: Reactome:R-HSA-9817362 "SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex"
xref: Reactome:R-HSA-983140 "Transfer of Ub from E2 to substrate and release of E2"
xref: Reactome:R-HSA-983153 "E1 mediated ubiquitin activation"
xref: Reactome:R-HSA-983156 "Polyubiquitination of substrate"
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0005634
name: cell nucleus
name: nucleus
def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators]
synonym: "cell nucleus" EXACT []
synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757]
xref: NIF_Subcellular:sao1702920020
xref: Wikipedia:Cell_nucleus
is_a: BFO:0000040 ! material entity
[Term]
id: GO:0008150
name: biological process
name: biological_process
def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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]
def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." []
comment: A biological process is an evolved process
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.
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
disjoint_from: OBI:0000011 ! planned process
created_by: jl
creation_date: 2012-09-19T15:05:24Z
[Term]
id: GO:0016301
name: kinase activity
def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732]
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
synonym: "phosphokinase activity" EXACT []
xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm"
xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines"
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0019107
name: myristoyltransferase activity
def: "Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule." [GOC:ai]
xref: Reactome:R-HSA-141367 "Myristoylation of tBID by NMT1"
xref: Reactome:R-HSA-162914 "Myristoylation of Nef"
is_a: GO:0003674 ! molecular_function
[Term]
id: IAO:0000030
name: information content entity
is_a: BFO:0000031 ! generically dependent continuant
property_value: IAO:0000111 "information content entity" xsd:string
[Term]
id: IAO:0000078
name: curation status specification
def: "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." []
property_value: IAO:0000111 "curation status specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string
property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string
property_value: IAO:0000119 "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>" xsd:string
property_value: IAO:0000119 "OBI_0000266" xsd:string
[Term]
id: OBI:0000011
name: planned process
def: "A process that realizes a plan which is the concretization of a plan specification." []
is_a: BFO:0000015 ! process
property_value: IAO:0000111 "planned process" xsd:string
property_value: IAO:0000111 "planned process" xsd:string
property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "'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.)" xsd:string
property_value: IAO:0000116 "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 \nobjectives is a planned process." xsd:string
property_value: IAO:0000117 "Bjoern Peters" xsd:string
property_value: IAO:0000119 "branch derived" xsd:string
[Term]
id: OBI:0000047
name: processed material
def: "Is a material entity that is created or changed during material processing." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000111 "processed material" xsd:string
property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
[Term]
id: OBI:0000070
name: assay
def: "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000111 "assay" xsd:string
property_value: IAO:0000112 "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string
property_value: IAO:0000118 "measuring" xsd:string
property_value: IAO:0000118 "scientific observation" xsd:string
property_value: IAO:0000119 "OBI branch derived" xsd:string
[Term]
id: OBI:0000967
name: container
def: "A device that can be used to restrict the location of material entities over time" []
is_a: OBI:0000968 ! device
property_value: IAO:0000111 "container" xsd:string
property_value: IAO:0000114 IAO:0000123
property_value: IAO:0000116 "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
[Term]
id: OBI:0000968
name: device
def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." []
is_a: OBI:0000047 ! processed material
property_value: IAO:0000111 "device" xsd:string
property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string
property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "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.\n\n2013-6-5 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:\n\n(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.\n\n(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.\n\n(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.\n\nIn 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 role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." xsd:string
property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string
property_value: IAO:0000118 "instrument" xsd:string
property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string
[Term]
id: OBI:0100026
name: organism
def: "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." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000111 "organism" xsd:string
property_value: IAO:0000112 "animal" xsd:string
property_value: IAO:0000112 "fungus" xsd:string
property_value: IAO:0000112 "plant" xsd:string
property_value: IAO:0000112 "virus" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "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')" xsd:string
property_value: IAO:0000116 "13-02-2009:\nOBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." xsd:string
property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string
property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" xsd:string
[Term]
id: OGMS:0000031
name: disease
def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." []
is_a: BFO:0000016 ! disposition
[Term]
id: PATO:0000001
name: quality
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 ! characteristic
[Term]
id: PATO:0000402
name: branched
def: "A branchiness quality inhering in a bearer by virtue of the bearer's having branches." [WordNet:WordNet]
synonym: "ramified" EXACT []
synonym: "ramiform" EXACT []
is_a: PATO:0000001 ! quality
property_value: RO:0002604 PATO:0000414
[Term]
id: PATO:0001199
name: linear
def: "A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel." [ISBN:0881923214]
is_a: PATO:0000001 ! quality
[Term]
id: PATO:0001470
name: proportionality to
def: "A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity." [PATOC:nw]
comment: Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right.
synonym: "proportion" EXACT []
synonym: "proportionality" EXACT []
synonym: "quotient" EXACT []
synonym: "rate" RELATED []
synonym: "ratio" EXACT []
is_a: PATO:0000001 ! quality
[Term]
id: PATO:0002124
name: laminar
def: "A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer." [PATOC:GVG]
is_a: PATO:0000001 ! quality
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X
creation_date: 2009-10-06T04:37:14Z
[Term]
id: RO:0002310
name: obsolete exposure event or process
def: "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." []
property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string
property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI
property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string
property_value: seeAlso "https://github.com/oborel/obo-relations/pull/173" xsd:anyURI
is_obsolete: true
created_by: https://orcid.org/0000-0002-6601-2165
creation_date: 2017-06-05T17:55:39Z
[Term]
id: RO:0002532
name: sequentially ordered entity
def: "Any entity that is ordered in discrete units along a linear axis." []
relationship: RO:0002524 RO:0002533 ! has subsequence sequence atomic unit
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
[Term]
id: RO:0002533
name: sequence atomic unit
def: "Any individual unit of a collection of like units arranged in a linear order" []
is_a: RO:0002532 ! sequentially ordered entity
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000232 "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." xsd:string
[Term]
id: RO:0002534
name: sequence bearer
def: "Any entity that can be divided into parts such that each part is an atomical unit of a sequence" []
is_a: RO:0002532 ! sequentially ordered entity
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000232 "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." xsd:string
[Term]
id: RO:0002577
name: system
def: "A material entity consisting of multiple components that are causally integrated." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 "http://www.jbiomedsem.com/content/4/1/43" xsd:string
[Term]
id: UBERON:0000061
name: anatomical structure
def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003]
subset: common_anatomy
subset: upper_level
synonym: "biological structure" EXACT []
synonym: "connected biological structure" EXACT [CARO:0000003]
xref: AAO:0010825
xref: AEO:0000003
xref: BILA:0000003
xref: CARO:0000003
xref: EHDAA2:0003003
xref: EMAPA:0
xref: FMA:305751
xref: FMA:67135
xref: GAID:781
xref: HAO:0000003
xref: http://dbpedia.org/ontology/AnatomicalStructure
xref: MA:0003000
xref: MESH:D000825
xref: SCTID:362889002
xref: TAO:0000037
xref: TGMA:0001823
xref: VHOG:0001759
xref: XAO:0003000
xref: ZFA:0000037
is_a: UBERON:0000465 ! material anatomical entity
property_value: RO:0002175 NCBITaxon:33090
property_value: RO:0002175 NCBITaxon:4751
[Term]
id: UBERON:0000122
name: neuron projection bundle
def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001, FBbt:00005099, FBC:DOS]
synonym: "funiculus" EXACT []
synonym: "nerve fiber bundle" EXACT [FBbt:00005099]
synonym: "neural fiber bundle" EXACT []
xref: CARO:0001001
xref: NLX:147821
is_a: UBERON:0000061 ! anatomical structure
[Term]
id: UBERON:0000465
name: material anatomical entity
def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737]
subset: common_anatomy
subset: upper_level
xref: AAO:0010264
xref: AEO:0000006
xref: BILA:0000006
xref: CARO:0000006
xref: EHDAA2:0003006
xref: FMA:67165
xref: HAO:0000006
xref: TAO:0001836
xref: TGMA:0001826
xref: VHOG:0001721
is_a: BFO:0000040 ! material entity
is_a: UBERON:0001062 ! anatomical entity
disjoint_from: UBERON:0000466 ! immaterial anatomical entity
property_value: RO:0002175 NCBITaxon:33090
property_value: RO:0002175 NCBITaxon:4751
[Term]
id: UBERON:0000466
name: immaterial anatomical entity
def: "Anatomical entity that has no mass." [http://orcid.org/0000-0001-9114-8737]
subset: common_anatomy
subset: upper_level
synonym: "immaterial physical anatomical entity" EXACT [FMA:67112]
xref: AAO:0010265
xref: AEO:0000007
xref: BILA:0000007
xref: CARO:0000007
xref: EHDAA2:0003007
xref: FMA:67112
xref: HAO:0000007
xref: TAO:0001835
xref: TGMA:0001827
xref: VHOG:0001727
is_a: BFO:0000141 ! immaterial entity
is_a: UBERON:0001062 ! anatomical entity
property_value: RO:0002175 NCBITaxon:33090
property_value: RO:0002175 NCBITaxon:4751
[Term]
id: UBERON:0001062
name: anatomical entity
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: common_anatomy
subset: upper_level
xref: AAO:0010841
xref: AEO:0000000
xref: BFO:0000004
xref: BILA:0000000
xref: BIRNLEX:6
xref: CARO:0000000
xref: EHDAA2:0002229
xref: FMA:62955
xref: HAO:0000000
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
is_a: BFO:0000004 ! independent continuant
property_value: RO:0002175 NCBITaxon:33090
property_value: RO:0002175 NCBITaxon:4751
[Term]
id: UBERON:0001981
name: blood vessel
def: "A vessel through which blood circulates in the body." [BTO:0001102, Wikipedia:Blood_vessel]
subset: efo_slim
subset: human_reference_atlas
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "region of vascular tree organ" EXACT [FMA:50722]
synonym: "vascular element" BROAD [EMAPA:35993]
synonym: "vascular tree organ region" EXACT [FMA:50722]
xref: AAO:0011004
xref: AEO:0000207
xref: BTO:0001102
xref: CALOHA:TS-0080
xref: EFO:0000817
xref: EHDAA2:0003252
xref: EHDAA:240
xref: EMAPA:32743
xref: EMAPA:35993
xref: FMA:50722
xref: FMA:63183
xref: GAID:169
xref: MA:0000060
xref: MAT:0000393
xref: MESH:D001808
xref: NCIT:C12679
xref: NLXANAT:090901
xref: SCTID:361097006
xref: TAO:0002137
xref: UMLS:C0005847 {source="ncithesaurus:Blood_Vessel"}
xref: VHOG:0001250
xref: Wikipedia:Blood_vessel
xref: XAO:0001011
xref: ZFA:0005314
is_a: UBERON:0010000 ! multicellular anatomical structure
property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string
[Term]
id: UBERON:0001982
name: capillary
def: "Any of the smallest blood vessels connecting arterioles with venules." [https://github.com/obophenotype/uberon/issues/137, ISBN:0073040584, Wikipedia:Capillary]
subset: efo_slim
subset: human_reference_atlas
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "blood capillary" EXACT []
synonym: "capillary vessel" EXACT []
xref: AAO:0010252
xref: BTO:0002045
xref: CALOHA:TS-2006
xref: EFO:0001906
xref: EMAPA:35198
xref: EV:0100035
xref: FMA:63194
xref: MA:0000065
xref: MESH:D002196
xref: NCIT:C12685
xref: NLXANAT:090902
xref: TAO:0005250
xref: UMLS:C0935624 {source="ncithesaurus:Capillary"}
xref: VHOG:0001253
xref: Wikipedia:Capillary
xref: XAO:0000116
xref: ZFA:0005250
is_a: UBERON:0001981 ! blood vessel
property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string
property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string
[Term]
id: UBERON:0010000
name: multicellular anatomical structure
def: "An anatomical structure that has more than one cell as a part." [CARO:0010000]
subset: common_anatomy
subset: upper_level
synonym: "multicellular structure" EXACT [FBbt:00100313]
xref: CARO:0010000
is_a: UBERON:0000061 ! anatomical structure
property_value: RO:0002175 NCBITaxon:33090
property_value: RO:0002175 NCBITaxon:4751
[Term]
id: UPHENO:0001001
name: phenotype
is_a: PATO:0000001 ! quality
[Typedef]
id: BFO:0000050
name: part of
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
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
property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI
is_transitive: true
is_a: RO:0002131 ! overlaps
inverse_of: BFO:0000051 ! has part
[Typedef]
id: BFO:0000051
name: has part
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
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
is_a: RO:0002131 ! overlaps
[Typedef]
id: BFO:0000054
name: realized in
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
property_value: IAO:0000111 "realized in" xsd:string
property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string
property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string
property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string
property_value: IAO:0000118 "is realized by" xsd:string
property_value: IAO:0000118 "realized_in" xsd:string
property_value: IAO:0000600 "[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])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000017 ! realizable entity
range: BFO:0000015 ! process
inverse_of: BFO:0000055 ! realizes
[Typedef]
id: BFO:0000055
name: realizes
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
property_value: IAO:0000111 "realizes" xsd:string
property_value: IAO:0000112 "this disease course realizes this disease" xsd:string
property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string
property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string
property_value: IAO:0000600 "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])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl
domain: BFO:0000015 ! process
range: BFO:0000017 ! realizable entity
[Typedef]
id: BFO:0000060
name: obsolete preceded by
comment: accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062
is_transitive: true
is_obsolete: true
[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/terms/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: BFO:0000050 BFO:0000062
holds_over_chain: RO:0002091 BFO:0000062
holds_over_chain: RO:0002092 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: BFO:0000050 BFO:0000063
holds_over_chain: RO:0002092 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
property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI
domain: BFO:0000003 ! occurrent
range: BFO:0000004 ! independent continuant
holds_over_chain: BFO:0000050 BFO:0000066
inverse_of: BFO:0000067 ! contains process
transitive_over: BFO:0000050 ! 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: ENVO:01003004
name: derives from part of
def: "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." []
[Typedef]
id: RO:0000052
name: characteristic of
def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." []
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
property_value: IAO:0000111 "inheres in" xsd:string
property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string
property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string
property_value: IAO:0000118 "inheres_in" xsd:string
property_value: RO:0001900 RO:0001901
is_functional: true
is_a: RO:0002314 ! characteristic of part of
inverse_of: RO:0000053 ! has characteristic
[Typedef]
id: RO:0000053
name: has characteristic
def: "Inverse of characteristic_of" []
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
range: BFO:0000020 ! characteristic
is_inverse_functional: true
[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/terms/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