format-version: 1.2 data-version: releases/2024-02-13 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 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 "2024-02-13" 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: BFO:0000050 BFO:0000015 {all_only="true"} ! part of process 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 relationship: BFO:0000051 BFO:0000020 {all_only="true"} ! has part 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 relationship: BFO:0000051 GO:0003674 ! has part molecular_function 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:" xsd:string property_value: IAO:0000119 "OBI_0000266" 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: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: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 domain: BFO:0000015 ! process 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 property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string 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 domain: BFO:0000015 ! process range: BFO:0000002 ! continuant holds_over_chain: BFO:0000051 RO:0000057 [Typedef] id: RO:0000058 name: is concretized as def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000031 ! generically dependent continuant range: BFO:0000020 ! characteristic inverse_of: RO:0000059 ! concretizes [Typedef] id: RO:0000059 name: concretizes def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000020 ! characteristic range: BFO:0000031 ! generically dependent continuant [Typedef] id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function [Typedef] id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role [Typedef] id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000086 name: has quality def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this apple has quality this red color" xsd:string property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string property_value: IAO:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000091 name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] domain: BFO:0000004 ! independent continuant range: BFO:0000016 ! disposition is_a: RO:0000053 ! has characteristic inverse_of: RO:0000092 ! disposition of [Typedef] id: RO:0000092 name: disposition of def: "inverse of has disposition" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. subset: RO:0002259 is_a: RO:0000052 ! characteristic of [Typedef] id: RO:0000300 name: obsolete in neural circuit with def: "OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons." [] comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_obsolete: true [Typedef] id: RO:0000301 name: obsolete upstream in neural circuit with def: "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first." [] comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_obsolete: true [Typedef] id: RO:0000302 name: obsolete downstream in neural circuit with def: "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first." [] comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_obsolete: true [Typedef] id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string property_value: IAO:0000118 "derives_from" xsd:string property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string inverse_of: RO:0001001 ! derives into [Typedef] id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string property_value: IAO:0000118 "derives_into" xsd:string [Typedef] id: RO:0001015 name: location of def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] property_value: IAO:0000111 "is location of" xsd:string property_value: IAO:0000112 "my head is the location of my brain" xsd:string property_value: IAO:0000112 "this cage is the location of this rat" xsd:string property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000118 "location_of" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true inverse_of: RO:0001025 ! located in [Typedef] id: RO:0001018 name: obsolete contained in property_value: IAO:0000111 "contained in" xsd:string property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string property_value: IAO:0000118 "contained_in" xsd:string property_value: seeAlso https://github.com/oborel/obo-relations/issues/693 is_obsolete: true [Typedef] id: RO:0001019 name: obsolete contains property_value: IAO:0000111 "contains" xsd:string property_value: seeAlso https://github.com/oborel/obo-relations/issues/693 is_obsolete: true [Typedef] id: RO:0001020 name: is allergic trigger for def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 ! material entity is_a: RO:0003302 ! causes or contributes to condition inverse_of: RO:0001022 ! has allergic trigger [Typedef] id: RO:0001021 name: is autoimmune trigger for def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] domain: BFO:0000040 ! material entity is_a: RO:0003302 ! causes or contributes to condition inverse_of: RO:0001023 ! has autoimmune trigger [Typedef] id: RO:0001022 name: has allergic trigger def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string range: BFO:0000040 ! material entity is_a: RO:0003302 ! causes or contributes to condition [Typedef] id: RO:0001023 name: has autoimmune trigger def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] range: BFO:0000040 ! material entity is_a: RO:0003302 ! causes or contributes to condition [Typedef] id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000118 "2D_boundary_of" xsd:string property_value: IAO:0000118 "boundary of" xsd:string property_value: IAO:0000118 "is 2D boundary of" xsd:string property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string property_value: RO:0001900 RO:0001901 is_a: RO:0002323 ! mereotopologically related to inverse_of: RO:0002002 ! has 2D boundary [Typedef] id: RO:0002001 name: aligned with property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_transitive: true [Typedef] id: RO:0002002 name: has 2D boundary def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has boundary" xsd:string property_value: IAO:0000118 "has_2D_boundary" xsd:string property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity range: BFO:0000141 ! immaterial entity is_a: RO:0002323 ! mereotopologically related to [Typedef] id: RO:0002003 name: electrically_synapsed_to def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002170 ! connected to [Typedef] id: RO:0002004 name: tracheates def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure is_a: RO:0001025 ! located in [Typedef] id: RO:0002005 name: innervated_by property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: UBERON:0000061 ! anatomical structure range: UBERON:0000122 ! neuron projection bundle inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002131 ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in [Typedef] id: RO:0002007 name: bounding layer of def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of [Typedef] id: RO:0002008 name: coincident with def: "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." [] comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. subset: ro-eco property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002323 ! mereotopologically related to [Typedef] id: RO:0002009 name: cell expresses def: "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." [] property_value: http://purl.org/dc/terms/description "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: CL:0000000 ! cell is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology synonym: "regulates in other organism" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002418 ! causally upstream of or within [Typedef] id: RO:0002011 name: regulates transport of def: "A relationship that holds between a process that regulates a transport process and the entity transported by that process." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 holds_over_chain: RO:0002211 RO:0002313 [Typedef] id: RO:0002012 name: occurrent part of def: "A part of relation that applies only between occurrents." [] domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: BFO:0000050 ! part of is_a: RO:0002418 ! causally upstream of or within [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: https://orcid.org/0000-0002-7073-9172 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: https://orcid.org/0000-0002-7073-9172 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: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] id: RO:0002016 name: has necessary component activity comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. is_a: RO:0002017 ! has component activity is_a: RO:0002336 ! positively regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:36:08Z [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: https://orcid.org/0000-0002-7073-9172 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: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] id: RO:0002019 name: has ligand def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] is_a: RO:0002233 ! has input created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-19T17:30:36Z [Typedef] id: RO:0002020 name: transports def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] is_a: RO:0002313 ! transports or maintains localization of created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:11:08Z [Typedef] id: RO:0002021 name: occurs across def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] is_a: RO:0002479 ! has part that occurs in created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-20T17:19:37Z [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="https://orcid.org/0000-0002-7073-9172"} is_a: RO:0002334 ! regulated by inverse_of: RO:0002578 ! directly regulates created_by: https://orcid.org/0000-0002-7073-9172 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." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002630 ! directly negatively regulates created_by: https://orcid.org/0000-0002-7073-9172 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." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002629 ! directly positively regulates created_by: https://orcid.org/0000-0002-7073-9172 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." [https://orcid.org/0000-0002-7073-9172] 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 created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] id: RO:0002026 name: in register with def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [https://orcid.org/0000-0002-7073-9172] domain: http://xmlns.com/foaf/0.1/image range: http://xmlns.com/foaf/0.1/image is_a: RO:0002323 ! mereotopologically related to created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-12-07T12:58:06Z [Typedef] id: RO:0002081 name: before or simultaneous with comment: Primitive instance level timing relation between events subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "<=" xsd:string is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002082 name: simultaneous with def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_symmetric: true is_transitive: true is_a: RO:0002081 ! before or simultaneous with [Typedef] id: RO:0002083 name: before comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002081 ! before or simultaneous with [Typedef] id: RO:0002084 name: during which ends comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: RO:0002222 ! temporally related to inverse_of: RO:0002093 ! ends during [Typedef] id: RO:0002085 name: encompasses comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "di" xsd:string is_transitive: true is_a: RO:0002088 ! during which starts inverse_of: RO:0002092 ! happens during [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 holds_over_chain: RO:0002093 BFO:0000062 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 holds_over_chain: RO:0002224 RO:0002230 is_a: BFO:0000062 ! preceded by inverse_of: RO:0002090 ! immediately precedes [Typedef] id: RO:0002088 name: during which starts comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: RO:0002222 ! temporally related to inverse_of: RO:0002091 ! starts during [Typedef] id: RO:0002089 name: starts before subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string holds_over_chain: RO:0002091 BFO:0000060 is_transitive: true is_a: RO:0002222 ! temporally related to [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:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "ends_at_start_of" xsd:string property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 holds_over_chain: RO:0002230 RO:0002224 is_a: BFO:0000063 ! precedes [Typedef] id: RO:0002091 name: starts during comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "io" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002092 name: happens during comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) 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:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Happens_during" xsd:anyURI is_transitive: true is_a: RO:0002091 ! starts during is_a: RO:0002093 ! ends during [Typedef] id: RO:0002093 name: ends during comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "o" xsd:string property_value: IAO:0000118 "overlaps" xsd:string is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002100 name: has soma location def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000465 ! material anatomical entity is_a: RO:0002131 ! overlaps transitive_over: BFO:0000050 ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002101 name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "fasciculates with" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000122 ! neuron projection bundle is_a: RO:0002131 ! overlaps inverse_of: RO:0002132 ! has fasciculating neuron projection [Typedef] id: RO:0002102 name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002113 ! has presynaptic terminal in transitive_over: BFO:0000050 ! part of expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] [Typedef] id: RO:0002103 name: synapsed by def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002485 ! receives input from inverse_of: RO:0002120 ! synapsed to expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] [Typedef] id: RO:0002104 name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: UBERON:0000465 ! material anatomical entity range: UBERON:0000465 ! material anatomical entity is_a: BFO:0000051 ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] id: RO:0002105 name: synapsed_via_type_Ib_bouton_to def: "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton." [] comment: Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002109 ! synapsed_by_via_type_Ib_bouton expand_expression_to: "BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" [] [Typedef] id: RO:0002106 name: synapsed_via_type_Is_bouton_to def: "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." [] comment: Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002112 ! synapsed_by_via_type_Is_bouton expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" [] [Typedef] id: RO:0002107 name: synapsed_via_type_II_bouton_to def: "A relation between a motor neuron and a muscle that it synapses to via a type II bouton." [] comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002108 ! synapsed_by_via_type_II_bouton expand_expression_to: "BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" [] [Typedef] id: RO:0002108 name: synapsed_by_via_type_II_bouton def: "Relation between a muscle and a motor neuron that synapses to it via a type II bouton." [] comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] [Typedef] id: RO:0002109 name: synapsed_by_via_type_Ib_bouton def: "Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton." [] comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] [Typedef] id: RO:0002110 name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "synapsed in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in inverse_of: RO:0002113 ! has presynaptic terminal in transitive_over: BFO:0000050 ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002111 name: releases neurotransmitter property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string domain: UBERON:0000061 ! anatomical structure range: BFO:0000040 ! material entity [Typedef] id: RO:0002112 name: synapsed_by_via_type_Is_bouton def: "Relation between a muscle and a motor neuron that synapses to it via a type Is bouton." [] comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] [Typedef] id: RO:0002113 name: has presynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "synapses in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in transitive_over: BFO:0000050 ! part of expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002114 name: synapsed_via_type_III_bouton_to def: "A relation between a motor neuron and a muscle that it synapses to via a type III bouton." [] comment: Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: RO:0001900 RO:0001901 is_a: RO:0002120 ! synapsed to inverse_of: RO:0002115 ! synapsed_by_via_type_III_bouton expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" [] [Typedef] id: RO:0002115 name: synapsed_by_via_type_III_bouton def: "Relation between a muscle and a motor neuron that synapses to it via a type III bouton.\n" [] comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: RO:0001900 RO:0001901 is_a: RO:0002103 ! synapsed by expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] [Typedef] id: RO:0002120 name: synapsed to def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] [Typedef] id: RO:0002121 name: dendrite synapsed in def: "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002110 ! has postsynaptic terminal in transitive_over: BFO:0000050 ! part of expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] [Typedef] id: RO:0002130 name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has synapse in" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002131 ! overlaps transitive_over: BFO:0000050 ! part of expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] [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: BFO:0000050 BFO:0000050 holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to transitive_over: BFO:0000050 ! 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:0002132 name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "has fasciculating component" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string property_value: RO:0001900 RO:0001901 domain: UBERON:0000122 ! neuron projection bundle is_a: RO:0002131 ! overlaps [Typedef] id: RO:0002134 name: innervates def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 domain: UBERON:0000122 ! neuron projection bundle transitive_over: BFO:0000050 ! part of expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] [Typedef] id: RO:0002150 name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_symmetric: true is_a: RO:0002323 ! mereotopologically related to [Typedef] id: RO:0002151 name: partially overlaps def: "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" xsd:string property_value: IAO:0000118 "proper overlaps" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (proper_overlaps ?x ?y)\n (and \n (overlaps ?x ?y)\n (not (part_of ?x ?y)) \n (not (part_of ?y ?x)))))" xsd:string property_value: RO:0001900 RO:0001901 is_a: RO:0002131 ! overlaps [Typedef] id: RO:0002156 name: derived by descent from def: "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "ancestral_stucture_of" xsd:string property_value: IAO:0000118 "evolutionarily_descended_from" xsd:string is_transitive: true is_a: RO:0002320 ! evolutionarily related to inverse_of: RO:0002157 ! has derived by descendant [Typedef] id: RO:0002157 name: has derived by descendant def: "inverse of derived by descent from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 is_transitive: true is_a: RO:0002320 ! evolutionarily related to [Typedef] id: RO:0002158 name: shares ancestor with def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] comment: VBO calls this homologous_to property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string holds_over_chain: RO:0002156 RO:0002157 is_symmetric: true is_transitive: true is_a: RO:0002320 ! evolutionarily related to [Typedef] id: RO:0002159 name: serially homologous to property_value: IAO:0000114 IAO:0000125 is_symmetric: true is_transitive: true is_a: RO:0002320 ! evolutionarily related to [Typedef] id: RO:0002160 name: only in taxon def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints is_a: RO:0002162 ! in taxon [Typedef] id: RO:0002162 name: in taxon def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] comment: Connects a biological entity to its taxon of origin. subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints range: OBI:0100026 ! organism holds_over_chain: BFO:0000050 RO:0002162 holds_over_chain: BFO:0000051 RO:0002162 holds_over_chain: RO:0002202 RO:0002162 holds_over_chain: RO:0002206 RO:0002162 holds_over_chain: RO:0002214 RO:0002162 holds_over_chain: RO:0002215 RO:0002162 holds_over_chain: RO:0002225 RO:0002162 holds_over_chain: RO:0002254 RO:0002162 holds_over_chain: RO:0002295 RO:0002162 is_a: RO:0002320 ! evolutionarily related to [Typedef] id: RO:0002163 name: spatially disjoint from def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002170 name: connected to def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to [Typedef] id: RO:0002176 name: connects def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 ! independent continuant is_a: RO:0002323 ! mereotopologically related to [Typedef] id: RO:0002177 name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure holds_over_chain: RO:0002371 BFO:0000050 {RO:0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to [Typedef] id: RO:0002178 name: supplies def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: RO:0002170 ! connected to [Typedef] id: RO:0002179 name: drains def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: RO:0002170 ! connected to [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: BFO:0000051 ! has part [Typedef] id: RO:0002200 name: has phenotype def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: UPHENO:0001001 ! phenotype is_a: RO:0016001 ! has phenotype or disease inverse_of: RO:0002201 ! phenotype of [Typedef] id: RO:0002201 name: phenotype of def: "inverse of has phenotype" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_functional: true [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 https://orcid.org/0000-0001-9114-8737 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true is_a: RO:0002254 ! has developmental contribution from 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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 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:0002204 name: gene product of def: "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000004 ! independent continuant range: BFO:0000002 ! continuant holds_over_chain: RO:0002512 RO:0002510 is_a: RO:0002330 ! genomically related to inverse_of: RO:0002205 ! has gene product [Typedef] id: RO:0002205 name: has gene product def: "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" [] property_value: IAO:0000112 "every HOTAIR lncRNA is the gene product of some HOXC gene" xsd:string property_value: IAO:0000112 "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: BFO:0000004 ! independent continuant holds_over_chain: RO:0002511 RO:0002513 is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002206 name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002207 name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS synonym: "has developmental precursor" EXACT [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: RO:0002202 ! develops from inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002208 name: parasitoid of def: "A parasite that kills or sterilizes its host" [] is_a: RO:0002444 ! parasite of inverse_of: RO:0002209 ! has parasitoid [Typedef] id: RO:0002209 name: has parasitoid def: "inverse of parasitoid of" [] subset: RO:0002259 is_a: RO:0002445 ! parasitized by [Typedef] id: RO:0002210 name: directly develops into def: "inverse of directly develops from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] 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:0000117 https://orcid.org/0000-0001-7476-6306 property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 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:0002230 RO:0002211 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: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] 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:0000117 https://orcid.org/0000-0002-6601-2165 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 holds_over_chain: RO:0002230 RO:0002212 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: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] 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:0000117 https://orcid.org/0000-0002-6601-2165 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 holds_over_chain: RO:0002230 RO:0002213 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:0002214 name: has prototype def: "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." [] property_value: IAO:0000112 "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" xsd:string property_value: IAO:0000112 "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" xsd:string property_value: IAO:0000116 "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." xsd:string property_value: IAO:0000116 "TODO: add homeomorphy axiom" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 [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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: RO:0002216 ! capable of part of [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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002217 name: obsolete actively participates in def: "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" [] comment: Obsoleted as the inverse property was obsoleted. property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "agent in" xsd:string is_obsolete: true replaced_by: RO:0002608 [Typedef] id: RO:0002218 name: obsolete has active participant def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has agent" xsd:string is_obsolete: true replaced_by: RO:0002500 [Typedef] id: RO:0002219 name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to inverse_of: RO:0002221 ! surrounds [Typedef] id: RO:0002220 name: adjacent to def: "x adjacent to y if and only if x and y share a boundary." [] 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:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_a: RO:0002163 ! spatially disjoint from [Typedef] id: RO:0002221 name: surrounds def: "inverse of surrounded by" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to [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 https://orcid.org/0000-0002-6601-2165 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:0002223 name: starts def: "inverse of starts with" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Allen" xsd:string is_a: BFO:0000050 ! part of is_a: RO:0002222 ! temporally related to inverse_of: RO:0002224 ! starts with [Typedef] id: RO:0002224 name: starts with def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002225 name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002207 BFO:0000050 is_a: RO:0002202 ! develops from [Typedef] id: RO:0002226 name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string domain: UBERON:0001062 ! anatomical entity holds_over_chain: RO:0002207 RO:0001025 is_a: RO:0002258 ! developmentally preceded by [Typedef] id: RO:0002227 name: obligate parasite of def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] is_a: RO:0002444 ! parasite of [Typedef] id: RO:0002228 name: facultative parasite of def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] is_a: RO:0002444 ! parasite of [Typedef] id: RO:0002229 name: ends def: "inverse of ends with" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000050 ! part of is_a: RO:0002222 ! temporally related to inverse_of: RO:0002230 ! ends with [Typedef] id: RO:0002230 name: ends with def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002222 ! temporally related to [Typedef] id: RO:0002231 name: has start location def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: RO:0002224 BFO:0000066 is_a: RO:0002479 ! has part that occurs in [Typedef] id: RO:0002232 name: has end location def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: RO:0002230 BFO:0000066 is_a: RO:0002479 ! has part that occurs in [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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: RO:0002224 RO:0002233 is_a: RO:0000057 ! has participant inverse_of: RO:0002352 ! input of [Typedef] id: RO:0002234 name: has output def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." [] 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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: RO:0002230 RO:0002234 is_a: RO:0000057 ! has participant inverse_of: RO:0002353 ! output of [Typedef] id: RO:0002235 name: stem parasite of def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] is_a: RO:0002444 ! parasite of [Typedef] id: RO:0002236 name: root parasite of def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] is_a: RO:0002444 ! parasite of [Typedef] id: RO:0002237 name: hemiparasite of def: "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." [] is_a: RO:0002444 ! parasite of [Typedef] id: RO:0002238 name: has component participant def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string is_a: RO:0000057 ! has participant [Typedef] id: RO:0002240 name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0002241 name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: RO:0002309 ! has exposure stimulus [Typedef] id: RO:0002242 name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0002243 name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0002244 name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string domain: COB:0001000 ! exposure of organism is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002245 name: over-expressed in def: "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." [] is_a: RO:0002206 ! expressed in [Typedef] id: RO:0002246 name: under-expressed in def: "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." [] is_a: RO:0002206 ! expressed in [Typedef] id: RO:0002248 name: has active ingredient def: "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." [] synonym: "has active pharmaceutical ingredient" RELATED [] synonym: "has active substance" EXACT [] property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: BFO:0000051 ! has part inverse_of: RO:0002249 ! active ingredient in [Typedef] id: RO:0002249 name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 is_a: BFO:0000050 ! part of [Typedef] id: RO:0002252 name: connecting branch of def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: RO:0002170 ! connected to is_a: RO:0002375 ! in branching relationship with inverse_of: RO:0002253 ! has connecting branch [Typedef] id: RO:0002253 name: has connecting branch def: "inverse of connecting branch of" [] subset: RO:0002259 property_value: RO:0004036 BFO:0000051 is_a: RO:0002375 ! in branching relationship with [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 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity holds_over_chain: BFO:0000051 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 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002203 BFO:0000050 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002385 ! has potential to developmentally contribute to [Typedef] id: RO:0002256 name: developmentally induced by def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: UBERON:0000465 ! material anatomical entity range: UBERON:0000465 ! material anatomical entity is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002257 ! developmentally induces [Typedef] id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce [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 https://orcid.org/0000-0002-6601-2165 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:0002260 name: has biological role def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] is_a: RO:0000087 ! has role [Typedef] id: RO:0002261 name: has application role def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] is_a: RO:0000087 ! has role [Typedef] id: RO:0002262 name: has chemical role def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] is_a: RO:0000087 ! has role [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 "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002285 name: developmentally replaces def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "replaces" xsd:string is_a: RO:0002258 ! developmentally preceded by [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002287 name: part of developmental precursor of property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002210 is_a: RO:0002286 ! developmentally succeeded by [Typedef] id: RO:0002291 name: ubiquitously expressed in def: "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002206 ! expressed in inverse_of: RO:0002293 ! ubiquitously expresses [Typedef] id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002293 name: ubiquitously expresses def: "inverse of ubiquiotously expressed in" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002292 ! expresses [Typedef] id: RO:0002295 name: results in developmental progression of def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to [Typedef] id: RO:0002296 name: results in development of def: "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." [] 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:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002297 name: results in formation of anatomical entity 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:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of [Typedef] id: RO:0002298 name: results in morphogenesis of def: "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." [] 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:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002299 name: results in maturation of def: "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." [] 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:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002300 name: results in disappearance of property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of [Typedef] id: RO:0002301 name: results in developmental regression of property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "May be merged into parent relation" xsd:string is_a: RO:0002552 ! results in ending of [Typedef] id: RO:0002302 name: is treated by substance def: "Inverse of 'is substance that treats'" [] subset: RO:0002259 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 is_a: RO:0002410 ! causally related to inverse_of: RO:0002606 ! is substance that treats [Typedef] id: RO:0002303 name: has habitat def: "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." [] comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. subset: ro-eco property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string domain: OBI:0100026 ! organism range: ENVO:01000254 ! environmental system is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002304 name: causally upstream of, positive effect def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect 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 def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] 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 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect [Typedef] id: RO:0002309 name: has exposure stimulus def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 is_a: RO:0002244 ! related via exposure to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:35:04Z [Typedef] id: RO:0002312 name: evolutionary variant of property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002320 ! evolutionarily related to [Typedef] id: RO:0002313 name: transports or maintains localization of def: "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." [] 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:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "regulates localization of" xsd:string is_a: RO:0002337 ! related via localization to is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002315 name: results in acquisition of features of def: "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" [] 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:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: UBERON:0000061 ! anatomical structure is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] id: RO:0002321 name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] id: RO:0002322 name: confers advantage in subset: ro-eco property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "adapted for" xsd:string range: ENVO:01000254 ! environmental system is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 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 https://orcid.org/0000-0002-6601-2165 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:0002325 name: colocalizes with def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002323 ! mereotopologically related to [Typedef] id: RO:0002326 name: contributes to subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string property_value: seeAlso "https://wiki.geneontology.org/Contributes_to" xsd:anyURI is_a: RO:0002216 ! capable of part of is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] 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 https://orcid.org/0000-0002-6601-2165 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: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! 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 https://orcid.org/0000-0002-6601-2165 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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant [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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002332 name: regulates levels of def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process range: BFO:0000040 ! material entity is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI 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 https://orcid.org/0000-0002-6601-2165 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 https://orcid.org/0000-0002-6601-2165 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 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant [Typedef] id: RO:0002338 name: has target start location def: "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." [] 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:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002344 ! results in transport to from or in transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002339 name: has target end location def: "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." [] 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:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002344 ! results in transport to from or in transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002340 name: imports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002020 ! transports [Typedef] id: RO:0002341 name: results in transport along def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] id: RO:0002342 name: results in transport across def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002021 ! occurs across is_a: RO:0002344 ! results in transport to from or in [Typedef] id: RO:0002343 name: results in growth of property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002344 name: results in transport to from or in property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] id: RO:0002345 name: exports def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002020 ! transports [Typedef] id: RO:0002348 name: results in commitment to def: "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." [] 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:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 ! cell is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002349 name: results in determination of def: "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment." [] 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:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 ! cell is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string property_value: IAO:0000118 "is member of" xsd:string property_value: IAO:0000118 "member part of" xsd:string property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 is_a: BFO:0000050 ! part of inverse_of: RO:0002351 ! has member [Typedef] id: RO:0002351 name: has member def: "has member is a mereological relation between a collection and an item." [] property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 is_a: BFO:0000051 ! has part [Typedef] id: RO:0002352 name: input of def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002353 name: output of def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002353 ! output of [Typedef] id: RO:0002355 name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002356 name: results in specification of def: "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. " [] 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:0000117 https://orcid.org/0000-0002-6601-2165 range: CL:0000000 ! cell is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002357 name: results in developmental induction of def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002360 name: has dendrite location property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps [Typedef] id: RO:0002371 name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: RO:0002170 ! connected to is_a: RO:0002177 ! attached to part of [Typedef] id: RO:0002372 name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to [Typedef] id: RO:0002373 name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to [Typedef] id: RO:0002374 name: derived from ancestral fusion of def: "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" [] comment: A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. synonym: "has fused element" BROAD [] property_value: IAO:0000112 "false" xsd:boolean property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: RO:0002156 ! derived by descent from [Typedef] id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002323 ! mereotopologically related to [Typedef] id: RO:0002376 name: tributary of def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] subset: ro-eco property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: RO:0002170 ! connected to is_a: RO:0002375 ! in branching relationship with [Typedef] id: RO:0002377 name: distributary of def: "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" [] comment: This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes subset: ro-eco property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: RO:0002170 ! connected to is_a: RO:0002375 ! in branching relationship with [Typedef] id: RO:0002378 name: anabranch of def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "anastomoses with" xsd:string is_a: RO:0002377 ! distributary of disjoint_from: RO:0002382 ! proper distributary of disjoint_from: RO:0002383 ! proper tributary of [Typedef] id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] property_value: IAO:0000112 "A lump of clay and a statue" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: RO:0002131 ! overlaps [Typedef] id: RO:0002380 name: branching part of def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 holds_over_chain: RO:0002377 RO:0002381 is_a: BFO:0000050 ! part of is_a: RO:0002375 ! in branching relationship with inverse_of: RO:0002569 ! has branching part [Typedef] id: RO:0002381 name: main stem of def: "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." [] subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: BFO:0000050 ! part of is_a: RO:0002375 ! in branching relationship with [Typedef] id: RO:0002382 name: proper distributary of def: "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002377 ! distributary of [Typedef] id: RO:0002383 name: proper tributary of def: "x proper_tributary_of y iff x tributary_of y and x does not originate from y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002376 ! tributary of [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 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! 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 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 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 https://orcid.org/0000-0002-6601-2165 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 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002400 name: has direct input def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly consumes" xsd:string property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string holds_over_chain: RO:0002224 RO:0002400 is_a: RO:0002233 ! has input [Typedef] id: RO:0002401 name: obsolete has indirect input comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_obsolete: true [Typedef] id: RO:0002402 name: obsolete has direct output def: "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " [] property_value: IAO:0000112 "translation SubClassOf has_direct_output some protein" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly produces" xsd:string is_obsolete: true [Typedef] id: RO:0002403 name: obsolete has indirect output comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002411 RO:0002402 is_obsolete: true [Typedef] id: RO:0002404 name: causally downstream of def: "inverse of upstream of" [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000062 ! preceded by is_a: RO:0002427 ! causally downstream of or within inverse_of: RO:0002411 ! causally upstream of [Typedef] id: RO:0002405 name: immediately causally downstream of property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002087 ! immediately preceded by is_a: RO:0002404 ! causally downstream of inverse_of: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002406 name: obsolete directly activates comment: This term was obsoleted because it has the same meaning as 'directly positively regulates'. is_obsolete: true replaced_by: RO:0002629 [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: RO:0002409 RO:0002409 holds_over_chain: RO:0002629 RO:0002407 holds_over_chain: RO:0002629 RO:0002629 is_transitive: true is_a: RO:0002213 ! positively regulates is_a: RO:0012012 ! indirectly regulates transitive_over: RO:0002629 ! directly positively regulates [Typedef] id: RO:0002408 name: obsolete directly inhibits comment: This term was obsoleted because it has the same meaning as 'directly negatively regulates'. is_obsolete: true replaced_by: RO:0002630 [Typedef] id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: RO:0002630 RO:0002409 holds_over_chain: RO:0002630 RO:0002630 is_transitive: true is_a: RO:0002212 ! negatively regulates is_a: RO:0012012 ! indirectly regulates transitive_over: RO:0002630 ! directly negatively regulates [Typedef] id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] id: RO:0002411 name: causally upstream of def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000063 ! precedes is_a: RO:0002418 ! causally upstream of or within [Typedef] id: RO:0002412 name: immediately causally upstream of def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: RO:0002090 ! immediately precedes is_a: RO:0002411 ! causally upstream of [Typedef] id: RO:0002413 name: provides input for def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "directly provides input for" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Provides_input_for" xsd:anyURI holds_over_chain: RO:0002402 RO:0002400 is_a: RO:0002412 ! immediately causally upstream of is_a: RO:0002414 ! transitively provides input for [Typedef] id: RO:0002414 name: transitively provides input for def: "transitive form of directly_provides_input_for" [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true is_a: RO:0004047 ! causally upstream of or within, positive effect [Typedef] id: RO:0002418 name: causally upstream of or within def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: RO:0002427 ! causally downstream of or within [Typedef] id: RO:0002424 name: differs in comment: This is an exploratory relation property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" xsd:anyURI [Typedef] id: RO:0002425 name: differs in attribute of property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002424 ! differs in [Typedef] id: RO:0002426 name: differs in attribute property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 range: BFO:0000020 ! characteristic is_a: RO:0002424 ! differs in [Typedef] id: RO:0002427 name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes [Typedef] id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 RO:0002211 holds_over_chain: RO:0002331 RO:0002211 is_a: RO:0002263 ! acts upstream of is_a: RO:0002431 ! involved in or involved in regulation of [Typedef] id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 RO:0002213 holds_over_chain: RO:0002331 RO:0002213 is_a: RO:0002428 ! involved in regulation of [Typedef] id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 RO:0002212 holds_over_chain: RO:0002331 RO:0002212 is_a: RO:0002428 ! involved in regulation of [Typedef] id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002433 name: contributes to morphology of def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps [Typedef] id: RO:0002434 name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_symmetric: true [Typedef] id: RO:0002435 name: genetically interacts with property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002437 name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_symmetric: true is_a: RO:0002321 ! ecologically related to is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002438 name: trophically interacts with def: "An interaction relationship in which the partners are related via a feeding relationship." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002439 name: preys on def: "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" [] subset: ro-eco property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002458 ! preyed upon by [Typedef] id: RO:0002440 name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002441 name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002442 name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002443 name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002444 name: parasite of subset: ro-eco synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002454 ! has host inverse_of: RO:0002445 ! parasitized by [Typedef] id: RO:0002445 name: parasitized by subset: ro-eco synonym: "directly parasitized by" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002453 ! host of [Typedef] id: RO:0002446 name: participates in a abiotic-biotic interaction with def: "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." [] subset: ro-eco synonym: "semibiotically interacts with" RELATED [] property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002447 name: phosphorylates property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with is_a: RO:0011002 ! regulates activity of [Typedef] id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002451 name: transmitted by def: "A relationship that holds between a disease and organism" [] property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string property_value: IAO:0000116 "Add domain and range constraints" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0002452 name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: OGMS:0000031 ! disease is_a: RO:0002200 ! has phenotype [Typedef] id: RO:0002453 name: host of subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002454 name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0002455 name: pollinates subset: ro-eco property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: RO:0002442 ! mutualistically interacts with inverse_of: RO:0002456 ! pollinated by [Typedef] id: RO:0002456 name: pollinated by subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: RO:0002442 ! mutualistically interacts with [Typedef] id: RO:0002457 name: acquires nutrients from subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002469 ! provides nutrients for [Typedef] id: RO:0002458 name: preyed upon by def: "inverse of preys on" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: RO:0002438 ! trophically interacts with [Typedef] id: RO:0002459 name: is vector for subset: ro-eco property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002460 ! has vector [Typedef] id: RO:0002460 name: has vector subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002461 name: partner in property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string is_a: RO:0000056 ! participates in [Typedef] id: RO:0002462 name: subject participant in property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: RO:0002461 ! partner in [Typedef] id: RO:0002463 name: target participant in property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 name: helper property (not for use in curation) property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string [Typedef] id: RO:0002465 name: is symbiosis property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002466 name: is commensalism property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002467 name: is mutualism property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002468 name: is parasitism property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002465 ! is symbiosis [Typedef] id: RO:0002469 name: provides nutrients for subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002438 ! trophically interacts with [Typedef] id: RO:0002470 name: eats subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of eating interaction with" xsd:string is_a: RO:0002438 ! trophically interacts with [Typedef] id: RO:0002471 name: is eaten by subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "eaten by" xsd:string property_value: IAO:0000118 "is target of eating interaction with" xsd:string is_a: RO:0002438 ! trophically interacts with [Typedef] id: RO:0002472 name: is evidence for def: "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002616 ! related via evidence or inference to inverse_of: RO:0002558 ! has evidence [Typedef] id: RO:0002473 name: composed primarily of def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] subset: ro-eco property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: BFO:0000051 ! has part [Typedef] id: RO:0002476 name: child nucleus of def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string domain: GO:0005634 ! nucleus range: GO:0005634 ! nucleus is_a: RO:0002258 ! developmentally preceded by [Typedef] id: RO:0002477 name: child nucleus of in hermaphrodite def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002476 ! child nucleus of [Typedef] id: RO:0002478 name: child nucleus of in male def: "A child nucleus relationship in which the cells are part of a male organism" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002476 ! child nucleus of [Typedef] id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002480 name: ubiquitinates def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002436 ! molecularly interacts with [Typedef] id: RO:0002481 name: is kinase activity property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002482 name: is ubiquitination property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from property_value: IAO:0000116 "See notes for inverse relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to [Typedef] id: RO:0002486 name: sends output to property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent [Typedef] id: RO:0002488 name: existence starts during def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002583 BFO:0000050 is_a: RO:0002490 ! existence overlaps is_a: RO:0002496 ! existence starts during or after transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002489 name: existence starts with def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002488 ! existence starts during [Typedef] id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage [Typedef] id: RO:0002491 name: existence starts and ends during def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. synonym: "exists during" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002488 ! existence starts during is_a: RO:0002492 ! existence ends during [Typedef] id: RO:0002492 name: existence ends during def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002593 BFO:0000050 is_a: RO:0002490 ! existence overlaps is_a: RO:0002497 ! existence ends during or before transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002493 name: existence ends with def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002492 ! existence ends during [Typedef] id: RO:0002494 name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002202 ! develops from [Typedef] id: RO:0002495 name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: RO:0002207 ! directly develops from is_a: RO:0002494 ! transformation of [Typedef] id: RO:0002496 name: existence starts during or after def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002496 holds_over_chain: RO:0002258 RO:0002496 is_a: RO:0002487 ! relation between physical entity and a process or stage transitive_over: BFO:0000050 ! part of transitive_over: BFO:0000062 ! preceded by transitive_over: RO:0002082 ! simultaneous with [Typedef] id: RO:0002497 name: existence ends during or before def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002497 holds_over_chain: RO:0002286 RO:0002497 is_a: RO:0002487 ! relation between physical entity and a process or stage transitive_over: BFO:0000050 ! part of transitive_over: BFO:0000063 ! precedes transitive_over: RO:0002082 ! simultaneous with [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: RO:0002608 ! process has causal agent [Typedef] id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002503 name: towards def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: RO:0002502 ! depends on [Typedef] id: RO:0002505 name: has intermediate def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" [] subset: ro-eco property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string is_a: RO:0000057 ! has participant [Typedef] id: RO:0002506 name: causal relation between entities property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002507 name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 ! system range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of is_a: RO:0002509 ! determined by part of is_a: RO:0002559 ! causally influenced by inverse_of: RO:0002508 ! determines [Typedef] id: RO:0002508 name: determines def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: RO:0002566 ! causally influences [Typedef] id: RO:0002509 name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 ! system range: BFO:0000040 ! material entity holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities [Typedef] id: RO:0002510 name: transcribed from def: "x is transcribed from y if and only if x is synthesized from template y" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002511 ! transcribed to [Typedef] id: RO:0002511 name: transcribed to def: "inverse of transcribed from" [] subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002512 name: ribosomal translation of def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002513 ! ribosomally translates to [Typedef] id: RO:0002513 name: ribosomally translates to def: "inverse of ribosomal translation of" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002514 name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 ! sequentially ordered entity range: RO:0002532 ! sequentially ordered entity [Typedef] id: RO:0002515 name: sequentially adjacent to def: "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002527 ! does not overlap sequence of [Typedef] id: RO:0002516 name: has start sequence def: "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002524 ! has subsequence inverse_of: RO:0002517 ! is start sequence of [Typedef] id: RO:0002517 name: is start sequence of def: "inverse of has start sequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002525 ! is subsequence of [Typedef] id: RO:0002518 name: has end sequence def: "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002524 ! has subsequence inverse_of: RO:0002519 ! is end sequence of [Typedef] id: RO:0002519 name: is end sequence of def: "inverse of has end sequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002525 ! is subsequence of [Typedef] id: RO:0002520 name: is consecutive sequence of def: "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002524 ! has subsequence [Typedef] id: RO:0002521 name: is sequentially aligned with def: "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_symmetric: true is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002522 name: bounds sequence of def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002514 ! sequentially related to inverse_of: RO:0002523 ! is bound by sequence of [Typedef] id: RO:0002523 name: is bound by sequence of def: "inverse of bounds sequence of" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002524 name: has subsequence def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002522 ! bounds sequence of is_a: RO:0002526 ! overlaps sequence of inverse_of: RO:0002525 ! is subsequence of [Typedef] id: RO:0002525 name: is subsequence of def: "inverse of has subsequence" [] subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: BFO:0000050 ! part of is_a: RO:0002523 ! is bound by sequence of is_a: RO:0002526 ! overlaps sequence of [Typedef] id: RO:0002526 name: overlaps sequence of def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002524 RO:0002525 is_symmetric: true is_a: RO:0002131 ! overlaps is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002527 name: does not overlap sequence of def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "disconnected from" xsd:string is_symmetric: true is_a: RO:0002514 ! sequentially related to [Typedef] id: RO:0002528 name: is upstream of sequence of def: "inverse of downstream of sequence of" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002527 ! does not overlap sequence of [Typedef] id: RO:0002529 name: is downstream of sequence of def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002527 ! does not overlap sequence of inverse_of: RO:0002529 ! is downstream of sequence of [Typedef] id: RO:0002530 name: is immediately downstream of sequence of def: "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002529 is_a: RO:0002515 ! sequentially adjacent to is_a: RO:0002529 ! is downstream of sequence of [Typedef] id: RO:0002531 name: is immediately upstream of sequence of def: "inverse of immediately downstream of" [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002515 ! sequentially adjacent to is_a: RO:0002528 ! is upstream of sequence of [Typedef] id: RO:0002551 name: has skeleton def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of is_asymmetric: true [Typedef] id: RO:0002552 name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002553 name: hyperparasite of def: "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" [] subset: ro-eco synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string holds_over_chain: RO:0002444 RO:0002444 is_a: RO:0002454 ! has host inverse_of: RO:0002554 ! hyperparasitized by [Typedef] id: RO:0002554 name: hyperparasitized by def: "inverse of hyperparasite of" [] subset: ro-eco subset: RO:0002259 synonym: "has epiparasite" RELATED [] synonym: "has hyperparasite" RELATED [] synonym: "hyperparasitoidized by" RELATED [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002445 RO:0002445 is_a: RO:0002453 ! host of [Typedef] id: RO:0002555 name: allelopath of subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002556 name: pathogen of subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002454 ! has host inverse_of: RO:0002557 ! has pathogen [Typedef] id: RO:0002557 name: has pathogen subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002453 ! host of [Typedef] id: RO:0002558 name: has evidence def: "inverse of is evidence for" [] comment: x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. subset: ro-eco subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/25052702 is_a: RO:0002616 ! related via evidence or inference to [Typedef] id: RO:0002559 name: causally influenced by property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002565 name: results in movement of def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] 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:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "" xsd:string is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities [Typedef] id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002568 name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: RO:0002567 ! biomechanically related to [Typedef] id: RO:0002569 name: has branching part def: "inverse of branching part of" [] subset: ro-eco subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002375 ! in branching relationship with [Typedef] id: RO:0002570 name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002131 ! overlaps [Typedef] id: RO:0002571 name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of [Typedef] id: RO:0002572 name: luminal space of def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000141 ! immaterial entity is_a: RO:0002571 ! lumen of [Typedef] id: RO:0002573 name: has modifier def: "A relation that holds between an attribute or a qualifier and another attribute." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string domain: BFO:0000020 ! characteristic range: BFO:0000020 ! characteristic [Typedef] id: RO:0002574 name: participates in a biotic-biotic interaction with subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 domain: OBI:0100026 ! organism range: OBI:0100026 ! organism is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002576 name: skeleton of def: "inverse of has skeleton" [] subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure is_a: BFO:0000050 ! part of [Typedef] id: RO:0002578 name: directly regulates def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] 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:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string property_value: RO:0002575 RO:0002211 is_a: RO:0002211 ! regulates is_a: RO:0002412 ! immediately causally upstream of [Typedef] id: RO:0002583 name: existence starts at end of def: "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y)." [] is_a: RO:0002496 ! existence starts during or after [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000051 RO:0002215 is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] id: RO:0002585 name: results in closure of property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002586 name: results in breakdown of def: "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" [] is_a: RO:0002233 ! has input [Typedef] id: RO:0002587 name: results in synthesis of is_a: RO:0002297 ! results in formation of anatomical entity [Typedef] id: RO:0002588 name: results in assembly of 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 is_a: RO:0002297 ! results in formation of anatomical entity is_a: RO:0002592 ! results in organization of [Typedef] id: RO:0002589 name: results in catabolism of def: "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." [] is_a: RO:0002586 ! results in breakdown of [Typedef] id: RO:0002590 name: results in disassembly of is_a: RO:0002586 ! results in breakdown of is_a: RO:0002592 ! results in organization of [Typedef] id: RO:0002591 name: results in remodeling of is_a: RO:0002233 ! has input is_a: RO:0002592 ! results in organization of [Typedef] id: RO:0002592 name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002593 name: existence ends at start of def: "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y)." [] is_a: RO:0002497 ! existence ends during or before [Typedef] id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] property_value: IAO:0000112 "pyrethroid -> growth" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: RO:0002215 RO:0002211 is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: RO:0002215 RO:0002212 is_a: RO:0002596 ! capable of regulating [Typedef] id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: RO:0002215 RO:0002213 is_a: RO:0002596 ! capable of regulating [Typedef] id: RO:0002599 name: capable of inhibiting or preventing pathological process def: "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." [] property_value: IAO:0000112 "pazopanib -> pathological angiogenesis" xsd:string property_value: IAO:0000118 "treats" xsd:string {comment="Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship"} property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." xsd:string is_a: RO:0002597 ! capable of negatively regulating [Typedef] id: RO:0002600 name: capable of upregulating or causing pathological process def: "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." [] property_value: IAO:0000112 "benzene -> cancer [CHEBI]" xsd:string property_value: IAO:0000118 "causes disease" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002598 ! capable of positively regulating [Typedef] id: RO:0002606 name: is substance that treats def: "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." [] property_value: IAO:0000118 "treats" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 is_a: RO:0002599 ! capable of inhibiting or preventing pathological process [Typedef] id: RO:0002607 name: is marker for def: "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." [] property_value: IAO:0000116 "May be ceded to OBI" xsd:string is_a: RO:0002610 ! correlated with [Typedef] id: RO:0002608 name: process has causal agent def: "Inverse of 'causal agent in process'" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002609 name: obsolete related via dependence to def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string is_obsolete: true [Typedef] id: RO:0002610 name: correlated with def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string [Typedef] id: RO:0002614 name: is evidence with support from def: "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." [] comment: In the Gene Ontology association model, this corresponds to the With/From field property_value: IAO:0000112 "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." xsd:string is_a: RO:0002616 ! related via evidence or inference to [Typedef] id: RO:0002615 name: has model def: "Inverse of is-model-of" [] inverse_of: RO:0003301 ! has role in modeling [Typedef] id: RO:0002616 name: related via evidence or inference to property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string [Typedef] id: RO:0002618 name: visits property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002619 ! visited by [Typedef] id: RO:0002619 name: visited by is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002622 name: visits flowers of is_a: RO:0002618 ! visits inverse_of: RO:0002623 ! has flowers visited by [Typedef] id: RO:0002623 name: has flowers visited by is_a: RO:0002619 ! visited by [Typedef] id: RO:0002624 name: lays eggs in is_a: RO:0002444 ! parasite of is_a: RO:0002618 ! visits inverse_of: RO:0002625 ! has eggs laid in by [Typedef] id: RO:0002625 name: has eggs laid in by is_a: RO:0002445 ! parasitized by is_a: RO:0002619 ! visited by [Typedef] id: RO:0002626 name: kills property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002627 ! is killed by [Typedef] id: RO:0002627 name: is killed by is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly positively regulates def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] 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:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] 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:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002632 name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] property_value: IAO:0000119 Types is_a: RO:0002444 ! parasite of inverse_of: RO:0002633 ! has ectoparasite [Typedef] id: RO:0002633 name: has ectoparasite def: "inverse of ectoparasite of" [] subset: RO:0002259 is_a: RO:0002445 ! parasitized by [Typedef] id: RO:0002634 name: endoparasite of synonym: "lives inside of" RELATED [] property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string property_value: IAO:0000119 Types is_a: RO:0002444 ! parasite of inverse_of: RO:0002635 ! has endoparasite [Typedef] id: RO:0002635 name: has endoparasite is_a: RO:0002445 ! parasitized by [Typedef] id: RO:0002636 name: mesoparasite of def: "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" [] is_a: RO:0002444 ! parasite of inverse_of: RO:0002637 ! has mesoparasite [Typedef] id: RO:0002637 name: has mesoparasite def: "inverse of mesoparasite of" [] subset: RO:0002259 is_a: RO:0002445 ! parasitized by [Typedef] id: RO:0002638 name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] property_value: IAO:0000119 Types is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002639 ! has intercellular endoparasite [Typedef] id: RO:0002639 name: has intercellular endoparasite def: "inverse of intercellular endoparasite of" [] subset: RO:0002259 is_a: RO:0002635 ! has endoparasite [Typedef] id: RO:0002640 name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] property_value: IAO:0000119 Types is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002641 ! has intracellular endoparasite [Typedef] id: RO:0002641 name: has intracellular endoparasite def: "inverse of intracellular endoparasite of" [] subset: RO:0002259 is_a: RO:0002635 ! has endoparasite [Typedef] id: RO:0002801 name: co-roosts with def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] property_value: IAO:0000119 Communal:roosting is_symmetric: true is_a: RO:0008506 ! ecologically co-occurs with [Typedef] id: RO:0002802 name: reservoir host of def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string property_value: IAO:0000119 https://doi.org/10.3390/v13071356 is_a: RO:0002453 ! host of inverse_of: RO:0002803 ! has reservoir host [Typedef] id: RO:0002803 name: has reservoir host def: "inverse of reservoir host of" [] subset: RO:0002259 property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string is_a: RO:0002454 ! has host [Typedef] id: RO:0003000 name: produces def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: RO:0003001 ! produced by [Typedef] id: RO:0003001 name: produced by def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity [Typedef] id: RO:0003002 name: represses expression of def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002449 ! directly negatively regulates activity of [Typedef] id: RO:0003003 name: increases expression of def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002450 ! directly positively regulates activity of [Typedef] id: RO:0003301 name: has role in modeling def: "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] comment: The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. property_value: IAO:0000117 https://orcid.org/0000-0002-1048-5019 property_value: IAO:0000118 "is used to study" xsd:string is_asymmetric: true [Typedef] id: RO:0003302 name: causes or contributes to condition def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." [] comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." xsd:string property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: RO:0002410 ! causally related to [Typedef] id: RO:0003303 name: causes condition def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." [] is_a: RO:0003302 ! causes or contributes to condition [Typedef] id: RO:0003304 name: contributes to condition def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." [] is_a: RO:0003302 ! causes or contributes to condition [Typedef] id: RO:0003305 name: contributes to severity of condition def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." [] property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string is_a: RO:0003304 ! contributes to condition [Typedef] id: RO:0003306 name: contributes to frequency of condition def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." [] property_value: IAO:0000118 "contributes to penetrance of condition" xsd:string is_a: RO:0003304 ! contributes to condition [Typedef] id: RO:0003307 name: ameliorates condition def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." [] comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. property_value: IAO:0000118 "is preventative for condition" xsd:string is_a: RO:0003305 ! contributes to severity of condition [Typedef] id: RO:0003308 name: correlated with condition def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] is_a: RO:0002610 ! correlated with [Typedef] id: RO:0003309 name: exacerbates condition def: "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." [] is_a: RO:0003305 ! contributes to severity of condition [Typedef] id: RO:0003310 name: condition ameliorated by def: "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity." [] is_a: RO:0002410 ! causally related to [Typedef] id: RO:0003311 name: condition exacerbated by def: "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity." [] is_a: RO:0002410 ! causally related to [Typedef] id: RO:0004000 name: condition has genetic basis in property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string domain: BFO:0000017 ! realizable entity is_a: RO:0002410 ! causally related to inverse_of: RO:0004010 ! is genetic basis for condition created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:38:20Z [Typedef] id: RO:0004001 name: has material basis in gain of function germline mutation in property_value: seeAlso Orphanet:410295 property_value: seeAlso Orphanet:410296 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004011 ! is causal gain of function germline mutation of in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:20Z [Typedef] id: RO:0004002 name: has material basis in loss of function germline mutation in is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004012 ! is causal loss of function germline mutation of in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:37Z [Typedef] id: RO:0004003 name: has material basis in germline mutation in property_value: seeAlso Orphanet:317343 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004013 ! is causal germline mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:45:54Z [Typedef] id: RO:0004004 name: has material basis in somatic mutation in property_value: seeAlso Orphanet:317344 is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004014 ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z [Typedef] id: RO:0004005 name: has major susceptibility factor is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004015 ! is causal susceptibility factor for created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:26Z [Typedef] id: RO:0004006 name: has partial material basis in germline mutation in is_a: RO:0004000 ! condition has genetic basis in inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:57Z [Typedef] id: RO:0004007 name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0000057 ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z [Typedef] id: RO:0004008 name: has primary output def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002234 ! has output is_a: RO:0004007 ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z [Typedef] id: RO:0004009 name: has primary input def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:dph, GOC:kva, GOC:pt, https://orcid.org/0000-0002-6601-2165] {comment="PMID:27812932"} subset: http://purl.obolibrary.org/obo/valid_for_go_ontology is_a: RO:0002233 ! has input is_a: RO:0004007 ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:56Z [Typedef] id: RO:0004010 name: is genetic basis for condition property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string range: BFO:0000017 ! realizable entity is_a: RO:0004018 ! is basis for realizable created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:53:08Z [Typedef] id: RO:0004011 name: is causal gain of function germline mutation of in def: "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:410296 is_a: RO:0004010 ! is genetic basis for condition created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:55:51Z [Typedef] id: RO:0004012 name: is causal loss of function germline mutation of in def: "Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:410295 is_a: RO:0004010 ! is genetic basis for condition created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:06Z [Typedef] id: RO:0004013 name: is causal germline mutation in def: "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:317343 is_a: RO:0003303 ! causes condition is_a: RO:0004010 ! is genetic basis for condition created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:56:40Z [Typedef] id: RO:0004014 name: is causal somatic mutation in def: "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]." [] property_value: seeAlso Orphanet:317344 is_a: RO:0003303 ! causes condition is_a: RO:0004010 ! is genetic basis for condition created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:07Z [Typedef] id: RO:0004015 name: is causal susceptibility factor for def: "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." [] property_value: seeAlso Orphanet:317345 is_a: RO:0004010 ! is genetic basis for condition created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:57:43Z [Typedef] id: RO:0004016 name: is causal germline mutation partially giving rise to def: "Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]." [] property_value: seeAlso Orphanet:317346 is_a: RO:0003304 ! contributes to condition is_a: RO:0004010 ! is genetic basis for condition created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:58:43Z [Typedef] id: RO:0004017 name: realizable has basis in is_a: RO:0002410 ! causally related to inverse_of: RO:0004018 ! is basis for realizable created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:01Z [Typedef] id: RO:0004018 name: is basis for realizable is_a: RO:0002410 ! causally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:20:29Z [Typedef] id: RO:0004019 name: disease has basis in domain: OGMS:0000031 ! disease is_a: RO:0004017 ! realizable has basis in is_a: RO:0004023 ! causal relationship with disease as subject created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:26:47Z [Typedef] id: RO:0004020 name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string range: UBERON:0000465 ! material anatomical entity is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:29:32Z [Typedef] id: RO:0004021 name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 ! process is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:37:52Z [Typedef] id: RO:0004022 name: disease has basis in feature def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] domain: OGMS:0000031 ! disease is_a: RO:0002200 ! has phenotype is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:46:07Z [Typedef] id: RO:0004023 name: causal relationship with disease as subject property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string domain: OGMS:0000031 ! disease is_a: RO:0002410 ! causally related to is_a: RO:0040035 ! disease relationship created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:50:54Z [Typedef] id: RO:0004024 name: disease causes disruption of def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string domain: OGMS:0000031 ! disease range: BFO:0000015 ! process holds_over_chain: RO:0004025 RO:0002215 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:51:09Z [Typedef] id: RO:0004025 name: disease causes dysfunction of property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string domain: OGMS:0000031 ! disease range: UBERON:0000465 ! material anatomical entity is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T03:58:20Z [Typedef] id: RO:0004026 name: disease has location def: "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." [] property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string domain: OGMS:0000031 ! disease range: BFO:0000004 ! independent continuant is_a: RO:0040035 ! disease relationship created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T04:06:02Z [Typedef] id: RO:0004027 name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] domain: OGMS:0000031 ! disease range: BFO:0000004 ! independent continuant is_a: RO:0004026 ! disease has location created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:37:31Z [Typedef] id: RO:0004028 name: realized in response to stimulus def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] domain: BFO:0000017 ! realizable entity range: BFO:0000040 ! material entity holds_over_chain: RO:0009501 RO:0002233 is_a: RO:0002410 ! causally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z [Typedef] id: RO:0004029 name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] domain: OGMS:0000031 ! disease is_a: RO:0040035 ! disease relationship created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:50:53Z [Typedef] id: RO:0004030 name: disease arises from alteration in structure def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] range: UBERON:0000061 ! anatomical structure is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:58:44Z [Typedef] id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 BFO:0000051 is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z [Typedef] id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:30Z [Typedef] id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:49:51Z [Typedef] id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:14Z [Typedef] id: RO:0004035 name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-26T23:53:22Z [Typedef] id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] id: RO:0004096 name: DEPRECATED inheres in comment: DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. is_obsolete: true [Typedef] id: RO:0004097 name: DEPRECATED bearer of is_obsolete: true [Typedef] id: RO:0007000 name: has driver def: "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8910-9851 property_value: seeAlso https://github.com/oborel/obo-relations/issues/506 [Typedef] id: RO:0007001 name: has disease driver def: "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8910-9851 property_value: seeAlso https://github.com/oborel/obo-relations/issues/506 is_a: RO:0007000 ! has driver [Typedef] id: RO:0008501 name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: RO:0002440 ! symbiotically interacts with inverse_of: RO:0008502 ! has epiphyte [Typedef] id: RO:0008502 name: has epiphyte def: "inverse of epiphyte of" [] subset: RO:0002259 is_a: RO:0002440 ! symbiotically interacts with [Typedef] id: RO:0008503 name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: RO:0002444 ! parasite of inverse_of: RO:0008504 ! kleptoparasitized by [Typedef] id: RO:0008504 name: kleptoparasitized by def: "inverse of kleptoparasite of" [] subset: RO:0002259 is_a: RO:0002445 ! parasitized by [Typedef] id: RO:0008505 name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] domain: OBI:0100026 ! organism range: OBI:0100026 ! organism is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0008506 name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] domain: OBI:0100026 ! organism range: OBI:0100026 ! organism is_symmetric: true is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0008507 name: lays eggs on def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] is_a: RO:0002618 ! visits inverse_of: RO:0008508 ! has eggs laid on by [Typedef] id: RO:0008508 name: has eggs laid on by def: "inverse of lays eggs on" [] is_a: RO:0002619 ! visited by [Typedef] id: RO:0008509 name: has roost def: "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x." [] comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. subset: ro-eco property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2908-3327 property_value: http://purl.org/dc/terms/date "2023-01-18T14:28:21Z" xsd:dateTime property_value: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string domain: OBI:0100026 ! organism range: ENVO:01000739 ! habitat is_a: RO:0002303 ! has habitat [Typedef] id: RO:0009001 name: has substance added def: "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." [] property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity [Typedef] id: RO:0009002 name: has substance removed def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity [Typedef] id: RO:0009003 name: immersed in def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity [Typedef] id: RO:0009004 name: has consumer def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 domain: BFO:0000040 ! material entity range: OBI:0100026 ! organism [Typedef] id: RO:0009005 name: has primary substance added def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] property_value: IAO:0000112 "bread 'has primary substance added' some 'flour'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 is_a: RO:0009001 ! has substance added [Typedef] id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 ! realizable entity range: BFO:0000015 ! process holds_over_chain: BFO:0000054 RO:0002404 is_a: RO:0002410 ! causally related to [Typedef] id: RO:0010001 name: generically depends on def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] synonym: "g-depends on" EXACT [] property_value: IAO:0000112 "Genetic information generically depend on molecules of DNA." xsd:string property_value: IAO:0000112 "The novel *War and Peace* generically depends on this copy of the novel." xsd:string property_value: IAO:0000112 "The pattern shared by chess boards generically depends on any chess board." xsd:string property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string property_value: IAO:0000119 "[072-ISO]" xsd:string domain: BFO:0000031 ! generically dependent continuant range: BFO:0000004 ! independent continuant holds_over_chain: RO:0000052 RO:0000058 inverse_of: RO:0010002 ! is carrier of [Typedef] id: RO:0010002 name: is carrier of def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] property_value: IAO:0000112 "Molecules of DNA are carriers of genetic information." xsd:string property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string property_value: IAO:0000119 "[072-ISO]" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000031 ! generically dependent continuant holds_over_chain: RO:0000059 RO:0000053 [Typedef] id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences [Typedef] id: RO:0011003 name: regulates quantity of def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences [Typedef] id: RO:0011004 name: indirectly regulates activity of def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011002 ! regulates activity of [Typedef] id: RO:0011007 name: decreases by repression quantity of def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011023 ! indirectly negatively regulates quantity of [Typedef] id: RO:0011008 name: increases by expression quantity of def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011024 ! indirectly positively regulates quantity of [Typedef] id: RO:0011009 name: directly positively regulates quantity of def: "The entity A has an activity that directly positively regulates the quantity of B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011021 ! directly regulates quantity of [Typedef] id: RO:0011010 name: directly negatively regulates quantity of def: "The entity A has an activity that directly negatively regulates the quantity of B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011021 ! directly regulates quantity of [Typedef] id: RO:0011013 name: indirectly positively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011004 ! indirectly regulates activity of [Typedef] id: RO:0011014 name: destabilizes quantity of def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011010 ! directly negatively regulates quantity of [Typedef] id: RO:0011015 name: stabilizes quantity of def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0011009 ! directly positively regulates quantity of [Typedef] id: RO:0011016 name: indirectly negatively regulates activity of def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000118 "indirectly inhibits" xsd:string is_a: RO:0011004 ! indirectly regulates activity of [Typedef] id: RO:0011021 name: directly regulates quantity of def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011003 ! regulates quantity of [Typedef] id: RO:0011022 name: indirectly regulates quantity of def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011003 ! regulates quantity of [Typedef] id: RO:0011023 name: indirectly negatively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011022 ! indirectly regulates quantity of [Typedef] id: RO:0011024 name: indirectly positively regulates quantity of def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: RO:0011022 ! indirectly regulates quantity of [Typedef] id: RO:0012000 name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] is_a: RO:0000057 ! has participant inverse_of: RO:0012004 ! is small molecule regulator of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:27:26Z [Typedef] id: RO:0012001 name: has small molecule activator def: "a relation between a process and a continuant, in which the process is activated by the small molecule continuant" [] is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012005 ! is small molecule activator of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:37Z [Typedef] id: RO:0012002 name: has small molecule inhibitor def: "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant" [] is_a: RO:0012000 ! has small molecule regulator inverse_of: RO:0012006 ! is small molecule inhibitor of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-04-22T20:28:54Z [Typedef] id: RO:0012003 name: acts on population of def: "p acts on population of c iff c' is a collection, has members of type c, and p has participant c" [] 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 is_a: RO:0000057 ! has participant created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-08T17:21:33Z [Typedef] id: RO:0012004 name: is small molecule regulator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] is_a: RO:0002596 ! capable of regulating created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:17Z [Typedef] id: RO:0012005 name: is small molecule activator of def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_activator_of" xsd:anyURI is_a: RO:0002598 ! capable of positively regulating is_a: RO:0012004 ! is small molecule regulator of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:26Z [Typedef] id: RO:0012006 name: is small molecule inhibitor of def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] property_value: seeAlso "https://wiki.geneontology.org/Is_small_molecule_inhibitor_of" xsd:anyURI is_a: RO:0002597 ! capable of negatively regulating is_a: RO:0012004 ! is small molecule regulator of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-06-24T13:15:35Z [Typedef] id: RO:0012007 name: results in adhesion of def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] is_a: RO:0040036 ! results in changes to anatomical or cellular structure created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2020-08-27T08:13:59Z [Typedef] id: RO:0012008 name: results in fusion of 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 is_a: RO:0002592 ! results in organization of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2021-02-26T07:28:29Z [Typedef] id: RO:0012009 name: constitutively upstream of def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: seeAlso "https://wiki.geneontology.org/Constitutively_upstream_of" xsd:anyURI is_a: RO:0002304 ! causally upstream of, positive effect created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:01:01Z [Typedef] id: RO:0012010 name: removes input for def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: seeAlso "https://wiki.geneontology.org/Removes_input_for" xsd:anyURI is_a: RO:0002305 ! causally upstream of, negative effect created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:06:20Z [Typedef] id: RO:0012011 name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: RO:0002411 ! causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] id: RO:0012012 name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] id: RO:0012013 name: positively regulates in another organism def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology synonym: "positively regulates in other organism" EXACT [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 property_value: RO:0004049 RO:0002010 is_a: RO:0002010 ! regulates in another organism creation_date: 2023-10-12T10:02:28Z [Typedef] id: RO:0012014 name: negatively regulates in another organism def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology synonym: "negatively regulates in other organism" EXACT [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 property_value: RO:0004050 RO:0002010 is_a: RO:0002010 ! regulates in another organism creation_date: 2023-10-12T10:02:42Z [Typedef] id: RO:0013001 name: has synaptic IO in region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in transitive_over: BFO:0000050 ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z [Typedef] id: RO:0013002 name: receives synaptic input in region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region." [] is_a: RO:0002110 ! has postsynaptic terminal in is_a: RO:0013001 ! has synaptic IO in region transitive_over: BFO:0000050 ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:42:23Z [Typedef] id: RO:0013003 name: sends synaptic output to region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region." [] is_a: RO:0002113 ! has presynaptic terminal in is_a: RO:0013001 ! has synaptic IO in region transitive_over: BFO:0000050 ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:45:06Z [Typedef] id: RO:0013004 name: has synaptic IO throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013001 ! has synaptic IO in region created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:52:19Z [Typedef] id: RO:0013005 name: receives synaptic input throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013002 ! receives synaptic input in region is_a: RO:0013004 ! has synaptic IO throughout created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:55:36Z [Typedef] id: RO:0013006 name: sends synaptic output throughout def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." [] is_a: RO:0013003 ! sends synaptic output to region is_a: RO:0013004 ! has synaptic IO throughout created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:57:27Z [Typedef] id: RO:0013007 name: has sensory dendrite in def: "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." [] synonym: "has sensory dendrite location" EXACT [] synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location transitive_over: BFO:0000050 ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z [Typedef] id: RO:0013008 name: receives synaptic input from neuron def: "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." [] is_a: RO:0002103 ! synapsed by inverse_of: RO:0013009 ! sends synaptic output to cell created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:40:18Z [Typedef] id: RO:0013009 name: sends synaptic output to cell def: "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." [] comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. is_a: RO:0002120 ! synapsed to created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2021-05-26T08:41:07Z [Typedef] id: RO:0014001 name: disease has infectious agent def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] is_a: RO:0004019 ! disease has basis in created_by: https://orcid.org/0000-0001-5208-3432 [Typedef] id: RO:0015001 name: has exemplar data def: "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." [] property_value: IAO:0000112 "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" xsd:string property_value: IAO:0000116 "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 property_value: IAO:0000232 "This relation is not meant to capture the relation between occurrents and data." xsd:string inverse_of: RO:0015002 ! exemplar data of transitive_over: RO:0015003 ! subcluster of [Typedef] id: RO:0015002 name: exemplar data of property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 [Typedef] id: RO:0015003 name: subcluster of def: "A relation between a group and another group it is part of but does not fully constitute." [] property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true is_a: BFO:0000050 ! part of [Typedef] id: RO:0015004 name: has characterizing marker set def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] synonym: "has marker gene combination" EXACT [] synonym: "has marker signature set" EXACT [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000112 "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1')." xsd:string property_value: IAO:0000112 "transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3." xsd:string property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string property_value: IAO:0000232 "This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context." xsd:string domain: CL:0000000 ! cell [Typedef] id: RO:0015006 name: different in magnitude relative to def: "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] domain: PATO:0000001 ! quality range: PATO:0000001 ! quality [Typedef] id: RO:0015007 name: increased in magnitude relative to def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. domain: PATO:0000001 ! quality range: PATO:0000001 ! quality is_a: RO:0015006 ! different in magnitude relative to [Typedef] id: RO:0015008 name: decreased in magnitude relative to def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. domain: PATO:0000001 ! quality range: PATO:0000001 ! quality is_a: RO:0015006 ! different in magnitude relative to [Typedef] id: RO:0015009 name: similar in magnitude relative to def: "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] [Typedef] id: RO:0015010 name: has relative magnitude [Typedef] id: RO:0015011 name: has cross section def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [https://orcid.org/0000-0002-6601-2165] comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. [Typedef] id: RO:0015012 name: reciprocal of def: "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e." [https://orcid.org/0000-0002-6601-2165] comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. [Typedef] id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part [Typedef] id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part [Typedef] id: RO:0016001 name: has phenotype or disease property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: RO:0016001 ! has phenotype or disease [Typedef] id: RO:0016004 name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-12-14T20:41:45Z" xsd:dateTime property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: RO:0002215 RO:0002233 creation_date: 2021-11-08T12:00:00Z [Typedef] id: RO:0017003 name: positively correlated with def: "A relation between entities in which one increases or decreases as the other does the same." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 property_value: IAO:0000118 "directly correlated with" xsd:string is_symmetric: true is_a: RO:0002610 ! correlated with [Typedef] id: RO:0017004 name: negatively correlated with def: "A relation between entities in which one increases as the other decreases." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 property_value: IAO:0000118 "inversely correlated with" xsd:string is_symmetric: true is_a: RO:0002610 ! correlated with [Typedef] id: RO:0017005 name: contains measured amount def: "A relation between a container and measurement datum that specifies the actual amount of material in the container." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2999-0103 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-5714-991X property_value: IAO:0000112 "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." xsd:string domain: OBI:0000967 ! container range: COB:0000121 ! measurement datum [Typedef] id: RO:0018001 name: is myristoyltransferase activity def: "Helper relation for OWL definition of RO:0018002 myristoylates" [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4423-4370 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0018002 name: myristoylates def: "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" [] property_value: http://purl.org/dc/terms/conformsTo http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4423-4370 is_a: RO:0002436 ! molecularly interacts with inverse_of: RO:0018003 ! myristoylated by [Typedef] id: RO:0018003 name: myristoylated by def: "inverse of myristoylates" [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4423-4370 [Typedef] id: RO:0018027 name: is agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 is_a: RO:0002450 ! directly positively regulates activity of [Typedef] id: RO:0018028 name: is inverse agonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 is_a: RO:0002449 ! directly negatively regulates activity of [Typedef] id: RO:0018029 name: is antagonist of def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 is_a: RO:0002449 ! directly negatively regulates activity of [Typedef] id: RO:0018030 name: chemical relationship property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical." xsd:string [Typedef] id: RO:0018031 name: is direct conjugate base of def: "A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B." [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816)" xsd:string property_value: RO:0002575 RO:0018033 property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 is_a: RO:0018033 ! is deprotonated form of inverse_of: RO:0018032 ! is direct conjugate acid of [Typedef] id: RO:0018032 name: is direct conjugate acid of def: "A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B." [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361)" xsd:string property_value: RO:0002575 RO:0018034 property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 is_a: RO:0018034 ! is protonated form of [Typedef] id: RO:0018033 name: is deprotonated form of def: "A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B.\n\nThis is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations." [] xref: obo:chebi#is_conjugate_base_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "(E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons." xsd:string property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 is_transitive: true is_a: RO:0018030 ! chemical relationship inverse_of: RO:0018034 ! is protonated form of [Typedef] id: RO:0018034 name: is protonated form of def: "A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B.\n\nThis is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations." [] xref: obo:chebi#is_conjugate_acid_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: IAO:0000112 "(E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons." xsd:string property_value: seeAlso https://github.com/oborel/obo-relations/issues/643 is_transitive: true is_a: RO:0018030 ! chemical relationship [Typedef] id: RO:0018035 name: is matched small molecular pair with def: "A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification.\n\nWhile this is normally called \"matched molecular pair\" in the cheminformatics literaturel, it is labeled as \"matched small molecular pair\" so as to reduce confusion with peptides and other macromolecules, which are also referenced as \"molecules\" in some contexts.\n\nThis relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A.\n\nThis relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C." [] {http://purl.org/dc/terms/source="https://doi.org/10.1021/jm200452d", http://purl.org/dc/terms/source="https://doi.org/10.1002/ddr.21045", http://purl.org/dc/terms/source="https://en.wikipedia.org/wiki/Matched_molecular_pair_analysis"} synonym: "is matched molecular pair with" EXACT [] synonym: "is MMP with" EXACT [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-02-28T18:53:32Z" xsd:dateTime property_value: IAO:0000112 "phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol." xsd:string is_symmetric: true is_a: RO:0018030 ! chemical relationship [Typedef] id: RO:0018036 name: is tautomer of def: "Two chemicals are tautomers if they can be readily interconverted.\n\nThis commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms." [] synonym: "is desmotrope of" EXACT [] xref: obo:chebi#is_tautomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {seeAlso="CHEBI:38707", seeAlso="CHEBI:38709"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship [Typedef] id: RO:0018037 name: is substitutent group from def: "Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization." [] xref: obo:chebi#is_substituent_group_from property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {seeAlso="CHEBI:30795", seeAlso="CHEBI:58957"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship [Typedef] id: RO:0018038 name: has functional parent def: "Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. \n\nFor example, the relationship between a salt and a freebased compound is a \"has functional parent\" relationship." [] xref: obo:chebi#has_functional_parent property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {seeAlso="CHEBI:50851", seeAlso="CHEBI:50854"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship [Typedef] id: RO:0018039 name: is enantiomer of def: "Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center.\n\nA chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers)." [] synonym: "is optical isomer of" EXACT [] xref: obo:chebi#is_enantiomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", seeAlso="CHEBI:31472"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship [Typedef] id: RO:0018040 name: has parent hydride def: "Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B." [] xref: obo:chebi#has_parent_hydride property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {seeAlso="CHEBI:39106", seeAlso="CHEBI:52083"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship [Typedef] id: RO:0019000 name: regulates characteristic def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: RO:0002211 RO:0019000 is_a: RO:0002410 ! causally related to [Typedef] id: RO:0019001 name: positively regulates characteristic def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: RO:0002213 RO:0019001 is_a: RO:0019000 ! regulates characteristic [Typedef] id: RO:0019002 name: negatively regulates characteristic def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: RO:0002212 RO:0019001 holds_over_chain: RO:0002213 RO:0019002 is_a: RO:0019000 ! regulates characteristic [Typedef] id: RO:0019501 name: confers susceptibility to condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] is_a: RO:0003304 ! contributes to condition created_by: https://orcid.org/0000-0002-4142-7153 [Typedef] id: RO:0020101 name: vessel supplies blood to def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string domain: UBERON:0001981 ! blood vessel range: UBERON:0000061 ! anatomical structure is_a: RO:0002178 ! supplies [Typedef] id: RO:0020102 name: vessel drains blood from def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string domain: UBERON:0001981 ! blood vessel range: UBERON:0000061 ! anatomical structure is_a: RO:0002179 ! drains [Typedef] id: RO:0020103 name: directly supplies and drains def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string domain: UBERON:0001982 ! capillary range: UBERON:0000061 ! anatomical structure is_a: RO:0002178 ! supplies is_a: RO:0002179 ! drains [Typedef] id: RO:0040035 name: disease relationship def: "This relation groups relations between diseases and any other kind of entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z [Typedef] id: RO:0040036 name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] is_a: RO:0000057 ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z [Typedef] id: RO:HOM0000000 name: in similarity relationship with def: "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000000] synonym: "correspondence" RELATED [http://dx.doi.org/10.1007/BF02814479] synonym: "resemblance" RELATED [] synonym: "sameness" EXACT [] synonym: "similar to" EXACT [] xref: ECO:0000041 xref: SO:similar_to property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: IAO:0000116 "TODO: Add homeomorphy axiom" xsd:string property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: seeAlso HOM:0000000 is_symmetric: true [Typedef] id: RO:HOM0000001 name: in homology relationship with def: "Similarity that results from common evolutionary origin." [http://dx.doi.org/10.1002/bies.950180611, http://dx.doi.org/10.1002/jmor.1051730307, http://dx.doi.org/10.1007/BF02814480, http://purl.obolibrary.org/obo/HOM_0000001] comment: This broad definition encompasses all the working definitions proposed so far in the literature. synonym: "homologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000001 is_symmetric: true is_a: RO:0002158 ! shares ancestor with is_a: RO:HOM0000000 ! in similarity relationship with disjoint_from: RO:HOM0000002 ! in homoplasy relationship with [Typedef] id: RO:HOM0000002 name: in homoplasy relationship with def: "Similarity that results from independent evolution." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000002] synonym: "analogy" RELATED [] synonym: "homoplasous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000002 is_symmetric: true is_a: RO:HOM0000000 ! in similarity relationship with [Typedef] id: RO:HOM0000003 name: in homocracy relationship with def: "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/s00427-003-0301-4, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000003] comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. synonym: "homocracous to" EXACT [] xref: ECO:0000075 property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000003 is_symmetric: true is_a: RO:0002320 ! evolutionarily related to is_a: RO:HOM0000000 ! in similarity relationship with [Typedef] id: RO:HOM0000004 name: in convergence relationship with def: "Homoplasy that involves different underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000004] comment: Convergence usually implies a notion of adaptation. synonym: "analogy" RELATED [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000004 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with [Typedef] id: RO:HOM0000005 name: in parallelism relationship with def: "Homoplasy that involves homologous underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000005] comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. synonym: "parallel evolution" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000005 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with [Typedef] id: RO:HOM0000006 name: in structural homology relationship with def: "Homology that is defined by similarity with regard to selected structural parameters." [http://dx.doi.org/10.1016/j.jhevol.2006.11.014, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000006, ISBN:0123195837] synonym: "idealistic homology" RELATED [] synonym: "structural homologous to" EXACT [] xref: ECO:0000071 xref: MI:2163 property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000006 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with [Typedef] id: RO:HOM0000007 name: in historical homology relationship with def: "Homology that is defined by common descent." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://purl.obolibrary.org/obo/HOM_0000007, ISBN:0123195837] synonym: "cladistic homology" EXACT [] synonym: "historical homologous to" EXACT [] synonym: "homology" BROAD [] synonym: "phylogenetic homology" EXACT [] synonym: "taxic homology" EXACT [] synonym: "true homology" RELATED [] xref: ECO:0000080 xref: RO_proposed_relation:homologous_to xref: SO:0000330 xref: SO:0000853 xref: SO:0000857 xref: SO:homologous_to xref: TAO:homologous_to property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000007 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with [Typedef] id: RO:HOM0000008 name: in biological homology relationship with def: "Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000008] comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. synonym: "biological homologous to" EXACT [] synonym: "transformational homology" RELATED [] xref: ECO:0000067 property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000008 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with [Typedef] id: RO:HOM0000009 name: in reversal relationship with def: "Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000009] synonym: "atavism" EXACT [] synonym: "reversion" RELATED [] synonym: "rudiment" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000009 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with [Typedef] id: RO:HOM0000010 name: in syntenic homology relationship with def: "Structural homology that is detected by similarity in content and organization between chromosomes." [http://purl.obolibrary.org/obo/HOM_0000010, MeSH:Synteny] synonym: "syntenic homologous to" EXACT [] synonym: "synteny" RELATED [] xref: MeSH:Synteny xref: SO:0000860 xref: SO:0005858 property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000010 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with [Typedef] id: RO:HOM0000011 name: in paralogy relationship with def: "Historical homology that involves genes that diverged after a duplication event." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000011, http://www.ncbi.nlm.nih.gov/pubmed/5449325] synonym: "paralogous to" EXACT [] xref: SO:0000854 xref: SO:0000859 xref: SO:paralogous_to property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000011 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with disjoint_from: RO:HOM0000017 ! in orthology relationship with [Typedef] id: RO:HOM0000012 name: in syntenic paralogy relationship with def: "Paralogy that involves sets of syntenic blocks." [DOI:10.1002/1097-010X(20001215)288\:4<345\:\:AID-JEZ7>3.0.CO;2-Y, http://dx.doi.org/10.1186/1471-213X-7-100, http://purl.obolibrary.org/obo/HOM_0000012] synonym: "duplicon" RELATED [] synonym: "paralogon" RELATED [] synonym: "syntenic paralogous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000012 is_symmetric: true is_a: RO:HOM0000010 ! in syntenic homology relationship with is_a: RO:HOM0000011 ! in paralogy relationship with [Typedef] id: RO:HOM0000013 name: in syntenic orthology relationship with def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013] synonym: "syntenic orthologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000013 is_symmetric: true is_a: RO:HOM0000010 ! in syntenic homology relationship with [Typedef] id: RO:HOM0000014 name: in partial homology relationship with def: "Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous." [http://purl.obolibrary.org/obo/HOM_0000014, ISBN:0123195837, ISBN:978-0471984931] synonym: "fractional homology" EXACT [] synonym: "mixed homology" RELATED [] synonym: "modular homology" RELATED [] synonym: "partial correspondence" RELATED [] synonym: "partial homologous to" EXACT [] synonym: "percent homology" RELATED [] synonym: "segmental homology" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000014 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with [Typedef] id: RO:HOM0000015 name: in protein structural homology relationship with def: "Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence." [http://dx.doi.org/10.1016/0022-2836(76)90195-9, http://purl.obolibrary.org/obo/HOM_0000015] synonym: "protein structural homologous to" EXACT [] xref: MeSH:Structural_Homology\,_Protein property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000015 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with [Typedef] id: RO:HOM0000016 name: in non functional homology relationship with def: "Structural homology that involves a pseudogenic feature and its functional ancestor." [http://purl.obolibrary.org/obo/HOM_0000016, SO:non_functional_homolog_of] synonym: "non functional homologous to" EXACT [] synonym: "pseudogene" BROAD [] xref: SO:non_functional_homolog_of property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000016 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with disjoint_from: RO:HOM0000062 ! in equivalogy relationship with [Typedef] id: RO:HOM0000017 name: in orthology relationship with def: "Historical homology that involves genes that diverged after a speciation event." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000017, http://www.ncbi.nlm.nih.gov/pubmed/5449325] comment: The term is sometimes also used for anatomical structures. synonym: "orthologous to" EXACT [] xref: ECO:00000060 xref: SO:0000855 xref: SO:0000858 xref: SO:orthologous_to property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000017 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with [Typedef] id: RO:HOM0000018 name: in xenology relationship with def: "Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000018] comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). synonym: "xenologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000018 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with [Typedef] id: RO:HOM0000019 name: in 1 to 1 homology relationship with def: "Historical homology that involves two members sharing no other homologs in the lineages considered." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000019] synonym: "1 to 1 homologous to" EXACT [] synonym: "1:1 homology" EXACT [] synonym: "one-to-one homology" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000019 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with [Typedef] id: RO:HOM0000020 name: in 1 to 1 orthology relationship with def: "Orthology that involves two genes that did not experience any duplication after the speciation event that created them." [http://dx.doi.org/10.1007/BF02814484, http://purl.obolibrary.org/obo/HOM_0000020, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "1 to 1 orthologous to" EXACT [] synonym: "1:1 orthology" EXACT [] synonym: "one-to-one orthology" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000020 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with [Typedef] id: RO:HOM0000022 name: in ohnology relationship with def: "Paralogy that results from a whole genome duplication event." [http://dx.doi.org/10.1038/75560, http://purl.obolibrary.org/obo/HOM_0000022] synonym: "homoeology" RELATED [] synonym: "ohnologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000022 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with [Typedef] id: RO:HOM0000023 name: in in-paralogy relationship with def: "Paralogy that results from a lineage-specific duplication subsequent to a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000023] synonym: "in-paralogous to" EXACT [] synonym: "inparalogy" EXACT [] synonym: "symparalogy" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000023 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with disjoint_from: RO:HOM0000024 ! in out-paralogy relationship with [Typedef] id: RO:HOM0000024 name: in out-paralogy relationship with def: "Paralogy that results from a duplication preceding a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000024] synonym: "alloparalogy" EXACT [] synonym: "out-paralogous to" EXACT [] synonym: "outparalogy" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000024 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with [Typedef] id: RO:HOM0000025 name: in pro-orthology relationship with def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025] synonym: "pro-orthologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000025 is_symmetric: true is_a: RO:HOM0000034 ! in 1 to many orthology relationship with [Typedef] id: RO:HOM0000026 name: in semi-orthology relationship with def: "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000026] comment: The converse of pro-orthologous. synonym: "semi-orthologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000026 is_symmetric: true is_a: RO:HOM0000034 ! in 1 to many orthology relationship with [Typedef] id: RO:HOM0000027 name: in serial homology relationship with def: "Iterative homology that involves structures arranged along the main body axis." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000027] synonym: "homonomy" RELATED [] synonym: "serial homologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000027 is_symmetric: true is_a: RO:HOM0000066 ! in iterative homology relationship with [Typedef] id: RO:HOM0000028 name: in heterochronous homology relationship with def: "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [http://purl.obolibrary.org/obo/HOM_0000028, ISBN:978-0674639416] synonym: "heterochronous homologous to" EXACT [] synonym: "heterochrony" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000028 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with [Typedef] id: RO:HOM0000029 name: in paedomorphorsis relationship with def: "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000029, ISBN:978-0674639416] synonym: "juvenification" EXACT [] synonym: "pedomorphosis" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000029 is_symmetric: true is_a: RO:HOM0000028 ! in heterochronous homology relationship with disjoint_from: RO:HOM0000030 ! in peramorphosis relationship with [Typedef] id: RO:HOM0000030 name: in peramorphosis relationship with def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000030 is_symmetric: true is_a: RO:HOM0000028 ! in heterochronous homology relationship with [Typedef] id: RO:HOM0000031 name: in progenesis relationship with def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000031 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with [Typedef] id: RO:HOM0000032 name: in neoteny relationship with def: "Paedomorphosis that is produced by a retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny, http://purl.obolibrary.org/obo/HOM_0000032, ISBN:978-0674639416] synonym: "juvenilization" EXACT [] synonym: "neotenous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000032 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with [Typedef] id: RO:HOM0000033 name: in mimicry relationship with def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://en.wikipedia.org/wiki/Mimicry, http://purl.obolibrary.org/obo/HOM_0000033] synonym: "mimicrous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000033 is_symmetric: true is_a: RO:HOM0000004 ! in convergence relationship with [Typedef] id: RO:HOM0000034 name: in 1 to many orthology relationship with def: "Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000034, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "1 to many orthologous to" EXACT [] synonym: "1:many orthology" EXACT [] synonym: "co-orthology" RELATED [] synonym: "many to 1 orthology" RELATED [] synonym: "one-to-many orthology" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000034 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with is_a: RO:HOM0000037 ! in 1 to many homology relationship with [Typedef] id: RO:HOM0000036 name: in many to many homology relationship with def: "Historical homology that involves two members of a larger set of homologs." [http://dx.doi.org/10.1093/molbev/msp002, http://purl.obolibrary.org/obo/HOM_0000036] synonym: "many to many homologous to" EXACT [] synonym: "many-to-many homology" EXACT [] synonym: "many:many homology " EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000036 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with [Typedef] id: RO:HOM0000037 name: in 1 to many homology relationship with def: "Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000037] synonym: "1 to many homologous to" EXACT [] synonym: "1:many homology" RELATED [] synonym: "one-to-many homology" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000037 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with [Typedef] id: RO:HOM0000042 name: in apomorphy relationship with def: "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group." [http://purl.obolibrary.org/obo/HOM_0000042, ISBN:978-0252068140] synonym: "apomorphous to" EXACT [] synonym: "synapomorphy" RELATED [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000042 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with disjoint_from: RO:HOM0000043 ! in plesiomorphy relationship with [Typedef] id: RO:HOM0000043 name: in plesiomorphy relationship with def: "Historical homology that is based on distant shared ancestry." [http://purl.obolibrary.org/obo/HOM_0000043, ISBN:978-0252068140] comment: This term is usually contrasted to apomorphy. synonym: "plesiomorphous to" EXACT [] synonym: "symplesiomorphy" RELATED [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000043 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with [Typedef] id: RO:HOM0000044 name: in deep homology relationship with def: "Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1038/nature07891, http://purl.obolibrary.org/obo/HOM_0000044] comment: Used for structures in distantly related taxa. synonym: "deep genetic homology" EXACT [] synonym: "deep homologous to" EXACT [] synonym: "generative homology" RELATED [] synonym: "homoiology" RELATED [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000044 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with is_a: RO:HOM0000005 ! in parallelism relationship with [Typedef] id: RO:HOM0000045 name: in hemiplasy relationship with def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045] synonym: "hemiplasous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000045 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with [Typedef] id: RO:HOM0000046 name: in gametology relationship with def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898] synonym: "gametologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000046 is_symmetric: true is_a: RO:HOM0000047 ! in chromosomal homology relationship with [Typedef] id: RO:HOM0000047 name: in chromosomal homology relationship with def: "Historical homology that involves the chromosomes able to pair (synapse) during meiosis." [http://purl.obolibrary.org/obo/HOM_0000047, ISBN:0195307615] synonym: "chromosomal homologous to" EXACT [] xref: MeSH:Chromosome_Pairing property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000047 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with [Typedef] id: RO:HOM0000048 name: in many to many orthology relationship with def: "Orthology that involves two genes that experienced duplications more recent than the species split that created them." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000048, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "co-orthology" RELATED [] synonym: "many to many orthologous to" EXACT [] synonym: "many-to-many orthology" EXACT [] synonym: "many:many orthology" EXACT [] synonym: "trans-homology" RELATED [] synonym: "trans-orthology" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000048 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with is_a: RO:HOM0000036 ! in many to many homology relationship with [Typedef] id: RO:HOM0000049 name: in within-species paralogy relationship with def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "within-species paralogous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000049 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with disjoint_from: RO:HOM0000050 ! in between-species paralogy relationship with [Typedef] id: RO:HOM0000050 name: in between-species paralogy relationship with def: "Paralogy that involves genes from different species." [http://purl.obolibrary.org/obo/HOM_0000050, http://www.ensembl.org/info/docs/compara/homology_method.html] comment: The genes have diverged before a speciation event. synonym: "between-species paralogous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000050 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with [Typedef] id: RO:HOM0000051 name: in postdisplacement relationship with def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051] synonym: "post-displacement" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000051 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with [Typedef] id: RO:HOM0000052 name: in hypermorphosis relationship with def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000052 is_symmetric: true is_a: RO:HOM0000030 ! in peramorphosis relationship with [Typedef] id: RO:HOM0000053 name: in synology relationship with def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053] synonym: "synologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000053 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with [Typedef] id: RO:HOM0000054 name: in isoorthology relationship with def: "Orthology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000054] synonym: "isoorthologous to" EXACT [] xref: ECO:0000080 property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000054 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with is_a: RO:HOM0000062 ! in equivalogy relationship with [Typedef] id: RO:HOM0000055 name: in tandem paralogy relationship with def: "Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000055, ISBN:978-0878932665] synonym: "iterative paralogy" RELATED [] synonym: "serial paralogy" RELATED [] synonym: "tandem paralogous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000055 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with [Typedef] id: RO:HOM0000057 name: in latent homology relationship with def: "Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character)." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000057, ISBN:0199141118] comment: Used for structures in closely related taxa. synonym: "apomorphic tendency" EXACT [] synonym: "cryptic homology" EXACT [] synonym: "homoiology" RELATED [] synonym: "homoplastic tendency" RELATED [] synonym: "latent homologous to" EXACT [] synonym: "re-awakening" RELATED [] synonym: "underlying synapomorphy" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000057 is_symmetric: true is_a: RO:HOM0000005 ! in parallelism relationship with is_a: RO:HOM0000058 ! in syngeny relationship with [Typedef] id: RO:HOM0000058 name: in syngeny relationship with def: "Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual." [DOI:10.1002/1521-1878(200009)22\:9<846\:\:AID-BIES10>3.0.CO;2-R, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000058] comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. synonym: "generative homology" EXACT [] synonym: "syngenous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000058 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with [Typedef] id: RO:HOM0000060 name: in apparent orthology relationship with def: "Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000060, http://www.ensembl.org/info/docs/compara/homology_method.html] comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. synonym: "1:1 paralogy" EXACT [] synonym: "apparent 1:1 orthology" EXACT [] synonym: "apparent orthologous to" EXACT [] synonym: "pseudoorthology" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000060 is_symmetric: true is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with is_a: RO:HOM0000050 ! in between-species paralogy relationship with [Typedef] id: RO:HOM0000061 name: in pseudoparalogy relationship with def: "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000061] comment: These genes may come out as paralogs in a single-genome analysis. synonym: "pseudoparalogous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000061 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with [Typedef] id: RO:HOM0000062 name: in equivalogy relationship with def: "Historical homology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1093/nar/gkl1043, http://purl.obolibrary.org/obo/HOM_0000062] comment: This may include examples of orthology, paralogy and xenology. synonym: "equivalogous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000062 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with is_a: RO:HOM0000065 ! in functional equivalence relationship with [Typedef] id: RO:HOM0000063 name: in interology relationship with def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063] synonym: "interologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000063 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with [Typedef] id: RO:HOM0000065 name: in functional equivalence relationship with def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065] synonym: "functional similarity" RELATED [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000065 is_symmetric: true is_a: RO:HOM0000000 ! in similarity relationship with [Typedef] id: RO:HOM0000066 name: in iterative homology relationship with def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066] synonym: "iterative homologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000066 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with [Typedef] id: RO:HOM0000068 name: in paraxenology relationship with def: "Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome." [http://purl.obolibrary.org/obo/HOM_0000068, http://www.ncbi.nlm.nih.gov/pubmed/3065587] synonym: "duplicate xenology" EXACT [] synonym: "multiple xenology" EXACT [] synonym: "paraxenologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000068 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with [Typedef] id: RO:HOM0000069 name: in plerology relationship with def: "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution." [http://purl.obolibrary.org/obo/HOM_0000069, http://www.ncbi.nlm.nih.gov/pubmed/3065587] comment: This phenomenon is usually due to gene conversion process. synonym: "plerologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000069 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with [Typedef] id: RO:HOM0000071 name: in homotopy relationship with def: "Structural homology that involves structures with the same or similar relative positions." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/BF02814485, http://purl.obolibrary.org/obo/HOM_0000071, ISBN:0123195837] comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. synonym: "homotopous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000071 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with disjoint_from: RO:HOM0000072 ! in homeosis relationship with [Typedef] id: RO:HOM0000072 name: in homeosis relationship with def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072] synonym: "heterotopy" RELATED [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000072 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with [Typedef] id: RO:HOM0000073 name: in homoeology relationship with def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pnas.0505156102, http://purl.obolibrary.org/obo/HOM_0000073] comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. synonym: "homoeologous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000073 is_symmetric: true is_a: RO:HOM0000022 ! in ohnology relationship with is_a: RO:HOM0000053 ! in synology relationship with [Typedef] id: RO:HOM0000074 name: in paramorphism relationship with def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074] synonym: "axis paramorphism" RELATED [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000074 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with is_a: RO:HOM0000066 ! in iterative homology relationship with [Typedef] id: RO:HOM0000075 name: in regulogy relationship with def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075] synonym: "regulogous to" EXACT [] property_value: http://purl.org/dc/terms/creator http://bgee.unil.ch property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000075 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with