ro.obo

format-version: 1.2
data-version: releases/2025-12-17
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: human_subset ""
subsetdef: mouse_subset ""
subsetdef: pheno_slim ""
subsetdef: ro-eco ""
subsetdef: RO:0002259 ""
subsetdef: uberon_slim ""
subsetdef: upper_level ""
subsetdef: vertebrate_core ""
idspace: cito http://purl.org/spar/cito/ 
idspace: dc http://purl.org/dc/elements/1.1/ 
idspace: foaf http://xmlns.com/foaf/0.1/ 
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# 
idspace: skos http://www.w3.org/2004/02/skos/core# 
idspace: swrl http://www.w3.org/2003/11/swrl# 
idspace: swrla http://swrl.stanford.edu/ontologies/3.3/swrla.owl# 
idspace: swrlb http://www.w3.org/2003/11/swrlb# 
idspace: terms http://purl.org/dc/terms/ 
ontology: ro
property_value: foaf:homepage " https://github.com/oborel/obo-relations/" xsd:anyURI
property_value: owl:versionInfo "2025-12-17" xsd:string
property_value: 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: terms:license https://creativecommons.org/publicdomain/zero/1.0/
property_value: terms:title "OBO Relations Ontology" 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 ! specifically dependent continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant

[Term]
id: BFO:0000006
name: spatial region
is_a: BFO:0000141 ! immaterial entity

[Term]
id: BFO:0000015
name: process
def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" []
comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
is_a: BFO:0000003 ! occurrent
relationship: RO:0002214 BFO:0000015 {all_only="true"} ! has prototype process

[Term]
id: BFO:0000016
name: disposition
is_a: BFO:0000017 ! realizable entity
disjoint_from: BFO:0000023 ! role

[Term]
id: BFO:0000017
name: realizable 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 ! specifically dependent continuant
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 ! specifically dependent continuant
relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality

[Term]
id: BFO:0000020
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 specifically dependent continuant

[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
property_value: IAO:0000116 "Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." xsd:string

[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]
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).
xref: CALOHA:TS-2035
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
property_value: IAO:0000116 "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc." xsd:string
property_value: IAO:0000116 "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism." xsd:string

[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: FMA:84649
xref: MESH:D011984
xref: WBbt:0005759
is_a: CL:0000540 ! neuron
property_value: RO:0002175 NCBITaxon:9606

[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: FMA:54527
xref: VHOG:0001483
xref: WBbt:0003679
is_a: CL:0000000 ! cell
property_value: RO:0002175 NCBITaxon:9606

[Term]
id: COB:0000022
name: organism
def: "A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome" []
is_a: UBERON:0000465 ! material anatomical entity
property_value: IAO:0000116 "'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'." xsd:string
property_value: IAO:0000116 "Includes virus - we will later have a class for cellular organisms." xsd:string

[Term]
id: COB:0000026
name: processed material entity
def: "A material entity processed by human activity with an intent to produce it." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000116 "In the COB 2024 workshop there was much disagreement about this label." xsd:string

[Term]
id: COB:0000035
name: completely executed planned process
is_a: BFO:0000015 ! process

[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: COB:0001300
name: device
def: "A processed material entity which is designed to be capable of a process." []
is_a: COB:0000026 ! processed material entity

[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: 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 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.
synonym: "molecular function" EXACT []
is_a: BFO:0000015 ! process
property_value: IAO:0000116 "This is the same as GO molecular function" xsd:string

[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-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-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-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-9766227 "MDM2 mediates CDH1 ubiquitination"
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"
xref: Reactome:R-HSA-9833155 "Ubiquitination of STAT2"
xref: Reactome:R-HSA-9833973 "ISGylation of PKR"
xref: Reactome:R-HSA-9834070 "PRKN ubiquitinates MOM substrates"
xref: Reactome:R-HSA-9861563 "CTLH E3 ligase ubiquitinates LDHA"
xref: Reactome:R-HSA-9861640 "CTLH E3 ligase ubiquitinates PKM-1"
xref: Reactome:R-HSA-9929350 "Ubiquitination of CD274 by BTRC-SCF E3-ligase complex"
xref: Reactome:R-HSA-9934753 "CBLL1 ubiquitinates CDH1"
xref: Reactome:R-HSA-9948301 "ZNF598 K63 polyubiquitinates RPS10 (eS10) and RPS20 (uS10) of the 40S ribosomal subunit"
xref: Reactome:R-HSA-9954721 "NEDD8-K699-CUL2:ELOB:ELOC:RBX1:KLHDC10 K48 polyubiquitinates alanine-tailed nascent peptide"
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0005634
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

[Term]
id: GO:0008150
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]
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended 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
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:0000078
name: curation status specification
def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." []
property_value: IAO:0000111 "curation status specification" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string
property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string
property_value: IAO:0000119 "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>" xsd:string
property_value: IAO:0000119 "OBI_0000266" xsd:string

[Term]
id: OBI:0000070
name: assay
def: "A planned process that has the objective to produce information about a material entity (the evaluant) by examining it." []
is_a: COB:0000035 ! completely executed planned process
property_value: IAO:0000111 "assay" xsd:string
property_value: IAO:0000112 "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house." xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000116 "12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation." xsd:string
property_value: IAO:0000116 "Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'.  https://github.com/obi-ontology/obi/issues/1683." xsd:string
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string
property_value: IAO:0000118 "measuring" xsd:string
property_value: IAO:0000118 "scientific observation" xsd:string
property_value: IAO:0000119 "OBI branch derived" xsd:string

[Term]
id: OBI:0000967
name: container
def: "A device that can be used to restrict the location of material entities over time" []
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: 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 ! specifically dependent continuant

[Term]
id: PATO:0000402
name: branched
def: "A branchiness quality inhering in a bearer by virtue of the bearer's having branches." [WordNet:WordNet]
synonym: "ramified" EXACT []
synonym: "ramiform" EXACT []
is_a: PATO:0000001 ! quality
property_value: RO:0002604 PATO:0000414

[Term]
id: PATO:0001199
name: linear
def: "A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel." [ISBN:0881923214]
is_a: PATO:0000001 ! quality

[Term]
id: PATO:0001470
name: ratio
def: "A quality inhering in a bearer by virtue of the bearer's magnitude in proportion to the magnitude of another entity." [] {terms:contributor="https://orcid.org/0000-0001-8314-2140"}
comment: Examples: height to weight; brain size to body size; root to shoot ratio; urinary sodium to potassium ratio. waist-hip ratio. {terms:contributor="https://orcid.org/0000-0001-8314-2140"}
synonym: "proportion" EXACT []
synonym: "proportionality" EXACT []
synonym: "proportionality to" EXACT []
synonym: "quotient" EXACT []
synonym: "rate" RELATED []
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: 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: 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
property_value: terms:creator https://orcid.org/0000-0002-6601-2165
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: human_reference_atlas
subset: human_subset
subset: mouse_subset
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: FAO:0000001
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]
subset: human_subset
subset: mouse_subset
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: human_subset
subset: mouse_subset
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: human_subset
subset: mouse_subset
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: human_subset
subset: mouse_subset
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: human_subset
subset: mouse_subset
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: human_subset
subset: mouse_subset
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: human_subset
subset: mouse_subset
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
def: "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" []
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_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: 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
property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
holds_over_chain: BFO:0000050 BFO:0000062
holds_over_chain: RO:0002091 BFO:0000062
holds_over_chain: RO:0002092 BFO:0000062
is_transitive: true
is_a: RO:0002086 ! ends after
inverse_of: BFO:0000063 ! precedes

[Typedef]
id: BFO:0000063
name: precedes
def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: IAO:0000111 "precedes" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
holds_over_chain: BFO:0000050 BFO:0000063
holds_over_chain: RO:0002092 BFO:0000063
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: BFO:0000066
name: occurs in
def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000111 "occurs in" xsd:string
property_value: IAO:0000118 "occurs_in" xsd:string
property_value: IAO:0000118 "unfolds in" xsd:string
property_value: IAO:0000118 "unfolds_in" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI
domain: BFO:0000003 ! occurrent
range: BFO:0000004 ! independent continuant
holds_over_chain: BFO:0000050 BFO:0000066
inverse_of: BFO:0000067 ! contains process
transitive_over: BFO:0000050 ! part of

[Typedef]
id: BFO:0000067
name: contains process
def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
property_value: IAO:0000111 "site of" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Typedef]
id: CL:4030045
name: lacks_part
expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" []

[Typedef]
id: CL:4030046
name: lacks_plasma_membrane_part
expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" []

[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: ENVO:02000200
name: has increased levels of
def: "A has part relationship between a whole and a part, where the number of parts present in the whole is higher than in comparable entities." []
comment: This relation is present in ENVO to support compositional classes such as "X-enriched soil". These will later be formalized, and a different relation from RO may be chosen.
property_value: seeAlso https://github.com/EnvironmentOntology/envo/issues/1380
is_a: RO:0002180 ! has component

[Typedef]
id: RO:0000052
name: characteristic of
def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." []
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
property_value: IAO:0000111 "inheres in" xsd:string
property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string
property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string
property_value: IAO:0000118 "inheres_in" xsd:string
property_value: RO:0001900 RO:0001901
is_functional: true
is_a: RO:0002314 ! characteristic of part of
inverse_of: RO:0000053 ! has characteristic

[Typedef]
id: RO:0000053
name: has characteristic
def: "Inverse of characteristic_of" []
property_value: IAO:0000111 "bearer of" xsd:string
property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string
property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string
property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "bearer_of" xsd:string
property_value: IAO:0000118 "is bearer of" xsd:string
property_value: RO:0001900 RO:0001901
range: BFO:0000020 ! specifically dependent continuant
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: 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
property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string
domain: BFO:0000003 ! occurrent
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 or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes." []
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
inverse_of: RO:0000059 ! concretizes

[Typedef]
id: RO:0000059
name: concretizes
def: "A relationship between a specifically dependent continuant or process 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 or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes 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
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: 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: 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: 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: 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
property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string
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: 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
def: "relation between an anatomical structure and a neuron projection bundle that has synaptic terminals in the structure." []
property_value: 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
transitive_over: RO:0002380 ! branching part of

[Typedef]
id: RO:0002006
name: has synaptic terminal of
property_value: 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: IAO:0000117 https://orcid.org/0000-0002-7073-9172
property_value: 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
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: foaf:image
range: foaf: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 https://orcid.org/0000-0002-7073-9172
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 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 https://orcid.org/0000-0002-7073-9172
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 https://orcid.org/0000-0002-7073-9172
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 https://orcid.org/0000-0002-7073-9172
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 https://orcid.org/0000-0002-7073-9172
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 https://orcid.org/0000-0002-7073-9172
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 https://orcid.org/0000-0002-7073-9172
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 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 https://orcid.org/0000-0002-7073-9172
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 https://orcid.org/0000-0002-7073-9172
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 https://orcid.org/0000-0002-7073-9172
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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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
synonym: "life cycle stage of" NARROW []
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: COB:0000022 ! organism
holds_over_chain: RO:0002005 RO:0002162
holds_over_chain: RO:0002131 RO:0002162
holds_over_chain: RO:0002134 RO:0002162
holds_over_chain: RO:0002150 RO:0002162
holds_over_chain: RO:0002170 RO:0002162
holds_over_chain: RO:0002176 RO:0002162
holds_over_chain: RO:0002206 RO:0002162
holds_over_chain: RO:0002211 RO:0002162
holds_over_chain: RO:0002214 RO:0002162
holds_over_chain: RO:0002215 RO:0002162
holds_over_chain: RO:0002254 RO:0002162
holds_over_chain: RO:0002256 RO:0002162
holds_over_chain: RO:0002295 RO:0002162
holds_over_chain: RO:0002387 RO:0002162
holds_over_chain: RO:0002490 RO:0002162
holds_over_chain: RO:0003000 RO:0002162
holds_over_chain: RO:0003001 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: 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
property_value: terms:source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI
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 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 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 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 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: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
property_value: terms:contributor https://orcid.org/0000-0001-9625-1899
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:0002254
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: 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: COB:0000022 ! 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: RO:0004049 RO:0002411
property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect
property_value: terms:creator https://orcid.org/0000-0002-6601-2165
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: RO:0004050 RO:0002411
property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect
property_value: terms:creator https://orcid.org/0000-0002-6601-2165
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: terms:contributor https://orcid.org/0000-0001-6996-0040
property_value: terms:contributor https://orcid.org/0000-0002-6601-2165
property_value: 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: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: terms:source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI
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" []
comment: This relation has a stronger meaning than merely indicating that X may develop into Y, in that the capability of developing into Y is always present, even if X does not always actually develop into Y. In particular, this means that if Y is restricted to a given taxon T, X is necessarily likewise restricted.
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: seeAlso https://github.com/oborel/obo-relations/issues/810
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:0002234 RO:0002233
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
transitive_over: BFO:0000050 ! part of

[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 ! specifically dependent continuant
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: 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
property_value: skos:closeMatch "http://purl.obolibrary.org/obo/MI_0914" 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: 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
property_value: skos:closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI
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: 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
property_value: skos:closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI
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:0000112 "lions trophically interact with the zebras that they eat" 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: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:0000112 "whales symbiotically interact with the barnacles that attach to them" xsd:string
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
def: "A parasite-host relationship where an organism benefits at the expense of another." []
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
def: "Inverse of parasite of" []
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
inverse_of: RO:0017007 ! symptom of

[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
def: "Inverse of provides nutrients for" []
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:0002437 ! biotically 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
def: "A biotic interaction where a material entity provides nutrition for an organism." []
subset: ro-eco
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
is_a: RO:0002437 ! biotically interacts with

[Typedef]
id: RO:0002470
name: eats
def: "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening." []
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:0002437 ! biotically interacts with

[Typedef]
id: RO:0002471
name: is eaten by
def: "Inverse of eats" []
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:0002437 ! biotically 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: 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
property_value: terms:creator https://orcid.org/0000-0002-4366-3088
property_value: terms:creator https://orcid.org/0000-0002-6601-2165
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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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
def: "A relationship between organisms where one organism is influenced by the biochemicals produced by another." []
comment: Allelopathy is a phenomenon in which one organism releases chemicals to positively or negatively influence the growth, survival or reproduction of other organisms in its vicinity.
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 "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172429/" xsd:string
property_value: seeAlso "x is an allelopath of y if x 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
inverse_of: RO:0020301 ! has allelopath

[Typedef]
id: RO:0002556
name: pathogen of
def: "Inverse of has pathogen" []
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
def: "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member" []
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
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 ! specifically dependent continuant
range: BFO:0000020 ! specifically dependent continuant

[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: COB:0000022 ! organism
range: COB:0000022 ! 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." []
synonym: "indicates" RELATED []
property_value: IAO:0000116 "May be ceded to OBI" xsd:string
is_a: RO:0002610 ! correlated with
inverse_of: RO:0017011 ! has marker

[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: 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
property_value: terms:contributor https://orcid.org/0000-0002-3120-4802
property_value: terms:contributor https://orcid.org/0000-0003-3138-4118
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:0002804
name: ectomycorrhizal host of
def: "x is an ectomycorrhizal host of y if and only if x is a plant (Plantae) whose roots form an intercellular interface (aka Hartig net) with fungus (Fungi) y. This interface consists of highly branched hyphae forming a latticework between epidermal and cortical root cells." []
comment: An ectomycorrhiza is a form of symbiotic relationship that occurs between a fungal symbiont, or mycobiont, and the roots of various plant species. The mycobiont is often from the phyla Basidiomycota and Ascomycota, and more rarely from the Zygomycota. Ectomycorrhizae form on the roots of around 2% of plant species, usually woody plants, including species from the birch, dipterocarp, myrtle, beech, willow, pine and rose families. Research on ectomycorrhizae is increasingly important in areas such as ecosystem management and restoration, forestry, and agriculture. Unlike other mycorrhizal relationships, such as arbuscular mycorrhiza and ericoid mycorrhiza, ectomycorrhizal fungi do not penetrate their host's cell wall. Instead they form an entirely intercellular interfaces known as the Hartig net, consisting of highly branched hyphae forming a latticework between epidermal and cortical root cells. 
property_value: IAO:0000112 "According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle)." xsd:string
property_value: IAO:0000119 https://doi.org/10.1128/AEM.01558-12
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Ectomycorrhiza
property_value: terms:contributor https://orcid.org/0000-0003-3138-4118
domain: NCBITaxon:33090
range: NCBITaxon:4751
is_a: RO:0002453 ! host of
inverse_of: RO:0002805 ! has ectomycorrhizal host

[Typedef]
id: RO:0002805
name: has ectomycorrhizal host
def: "inverse of ectomycorrhizal host of" []
subset: RO:0002259
property_value: IAO:0000112 "According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle)." xsd:string
is_a: RO:0002454 ! has host

[Typedef]
id: RO:0002806
name: arbuscular mycorrhizal host of
def: "x is an arbuscular mycorrhizal host of y if and only if x is a vascular plant (Plantae) whose cortical cells of the roots are penetrated by fungus (Fungi) y and form arbuscules." []
comment: An arbuscular mycorrhiza (AM) (plural mycorrhizae) is a type of mycorrhiza in which the symbiont fungus (Arbuscular mycorrhizal fungi, or AMF) penetrates the cortical cells of the roots of a vascular plant forming arbuscules. Arbuscular mycorrhiza is a type of endomycorrhiza along with ericoid mycorrhiza and orchid mycorrhiza (not to be confused with ectomycorrhiza). They are characterized by the formation of unique tree-like structures, the arbuscules. In addition, globular storage structures called vesicles are often encountered. Arbuscular mycorrhizae are formed by fungi in the subphylum Glomeromycotina and some fungi from the Mucoromycotina. These subphyla, along with the Mortierellomycotina, form the phylum Mucoromycota, a sister clade of the more well-known and diverse dikaryan fungi. AM fungi help plants to capture nutrients such as phosphorus, sulfur, nitrogen and micronutrients from the soil. It is believed that the development of the arbuscular mycorrhizal symbiosis played a crucial role in the initial colonisation of land by plants and in the evolution of the vascular plants. It has been said that it is quicker to list the plants that do not form endomycorrhizae than those that do. This symbiosis is a highly evolved mutualistic relationship found between fungi and plants, the most prevalent plant symbiosis known, and AMF is found in 80% of vascular plant families in existence today.
property_value: IAO:0000112 "According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae)." xsd:string
property_value: IAO:0000119 Arbuscular:mycorrhiza
property_value: IAO:0000119 https://doi.org/10.1016/S0929-1393(02)00112-9
property_value: terms:contributor https://orcid.org/0000-0003-3138-4118
domain: NCBITaxon:33090
range: NCBITaxon:4751
is_a: RO:0002453 ! host of
inverse_of: RO:0002807 ! has arbuscular mycorrhizal host

[Typedef]
id: RO:0002807
name: has arbuscular mycorrhizal host
def: "inverse of arbuscular mycorrhizal host of" []
subset: RO:0002259
property_value: IAO:0000112 "According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae)." xsd:string
property_value: IAO:0000119 https://doi.org/10.1016/S0929-1393(02)00112-9
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: seeAlso https://github.com/oborel/obo-relations/issues/506
property_value: terms:contributor https://orcid.org/0000-0001-8910-9851

[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: seeAlso https://github.com/oborel/obo-relations/issues/506
property_value: terms:contributor https://orcid.org/0000-0001-8910-9851
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: COB:0000022 ! organism
range: COB:0000022 ! 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: COB:0000022 ! organism
range: COB:0000022 ! 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: IAO:0000112 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)" xsd:string
property_value: terms:contributor https://orcid.org/0000-0002-2908-3327
property_value: terms:date "2023-01-18T14:28:21Z" xsd:dateTime
domain: COB:0000022 ! organism
range: ENVO:01000739 ! habitat
is_a: RO:0002303 ! has habitat

[Typedef]
id: RO:0008510
name: symbiotrophically interacts with
def: "A trophic interaction in which one organism acquires nutrients through a symbiotic relationship with another organism" []
subset: ro-eco
property_value: IAO:0000112 "frog symbiotrophically interacts with the pitcher plant it lives inside of" xsd:string
property_value: terms:contributor https://orcid.org/0000-0002-2908-3327
property_value: terms:date "2023-07-17T14:39:56Z" xsd:dateTime
is_a: RO:0002438 ! trophically interacts with

[Typedef]
id: RO:0008511
name: trophic parasite of
def: "A symbiotrophic interaction in which one organism acquires nutrients through a parasitic relationship with another organism" []
subset: ro-eco
property_value: IAO:0000112 "tapeworm is trophic parasite of the cow it lives inside of" xsd:string
property_value: terms:contributor https://orcid.org/0000-0002-2908-3327
property_value: terms:date "2023-07-17T14:41:07Z" xsd:dateTime
is_a: RO:0008510 ! symbiotrophically interacts with

[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: COB:0000022 ! 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:0009006
name: assay measures characteristic
def: "A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic." []
property_value: IAO:0000112 "A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material." xsd:string
property_value: terms:contributor https://orcid.org/0000-0002-8844-9165
property_value: terms:date "2023-05-23T15:24:15Z" xsd:dateTime
domain: OBI:0000070 ! assay
range: BFO:0000020 ! specifically dependent continuant
inverse_of: RO:0009007 ! characteristic measured by assay

[Typedef]
id: RO:0009007
name: characteristic measured by assay
def: "Inverse of 'assay measures characteristic'" []
property_value: terms:contributor https://orcid.org/0000-0002-8844-9165
property_value: terms:date "2023-05-23T15:29:50Z" xsd:dateTime
domain: BFO:0000020 ! specifically dependent continuant
range: OBI:0000070 ! assay

[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: 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
property_value: terms:contributor https://orcid.org/0000-0001-6996-0040
property_value: terms:contributor https://orcid.org/0000-0002-6601-2165
property_value: terms:contributor https://orcid.org/0000-0002-7073-9172
property_value: terms:contributor https://orcid.org/0000-0002-8461-9745
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: RO:0004049 RO:0002010
property_value: terms:contributor https://orcid.org/0000-0003-1813-6857
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: RO:0004050 RO:0002010
property_value: terms:contributor https://orcid.org/0000-0003-1813-6857
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:0013010
name: synapses restricted to region
def: "A relationship between a neuron and a region, where all of the functionally relevant input and output synapses are in that region." []
comment: This relation may still be used if a very small number of synapses fall slightly outside the boundaries of the region, but any class using this relation should not have another restriction using this relation to another non-overlapping region.
synonym: "intrinsic to" EXACT []
property_value: IAO:0000112 "An optic lobe intrinsic neuron has its synapses restricted to optic lobe neuropil." xsd:string
property_value: terms:contributor https://orcid.org/0000-0002-1373-1705
property_value: terms:date "2023-08-17T12:17:24Z" xsd:dateTime
is_a: RO:0013001 ! has synaptic IO in region
transitive_over: BFO:0000050 ! part of

[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: 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
property_value: terms:contributor https://orcid.org/0000-0001-7258-9596
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: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string
property_value: terms:contributor https://orcid.org/0000-0003-1617-8244
property_value: terms:contributor https://orcid.org/0000-0003-1940-6740
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: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string
property_value: terms:contributor https://orcid.org/0000-0003-1617-8244
property_value: terms:contributor https://orcid.org/0000-0003-1940-6740
domain: CL:0000000 ! cell
is_a: RO:0002104 ! has plasma membrane part

[Typedef]
id: RO:0016001
name: has phenotype or disease
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
property_value: terms:contributor https://orcid.org/0000-0002-7463-6306
property_value: terms:date "2021-11-05T17:30:14Z" xsd:dateTime

[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: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string
property_value: terms:contributor https://orcid.org/0000-0002-7463-6306
property_value: terms:date "2021-11-05T17:30:44Z" xsd:dateTime
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: IAO:0000119 "ExO:0000083" xsd:string
property_value: terms:creator https://orcid.org/0000-0002-7463-6306
property_value: terms:date "2021-12-14T20:41:45Z" xsd:dateTime
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: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
property_value: terms:contributor https://orcid.org/0000-0001-9625-1899
property_value: terms:contributor https://orcid.org/0000-0003-2620-0345
holds_over_chain: RO:0002215 RO:0002233
creation_date: 2021-11-08T12:00:00Z

[Typedef]
id: RO:0017002
name: information specifies
def: "A relation between information and an entity such that the information serves as a rule or guide if the entity is an occurrent, or the information serves as a model if the entity is a continuant." []
synonym: "prescribes" EXACT []
synonym: "specifies" EXACT []
property_value: IAO:0000112 "The information in a blueprint specifies the dimensions of a building." xsd:string
property_value: IAO:0000112 "The information in a recipe specifies what interredients to use and the steps needed to prepare a meal." xsd:string
property_value: IAO:0000112 "The information in a software program specifies the order of computations." xsd:string
property_value: skos:exactMatch "https://www.ontologyrepository.com/CommonCoreOntologies/prescribes" xsd:string
property_value: terms:contributor https://orcid.org/0000-0001-9625-1899
property_value: terms:created "2025-06-16T17:08:04Z" xsd:dateTime
inverse_of: RO:0017010 ! specified by information

[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: IAO:0000118 "directly correlated with" xsd:string
property_value: terms:contributor https://orcid.org/0000-0003-1909-9269
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: IAO:0000118 "inversely correlated with" xsd:string
property_value: terms:contributor https://orcid.org/0000-0003-1909-9269
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: IAO:0000112 "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." xsd:string
property_value: terms:contributor https://orcid.org/0000-0002-2999-0103
property_value: terms:contributor https://orcid.org/0000-0002-5714-991X
domain: OBI:0000967 ! container
range: COB:0000121

[Typedef]
id: RO:0017006
name: has maximum capacity
def: "A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume." []
property_value: IAO:0000112 "anticoagulant-containing test tube has maximum capacity 10 ml." xsd:string
property_value: terms:contributor https://orcid.org/0000-0002-2999-0103
property_value: terms:contributor https://orcid.org/0000-0002-5714-991X
domain: OBI:0000967 ! container
range: COB:0000121

[Typedef]
id: RO:0017007
name: symptom of
def: "inverse of 'has symptom'" []
property_value: terms:contributor https://orcid.org/0009-0002-7282-0836
property_value: terms:created "2025-06-16T17:42:05Z" xsd:dateTime

[Typedef]
id: RO:0017008
name: owns
def: "A primitive relation that holds between entities x and y in which y is at x's full disposal." []
property_value: IAO:0000112 "biobank organization owns a specimen" xsd:string
property_value: IAO:0000112 "hospital owns a laboratory facility" xsd:string
property_value: terms:contributor https://orcid.org/0000-0001-9625-1899
property_value: terms:contributor https://orcid.org/0000-0003-1834-3856
property_value: terms:contributor https://orcid.org/0000-0003-1909-9269
property_value: terms:description "This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal." xsd:string
inverse_of: RO:0017009 ! is owned by
creation_date: 2023-03-29T16:57:03Z

[Typedef]
id: RO:0017009
name: is owned by
def: "Inverse of the owns relation." []
subset: RO:0002259
property_value: IAO:0000112 "freezer is owned by a biobank organization" xsd:string
property_value: terms:contributor https://orcid.org/0000-0001-9625-1899
property_value: terms:contributor https://orcid.org/0000-0003-1834-3856
property_value: terms:contributor https://orcid.org/0000-0003-1909-9269
creation_date: 2023-03-29T17:06:06Z

[Typedef]
id: RO:0017010
name: specified by information
def: "Inverse of information specifies." []
property_value: terms:contributor https://orcid.org/0000-0001-9625-1899
property_value: terms:created "2025-06-16T17:13:17Z" xsd:dateTime

[Typedef]
id: RO:0017011
name: has marker
def: "Inverse relation of 'is marker for'." []
property_value: terms:contributor https://orcid.org/0000-0001-9625-1899
property_value: terms:created "2025-07-14T20:57:25Z" xsd:dateTime
is_a: RO:0002610 ! correlated with

[Typedef]
id: RO:0017502
name: collected during
def: "A relation between a material entity and an occurrent in which the material entity is collected during the existence of the occurrent." []
property_value: IAO:0000112 "A thorax specimen was collected during the larval stage." xsd:string
property_value: IAO:0000112 "An oyster was collected during low tide." xsd:string
property_value: terms:contributor https://orcid.org/0000-0002-8844-9165
property_value: terms:date "2023-09-13T04:12:32Z" xsd:dateTime
domain: BFO:0000040 ! material entity
range: BFO:0000003 ! occurrent

[Typedef]
id: RO:0018001
name: is myristoyltransferase activity
def: "Helper relation for OWL definition of RO:0018002 myristoylates" []
property_value: 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: terms:conformsTo http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess
property_value: 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: 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: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string
property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
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: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string
property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
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: 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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
is_a: RO:0002449 ! directly negatively regulates activity of

[Typedef]
id: RO:0018030
name: chemical relationship
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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370

[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: 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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
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: 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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
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: 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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
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: 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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
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." [] {terms:source="https://doi.org/10.1021/jm200452d", terms:source="https://doi.org/10.1002/ddr.21045", 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: 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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
property_value: terms:date "2023-02-28T18:53:32Z" xsd:dateTime
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: 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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
property_value: terms:date "2023-03-18T23:49:31Z" xsd:dateTime
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: 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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
property_value: terms:date "2023-03-18T23:49:31Z" xsd:dateTime
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: 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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
property_value: terms:date "2023-03-18T23:49:31Z" xsd:dateTime
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: 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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
property_value: terms:date "2023-03-18T23:49:31Z" xsd:dateTime
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: 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
property_value: terms:creator https://orcid.org/0000-0003-4423-4370
property_value: terms:date "2023-03-18T23:49:31Z" xsd:dateTime
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: 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: 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: 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:0019003
name: has substitutable entity
def: "Relates one individual to another which is capable of standing in for the first individual in its other relations to other individuals." []
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000112 "Given individuals f, i, x, and y, where f is a 'molecular function', i is an 'information biomacromolecule', and x and y are instances of different types of gene products, if f 'enabled by' i within an OWL model of a biological pathway, and i 'has substitutable entity' both x and y, then either x or y are valid enablers of function f within the modeled biological context." xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-8688-6599

[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: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string
property_value: terms:contributor https://orcid.org/0000-0001-6677-8489
property_value: terms:date "2024-02-01T10:09:22Z" xsd:dateTime
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: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string
property_value: terms:contributor https://orcid.org/0000-0001-6677-8489
property_value: terms:date "2024-02-01T10:09:41Z" xsd:dateTime
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: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string
property_value: terms:contributor https://orcid.org/0000-0001-6677-8489
property_value: terms:date "2024-02-01T10:09:59Z" xsd:dateTime
domain: UBERON:0001982 ! capillary
range: UBERON:0000061 ! anatomical structure
is_a: RO:0002178 ! supplies
is_a: RO:0002179 ! drains

[Typedef]
id: RO:0020104
name: is neuron
def: "This property only applies to neurons" []
property_value: terms:contributor https://orcid.org/0000-0001-6677-8489
property_value: terms:date "2024-10-23T14:34:52Z" xsd:dateTime
domain: CL:0000540 ! neuron

[Typedef]
id: RO:0020105
name: is anatomical entity
def: "This property only applies to anatomical entities." []
property_value: terms:contributor https://orcid.org/0000-0001-6677-8489
property_value: terms:date "2024-10-29T09:55:07Z" xsd:dateTime
domain: UBERON:0001062 ! anatomical entity

[Typedef]
id: RO:0020202
name: has numerator
def: "A relationship between a ratio or proportion and its dividend." []
synonym: "has dividend" EXACT []
property_value: terms:contributor https://orcid.org/0000-0001-8314-2140
domain: PATO:0001470 ! ratio
range: PATO:0000001 ! quality
is_a: BFO:0000051 ! has part

[Typedef]
id: RO:0020203
name: has denominator
def: "A relationship between a ratio or proportion and its divisor." []
synonym: "has divisor" EXACT []
property_value: terms:contributor https://orcid.org/0000-0001-8314-2140
domain: PATO:0001470 ! ratio
range: PATO:0000001 ! quality
is_a: BFO:0000051 ! has part

[Typedef]
id: RO:0020301
name: has allelopath
def: "inverse of allelopath of" []
property_value: IAO:0000117 https://orcid.org/0009-0005-5515-1230
property_value: seeAlso "https://en.wikipedia.org/wiki/Allelopathy" xsd:string
is_a: RO:0002574 ! participates in a biotic-biotic interaction with

[Typedef]
id: RO:0020326
name: provides clinical information for
def: "A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' provides clinical information about 'd'." []
comment: Usage note: This does not imply that 'b' and 'd' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and 'd'.\n\nBasis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
property_value: IAO:0000112 "A cancer biomarker provides_clinical_information_for some cancer, which is to say that the presence of or features of the biomarker is clinically informative for the presence of or features of the cancer." xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-5809-9523" xsd:string
is_a: RO:0002607 ! is marker for
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020327
name: diagnostic for
def: "A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the presence or occurrence of 'd' or determine its subtype." []
comment: Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
property_value: IAO:0000112 "A below-normal level of creatine in cerebrospinal fluid is diagnostic_for guanidinoacetate methyltransferase deficiency, which is to say that such levels indicate that the patient has the indicated clinical issue." xsd:string
property_value: IAO:0000112 "An above-normal level of succinylacetone in urine is diagnostic_for type 1 tyrosinemia, while an above-normal level of 4-hydroxyphenylpyruvate is diagnostic_for either type 2 or type 3 tyrosinemia." xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-5809-9523" xsd:string
is_a: RO:0020326 ! provides clinical information for
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020328
name: monitors status of
def: "A relationship between a serially-measured biomarker 'b' and a disease or condition of clinical interest 'd', where 'b' is used to infer the status of 'd'." []
comment: Usage note: The status of 'd' refers to disease progression/remission or treatment response.\n\nBasis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
property_value: IAO:0000112 "Hemoglobin A1c (HbA1c) level in blood monitors_status_of diabetes since HbA1c levels reflect a three-month average of blood glucose levels, and can thus be used to monitor the disease progression." xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-5809-9523" xsd:string
is_a: RO:0020326 ! provides clinical information for
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020329
name: indicates response to
def: "A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to show that a biological response to 'e' has occurred." []
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment.\n\nBasis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
property_value: IAO:0000112 "The level of urinary glycosaminoglycans indicates_response_to enzyme replacement therapy for patients with mucopolysaccharidosis type 1." xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-5809-9523" xsd:string
is_a: RO:0020334 ! indicates clinical effect of
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020330
name: predicts effect of
def: "A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to identify individuals who are likely to experience a favorable or unfavorable effect from exposure to 'e'." []
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. In the context of predictive biomarkers, 'e' is typically a medical product such as a drug.\n\nUsage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (RO:0020331), and 'predicts effect of' (this relation) are each used to relate biomarkers to possible future clinical outcomes:\n	- 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue;\n	- 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest;\n	- 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment.\n\nBasis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
property_value: IAO:0000112 "The incidence of squamous cell differentiation (indicated, for example, by keratinization) in non-small cell lung cancer patients predicts_effect_of the drug pemetrexed, where the prediction is that such patients will have a poor outcome with use of the drug." xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-5809-9523" xsd:string
is_a: RO:0020334 ! indicates clinical effect of
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020331
name: prognostic for
def: "A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the likelihood of a clinical event, disease recurrence or progression in patients who have 'd'." []
comment: Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (this relation), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes:\n	- 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue;\n	- 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest;\n	- 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment.\n\nBasis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
property_value: IAO:0000112 "A high number of tumor cells expressing the nuclear protein Ki-67 is prognostic_for an aggressive cancer." xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-5809-9523" xsd:string
is_a: RO:0020326 ! provides clinical information for
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020332
name: assesses toxicity of
def: "A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to indicate the likelihood, presence, or extent of toxicity as an adverse effect of exposure to 'e'." []
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment.\n\nBasis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
property_value: IAO:0000112 "As an indicator of kidney issues, reduced creatinine clearance capability assesses_toxicity_of certain drugs (such as antibiotics or chemotherapy agents) to the kidneys." xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-5809-9523" xsd:string
is_a: RO:0020334 ! indicates clinical effect of
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020333
name: indicates risk of developing
def: "A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the potential for developing 'd' in an individual that currently does not have 'd'." []
comment: Usage note: The relations 'indicates risk of developing' (this relation), 'prognostic for' (RO:0020331), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes:\n	- 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue;\n	- 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest;\n	- 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment.\n\nBasis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
property_value: IAO:0000112 "The presence of a certain BRCA1 mutation indicates_risk_of_developing breast cancer in those who don't currently have the cancer." xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-5809-9523" xsd:string
is_a: RO:0020326 ! provides clinical information for
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020334
name: indicates clinical effect of
def: "A relationship between a biomarker 'b' and an exposure agent 'e', where the effect of exposure to 'e' is correlated with the presence or occurrence of 'b', and the observation of 'b' is used to infer exposure to 'e'." []
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment.\n\nUsage note: This does not imply that 'b' and exposure to 'e' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and exposure to 'e'.\n\nBasis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
property_value: IAO:0000112 "An image biomarker showing tumor size indicates_clinical_effect_of some radiotherapy." xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-5809-9523" xsd:string
is_a: RO:0002607 ! is marker for
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020335
name: monitors effect of
def: "A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of a biological effect of 'e'." []
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment.\n		\nBasis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
property_value: IAO:0000112 "The level of prostate-specific antigen (PSA) monitors_effect_of therapies applied for the treatment of prostate cancers." xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-5809-9523" xsd:string
is_a: RO:0020334 ! indicates clinical effect of
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020336
name: monitors exposure to
def: "A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of exposure to 'e'." []
comment: Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment.\n		\nUsage note: The relations 'monitors status of' (RO:0020328), 'monitors exposure to' (this relation), and 'monitors effect of' (RO:0020335) are each used for serially-measured biomarkers:\n	- 'monitors status of' pertains to cases where the biomarker is used to assess the progression/remission of a disease or condition of clinical interest;\n	- 'monitors exposure to' pertains to cases where the biomarker is used to assess the occurrence of or amount of exposure to some exposure agent;\n	- 'monitors effect of' pertains to cases where the biomarker is used to assess any possible biological effect arising from exposure to some exposure agent.  \n	\n	Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts.
property_value: IAO:0000112 "The concentration of tobacco specific nitrosamines in urine monitors_exposure_to tobacco/tobacco smoke." xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-5809-9523" xsd:string
is_a: RO:0020334 ! indicates clinical effect of
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020337
name: has constituent monomer
def: "A relation that holds between a polymer and its constituent monomers. P has_constituent_monomer 'm' if and only if P has_component multiple instances of 'm' and each instance of 'm' is covalently attached to another instance of 'm'." []
comment: Usage note: The constituent monomers need not be covalently attached in an end-to-end manner; that is, polymers with internal connections (e.g., polyubiquitin) can use this relation, as can circular polymers (e.g., plasmids) and multi-branched polymers (e.g., glycans). This relation, as non-transitive, allows the number of instances of 'm' to be indicated.
property_value: IAO:0000112 "A polyubiquitin has_constituent_monomer some ubiquitin." xsd:string
property_value: IAO:0000112 "An amino acid chain has_constituent_monomer at least two amino acid residues." xsd:string
is_a: RO:0002180 ! has component
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020338
name: covalently bound to
def: "A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of covalent interactions." []
comment: Such entities will colocalize at all times of the interaction.
property_value: IAO:0000112 "Charged tRNA (i.e., aminoacyl-tRNA) is a tRNA that is covalently_bound_to some amino acid." xsd:string
is_symmetric: true
is_a: RO:0002436 ! molecularly interacts with
created_by: https://orcid.org/0000-0001-5809-9523

[Typedef]
id: RO:0020339
name: non-covalently bound to
def: "A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of non-covalent interactions." []
comment: Such entities will colocalize at all times of the interaction.
property_value: IAO:0000112 "Holo-calmodulin is a calmodulin that is non-covalently_bound_to calcium." xsd:string
is_symmetric: true
is_a: RO:0002436 ! molecularly interacts with
created_by: https://orcid.org/0000-0001-5809-9523

[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: 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
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000001
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000002
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000003
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000004
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000005
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000006
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000007
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000008
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000009
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000010
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000011
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000012
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000013
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000014
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000015
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000016
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000017
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000018
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000019
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000020
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000022
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000023
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000024
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000025
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000026
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000027
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000028
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000029
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000030
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000031
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000032
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000033
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000034
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000036
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000037
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000042
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000043
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000044
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000045
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000046
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000047
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000048
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000049
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000050
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000051
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000052
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000053
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000054
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000055
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000057
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000058
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000060
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000061
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000062
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000063
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000065
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000066
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000068
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000069
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000071
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000072
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000073
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000074
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
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: seeAlso HOM:0000075
property_value: terms:creator https://www.wikidata.org/wiki/Q54985720
property_value: terms:source http://www.ncbi.nlm.nih.gov/pubmed/20116127
is_symmetric: true
is_a: RO:HOM0000007 ! in historical homology relationship with