From fc42248de75e6b3c6ce6df6c25188271685e0725 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Wed, 24 Aug 2016 19:24:54 -0700 Subject: [PATCH] new release --- ro.obo | 159 +++++- ro.owl | 305 +++++++---- src/ontology/Makefile | 17 + src/ontology/reports/ro-objectProperties.csv | 506 +++++++++++++++++++ src/ontology/ro-edit.owl | 174 ++----- src/ontology/ro.obo | 159 +++++- src/ontology/ro.owl | 305 +++++++---- src/ontology/subsets/ro-causal.obo | 129 ++++- src/ontology/subsets/ro-causal.owl | 228 +++++---- src/ontology/subsets/ro-developmental.obo | 129 ++++- src/ontology/subsets/ro-developmental.owl | 228 +++++---- src/ontology/subsets/ro-eco.obo | 157 +++++- src/ontology/subsets/ro-eco.owl | 309 ++++++----- src/ontology/subsets/ro-interaction.obo | 129 ++++- src/ontology/subsets/ro-interaction.owl | 228 +++++---- src/ontology/subsets/ro-mereotopology.obo | 129 ++++- src/ontology/subsets/ro-mereotopology.owl | 228 +++++---- src/ontology/subsets/ro-sequence.obo | 129 ++++- src/ontology/subsets/ro-sequence.owl | 228 +++++---- src/ontology/subsets/ro-time-interval.obo | 129 ++++- src/ontology/subsets/ro-time-interval.owl | 228 +++++---- subsets/ro-causal.obo | 129 ++++- subsets/ro-causal.owl | 228 +++++---- subsets/ro-chado.obo | 7 +- subsets/ro-developmental.obo | 129 ++++- subsets/ro-developmental.owl | 228 +++++---- subsets/ro-eco.obo | 157 +++++- subsets/ro-eco.owl | 309 ++++++----- subsets/ro-interaction.obo | 129 ++++- subsets/ro-interaction.owl | 228 +++++---- subsets/ro-mereotopology.obo | 129 ++++- subsets/ro-mereotopology.owl | 228 +++++---- subsets/ro-sequence.obo | 129 ++++- subsets/ro-sequence.owl | 228 +++++---- subsets/ro-time-interval.obo | 129 ++++- subsets/ro-time-interval.owl | 228 +++++---- 36 files changed, 4836 insertions(+), 2012 deletions(-) create mode 100644 src/ontology/reports/ro-objectProperties.csv diff --git a/ro.obo b/ro.obo index 18316286..9bb2fef7 100644 --- a/ro.obo +++ b/ro.obo @@ -1,6 +1,9 @@ format-version: 1.2 -data-version: releases/2016-06-15 +data-version: releases/2016-08-24 subsetdef: ro-eco "" +subsetdef: RO:0002259 "" +remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] +remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 276 Logical Axioms: 56] @@ -721,6 +724,8 @@ inverse_of: RO:0000092 ! disposition of [Typedef] id: RO:0000092 name: disposition of +def: "inverse of has disposition" [] +subset: RO:0002259 is_a: RO:0000052 ! inheres in [Typedef] @@ -824,6 +829,7 @@ def: "A relation between a material entity and a condition (a phenotype or disea 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 @@ -831,6 +837,22 @@ 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 @@ -954,7 +976,7 @@ 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." [GOC:dos] +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 "David Osumi-Sutherland" xsd:string holds_over_chain: RO:0002211 RO:0002313 @@ -962,7 +984,7 @@ holds_over_chain: RO:0002211 RO:0002313 [Typedef] id: RO:0002012 name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: BFO:0000050 ! part of @@ -1383,7 +1405,7 @@ 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 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -1416,6 +1438,8 @@ 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 @@ -1566,7 +1590,9 @@ 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 "Chris Mungall" xsd:string is_functional: true @@ -1590,6 +1616,8 @@ inverse_of: RO:0002203 ! develops into [Typedef] id: RO:0002203 name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string @@ -1655,18 +1683,22 @@ inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002208 name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +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 @@ -1810,6 +1842,8 @@ 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 "Chris Mungall" xsd:string property_value: RO:0001900 RO:0001901 @@ -1877,13 +1911,13 @@ 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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] @@ -1962,19 +1996,19 @@ 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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] @@ -2022,6 +2056,35 @@ 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." [] +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +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." [] +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 +is_a: RO:0002375 ! in branching relationship with + [Typedef] id: RO:0002254 name: has developmental contribution from @@ -2038,6 +2101,8 @@ inverse_of: RO:0002255 ! developmentally contributes to [Typedef] id: RO:0002255 name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002203 BFO:0000050 @@ -2083,6 +2148,24 @@ property_value: IAO:0000232 "In general you should not use this relation to make 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:0002285 name: developmentally replaces @@ -2132,6 +2215,7 @@ is_a: RO:0002330 ! genomically related to 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 "Chris Mungall" xsd:string is_a: RO:0002292 ! expresses @@ -2255,7 +2339,7 @@ is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string @@ -2324,6 +2408,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002334 name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process @@ -2334,12 +2419,16 @@ is_a: RO:0002427 ! causally downstream of or within [Typedef] id: RO:0002335 name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002336 name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002334 ! regulated by @@ -2453,7 +2542,9 @@ 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 "Chris Mungall" xsd:string is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to @@ -2461,7 +2552,9 @@ 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 "Chris Mungall" xsd:string is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to @@ -2548,10 +2641,13 @@ is_a: RO:0002320 ! evolutionarily related to [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: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of @@ -2562,12 +2658,12 @@ 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 {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 @@ -2580,8 +2676,9 @@ is_a: RO:0002375 ! in branching relationship with 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 {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -2887,6 +2984,8 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true @@ -3028,7 +3127,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -3196,7 +3295,9 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string @@ -3570,7 +3671,9 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: RO:0002566 ! causally influences @@ -3599,6 +3702,8 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -3660,6 +3765,7 @@ inverse_of: RO:0002517 ! is start sequence of id: RO:0002517 name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "starts" xsd:string @@ -3684,6 +3790,7 @@ inverse_of: RO:0002519 ! is end sequence of id: RO:0002519 name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "ends" xsd:string @@ -3726,6 +3833,7 @@ inverse_of: RO:0002523 ! is bound by sequence of id: RO:0002523 name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true @@ -3749,6 +3857,7 @@ inverse_of: RO:0002525 ! is subsequence of id: RO:0002525 name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "contained by" xsd:string @@ -3853,7 +3962,9 @@ inverse_of: RO:0002554 ! hyperparasitized by [Typedef] id: RO:0002554 name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002445 RO:0002445 is_a: RO:0002453 ! host of @@ -3886,8 +3997,10 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/25052702 is_a: RO:0002616 ! related via evidence or inference to @@ -3918,7 +4031,7 @@ 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string domain: GO:0040011 @@ -3952,7 +4065,9 @@ 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 "Chris Mungall" xsd:string is_a: RO:0002375 ! in branching relationship with @@ -4008,6 +4123,8 @@ 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 "Chris Mungall" xsd:string domain: CARO:0000003 ! anatomical structure range: CARO:0000003 ! anatomical structure @@ -4281,6 +4398,8 @@ 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] @@ -4306,6 +4425,8 @@ 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] @@ -4319,6 +4440,8 @@ 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] @@ -4332,6 +4455,8 @@ 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] diff --git a/ro.owl b/ro.owl index 5f24085f..45030cfb 100644 --- a/ro.owl +++ b/ro.owl @@ -13,7 +13,7 @@ xmlns:cito="http://purl.org/spar/cito/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"> - + @@ -24,6 +24,8 @@ The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. https://github.com/oborel/obo-relations/ + Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] + Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] OBO Relations Ontology @@ -41,6 +43,12 @@ + + + + + + @@ -155,6 +163,21 @@ + + + + + + + + + + defined by inverse + + + + + @@ -722,7 +745,6 @@ Where we have an annotation assertion - @@ -905,6 +927,7 @@ range: spatial region or site (immaterial continuant) + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -917,6 +940,7 @@ range: spatial region or site (immaterial continuant) + 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. is autoimmune trigger for @@ -924,6 +948,29 @@ range: spatial region or site (immaterial continuant) + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + has allergic trigger + + + + + + + + + + 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. + has autoimmune trigger + + + + @@ -1110,12 +1157,6 @@ AND t has_input y regulates transport of - - - - A relationship that holds between a process that regulates a transport process and the entity transported by that process. - GOC:dos - @@ -1129,12 +1170,6 @@ AND t has_input y A part of relation that applies only between occurents. occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -1767,12 +1802,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -1819,6 +1848,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of derived by descent from + has derived by descendant @@ -2093,7 +2124,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of has phenotype Chris Mungall + phenotype of @@ -2128,9 +2161,11 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan + develops into @@ -2238,13 +2273,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite that kills or sterilizes its host parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -2252,6 +2280,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of parasitoid of + has parasitoid @@ -2262,7 +2292,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of directly develops from developmental precursor of + directly develops into @@ -2485,24 +2517,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of surrounded by Chris Mungall + surrounds - - - - Chris Mungall - 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. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - - - - @@ -2565,12 +2588,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -2581,12 +2598,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -2695,12 +2706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -2711,12 +2716,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -2727,12 +2726,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.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. hemiparasite of - - - - 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. - - @@ -2809,6 +2802,53 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + has active substance + has active pharmaceutical ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + + active ingredient in' + + + + + + + + + + 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. + connecting branch of + + + + + + + + + inverse of connecting branch of + + has connecting branch + + + + @@ -2839,7 +2879,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of has developmental contribution from Chris Mungall + developmentally contributes to @@ -2896,6 +2938,36 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + has chemical role + + + + @@ -2971,6 +3043,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of ubiquiotously expressed in Chris Mungall + ubiquitously expresses @@ -3301,12 +3374,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables - - - - enables - http://www.arabidopsis.org/ - @@ -3419,6 +3486,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates Chris Mungall regulated by (processual) + regulated by @@ -3428,7 +3496,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall + negatively regulated by @@ -3438,7 +3508,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall + positively regulated by @@ -3592,7 +3664,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall + input of @@ -3604,7 +3678,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall + output of @@ -3734,9 +3810,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -3762,24 +3841,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -3795,14 +3856,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati distributary channel of http://en.wikipedia.org/wiki/Distributary + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -4301,8 +4357,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall + causally downstream of or within @@ -4536,12 +4594,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -4828,9 +4880,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with + preyed upon by http://eol.org/schema/terms/HasPredator @@ -5460,8 +5514,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of determined by Chris Mungall determines (material entity to system) + determines @@ -5513,8 +5569,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of transcribed from Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 + transcribed to @@ -5603,6 +5661,7 @@ the a supports either the existence of b, or the truth value of b.starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 + is start sequence of @@ -5635,6 +5694,7 @@ the a supports either the existence of b, or the truth value of b.ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 + is end sequence of @@ -5691,6 +5751,7 @@ the a supports either the existence of b, or the truth value of b.inverse of bounds sequence of Chris Mungall + is bound by sequence of @@ -5725,6 +5786,7 @@ the a supports either the existence of b, or the truth value of b.Chris Mungall contained by + is subsequence of @@ -5875,10 +5937,12 @@ the a supports either the existence of b, or the truth value of b. + inverse of hyperparasite of Chris Mungall has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized by @@ -5926,8 +5990,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of is evidence for Chris Mungall + 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. has evidence @@ -5980,12 +6046,6 @@ the a supports either the existence of b, or the truth value of b. results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -6040,7 +6100,9 @@ the a supports either the existence of b, or the truth value of b. + inverse of branching part of Chris Mungall + has branching part @@ -6122,7 +6184,9 @@ the a supports either the existence of b, or the truth value of b. + inverse of has skeleton Chris Mungall + skeleton of @@ -6563,6 +6627,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of ectoparasite of + has ectoparasite @@ -6605,6 +6671,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of mesoparasite of + has mesoparasite @@ -6626,6 +6694,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of intercellular endoparasite of + has intercellular endoparasite @@ -6647,6 +6717,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of intracellular endoparasite of + has intracellular endoparasite @@ -7292,6 +7364,9 @@ Environments include natural environments or exposures, experimentally applied c /////////////////////////////////////////////////////////////////////////////////////// --> + + + curation status specification @@ -7316,6 +7391,10 @@ Environments include natural environments or exposures, experimentally applied c term replaced by + + inverse of has disposition + + 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. @@ -7344,6 +7423,12 @@ Environments include natural environments or exposures, experimentally applied c + + 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. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + Chris Mungall + + is defined by diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 1387a70d..eca6015a 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -18,6 +18,10 @@ ro.owl: ro-edit.owl core.owl temporal-intervals.owl validate-using-oort owltools $< --set-ontology-id -v $(OBO)/ro/releases/`date +%Y-%m-%d`/ro.owl $(OBO)/ro.owl -o file://`pwd`/$@ # grep versionIRI $< && (echo "check the version:" && echo versionIRI: `grep versionIRI $<` && cp $< $@) || echo 'You must set the versionIRI!!' +# turtle file is merged, for querying via arq +ro.ttl: ro.owl + owltools --use-catalog $< --merge-import-closure -o -f ttl $@.tmp && mv $@.tmp $@ + %.obo: %.owl owltools --use-catalog $< --merge-import-closure -o -f obo $@.tmp && grep -v ^synonym $@.tmp > $@ # obolib-owl2obo -o $@.tmp $< && grep -v ^import: $@.tmp > $@ @@ -125,6 +129,19 @@ odp/%.owl: wget http://www.ontologydesignpatterns.org/cp/owl/$*.owl -O $@ +# ---------------------------------------- +# Reports +# ---------------------------------------- +REPORTS=basicReport +all_reports: $(patsubst %, reports/envo-%.csv, $(REPORTS)) + +reports/ro-%.csv: ro.ttl sparql/%.sparql + arq --data $< --query sparql/$*.sparql --results csv > $@.tmp && mv $@.tmp $@ + +reports/ro-%.ttl: ro.ttl sparql/%.sparql + arq --data $< --query sparql/$*.sparql --results ttl > $@.tmp && mv $@.tmp $@ + + # ---------------------------------------- # MARKDOWN EXPORT # ---------------------------------------- diff --git a/src/ontology/reports/ro-objectProperties.csv b/src/ontology/reports/ro-objectProperties.csv new file mode 100644 index 00000000..a5a83a93 --- /dev/null +++ b/src/ontology/reports/ro-objectProperties.csv @@ -0,0 +1,506 @@ +property,def,superPropertyList +http://purl.obolibrary.org/obo/RO_0002257,Inverse of developmentally induced by,http://purl.obolibrary.org/obo/RO_0002286 http://purl.obolibrary.org/obo/RO_0002386 +http://purl.obolibrary.org/obo/RO_0000302,"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.",http://purl.obolibrary.org/obo/RO_0000300 +http://purl.obolibrary.org/obo/BFO_0000063,"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.",http://purl.obolibrary.org/obo/RO_0002222 +http://purl.obolibrary.org/obo/RO_0002093,,http://purl.obolibrary.org/obo/RO_0002222 +http://purl.obolibrary.org/obo/RO_0002081,,http://purl.obolibrary.org/obo/RO_0002222 +http://purl.obolibrary.org/obo/RO_0002593,x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends.,http://purl.obolibrary.org/obo/RO_0002487 +http://purl.obolibrary.org/obo/RO_0002636,A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite,http://purl.obolibrary.org/obo/RO_0002444 +http://purl.obolibrary.org/obo/RO_0000056,"a relation between a continuant and a process, in which the continuant is somehow involved in the process", +http://purl.obolibrary.org/obo/RO_0002624,,http://purl.obolibrary.org/obo/RO_0002444 http://purl.obolibrary.org/obo/RO_0002618 +http://purl.obolibrary.org/obo/RO_HOM0000013,Syntenic homology that involves chromosomes of different species.,http://purl.obolibrary.org/obo/RO_HOM0000010 +http://purl.obolibrary.org/obo/RO_0002491,x existence starts and ends during y if and only if the start of x is part of y and 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) & ω(x) <= ω(y) & ω(x) >= α(y),http://purl.obolibrary.org/obo/RO_0002488 http://purl.obolibrary.org/obo/RO_0002492 +http://purl.obolibrary.org/obo/RO_0000301,"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.",http://purl.obolibrary.org/obo/RO_0000300 +http://purl.obolibrary.org/obo/RO_0002441,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).,http://purl.obolibrary.org/obo/RO_0002440 +http://purl.obolibrary.org/obo/RO_0000052,"a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence",http://purl.obolibrary.org/obo/RO_0002314 +http://purl.obolibrary.org/obo/RO_0002223,inverse of starts with,http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/RO_0002222 +http://purl.obolibrary.org/obo/RO_0002610,"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.",http://purl.obolibrary.org/obo/RO_0002609 +http://purl.obolibrary.org/obo/RO_0002082,,http://purl.obolibrary.org/obo/RO_0002081 +http://purl.obolibrary.org/obo/RO_0002320,A relationship that holds via some environmental process, +http://purl.obolibrary.org/obo/RO_0002592,"p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c",http://purl.obolibrary.org/obo/RO_0000057 +http://purl.obolibrary.org/obo/RO_HOM0000017,Historical homology that involves genes that diverged after a speciation event.,http://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_HOM0000068,"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/RO_HOM0000018 +http://purl.obolibrary.org/obo/RO_0002551,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.,http://purl.obolibrary.org/obo/BFO_0000051 +http://purl.obolibrary.org/obo/RO_0002625,,http://purl.obolibrary.org/obo/RO_0002619 http://purl.obolibrary.org/obo/RO_0002445 +http://purl.obolibrary.org/obo/RO_0002637,,http://purl.obolibrary.org/obo/RO_0002445 +http://purl.obolibrary.org/obo/RO_0002334,inverse of regulates,http://purl.obolibrary.org/obo/RO_0002427 +http://purl.obolibrary.org/obo/RO_0002226,x develops_in y if x is located in y whilst x is developing,http://purl.obolibrary.org/obo/RO_0002258 +http://purl.obolibrary.org/obo/RO_0002216,"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.",http://purl.obolibrary.org/obo/RO_0002328 http://purl.obolibrary.org/obo/RO_0002500 +http://purl.obolibrary.org/obo/RO_0002341,"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 ",http://purl.obolibrary.org/obo/RO_0002337 +http://purl.obolibrary.org/obo/RO_0002091,,http://purl.obolibrary.org/obo/RO_0002222 +http://purl.obolibrary.org/obo/RO_HOM0000037,"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.",http://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_0002440,A biotic interaction in which the two organisms live together in more or less intimate association.,http://purl.obolibrary.org/obo/RO_0002574 +http://purl.obolibrary.org/obo/RO_0002241,"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.",http://purl.obolibrary.org/obo/RO_0002244 +http://purl.obolibrary.org/obo/RO_0002583,x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends.,http://purl.obolibrary.org/obo/RO_0002487 +http://purl.obolibrary.org/obo/RO_0002433,"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.",http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002514,A relation that holds between two entities that have the property of being sequences or having sequences. , +http://purl.obolibrary.org/obo/BFO_0000050,a core relation that holds between a part and its whole,http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_HOM0000046,Historical homology that involves not recombining and subsequently differentiated sex chromosomes.,http://purl.obolibrary.org/obo/RO_HOM0000047 +http://purl.obolibrary.org/obo/RO_0002634,,http://purl.obolibrary.org/obo/RO_0002444 +http://purl.obolibrary.org/obo/RO_0002629,"p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p",http://purl.obolibrary.org/obo/RO_0002578 http://purl.obolibrary.org/obo/RO_0002213 +http://purl.obolibrary.org/obo/RO_0002622,,http://purl.obolibrary.org/obo/RO_0002618 +http://purl.obolibrary.org/obo/RO_0001023,"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.",http://purl.obolibrary.org/obo/RO_0003302 +http://purl.obolibrary.org/obo/RO_0001015,"a relation between two independent continuants, the location and the target, in which the target is entirely within the location", +http://purl.obolibrary.org/obo/RO_0002108,Relation between a muscle and a motor neuron that synapses to it via a type II bouton.,http://purl.obolibrary.org/obo/RO_0002103 +http://purl.obolibrary.org/obo/RO_0002586,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,http://purl.obolibrary.org/obo/RO_0002233 +http://purl.obolibrary.org/obo/RO_0002092,,http://purl.obolibrary.org/obo/RO_0002093 +http://purl.obolibrary.org/obo/RO_0002599,"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.",http://purl.obolibrary.org/obo/RO_0002597 +http://purl.obolibrary.org/obo/RO_0002565,Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c,http://purl.obolibrary.org/obo/RO_0000057 +http://purl.obolibrary.org/obo/RO_0002120," Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. + ",http://purl.obolibrary.org/obo/RO_0000302 +http://purl.obolibrary.org/obo/RO_0003003,Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.,http://purl.obolibrary.org/obo/RO_0002450 +http://purl.obolibrary.org/obo/RO_0002355,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.,http://purl.obolibrary.org/obo/RO_0000057 http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0002515,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,http://purl.obolibrary.org/obo/RO_0002527 +http://purl.obolibrary.org/obo/RO_0002521,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,http://purl.obolibrary.org/obo/RO_0002514 +http://purl.obolibrary.org/obo/RO_0002219,"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",http://purl.obolibrary.org/obo/RO_0002220 +http://purl.obolibrary.org/obo/RO_0002383,x proper_tributary_of y iff x tributary_of y and x does not originate from y,http://purl.obolibrary.org/obo/RO_0002376 +http://purl.obolibrary.org/obo/RO_0002623,,http://purl.obolibrary.org/obo/RO_0002619 +http://purl.obolibrary.org/obo/RO_0002502,, +http://purl.obolibrary.org/obo/RO_0002333,inverse of enables, +http://purl.obolibrary.org/obo/RO_0002635,,http://purl.obolibrary.org/obo/RO_0002445 +http://purl.obolibrary.org/obo/RO_0002429,,http://purl.obolibrary.org/obo/RO_0002428 +http://purl.obolibrary.org/obo/RO_0002405,,http://purl.obolibrary.org/obo/RO_0002404 http://purl.obolibrary.org/obo/RO_0002087 +http://purl.obolibrary.org/obo/RO_0002085,,http://purl.obolibrary.org/obo/RO_0002088 +http://purl.obolibrary.org/obo/RO_0002114,A relation between a motor neuron and a muscle that it synapses to via a type III bouton.,http://purl.obolibrary.org/obo/RO_0002120 +http://purl.obolibrary.org/obo/RO_0002254,x has developmental contribution from y iff x has some part z such that z develops from y,http://purl.obolibrary.org/obo/RO_0002258 +http://purl.obolibrary.org/obo/RO_0002584,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,http://purl.obolibrary.org/obo/RO_0002595 http://purl.obolibrary.org/obo/RO_0002328 +http://purl.obolibrary.org/obo/RO_0002357,"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.",http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0002332,p regulates levels of c if p regulates some amount (PATO:0000070) of c,http://purl.obolibrary.org/obo/RO_0002328 +http://purl.obolibrary.org/obo/RO_0002449,Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b.,http://purl.obolibrary.org/obo/RO_0002448 +http://purl.obolibrary.org/obo/RO_HOM0000003,Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.,http://purl.obolibrary.org/obo/RO_HOM0000000 http://purl.obolibrary.org/obo/RO_0002320 +http://purl.obolibrary.org/obo/RO_0002112,Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.,http://purl.obolibrary.org/obo/RO_0002103 +http://purl.obolibrary.org/obo/RO_0002400,"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.",http://purl.obolibrary.org/obo/RO_0002233 +http://purl.obolibrary.org/obo/RO_0002616,, +http://purl.obolibrary.org/obo/RO_0002003,A relation that holds between two neurons that are electrically coupled via gap junctions.,http://purl.obolibrary.org/obo/RO_0000300 +http://purl.obolibrary.org/obo/RO_0002086,,http://purl.obolibrary.org/obo/RO_0002222 +http://purl.obolibrary.org/obo/RO_0002472,"A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and +the a supports either the existence of b, or the truth value of b.",http://purl.obolibrary.org/obo/RO_0002616 +http://purl.obolibrary.org/obo/RO_0002340,"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.",http://purl.obolibrary.org/obo/RO_0002313 +http://purl.obolibrary.org/obo/RO_0002479,"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.", +http://purl.obolibrary.org/obo/RO_HOM0000001,Similarity that results from common evolutionary origin.,http://purl.obolibrary.org/obo/RO_0002158 http://purl.obolibrary.org/obo/RO_HOM0000000 +http://purl.obolibrary.org/obo/RO_0002342,"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.",http://purl.obolibrary.org/obo/RO_0002344 +http://purl.obolibrary.org/obo/RO_0002404,inverse of upstream of,http://purl.obolibrary.org/obo/BFO_0000062 http://purl.obolibrary.org/obo/RO_0002427 +http://purl.obolibrary.org/obo/RO_0002508,,http://purl.obolibrary.org/obo/RO_0002566 +http://purl.obolibrary.org/obo/RO_0002100,Relation between a neuron and an anatomical structure that its soma is part of.,http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002228,A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.,http://purl.obolibrary.org/obo/RO_0002444 +http://purl.obolibrary.org/obo/RO_0002102,Relation between a neuron and some structure its axon forms (chemical) synapses in.,http://purl.obolibrary.org/obo/RO_0002113 +http://purl.obolibrary.org/obo/RO_0002431,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,http://purl.obolibrary.org/obo/RO_0002328 http://purl.obolibrary.org/obo/RO_0002500 +http://purl.obolibrary.org/obo/RO_0002083,,http://purl.obolibrary.org/obo/RO_0002081 +http://purl.obolibrary.org/obo/RO_0002375,"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.",http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/RO_0002323 +http://purl.obolibrary.org/obo/RO_0002524,x has subsequence y iff all of the sequence parts of x are sequence parts of y,http://purl.obolibrary.org/obo/BFO_0000051 http://purl.obolibrary.org/obo/RO_0002522 http://purl.obolibrary.org/obo/RO_0002526 +http://purl.obolibrary.org/obo/RO_0002386,x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y,http://purl.obolibrary.org/obo/RO_0002384 +http://purl.obolibrary.org/obo/RO_0002516,"x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence",http://purl.obolibrary.org/obo/RO_0002524 +http://purl.obolibrary.org/obo/RO_0002408,,http://purl.obolibrary.org/obo/RO_0002630 +http://purl.obolibrary.org/obo/RO_0002291,"x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x",http://purl.obolibrary.org/obo/RO_0002206 +http://purl.obolibrary.org/obo/RO_0002626,,http://purl.obolibrary.org/obo/RO_0002574 +http://purl.obolibrary.org/obo/RO_HOM0000051,Paedomorphosis that is produced by delayed growth of immature structures into the adult form.,http://purl.obolibrary.org/obo/RO_HOM0000029 +http://purl.obolibrary.org/obo/RO_HOM0000036,Historical homology that involves two members of a larger set of homologs.,http://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_0002084,,http://purl.obolibrary.org/obo/RO_0002222 +http://purl.obolibrary.org/obo/RO_0002597,"Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.",http://purl.obolibrary.org/obo/RO_0002596 +http://purl.obolibrary.org/obo/RO_0002436,An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected.,http://purl.obolibrary.org/obo/RO_0002434 +http://purl.obolibrary.org/obo/RO_0002409,,http://purl.obolibrary.org/obo/RO_0002212 +http://purl.obolibrary.org/obo/RO_0002176,"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.",http://purl.obolibrary.org/obo/RO_0002323 +http://purl.obolibrary.org/obo/RO_HOM0000065,Similarity that is characterized by interchangeability in function.,http://purl.obolibrary.org/obo/RO_HOM0000000 +http://purl.obolibrary.org/obo/RO_0002627,,http://purl.obolibrary.org/obo/RO_0002574 +http://purl.obolibrary.org/obo/RO_0002331,"c involved_in p if and only if c enables some process p', and p' is part of p",http://purl.obolibrary.org/obo/RO_0002431 +http://purl.obolibrary.org/obo/RO_0002506,,http://purl.obolibrary.org/obo/RO_0002410 +http://purl.obolibrary.org/obo/RO_0002639,,http://purl.obolibrary.org/obo/RO_0002635 +http://purl.obolibrary.org/obo/RO_0002500,A relationship between a material entity and a process where the material entity has some causal role that influences the process,http://purl.obolibrary.org/obo/RO_0002595 +http://purl.obolibrary.org/obo/RO_0002330,"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.", +http://purl.obolibrary.org/obo/RO_0002089,,http://purl.obolibrary.org/obo/RO_0002222 +http://purl.obolibrary.org/obo/RO_0002596,"Holds between c and p if and only if c is capable of some activity a, and a regulates p.",http://purl.obolibrary.org/obo/RO_0002500 +http://purl.obolibrary.org/obo/RO_0002356,"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. ",http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0001022,"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.",http://purl.obolibrary.org/obo/RO_0003302 +http://purl.obolibrary.org/obo/RO_0002503,"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",http://purl.obolibrary.org/obo/RO_0002502 +http://purl.obolibrary.org/obo/RO_0002518,"x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence",http://purl.obolibrary.org/obo/RO_0002524 +http://purl.obolibrary.org/obo/RO_0002349,"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.",http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_HOM0000063,Historical homology that involves orthologous pairs of interacting molecules in different organisms.,http://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_HOM0000053,"Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.",http://purl.obolibrary.org/obo/RO_HOM0000018 +http://purl.obolibrary.org/obo/RO_HOM0000072,Biological homology that involves an ectopic structure and the normally positioned structure.,http://purl.obolibrary.org/obo/RO_HOM0000008 +http://purl.obolibrary.org/obo/RO_0002314,q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.,http://purl.obolibrary.org/obo/RO_0002502 +http://purl.obolibrary.org/obo/RO_0002522,"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",http://purl.obolibrary.org/obo/RO_0002514 +http://purl.obolibrary.org/obo/RO_0002323,A mereological relationship or a topological relationship, +http://purl.obolibrary.org/obo/RO_0002411,p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain,http://purl.obolibrary.org/obo/BFO_0000063 http://purl.obolibrary.org/obo/RO_0002418 +http://purl.obolibrary.org/obo/BFO_0000062,"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.",http://purl.obolibrary.org/obo/RO_0002086 +http://purl.obolibrary.org/obo/RO_0002212,"x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y",http://purl.obolibrary.org/obo/RO_0002211 +http://purl.obolibrary.org/obo/RO_0002296,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.,http://purl.obolibrary.org/obo/RO_0000057 http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0002163,A is spatially_disjoint_from B if and only if they have no parts in common,http://purl.obolibrary.org/obo/RO_0002323 +http://purl.obolibrary.org/obo/RO_HOM0000032,Paedomorphosis that is produced by a retardation of somatic development.,http://purl.obolibrary.org/obo/RO_HOM0000029 +http://purl.obolibrary.org/obo/RO_0002385,x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y,http://purl.obolibrary.org/obo/RO_0002384 +http://purl.obolibrary.org/obo/RO_0002614,A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.,http://purl.obolibrary.org/obo/RO_0002616 +http://purl.obolibrary.org/obo/RO_0002528,inverse of downstream of sequence of,http://purl.obolibrary.org/obo/RO_0002527 +http://purl.obolibrary.org/obo/RO_HOM0000010,Structural homology that is detected by similarity in content and organization between chromosomes.,http://purl.obolibrary.org/obo/RO_HOM0000006 +http://purl.obolibrary.org/obo/RO_0002438,An interaction relationship in which the partners are related via a feeding relationship.,http://purl.obolibrary.org/obo/RO_0002574 +http://purl.obolibrary.org/obo/RO_0002087,,http://purl.obolibrary.org/obo/BFO_0000062 +http://purl.obolibrary.org/obo/RO_HOM0000073,Synology that results from allopolyploidy.,http://purl.obolibrary.org/obo/RO_HOM0000053 http://purl.obolibrary.org/obo/RO_HOM0000022 +http://purl.obolibrary.org/obo/RO_0002179,"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.",http://purl.obolibrary.org/obo/RO_0002170 +http://purl.obolibrary.org/obo/RO_0003301,"Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", +http://purl.obolibrary.org/obo/RO_0000092,,http://purl.obolibrary.org/obo/RO_0000052 +http://purl.obolibrary.org/obo/RO_0002495,"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",http://purl.obolibrary.org/obo/RO_0002207 http://purl.obolibrary.org/obo/RO_0002494 http://purl.obolibrary.org/obo/RO_0002087 +http://purl.obolibrary.org/obo/RO_0002286,Inverse of developmentally preceded by,http://purl.obolibrary.org/obo/RO_0002384 +http://purl.obolibrary.org/obo/RO_0002618,,http://purl.obolibrary.org/obo/RO_0002574 +http://purl.obolibrary.org/obo/RO_0002493,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).,http://purl.obolibrary.org/obo/RO_0002492 +http://purl.obolibrary.org/obo/RO_0002388,x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y,http://purl.obolibrary.org/obo/RO_0002387 +http://purl.obolibrary.org/obo/RO_0002008,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.,http://purl.obolibrary.org/obo/RO_0002323 +http://purl.obolibrary.org/obo/RO_0002570,"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.",http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002553,x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y,http://purl.obolibrary.org/obo/RO_0002454 +http://purl.obolibrary.org/obo/RO_0002229,inverse of ends with,http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/RO_0002222 +http://purl.obolibrary.org/obo/RO_0002630,"p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p",http://purl.obolibrary.org/obo/RO_0002212 http://purl.obolibrary.org/obo/RO_0002578 +http://purl.obolibrary.org/obo/RO_0002372,"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.",http://purl.obolibrary.org/obo/RO_0002371 http://purl.obolibrary.org/obo/RO_0002567 +http://purl.obolibrary.org/obo/RO_0002088,,http://purl.obolibrary.org/obo/RO_0002222 +http://purl.obolibrary.org/obo/RO_0002606,"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.",http://purl.obolibrary.org/obo/RO_0002599 +http://purl.obolibrary.org/obo/RO_0002107,A relation between a motor neuron and a muscle that it synapses to via a type II bouton.,http://purl.obolibrary.org/obo/RO_0002120 +http://purl.obolibrary.org/obo/RO_0002180,"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.",http://purl.obolibrary.org/obo/BFO_0000051 +http://purl.obolibrary.org/obo/RO_0002497,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.,http://purl.obolibrary.org/obo/RO_0002487 +http://purl.obolibrary.org/obo/RO_HOM0000007,Homology that is defined by common descent.,http://purl.obolibrary.org/obo/RO_HOM0000001 +http://purl.obolibrary.org/obo/RO_0002619,,http://purl.obolibrary.org/obo/RO_0002574 +http://purl.obolibrary.org/obo/RO_HOM0000025,"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://purl.obolibrary.org/obo/RO_HOM0000034 +http://purl.obolibrary.org/obo/RO_0002450,Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b.,http://purl.obolibrary.org/obo/RO_0002448 +http://purl.obolibrary.org/obo/RO_HOM0000074,"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://purl.obolibrary.org/obo/RO_HOM0000066 http://purl.obolibrary.org/obo/RO_HOM0000003 +http://purl.obolibrary.org/obo/RO_0002501,"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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.",http://purl.obolibrary.org/obo/RO_0002410 +http://purl.obolibrary.org/obo/RO_0002360,,http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002478,A child nucleus relationship in which the cells are part of a male organism,http://purl.obolibrary.org/obo/RO_0002476 +http://purl.obolibrary.org/obo/RO_0002481,,http://purl.obolibrary.org/obo/RO_0002564 +http://purl.obolibrary.org/obo/RO_HOM0000015,"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://purl.obolibrary.org/obo/RO_HOM0000006 +http://purl.obolibrary.org/obo/RO_0002287,,http://purl.obolibrary.org/obo/RO_0002286 +http://purl.obolibrary.org/obo/RO_0002293,inverse of ubiquiotously expressed in,http://purl.obolibrary.org/obo/RO_0002292 +http://purl.obolibrary.org/obo/RO_HOM0000049,Paralogy that involves genes from the same species.,http://purl.obolibrary.org/obo/RO_HOM0000011 +http://purl.obolibrary.org/obo/RO_0002590,,http://purl.obolibrary.org/obo/RO_0002592 http://purl.obolibrary.org/obo/RO_0002586 +http://purl.obolibrary.org/obo/RO_HOM0000000,Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison., +http://purl.obolibrary.org/obo/RO_HOM0000054,Orthology that involves functional equivalent genes with retention of the ancestral function.,http://purl.obolibrary.org/obo/RO_HOM0000062 http://purl.obolibrary.org/obo/RO_HOM0000017 +http://purl.obolibrary.org/obo/RO_0002232,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,http://purl.obolibrary.org/obo/RO_0002479 +http://purl.obolibrary.org/obo/RO_HOM0000062,Historical homology that involves functional equivalent genes with retention of the ancestral function.,http://purl.obolibrary.org/obo/RO_HOM0000007 http://purl.obolibrary.org/obo/RO_HOM0000065 +http://purl.obolibrary.org/obo/RO_0002482,,http://purl.obolibrary.org/obo/RO_0002564 +http://purl.obolibrary.org/obo/RO_0002470,,http://purl.obolibrary.org/obo/RO_0002438 +http://purl.obolibrary.org/obo/RO_0002591,,http://purl.obolibrary.org/obo/RO_0002233 http://purl.obolibrary.org/obo/RO_0002592 +http://purl.obolibrary.org/obo/RO_HOM0000047,Historical homology that involves the chromosomes able to pair (synapse) during meiosis.,http://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_HOM0000075,Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.,http://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_HOM0000052,Peramorphosis that is produced by a delay in the offset of development.,http://purl.obolibrary.org/obo/RO_HOM0000030 +http://purl.obolibrary.org/obo/RO_0002324,A relationship that holds between entities participating in some developmental process (GO:0032502), +http://purl.obolibrary.org/obo/RO_0002299,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.,http://purl.obolibrary.org/obo/RO_0000057 http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0002519,inverse of has end sequence,http://purl.obolibrary.org/obo/RO_0002525 +http://purl.obolibrary.org/obo/RO_0002573,A relation that holds between an attribute or a qualifier and another attribute., +http://purl.obolibrary.org/obo/RO_0002225,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,http://purl.obolibrary.org/obo/RO_0002202 +http://purl.obolibrary.org/obo/RO_0002113,Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.,http://purl.obolibrary.org/obo/RO_0002130 +http://purl.obolibrary.org/obo/RO_0003302,"A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition.",http://purl.obolibrary.org/obo/RO_0002410 +http://purl.obolibrary.org/obo/RO_0002233,"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.",http://purl.obolibrary.org/obo/RO_0000057 +http://purl.obolibrary.org/obo/RO_0002490,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)),http://purl.obolibrary.org/obo/RO_0002487 +http://purl.obolibrary.org/obo/RO_0001020,"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.",http://purl.obolibrary.org/obo/RO_0003302 +http://purl.obolibrary.org/obo/RO_HOM0000058,"Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.",http://purl.obolibrary.org/obo/RO_HOM0000003 +http://purl.obolibrary.org/obo/RO_0002297,,http://purl.obolibrary.org/obo/RO_0002234 http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0003307,"A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition.",http://purl.obolibrary.org/obo/RO_0002410 +http://purl.obolibrary.org/obo/BFO_0000060,, +http://purl.obolibrary.org/obo/RO_0002010,"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).",http://purl.obolibrary.org/obo/RO_0002418 +http://purl.obolibrary.org/obo/RO_0002496,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).,http://purl.obolibrary.org/obo/RO_0002487 +http://purl.obolibrary.org/obo/RO_0002162,"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.",http://purl.obolibrary.org/obo/RO_0002320 +http://purl.obolibrary.org/obo/RO_0002158,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.,http://purl.obolibrary.org/obo/RO_0002320 +http://purl.obolibrary.org/obo/RO_0002632,A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host,http://purl.obolibrary.org/obo/RO_0002444 +http://purl.obolibrary.org/obo/RO_0002205,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,http://purl.obolibrary.org/obo/RO_0002330 +http://purl.obolibrary.org/obo/RO_0002213,"x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y",http://purl.obolibrary.org/obo/RO_0002211 +http://purl.obolibrary.org/obo/RO_0002373,"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.",http://purl.obolibrary.org/obo/RO_0002371 http://purl.obolibrary.org/obo/RO_0002567 +http://purl.obolibrary.org/obo/RO_0002413,p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c,http://purl.obolibrary.org/obo/RO_0002414 http://purl.obolibrary.org/obo/RO_0002412 +http://purl.obolibrary.org/obo/RO_0003304,"A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition.",http://purl.obolibrary.org/obo/RO_0003302 +http://purl.obolibrary.org/obo/RO_0002567,A relation that holds between elements of a musculoskeletal system or its analogs.,http://purl.obolibrary.org/obo/RO_0002328 +http://purl.obolibrary.org/obo/RO_0002476,"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",http://purl.obolibrary.org/obo/RO_0002258 +http://purl.obolibrary.org/obo/RO_0002526,x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.,http://purl.obolibrary.org/obo/RO_0002514 http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002298,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.,http://purl.obolibrary.org/obo/RO_0000057 http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0000059,"A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.", +http://purl.obolibrary.org/obo/RO_0002134,"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. +T innervates some R +Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.",http://www.w3.org/2002/07/owl#topObjectProperty +http://purl.obolibrary.org/obo/RO_HOM0000027,Iterative homology that involves structures arranged along the main body axis.,http://purl.obolibrary.org/obo/RO_HOM0000066 +http://purl.obolibrary.org/obo/RO_0002381,"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.",http://purl.obolibrary.org/obo/RO_0002375 +http://purl.obolibrary.org/obo/RO_0002130,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.,http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002132,The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.,http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002237,"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.",http://purl.obolibrary.org/obo/RO_0002444 +http://purl.obolibrary.org/obo/RO_0002477,A child nucleus relationship in which the cells are part of a hermaphroditic organism,http://purl.obolibrary.org/obo/RO_0002476 +http://purl.obolibrary.org/obo/RO_0002451,A relationship that holds between a disease and organism,http://purl.obolibrary.org/obo/RO_0002321 +http://purl.obolibrary.org/obo/RO_0000053,"a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence", +http://purl.obolibrary.org/obo/RO_0002461,,http://purl.obolibrary.org/obo/RO_0000056 +http://purl.obolibrary.org/obo/RO_0002428,c involved in regulation of p if c is involved in some 'p' and p' regulates some p,http://purl.obolibrary.org/obo/RO_0002431 +http://purl.obolibrary.org/obo/RO_0002525,inverse of has subsequence,http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/RO_0002523 http://purl.obolibrary.org/obo/RO_0002526 +http://purl.obolibrary.org/obo/RO_HOM0000019,Historical homology that involves two members sharing no other homologs in the lineages considered.,http://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_0002012,A part of relation that applies only between occurents.,http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/RO_0002418 +http://purl.obolibrary.org/obo/RO_0002352,,http://purl.obolibrary.org/obo/RO_0002328 http://purl.obolibrary.org/obo/RO_0000056 +http://purl.obolibrary.org/obo/RO_0002231,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,http://purl.obolibrary.org/obo/RO_0002479 +http://purl.obolibrary.org/obo/RO_0002255,,http://purl.obolibrary.org/obo/RO_0002286 http://purl.obolibrary.org/obo/RO_0002385 +http://purl.obolibrary.org/obo/RO_0002001,, +http://purl.obolibrary.org/obo/RO_0000300,"A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.", +http://purl.obolibrary.org/obo/RO_0002485,,http://purl.obolibrary.org/obo/RO_0002170 +http://purl.obolibrary.org/obo/RO_0002106,A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.,http://purl.obolibrary.org/obo/RO_0002120 +http://purl.obolibrary.org/obo/RO_0002151,"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",http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_HOM0000044,Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.,http://purl.obolibrary.org/obo/RO_HOM0000003 http://purl.obolibrary.org/obo/RO_HOM0000005 +http://purl.obolibrary.org/obo/RO_HOM0000042,"Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.",http://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_0002159,,http://purl.obolibrary.org/obo/RO_0002320 +http://purl.obolibrary.org/obo/RO_0002434,A relationship that holds between two entities in which the processes executed by the two entities are causally connected., +http://purl.obolibrary.org/obo/RO_0002000,"a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity",http://purl.obolibrary.org/obo/RO_0002323 +http://purl.obolibrary.org/obo/RO_0002442,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).,http://purl.obolibrary.org/obo/RO_0002440 +http://purl.obolibrary.org/obo/RO_0002230,"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.",http://purl.obolibrary.org/obo/RO_0002222 http://purl.obolibrary.org/obo/BFO_0000051 +http://purl.obolibrary.org/obo/RO_0002011,A relationship that holds between a process that regulates a transport process and the entity transported by that process., +http://purl.obolibrary.org/obo/RO_0002462,,http://purl.obolibrary.org/obo/RO_0002461 +http://purl.obolibrary.org/obo/RO_0002160,"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.",http://purl.obolibrary.org/obo/RO_0002162 +http://purl.obolibrary.org/obo/RO_0002353,,http://purl.obolibrary.org/obo/RO_0002328 http://purl.obolibrary.org/obo/RO_0000056 +http://purl.obolibrary.org/obo/RO_0002111,,http://www.w3.org/2002/07/owl#topObjectProperty +http://purl.obolibrary.org/obo/RO_0002244,,http://purl.obolibrary.org/obo/RO_0002410 +http://purl.obolibrary.org/obo/RO_0002486,,http://purl.obolibrary.org/obo/RO_0002170 +http://purl.obolibrary.org/obo/RO_0002115,"Relation between a muscle and a motor neuron that synapses to it via a type III bouton. +",http://purl.obolibrary.org/obo/RO_0002103 +http://purl.obolibrary.org/obo/RO_0002571,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.,http://purl.obolibrary.org/obo/BFO_0000050 +http://purl.obolibrary.org/obo/RO_0002177,"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.",http://purl.obolibrary.org/obo/RO_0002323 http://purl.obolibrary.org/obo/RO_0002567 +http://purl.obolibrary.org/obo/RO_0002520,"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.",http://purl.obolibrary.org/obo/RO_0002524 +http://purl.obolibrary.org/obo/RO_0002578,"p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p",http://purl.obolibrary.org/obo/RO_0002211 http://purl.obolibrary.org/obo/RO_0002412 +http://purl.obolibrary.org/obo/RO_0002471,,http://purl.obolibrary.org/obo/RO_0002438 +http://purl.obolibrary.org/obo/RO_0002236,A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005),http://purl.obolibrary.org/obo/RO_0002444 +http://purl.obolibrary.org/obo/RO_0002253,,http://purl.obolibrary.org/obo/RO_0002375 +http://purl.obolibrary.org/obo/RO_0000081,"a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence",http://purl.obolibrary.org/obo/RO_0000052 +http://purl.obolibrary.org/obo/RO_0002488,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).,http://purl.obolibrary.org/obo/RO_0002490 http://purl.obolibrary.org/obo/RO_0002496 +http://purl.obolibrary.org/obo/RO_0000086,"a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence",http://purl.obolibrary.org/obo/RO_0000053 +http://purl.obolibrary.org/obo/RO_HOM0000055,Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.,http://purl.obolibrary.org/obo/RO_HOM0000011 +http://purl.obolibrary.org/obo/RO_0002615,Inverse of is-model-of, +http://purl.obolibrary.org/obo/RO_0002215,"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. ",http://purl.obolibrary.org/obo/RO_0002216 +http://purl.obolibrary.org/obo/RO_HOM0000069,Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.,http://purl.obolibrary.org/obo/RO_HOM0000011 +http://www.w3.org/2002/07/owl#topObjectProperty,, +http://purl.obolibrary.org/obo/RO_0002004,The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).,http://purl.obolibrary.org/obo/RO_0001018 +http://purl.obolibrary.org/obo/RO_0002202,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,http://purl.obolibrary.org/obo/RO_0002258 +http://purl.obolibrary.org/obo/RO_0002572,s is luminal space of x iff s is lumen_of x and s is an immaterial entity,http://purl.obolibrary.org/obo/RO_0002571 +http://purl.obolibrary.org/obo/RO_0000085,"a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence",http://purl.obolibrary.org/obo/RO_0000053 +http://purl.obolibrary.org/obo/RO_0002339,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.,http://purl.obolibrary.org/obo/RO_0002344 +http://purl.obolibrary.org/obo/RO_0002448,Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b,http://purl.obolibrary.org/obo/RO_0002566 http://purl.obolibrary.org/obo/RO_0002436 +http://purl.obolibrary.org/obo/RO_0002460,,http://purl.obolibrary.org/obo/RO_0002459 +http://purl.obolibrary.org/obo/RO_HOM0000011,Historical homology that involves genes that diverged after a duplication event.,http://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_HOM0000029,Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.,http://purl.obolibrary.org/obo/RO_HOM0000028 +http://purl.obolibrary.org/obo/RO_0002157,,http://purl.obolibrary.org/obo/RO_0002320 +http://purl.obolibrary.org/obo/RO_0002292,Inverse of 'expressed in',http://purl.obolibrary.org/obo/RO_0002330 +http://purl.obolibrary.org/obo/BFO_0000066,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, +http://purl.obolibrary.org/obo/RO_0002248,"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.",http://purl.obolibrary.org/obo/BFO_0000051 +http://purl.obolibrary.org/obo/RO_HOM0000004,Homoplasy that involves different underlying mechanisms or structures.,http://purl.obolibrary.org/obo/RO_HOM0000002 +http://purl.obolibrary.org/obo/RO_0003002,Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b.,http://purl.obolibrary.org/obo/RO_0002449 +http://purl.obolibrary.org/obo/RO_HOM0000012,Paralogy that involves sets of syntenic blocks.,http://purl.obolibrary.org/obo/RO_HOM0000011 http://purl.obolibrary.org/obo/RO_HOM0000010 +http://purl.obolibrary.org/obo/RO_0002465,,http://purl.obolibrary.org/obo/RO_0002563 +http://purl.obolibrary.org/obo/RO_0002344,,http://purl.obolibrary.org/obo/RO_0002337 +http://purl.obolibrary.org/obo/RO_0002574,,http://purl.obolibrary.org/obo/RO_0002437 +http://purl.obolibrary.org/obo/RO_0002453,,http://purl.obolibrary.org/obo/RO_0002440 +http://purl.obolibrary.org/obo/BFO_0000054,, +http://purl.obolibrary.org/obo/RO_HOM0000005,Homoplasy that involves homologous underlying mechanisms or structures.,http://purl.obolibrary.org/obo/RO_HOM0000002 +http://purl.obolibrary.org/obo/RO_0002110,Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. ,http://purl.obolibrary.org/obo/RO_0002130 +http://purl.obolibrary.org/obo/RO_0002566,"Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b",http://purl.obolibrary.org/obo/RO_0002506 +http://purl.obolibrary.org/obo/BFO_0000051,a core relation that holds between a whole and its part,http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002234,"p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.",http://purl.obolibrary.org/obo/RO_0000057 +http://purl.obolibrary.org/obo/RO_0002103,Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. ,http://purl.obolibrary.org/obo/RO_0000301 +http://purl.obolibrary.org/obo/RO_0002452,A relation that holds between a disease or an organism and a phenotype,http://purl.obolibrary.org/obo/RO_0002200 +http://purl.obolibrary.org/obo/RO_0002006,,http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002285,"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",http://purl.obolibrary.org/obo/RO_0002258 +http://purl.obolibrary.org/obo/RO_0002492,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).,http://purl.obolibrary.org/obo/RO_0002490 http://purl.obolibrary.org/obo/RO_0002497 +http://purl.obolibrary.org/obo/RO_0002517,inverse of has start sequence,http://purl.obolibrary.org/obo/RO_0002525 +http://purl.obolibrary.org/obo/RO_0002446,"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.",http://purl.obolibrary.org/obo/RO_0002437 +http://purl.obolibrary.org/obo/RO_HOM0000014,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/RO_HOM0000006 +http://purl.obolibrary.org/obo/RO_0002466,,http://purl.obolibrary.org/obo/RO_0002465 +http://purl.obolibrary.org/obo/RO_0002587,,http://purl.obolibrary.org/obo/RO_0002297 +http://purl.obolibrary.org/obo/RO_0002454,,http://purl.obolibrary.org/obo/RO_0002440 +http://purl.obolibrary.org/obo/RO_0002563,,http://purl.obolibrary.org/obo/RO_0002464 +http://purl.obolibrary.org/obo/RO_0002345,,http://purl.obolibrary.org/obo/RO_0002313 +http://purl.obolibrary.org/obo/RO_0002430,,http://purl.obolibrary.org/obo/RO_0002428 +http://purl.obolibrary.org/obo/RO_0002595,"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.",http://purl.obolibrary.org/obo/RO_0002410 +http://purl.obolibrary.org/obo/RO_0002505,"p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c",http://purl.obolibrary.org/obo/RO_0000057 +http://purl.obolibrary.org/obo/RO_HOM0000028,"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/RO_HOM0000008 +http://purl.obolibrary.org/obo/RO_0002589,"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.",http://purl.obolibrary.org/obo/RO_0002586 +http://purl.obolibrary.org/obo/RO_0002414,transitive form of directly_provides_input_for,http://purl.obolibrary.org/obo/RO_0002411 +http://purl.obolibrary.org/obo/RO_0002220,x adjacent to y if and only if x and y share a boundary.,http://purl.obolibrary.org/obo/RO_0002163 +http://purl.obolibrary.org/obo/RO_0002256,"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 anatomical structure type T to T', where T' develops_from T",http://purl.obolibrary.org/obo/RO_0002258 +http://purl.obolibrary.org/obo/RO_0002494,"x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships",http://purl.obolibrary.org/obo/RO_0002202 http://purl.obolibrary.org/obo/BFO_0000062 +http://purl.obolibrary.org/obo/RO_0002380,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,http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/RO_0002375 +http://purl.obolibrary.org/obo/RO_0002608,Inverse of 'causal agent in',http://purl.obolibrary.org/obo/RO_0002410 +http://purl.obolibrary.org/obo/RO_0002249,,http://purl.obolibrary.org/obo/BFO_0000050 +http://purl.obolibrary.org/obo/RO_0002467,,http://purl.obolibrary.org/obo/RO_0002465 +http://purl.obolibrary.org/obo/RO_0002588,,http://purl.obolibrary.org/obo/RO_0002592 http://purl.obolibrary.org/obo/RO_0002297 +http://purl.obolibrary.org/obo/RO_0002218,x has participant y if and only if x realizes some active role that inheres in y,http://purl.obolibrary.org/obo/RO_0000057 +http://purl.obolibrary.org/obo/RO_0002221,,http://purl.obolibrary.org/obo/RO_0002220 +http://purl.obolibrary.org/obo/RO_0002487,, +http://purl.obolibrary.org/obo/RO_0002354,,http://purl.obolibrary.org/obo/RO_0002353 +http://purl.obolibrary.org/obo/RO_0002463,,http://purl.obolibrary.org/obo/RO_0002461 +http://purl.obolibrary.org/obo/RO_HOM0000020,Orthology that involves two genes that did not experience any duplication after the speciation event that created them.,http://purl.obolibrary.org/obo/RO_HOM0000017 http://purl.obolibrary.org/obo/RO_HOM0000019 +http://purl.obolibrary.org/obo/RO_0002443,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).,http://purl.obolibrary.org/obo/RO_0002440 +http://purl.obolibrary.org/obo/RO_0002325,a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].,http://purl.obolibrary.org/obo/RO_0002323 +http://purl.obolibrary.org/obo/RO_HOM0000045,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://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_0002246,"g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.",http://purl.obolibrary.org/obo/RO_0002206 +http://purl.obolibrary.org/obo/RO_0002295,"p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure 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).",http://purl.obolibrary.org/obo/RO_0002324 +http://purl.obolibrary.org/obo/RO_0002382,x proper_distributary_of y iff x distributary_of y and x does not flow back into y,http://purl.obolibrary.org/obo/RO_0002377 +http://purl.obolibrary.org/obo/RO_0001025,"a relation between two independent continuants, the target and the location, in which the target is entirely within the location", +http://purl.obolibrary.org/obo/RO_0002210,,http://purl.obolibrary.org/obo/RO_0002203 +http://purl.obolibrary.org/obo/RO_0002222,, +http://purl.obolibrary.org/obo/RO_0002343,,http://purl.obolibrary.org/obo/RO_0000057 http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0002585,,http://purl.obolibrary.org/obo/RO_0000057 http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0002464,, +http://purl.obolibrary.org/obo/BFO_0000055,, +http://purl.obolibrary.org/obo/RO_0002489,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).,http://purl.obolibrary.org/obo/RO_0002488 +http://purl.obolibrary.org/obo/RO_0002412,"p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.",http://purl.obolibrary.org/obo/RO_0002090 http://purl.obolibrary.org/obo/RO_0002411 +http://purl.obolibrary.org/obo/RO_0002552,"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.",http://purl.obolibrary.org/obo/RO_0000057 http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0002350,is member of is a mereological relation between a item and a collection.,http://purl.obolibrary.org/obo/BFO_0000050 +http://purl.obolibrary.org/obo/RO_0002351,has member is a mereological relation between a collection and an item.,http://purl.obolibrary.org/obo/BFO_0000051 +http://purl.obolibrary.org/obo/RO_0003305,"A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual.",http://purl.obolibrary.org/obo/RO_0003304 +http://purl.obolibrary.org/obo/RO_0003001,a produced_by b iff some process that occurs_in b has_output a., +http://purl.obolibrary.org/obo/RO_0002005,, +http://purl.obolibrary.org/obo/RO_0002607,"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.",http://purl.obolibrary.org/obo/RO_0002610 +http://purl.obolibrary.org/obo/RO_0002105,A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.,http://purl.obolibrary.org/obo/RO_0002120 +http://purl.obolibrary.org/obo/RO_0002387,x has the potential to develop into y iff x develops into y or if x is capable of developing into y,http://purl.obolibrary.org/obo/RO_0002384 +http://purl.obolibrary.org/obo/RO_0002315,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,http://purl.obolibrary.org/obo/RO_0000057 http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0002337,A relationship that holds via some process of localization, +http://purl.obolibrary.org/obo/RO_0002554,,http://purl.obolibrary.org/obo/RO_0002453 +http://purl.obolibrary.org/obo/RO_0002204,"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""",http://purl.obolibrary.org/obo/RO_0002330 +http://purl.obolibrary.org/obo/RO_0002300,,http://purl.obolibrary.org/obo/RO_0002552 +http://purl.obolibrary.org/obo/RO_HOM0000071,Structural homology that involves structures with the same or similar relative positions.,http://purl.obolibrary.org/obo/RO_HOM0000006 +http://purl.obolibrary.org/obo/RO_0002312,,http://purl.obolibrary.org/obo/RO_0002320 +http://purl.obolibrary.org/obo/RO_0002510,x is transcribed from y if and only if x is synthesized from template y,http://purl.obolibrary.org/obo/RO_0002330 +http://purl.obolibrary.org/obo/RO_0001019,, +http://purl.obolibrary.org/obo/RO_0002156,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.,http://purl.obolibrary.org/obo/RO_0002320 +http://purl.obolibrary.org/obo/RO_0000058,"A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.", +http://purl.obolibrary.org/obo/RO_0001001,"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", +http://purl.obolibrary.org/obo/RO_HOM0000057,"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://purl.obolibrary.org/obo/RO_HOM0000058 http://purl.obolibrary.org/obo/RO_HOM0000005 +http://purl.obolibrary.org/obo/RO_0002600,"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.",http://purl.obolibrary.org/obo/RO_0002598 +http://purl.obolibrary.org/obo/RO_0002131,x overlaps y if and only if there exists some z such that x has part z and z part of y,http://purl.obolibrary.org/obo/RO_0002323 +http://purl.obolibrary.org/obo/RO_0002473,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.,http://purl.obolibrary.org/obo/BFO_0000051 +http://purl.obolibrary.org/obo/RO_0002458,,http://purl.obolibrary.org/obo/RO_0002438 +http://purl.obolibrary.org/obo/RO_0002406,p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q,http://purl.obolibrary.org/obo/RO_0002629 +http://purl.obolibrary.org/obo/RO_0002555,,http://purl.obolibrary.org/obo/RO_0002574 +http://purl.obolibrary.org/obo/RO_0002379,x spatially_coextensive_with y if and inly if x and y have the same location,http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002301,,http://purl.obolibrary.org/obo/RO_0002552 +http://purl.obolibrary.org/obo/RO_0001018,, +http://purl.obolibrary.org/obo/RO_0000080,"a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence",http://purl.obolibrary.org/obo/RO_0000052 +http://purl.obolibrary.org/obo/RO_HOM0000002,Similarity that results from independent evolution.,http://purl.obolibrary.org/obo/RO_HOM0000000 +http://purl.obolibrary.org/obo/BFO_0000067,[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, +http://purl.obolibrary.org/obo/RO_0002384,"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).",http://purl.obolibrary.org/obo/RO_0002324 +http://purl.obolibrary.org/obo/RO_HOM0000060,Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.,http://purl.obolibrary.org/obo/RO_HOM0000050 http://purl.obolibrary.org/obo/RO_HOM0000019 +http://purl.obolibrary.org/obo/RO_0002235,A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047),http://purl.obolibrary.org/obo/RO_0002444 +http://purl.obolibrary.org/obo/RO_0002640,A sub-relation of endoparasite-of in which the parasite inhabits host cells.,http://purl.obolibrary.org/obo/RO_0002634 +http://purl.obolibrary.org/obo/RO_0000079,"a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence",http://purl.obolibrary.org/obo/RO_0000052 +http://purl.obolibrary.org/obo/RO_0002459,,http://purl.obolibrary.org/obo/RO_0002574 +http://purl.obolibrary.org/obo/RO_0002447,,http://purl.obolibrary.org/obo/RO_0002436 +http://purl.obolibrary.org/obo/RO_0002407,p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q,http://purl.obolibrary.org/obo/RO_0002213 +http://purl.obolibrary.org/obo/RO_0002556,,http://purl.obolibrary.org/obo/RO_0002454 +http://purl.obolibrary.org/obo/RO_0002435,,http://purl.obolibrary.org/obo/RO_0002434 +http://purl.obolibrary.org/obo/RO_0002326,,http://purl.obolibrary.org/obo/RO_0002216 http://purl.obolibrary.org/obo/RO_0002329 +http://purl.obolibrary.org/obo/RO_HOM0000009,Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.,http://purl.obolibrary.org/obo/RO_HOM0000002 +http://purl.obolibrary.org/obo/RO_0002609,"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.", +http://purl.obolibrary.org/obo/RO_0002101,"relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. +",http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002410,This relation groups causal relations between material entities and causal relations between processes,http://purl.obolibrary.org/obo/RO_0002609 +http://purl.obolibrary.org/obo/RO_0002638,A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.,http://purl.obolibrary.org/obo/RO_0002634 +http://purl.obolibrary.org/obo/RO_HOM0000016,Structural homology that involves a pseudogenic feature and its functional ancestor.,http://purl.obolibrary.org/obo/RO_HOM0000006 +http://purl.obolibrary.org/obo/RO_0002245,"g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.",http://purl.obolibrary.org/obo/RO_0002206 +http://purl.obolibrary.org/obo/RO_0002576,,http://purl.obolibrary.org/obo/BFO_0000050 +http://purl.obolibrary.org/obo/RO_0002455,,http://purl.obolibrary.org/obo/RO_0002442 +http://purl.obolibrary.org/obo/RO_0002564,,http://purl.obolibrary.org/obo/RO_0002563 +http://purl.obolibrary.org/obo/RO_0002201,,http://www.w3.org/2002/07/owl#topObjectProperty +http://purl.obolibrary.org/obo/RO_0002322,,http://purl.obolibrary.org/obo/RO_0002321 +http://purl.obolibrary.org/obo/RO_0002418,"p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.",http://purl.obolibrary.org/obo/RO_0002501 +http://purl.obolibrary.org/obo/RO_0002432,c executes activity in d if and only if c enables p and p occurs_in d,http://purl.obolibrary.org/obo/RO_0002328 +http://purl.obolibrary.org/obo/RO_0002321,A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297), +http://purl.obolibrary.org/obo/RO_0001000,"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", +http://purl.obolibrary.org/obo/RO_HOM0000031,Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.,http://purl.obolibrary.org/obo/RO_HOM0000029 +http://purl.obolibrary.org/obo/RO_0002170,"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",http://purl.obolibrary.org/obo/RO_0002323 +http://purl.obolibrary.org/obo/RO_0002208,A parasite that kills or sterilizes its host,http://purl.obolibrary.org/obo/RO_0002444 +http://purl.obolibrary.org/obo/RO_0002530,"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",http://purl.obolibrary.org/obo/RO_0002515 http://purl.obolibrary.org/obo/RO_0002529 +http://purl.obolibrary.org/obo/RO_0002206,"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",http://purl.obolibrary.org/obo/RO_0002330 +http://purl.obolibrary.org/obo/RO_HOM0000023,Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.,http://purl.obolibrary.org/obo/RO_HOM0000011 +http://purl.obolibrary.org/obo/RO_0002335,,http://purl.obolibrary.org/obo/RO_0002334 +http://purl.obolibrary.org/obo/RO_0002468,,http://purl.obolibrary.org/obo/RO_0002465 +http://purl.obolibrary.org/obo/RO_0002456,,http://purl.obolibrary.org/obo/RO_0002442 +http://purl.obolibrary.org/obo/RO_0002512,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,http://purl.obolibrary.org/obo/RO_0002330 +http://purl.obolibrary.org/obo/RO_0002444,,http://purl.obolibrary.org/obo/RO_0002443 http://purl.obolibrary.org/obo/RO_0002454 +http://purl.obolibrary.org/obo/RO_0002568,"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.",http://purl.obolibrary.org/obo/RO_0002567 +http://purl.obolibrary.org/obo/RO_0002513,inverse of ribosomal translation of,http://purl.obolibrary.org/obo/RO_0002330 +http://purl.obolibrary.org/obo/RO_0002507,"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.",http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/RO_0002559 http://purl.obolibrary.org/obo/RO_0002509 +http://purl.obolibrary.org/obo/RO_0002527,x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.,http://purl.obolibrary.org/obo/RO_0002514 +http://purl.obolibrary.org/obo/RO_0002338,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.,http://purl.obolibrary.org/obo/RO_0002344 +http://purl.obolibrary.org/obo/RO_0002150,X continuous_with Y if and only if X and Y share a fiat boundary.,http://purl.obolibrary.org/obo/RO_0002323 +http://purl.obolibrary.org/obo/RO_HOM0000061,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://purl.obolibrary.org/obo/RO_HOM0000018 +http://purl.obolibrary.org/obo/RO_0002227,A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.,http://purl.obolibrary.org/obo/RO_0002444 +http://purl.obolibrary.org/obo/RO_0002439,"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",http://purl.obolibrary.org/obo/RO_0002438 +http://purl.obolibrary.org/obo/RO_0002509,"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.",http://purl.obolibrary.org/obo/RO_0002506 http://purl.obolibrary.org/obo/RO_0002131 +http://purl.obolibrary.org/obo/RO_0002009,"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.",http://purl.obolibrary.org/obo/RO_0002292 +http://purl.obolibrary.org/obo/RO_0002121,"Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. + + ",http://purl.obolibrary.org/obo/RO_0002110 +http://purl.obolibrary.org/obo/RO_0002203,,http://purl.obolibrary.org/obo/RO_0002388 http://purl.obolibrary.org/obo/RO_0002286 http://purl.obolibrary.org/obo/RO_0002387 +http://purl.obolibrary.org/obo/RO_0002303,"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.",http://purl.obolibrary.org/obo/RO_0002321 +http://purl.obolibrary.org/obo/RO_0002469,,http://purl.obolibrary.org/obo/RO_0002438 +http://purl.obolibrary.org/obo/RO_0002336,,http://purl.obolibrary.org/obo/RO_0002334 +http://purl.obolibrary.org/obo/RO_0002457,,http://purl.obolibrary.org/obo/RO_0002438 +http://purl.obolibrary.org/obo/RO_0002224,"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.",http://purl.obolibrary.org/obo/RO_0002222 http://purl.obolibrary.org/obo/BFO_0000051 +http://purl.obolibrary.org/obo/RO_0002445,,http://purl.obolibrary.org/obo/RO_0002443 http://purl.obolibrary.org/obo/RO_0002453 +http://purl.obolibrary.org/obo/RO_0000087,"a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence",http://purl.obolibrary.org/obo/RO_0000053 +http://purl.obolibrary.org/obo/RO_0003308,A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.,http://purl.obolibrary.org/obo/RO_0002610 +http://purl.obolibrary.org/obo/RO_0002104,"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.",http://purl.obolibrary.org/obo/BFO_0000051 +http://purl.obolibrary.org/obo/RO_0002178,"Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.",http://purl.obolibrary.org/obo/RO_0002170 +http://purl.obolibrary.org/obo/RO_0002200,"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).",http://www.w3.org/2002/07/owl#topObjectProperty +http://purl.obolibrary.org/obo/RO_0003306,"A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population.",http://purl.obolibrary.org/obo/RO_0003304 +http://purl.obolibrary.org/obo/RO_0002377,"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",http://purl.obolibrary.org/obo/RO_0002375 +http://purl.obolibrary.org/obo/RO_HOM0000050,Paralogy that involves genes from different species.,http://purl.obolibrary.org/obo/RO_HOM0000011 +http://purl.obolibrary.org/obo/RO_0002523,inverse of bounds sequence of,http://purl.obolibrary.org/obo/RO_0002514 +http://purl.obolibrary.org/obo/RO_0002243,A broad relationship between an exposure event or process and a the material an agent takes from the source to the target.,http://purl.obolibrary.org/obo/RO_0002244 +http://purl.obolibrary.org/obo/RO_0002437,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.,http://purl.obolibrary.org/obo/RO_0002434 http://purl.obolibrary.org/obo/RO_0002321 +http://purl.obolibrary.org/obo/RO_HOM0000018,Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.,http://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_0002426,,http://purl.obolibrary.org/obo/RO_0002424 +http://purl.obolibrary.org/obo/RO_HOM0000008,"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://purl.obolibrary.org/obo/RO_HOM0000001 +http://purl.obolibrary.org/obo/RO_0002511,,http://purl.obolibrary.org/obo/RO_0002330 +http://purl.obolibrary.org/obo/RO_HOM0000030,"Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.",http://purl.obolibrary.org/obo/RO_HOM0000028 +http://purl.obolibrary.org/obo/RO_0002217,x actively participates in y if and only if x participates in y and x realizes some active role,http://purl.obolibrary.org/obo/RO_0000056 +http://purl.obolibrary.org/obo/RO_0002559,,http://purl.obolibrary.org/obo/RO_0002506 +http://purl.obolibrary.org/obo/RO_0002374,"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",http://purl.obolibrary.org/obo/RO_0002320 +http://purl.obolibrary.org/obo/RO_0002529,"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.",http://purl.obolibrary.org/obo/RO_0002527 +http://purl.obolibrary.org/obo/RO_0002371,"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",http://purl.obolibrary.org/obo/RO_0002170 http://purl.obolibrary.org/obo/RO_0002177 +http://purl.obolibrary.org/obo/RO_0003303,"A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition.",http://purl.obolibrary.org/obo/RO_0003302 +http://purl.obolibrary.org/obo/RO_0002090,,http://purl.obolibrary.org/obo/BFO_0000063 +http://purl.obolibrary.org/obo/RO_HOM0000066,Biological homology that involves parts of the same organism.,http://purl.obolibrary.org/obo/RO_HOM0000008 +http://purl.obolibrary.org/obo/RO_0002313,Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c,http://purl.obolibrary.org/obo/RO_0002337 http://purl.obolibrary.org/obo/RO_0000057 +http://purl.obolibrary.org/obo/RO_0003000,"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.", +http://purl.obolibrary.org/obo/RO_0002109,Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.,http://purl.obolibrary.org/obo/RO_0002103 +http://purl.obolibrary.org/obo/RO_0002403,,http://purl.obolibrary.org/obo/RO_0002234 +http://purl.obolibrary.org/obo/RO_0002633,,http://purl.obolibrary.org/obo/RO_0002445 +http://purl.obolibrary.org/obo/RO_0002209,,http://purl.obolibrary.org/obo/RO_0002445 +http://purl.obolibrary.org/obo/RO_0002427,,http://purl.obolibrary.org/obo/RO_0002501 +http://purl.obolibrary.org/obo/RO_0002207,"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 participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y",http://purl.obolibrary.org/obo/RO_0002202 +http://purl.obolibrary.org/obo/RO_HOM0000022,Paralogy that results from a whole genome duplication event.,http://purl.obolibrary.org/obo/RO_HOM0000011 +http://purl.obolibrary.org/obo/RO_0002214,"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.", +http://purl.obolibrary.org/obo/RO_0001021,"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.",http://purl.obolibrary.org/obo/RO_0003302 +http://purl.obolibrary.org/obo/RO_0002402,"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. ", +http://purl.obolibrary.org/obo/RO_0000091,"a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence",http://purl.obolibrary.org/obo/RO_0000053 +http://purl.obolibrary.org/obo/RO_0002641,,http://purl.obolibrary.org/obo/RO_0002635 +http://purl.obolibrary.org/obo/RO_0002007,"X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000",http://purl.obolibrary.org/obo/BFO_0000050 +http://purl.obolibrary.org/obo/RO_0000057,"a relation between a process and a continuant, in which the continuant is somehow involved in the process", +http://purl.obolibrary.org/obo/RO_0002598,"Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.",http://purl.obolibrary.org/obo/RO_0002596 +http://purl.obolibrary.org/obo/RO_0002378,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., +http://purl.obolibrary.org/obo/RO_0002480,An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y,http://purl.obolibrary.org/obo/RO_0002436 +http://purl.obolibrary.org/obo/RO_0002258,"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",http://purl.obolibrary.org/obo/RO_0002324 +http://purl.obolibrary.org/obo/RO_HOM0000024,Paralogy that results from a duplication preceding a given speciation event.,http://purl.obolibrary.org/obo/RO_HOM0000011 +http://purl.obolibrary.org/obo/RO_0002569,,http://purl.obolibrary.org/obo/RO_0002375 +http://purl.obolibrary.org/obo/RO_0002531,inverse of immediately downstream of,http://purl.obolibrary.org/obo/RO_0002528 http://purl.obolibrary.org/obo/RO_0002515 +http://purl.obolibrary.org/obo/RO_0002557,,http://purl.obolibrary.org/obo/RO_0002453 +http://purl.obolibrary.org/obo/RO_0002424,, +http://purl.obolibrary.org/obo/RO_0002327,,http://purl.obolibrary.org/obo/RO_0002215 +http://purl.obolibrary.org/obo/RO_HOM0000006,Homology that is defined by similarity with regard to selected structural parameters.,http://purl.obolibrary.org/obo/RO_HOM0000001 +http://purl.obolibrary.org/obo/RO_0002240,"A broad relationship between an exposure event or process and any entity (e.g., a human, human population, or a human organ) that interacts with an exposure stressor during the exposure event",http://purl.obolibrary.org/obo/RO_0002244 +http://purl.obolibrary.org/obo/RO_0002002,"a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity",http://purl.obolibrary.org/obo/RO_0002323 +http://purl.obolibrary.org/obo/RO_0002376,"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.",http://purl.obolibrary.org/obo/RO_0002375 +http://purl.obolibrary.org/obo/RO_0002211,"x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y",http://purl.obolibrary.org/obo/RO_0002411 +http://purl.obolibrary.org/obo/RO_0002348,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.,http://purl.obolibrary.org/obo/RO_0002295 +http://purl.obolibrary.org/obo/RO_0002252,"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.",http://purl.obolibrary.org/obo/RO_0002375 +http://purl.obolibrary.org/obo/RO_HOM0000033,Convergence that results from co-evolution usually involving an evolutionary arms race.,http://purl.obolibrary.org/obo/RO_HOM0000004 +http://purl.obolibrary.org/obo/RO_HOM0000043,Historical homology that is based on distant shared ancestry.,http://purl.obolibrary.org/obo/RO_HOM0000007 +http://purl.obolibrary.org/obo/RO_HOM0000026,"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://purl.obolibrary.org/obo/RO_HOM0000034 +http://purl.obolibrary.org/obo/RO_0002329,"this relation holds between c and p when c is part of some c', and c' is capable of p.",http://purl.obolibrary.org/obo/RO_0002328 +http://purl.obolibrary.org/obo/RO_0002558,,http://purl.obolibrary.org/obo/RO_0002616 +http://purl.obolibrary.org/obo/RO_0002425,,http://purl.obolibrary.org/obo/RO_0002424 +http://purl.obolibrary.org/obo/RO_HOM0000034,Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.,http://purl.obolibrary.org/obo/RO_HOM0000017 http://purl.obolibrary.org/obo/RO_HOM0000037 +http://purl.obolibrary.org/obo/RO_0002401,, +http://purl.obolibrary.org/obo/RO_0002328,, +http://purl.obolibrary.org/obo/RO_HOM0000048,Orthology that involves two genes that experienced duplications more recent than the species split that created them.,http://purl.obolibrary.org/obo/RO_HOM0000036 http://purl.obolibrary.org/obo/RO_HOM0000017 +http://purl.obolibrary.org/obo/RO_0002242,A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor,http://purl.obolibrary.org/obo/RO_0002244 diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 81835da3..4842a86a 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -1,6 +1,6 @@ - + + + + + + + @@ -157,6 +165,17 @@ + + + + Chris Mungall + 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. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + + + + @@ -724,7 +743,6 @@ Where we have an annotation assertion - @@ -733,7 +751,6 @@ Where we have an annotation assertion - @@ -1146,12 +1163,6 @@ AND t has_input y regulates transport of - - - - A relationship that holds between a process that regulates a transport process and the entity transported by that process. - GOC:dos - @@ -1165,12 +1176,6 @@ AND t has_input y A part of relation that applies only between occurents. occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -1803,12 +1808,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -2280,13 +2279,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite that kills or sterilizes its host parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -2540,17 +2532,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - Chris Mungall - 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. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - - - - @@ -2613,12 +2594,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -2629,12 +2604,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -2743,12 +2712,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -2759,12 +2722,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -2775,12 +2732,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.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. hemiparasite of - - - - 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. - - @@ -2868,12 +2819,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.has active pharmaceutical ingredient has active ingredient - - - - 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. - https://en.wikipedia.org/wiki/Active_ingredient - @@ -2999,6 +2944,36 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + has chemical role + + + + @@ -3405,12 +3380,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables - - - - enables - http://www.arabidopsis.org/ - @@ -3878,24 +3847,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -3914,12 +3865,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -4655,12 +4600,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -6113,12 +6052,6 @@ the a supports either the existence of b, or the truth value of b. results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -7437,6 +7370,9 @@ Environments include natural environments or exposures, experimentally applied c /////////////////////////////////////////////////////////////////////////////////////// --> + + + curation status specification @@ -7550,5 +7486,5 @@ Environments include natural environments or exposures, experimentally applied c - + diff --git a/src/ontology/ro.obo b/src/ontology/ro.obo index 18316286..9bb2fef7 100644 --- a/src/ontology/ro.obo +++ b/src/ontology/ro.obo @@ -1,6 +1,9 @@ format-version: 1.2 -data-version: releases/2016-06-15 +data-version: releases/2016-08-24 subsetdef: ro-eco "" +subsetdef: RO:0002259 "" +remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] +remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 276 Logical Axioms: 56] @@ -721,6 +724,8 @@ inverse_of: RO:0000092 ! disposition of [Typedef] id: RO:0000092 name: disposition of +def: "inverse of has disposition" [] +subset: RO:0002259 is_a: RO:0000052 ! inheres in [Typedef] @@ -824,6 +829,7 @@ def: "A relation between a material entity and a condition (a phenotype or disea 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 @@ -831,6 +837,22 @@ 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 @@ -954,7 +976,7 @@ 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." [GOC:dos] +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 "David Osumi-Sutherland" xsd:string holds_over_chain: RO:0002211 RO:0002313 @@ -962,7 +984,7 @@ holds_over_chain: RO:0002211 RO:0002313 [Typedef] id: RO:0002012 name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: BFO:0000050 ! part of @@ -1383,7 +1405,7 @@ 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 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -1416,6 +1438,8 @@ 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 @@ -1566,7 +1590,9 @@ 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 "Chris Mungall" xsd:string is_functional: true @@ -1590,6 +1616,8 @@ inverse_of: RO:0002203 ! develops into [Typedef] id: RO:0002203 name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string @@ -1655,18 +1683,22 @@ inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002208 name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +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 @@ -1810,6 +1842,8 @@ 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 "Chris Mungall" xsd:string property_value: RO:0001900 RO:0001901 @@ -1877,13 +1911,13 @@ 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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] @@ -1962,19 +1996,19 @@ 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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] @@ -2022,6 +2056,35 @@ 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." [] +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +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." [] +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 +is_a: RO:0002375 ! in branching relationship with + [Typedef] id: RO:0002254 name: has developmental contribution from @@ -2038,6 +2101,8 @@ inverse_of: RO:0002255 ! developmentally contributes to [Typedef] id: RO:0002255 name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002203 BFO:0000050 @@ -2083,6 +2148,24 @@ property_value: IAO:0000232 "In general you should not use this relation to make 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:0002285 name: developmentally replaces @@ -2132,6 +2215,7 @@ is_a: RO:0002330 ! genomically related to 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 "Chris Mungall" xsd:string is_a: RO:0002292 ! expresses @@ -2255,7 +2339,7 @@ is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string @@ -2324,6 +2408,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002334 name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process @@ -2334,12 +2419,16 @@ is_a: RO:0002427 ! causally downstream of or within [Typedef] id: RO:0002335 name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002336 name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002334 ! regulated by @@ -2453,7 +2542,9 @@ 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 "Chris Mungall" xsd:string is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to @@ -2461,7 +2552,9 @@ 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 "Chris Mungall" xsd:string is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to @@ -2548,10 +2641,13 @@ is_a: RO:0002320 ! evolutionarily related to [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: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of @@ -2562,12 +2658,12 @@ 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 {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 @@ -2580,8 +2676,9 @@ is_a: RO:0002375 ! in branching relationship with 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 {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -2887,6 +2984,8 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true @@ -3028,7 +3127,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -3196,7 +3295,9 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string @@ -3570,7 +3671,9 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: RO:0002566 ! causally influences @@ -3599,6 +3702,8 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -3660,6 +3765,7 @@ inverse_of: RO:0002517 ! is start sequence of id: RO:0002517 name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "starts" xsd:string @@ -3684,6 +3790,7 @@ inverse_of: RO:0002519 ! is end sequence of id: RO:0002519 name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "ends" xsd:string @@ -3726,6 +3833,7 @@ inverse_of: RO:0002523 ! is bound by sequence of id: RO:0002523 name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true @@ -3749,6 +3857,7 @@ inverse_of: RO:0002525 ! is subsequence of id: RO:0002525 name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "contained by" xsd:string @@ -3853,7 +3962,9 @@ inverse_of: RO:0002554 ! hyperparasitized by [Typedef] id: RO:0002554 name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002445 RO:0002445 is_a: RO:0002453 ! host of @@ -3886,8 +3997,10 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/25052702 is_a: RO:0002616 ! related via evidence or inference to @@ -3918,7 +4031,7 @@ 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string domain: GO:0040011 @@ -3952,7 +4065,9 @@ 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 "Chris Mungall" xsd:string is_a: RO:0002375 ! in branching relationship with @@ -4008,6 +4123,8 @@ 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 "Chris Mungall" xsd:string domain: CARO:0000003 ! anatomical structure range: CARO:0000003 ! anatomical structure @@ -4281,6 +4398,8 @@ 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] @@ -4306,6 +4425,8 @@ 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] @@ -4319,6 +4440,8 @@ 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] @@ -4332,6 +4455,8 @@ 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] diff --git a/src/ontology/ro.owl b/src/ontology/ro.owl index 5f24085f..45030cfb 100644 --- a/src/ontology/ro.owl +++ b/src/ontology/ro.owl @@ -13,7 +13,7 @@ xmlns:cito="http://purl.org/spar/cito/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"> - + @@ -24,6 +24,8 @@ The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. https://github.com/oborel/obo-relations/ + Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] + Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] OBO Relations Ontology @@ -41,6 +43,12 @@ + + + + + + @@ -155,6 +163,21 @@ + + + + + + + + + + defined by inverse + + + + + @@ -722,7 +745,6 @@ Where we have an annotation assertion - @@ -905,6 +927,7 @@ range: spatial region or site (immaterial continuant) + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -917,6 +940,7 @@ range: spatial region or site (immaterial continuant) + 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. is autoimmune trigger for @@ -924,6 +948,29 @@ range: spatial region or site (immaterial continuant) + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + has allergic trigger + + + + + + + + + + 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. + has autoimmune trigger + + + + @@ -1110,12 +1157,6 @@ AND t has_input y regulates transport of - - - - A relationship that holds between a process that regulates a transport process and the entity transported by that process. - GOC:dos - @@ -1129,12 +1170,6 @@ AND t has_input y A part of relation that applies only between occurents. occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -1767,12 +1802,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -1819,6 +1848,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of derived by descent from + has derived by descendant @@ -2093,7 +2124,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of has phenotype Chris Mungall + phenotype of @@ -2128,9 +2161,11 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan + develops into @@ -2238,13 +2273,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite that kills or sterilizes its host parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -2252,6 +2280,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of parasitoid of + has parasitoid @@ -2262,7 +2292,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of directly develops from developmental precursor of + directly develops into @@ -2485,24 +2517,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of surrounded by Chris Mungall + surrounds - - - - Chris Mungall - 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. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - - - - @@ -2565,12 +2588,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -2581,12 +2598,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -2695,12 +2706,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -2711,12 +2716,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -2727,12 +2726,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.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. hemiparasite of - - - - 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. - - @@ -2809,6 +2802,53 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + has active substance + has active pharmaceutical ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + + active ingredient in' + + + + + + + + + + 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. + connecting branch of + + + + + + + + + inverse of connecting branch of + + has connecting branch + + + + @@ -2839,7 +2879,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of has developmental contribution from Chris Mungall + developmentally contributes to @@ -2896,6 +2938,36 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + has chemical role + + + + @@ -2971,6 +3043,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of ubiquiotously expressed in Chris Mungall + ubiquitously expresses @@ -3301,12 +3374,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables - - - - enables - http://www.arabidopsis.org/ - @@ -3419,6 +3486,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates Chris Mungall regulated by (processual) + regulated by @@ -3428,7 +3496,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall + negatively regulated by @@ -3438,7 +3508,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall + positively regulated by @@ -3592,7 +3664,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall + input of @@ -3604,7 +3678,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall + output of @@ -3734,9 +3810,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -3762,24 +3841,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -3795,14 +3856,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati distributary channel of http://en.wikipedia.org/wiki/Distributary + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -4301,8 +4357,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall + causally downstream of or within @@ -4536,12 +4594,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -4828,9 +4880,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with + preyed upon by http://eol.org/schema/terms/HasPredator @@ -5460,8 +5514,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of determined by Chris Mungall determines (material entity to system) + determines @@ -5513,8 +5569,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of transcribed from Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 + transcribed to @@ -5603,6 +5661,7 @@ the a supports either the existence of b, or the truth value of b.starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 + is start sequence of @@ -5635,6 +5694,7 @@ the a supports either the existence of b, or the truth value of b.ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 + is end sequence of @@ -5691,6 +5751,7 @@ the a supports either the existence of b, or the truth value of b.inverse of bounds sequence of Chris Mungall + is bound by sequence of @@ -5725,6 +5786,7 @@ the a supports either the existence of b, or the truth value of b.Chris Mungall contained by + is subsequence of @@ -5875,10 +5937,12 @@ the a supports either the existence of b, or the truth value of b. + inverse of hyperparasite of Chris Mungall has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized by @@ -5926,8 +5990,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of is evidence for Chris Mungall + 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. has evidence @@ -5980,12 +6046,6 @@ the a supports either the existence of b, or the truth value of b. results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -6040,7 +6100,9 @@ the a supports either the existence of b, or the truth value of b. + inverse of branching part of Chris Mungall + has branching part @@ -6122,7 +6184,9 @@ the a supports either the existence of b, or the truth value of b. + inverse of has skeleton Chris Mungall + skeleton of @@ -6563,6 +6627,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of ectoparasite of + has ectoparasite @@ -6605,6 +6671,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of mesoparasite of + has mesoparasite @@ -6626,6 +6694,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of intercellular endoparasite of + has intercellular endoparasite @@ -6647,6 +6717,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of intracellular endoparasite of + has intracellular endoparasite @@ -7292,6 +7364,9 @@ Environments include natural environments or exposures, experimentally applied c /////////////////////////////////////////////////////////////////////////////////////// --> + + + curation status specification @@ -7316,6 +7391,10 @@ Environments include natural environments or exposures, experimentally applied c term replaced by + + inverse of has disposition + + 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. @@ -7344,6 +7423,12 @@ Environments include natural environments or exposures, experimentally applied c + + 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. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + Chris Mungall + + is defined by diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index 36d440cb..377eda5d 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index af46745f..55abccb4 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index 5a9d335b..58603696 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index 56d3068b..0895ab92 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite diff --git a/src/ontology/subsets/ro-eco.obo b/src/ontology/subsets/ro-eco.obo index 6038cd87..72230f8e 100644 --- a/src/ontology/subsets/ro-eco.obo +++ b/src/ontology/subsets/ro-eco.obo @@ -1,8 +1,9 @@ format-version: 1.2 data-version: ro/ro-edit.owl/subsets/ro-eco.owl subsetdef: ro-eco "" +subsetdef: RO:0002259 "" ontology: ro/subsets/ro-eco -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\n) [Typedef] id: BFO:0000050 @@ -20,7 +21,6 @@ id: BFO:0000063 subset: ro-eco holds_over_chain: BFO:0000050 BFO:0000063 holds_over_chain: RO:0002092 BFO:0000063 -is_a: RO:0002222 [Typedef] id: RO:0000300 @@ -82,12 +82,27 @@ 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 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." [] 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 +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." [] +is_a: RO:0003302 ! causes or contributes to condition [Typedef] id: RO:0002001 @@ -168,7 +183,7 @@ 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." [GOC:dos] +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 "David Osumi-Sutherland" xsd:string holds_over_chain: RO:0002211 RO:0002313 @@ -176,7 +191,7 @@ holds_over_chain: RO:0002211 RO:0002313 [Typedef] id: RO:0002012 name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] is_a: BFO:0000050 is_a: RO:0002418 ! causally upstream of or within @@ -488,7 +503,7 @@ 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 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 is_a: RO:0002323 ! mereotopologically related to @@ -519,6 +534,8 @@ 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 @@ -662,7 +679,9 @@ 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 "Chris Mungall" xsd:string is_functional: true @@ -684,6 +703,8 @@ inverse_of: RO:0002203 ! develops into [Typedef] id: RO:0002203 name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string @@ -743,18 +764,22 @@ inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002208 name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +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 @@ -890,18 +915,13 @@ 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 "Chris Mungall" xsd:string property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to -[Typedef] -id: RO:0002222 -subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string - [Typedef] id: RO:0002223 subset: ro-eco @@ -935,13 +955,13 @@ 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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] @@ -1000,19 +1020,19 @@ 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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] @@ -1059,6 +1079,34 @@ 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." [] +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +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 + +[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." [] +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 +is_a: RO:0002375 ! in branching relationship with + [Typedef] id: RO:0002254 name: has developmental contribution from @@ -1072,6 +1120,8 @@ inverse_of: RO:0002255 ! developmentally contributes to [Typedef] id: RO:0002255 name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002203 BFO:0000050 @@ -1115,6 +1165,21 @@ property_value: IAO:0000232 "In general you should not use this relation to make 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)" [] + +[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)" [] + +[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)" [] + [Typedef] id: RO:0002285 name: developmentally replaces @@ -1164,6 +1229,7 @@ is_a: RO:0002330 ! genomically related to 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 "Chris Mungall" xsd:string is_a: RO:0002292 ! expresses @@ -1280,7 +1346,7 @@ is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string @@ -1347,6 +1413,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002334 name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string is_transitive: true @@ -1355,12 +1422,16 @@ is_a: RO:0002427 ! causally downstream of or within [Typedef] id: RO:0002335 name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002336 name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002334 ! regulated by @@ -1447,14 +1518,18 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: RO:0002352 name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO: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 "Chris Mungall" xsd:string is_a: RO:0002328 ! functionally related to @@ -1538,10 +1613,13 @@ is_a: RO:0002320 ! evolutionarily related to [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: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png is_a: BFO:0000050 is_a: RO:0002323 ! mereotopologically related to @@ -1550,12 +1628,12 @@ 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 {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 @@ -1568,8 +1646,9 @@ is_a: RO:0002375 ! in branching relationship with 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 {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -1871,6 +1950,8 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true @@ -2007,7 +2088,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -2175,7 +2256,9 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string @@ -2532,7 +2615,9 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: RO:0002566 ! causally influences @@ -2559,6 +2644,8 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -2618,6 +2705,7 @@ inverse_of: RO:0002517 ! is start sequence of id: RO:0002517 name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "starts" xsd:string @@ -2642,6 +2730,7 @@ inverse_of: RO:0002519 ! is end sequence of id: RO:0002519 name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "ends" xsd:string @@ -2684,6 +2773,7 @@ inverse_of: RO:0002523 ! is bound by sequence of id: RO:0002523 name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true @@ -2706,6 +2796,7 @@ inverse_of: RO:0002525 ! is subsequence of id: RO:0002525 name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "contained by" xsd:string @@ -2808,7 +2899,9 @@ inverse_of: RO:0002554 ! hyperparasitized by [Typedef] id: RO:0002554 name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002445 RO:0002445 is_a: RO:0002453 ! host of @@ -2841,8 +2934,10 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/25052702 is_a: RO:0002616 ! related via evidence or inference to @@ -2873,7 +2968,7 @@ 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2905,7 +3000,9 @@ 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 "Chris Mungall" xsd:string is_a: RO:0002375 ! in branching relationship with @@ -2956,6 +3053,8 @@ 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 "Chris Mungall" xsd:string is_a: BFO:0000050 @@ -3222,6 +3321,8 @@ 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] @@ -3247,6 +3348,8 @@ 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] @@ -3260,6 +3363,8 @@ 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] @@ -3273,6 +3378,8 @@ 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] diff --git a/src/ontology/subsets/ro-eco.owl b/src/ontology/subsets/ro-eco.owl index 8a9d2014..32c492aa 100644 --- a/src/ontology/subsets/ro-eco.owl +++ b/src/ontology/subsets/ro-eco.owl @@ -29,6 +29,14 @@ + + + + + + + + @@ -209,6 +217,26 @@ + + + + Chris Mungall + 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. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + + + + + + + + defined by inverse + + + + + @@ -689,12 +717,6 @@ Where we have an annotation assertion - - - - - - @@ -727,12 +749,6 @@ Where we have an annotation assertion - - - - - - @@ -801,7 +817,6 @@ Where we have an annotation assertion - @@ -810,7 +825,6 @@ Where we have an annotation assertion - @@ -963,6 +977,7 @@ range: spatial region or site (immaterial continuant) + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. is allergic trigger for @@ -974,12 +989,34 @@ range: spatial region or site (immaterial continuant) + 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. is autoimmune trigger for + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + has allergic trigger + + + + + + + + + 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. + has autoimmune trigger + + + + @@ -1121,12 +1158,6 @@ AND t has_input y regulates transport of - - - - A relationship that holds between a process that regulates a transport process and the entity transported by that process. - GOC:dos - @@ -1138,12 +1169,6 @@ AND t has_input y A part of relation that applies only between occurents. occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -1660,12 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -1712,6 +1731,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of derived by descent from + has derived by descendant @@ -1956,7 +1977,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of has phenotype Chris Mungall + phenotype of @@ -1989,9 +2012,11 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan + develops into @@ -2077,13 +2102,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite that kills or sterilizes its host parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -2091,6 +2109,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of parasitoid of + has parasitoid @@ -2101,7 +2121,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of directly develops from developmental precursor of + directly develops into @@ -2316,24 +2338,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of surrounded by Chris Mungall + surrounds - - - - Chris Mungall - 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. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - - - - @@ -2390,12 +2403,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -2406,12 +2413,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -2505,12 +2506,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -2521,12 +2516,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -2537,12 +2526,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.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. hemiparasite of - - - - 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. - - @@ -2618,6 +2601,52 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + has active substance + has active pharmaceutical ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + + active ingredient in' + + + + + + + + + + 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. + connecting branch of + + + + + + + + + inverse of connecting branch of + + has connecting branch + + + + @@ -2642,7 +2671,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of has developmental contribution from Chris Mungall + developmentally contributes to @@ -2697,6 +2728,33 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + has biological role + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + has application role + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + has chemical role + + + + @@ -2772,6 +2830,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of ubiquiotously expressed in Chris Mungall + ubiquitously expresses @@ -3073,12 +3132,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables - - - - enables - http://www.arabidopsis.org/ - @@ -3187,6 +3240,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates Chris Mungall regulated by (processual) + regulated by @@ -3196,7 +3250,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall + negatively regulated by @@ -3206,7 +3262,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall + positively regulated by @@ -3346,7 +3404,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall + input of @@ -3357,7 +3417,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall + output of @@ -3483,9 +3545,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -3511,24 +3576,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -3544,14 +3591,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati distributary channel of http://en.wikipedia.org/wiki/Distributary + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -4026,8 +4068,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall + causally downstream of or within @@ -4244,12 +4288,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -4536,9 +4574,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with + preyed upon by http://eol.org/schema/terms/HasPredator @@ -5139,8 +5179,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of determined by Chris Mungall determines (material entity to system) + determines @@ -5190,8 +5232,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of transcribed from Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 + transcribed to @@ -5278,6 +5322,7 @@ the a supports either the existence of b, or the truth value of b.starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 + is start sequence of @@ -5310,6 +5355,7 @@ the a supports either the existence of b, or the truth value of b.ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 + is end sequence of @@ -5366,6 +5412,7 @@ the a supports either the existence of b, or the truth value of b.inverse of bounds sequence of Chris Mungall + is bound by sequence of @@ -5399,6 +5446,7 @@ the a supports either the existence of b, or the truth value of b.Chris Mungall contained by + is subsequence of @@ -5547,10 +5595,12 @@ the a supports either the existence of b, or the truth value of b. + inverse of hyperparasite of Chris Mungall has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized by @@ -5598,8 +5648,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of is evidence for Chris Mungall + 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. has evidence @@ -5650,12 +5702,6 @@ the a supports either the existence of b, or the truth value of b. results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -5710,7 +5756,9 @@ the a supports either the existence of b, or the truth value of b. + inverse of branching part of Chris Mungall + has branching part @@ -5785,7 +5833,9 @@ the a supports either the existence of b, or the truth value of b. + inverse of has skeleton Chris Mungall + skeleton of @@ -6218,6 +6268,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of ectoparasite of + has ectoparasite @@ -6260,6 +6312,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of mesoparasite of + has mesoparasite @@ -6281,6 +6335,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of intercellular endoparasite of + has intercellular endoparasite @@ -6302,6 +6358,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of intracellular endoparasite of + has intracellular endoparasite @@ -6457,6 +6515,9 @@ Environments include natural environments or exposures, experimentally applied c /////////////////////////////////////////////////////////////////////////////////////// --> + + + curation status specification @@ -6481,6 +6542,10 @@ Environments include natural environments or exposures, experimentally applied c term replaced by + + inverse of has disposition + + 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. diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo index 5d86046f..b017cccd 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index 10492968..63235031 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index eadc4459..4c1103da 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index 7f065cf0..c3942036 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index 71715c8e..7844559e 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index 832a9f45..c332c69d 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index f29f5321..f985cbf2 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index 304a8939..d240aba1 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index 36d440cb..377eda5d 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index af46745f..55abccb4 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index bcae8f35..69ef8e09 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -9,7 +9,7 @@ remark: Includes Ontology(OntologyID(OntologyIRI())) [Axioms: 20 Logical Axioms: 6] remark: Includes Ontology(OntologyID(OntologyIRI())) [Axioms: 731 Logical Axioms: 148] remark: Includes Ontology(OntologyID(OntologyIRI())) [Axioms: 146 Logical Axioms: 45] -default-namespace: relationship +default-namespace: ro ontology: ro/subsets/ro-chado.obo property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/elements/1.1/source http://obofoundry.org/ro @@ -3032,3 +3032,8 @@ def: "The relationship that links an entity with the process that results in the is_a: results_in_developmental_progression_of ! results in developmental progression of is_a: RO:0000057 ! has participant +[Typedef] +id: OBO_REL:is_a +name: is_a +comment: This relation is added for backward compatibility with Chado + diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index 5a9d335b..58603696 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index 56d3068b..0895ab92 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite diff --git a/subsets/ro-eco.obo b/subsets/ro-eco.obo index 6038cd87..72230f8e 100644 --- a/subsets/ro-eco.obo +++ b/subsets/ro-eco.obo @@ -1,8 +1,9 @@ format-version: 1.2 data-version: ro/ro-edit.owl/subsets/ro-eco.owl subsetdef: ro-eco "" +subsetdef: RO:0002259 "" ontology: ro/subsets/ro-eco 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Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\n) [Typedef] id: BFO:0000050 @@ -20,7 +21,6 @@ id: BFO:0000063 subset: ro-eco holds_over_chain: BFO:0000050 BFO:0000063 holds_over_chain: RO:0002092 BFO:0000063 -is_a: RO:0002222 [Typedef] id: RO:0000300 @@ -82,12 +82,27 @@ 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 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." [] 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 +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." [] +is_a: RO:0003302 ! causes or contributes to condition [Typedef] id: RO:0002001 @@ -168,7 +183,7 @@ 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." [GOC:dos] +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 "David Osumi-Sutherland" xsd:string holds_over_chain: RO:0002211 RO:0002313 @@ -176,7 +191,7 @@ holds_over_chain: RO:0002211 RO:0002313 [Typedef] id: RO:0002012 name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] is_a: BFO:0000050 is_a: RO:0002418 ! causally upstream of or within @@ -488,7 +503,7 @@ 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 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 is_a: RO:0002323 ! mereotopologically related to @@ -519,6 +534,8 @@ 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 @@ -662,7 +679,9 @@ 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 "Chris Mungall" xsd:string is_functional: true @@ -684,6 +703,8 @@ inverse_of: RO:0002203 ! develops into [Typedef] id: RO:0002203 name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string @@ -743,18 +764,22 @@ inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002208 name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +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 @@ -890,18 +915,13 @@ 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 "Chris Mungall" xsd:string property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to -[Typedef] -id: RO:0002222 -subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string - [Typedef] id: RO:0002223 subset: ro-eco @@ -935,13 +955,13 @@ 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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] @@ -1000,19 +1020,19 @@ 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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] @@ -1059,6 +1079,34 @@ 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." [] +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +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 + +[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." [] +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 +is_a: RO:0002375 ! in branching relationship with + [Typedef] id: RO:0002254 name: has developmental contribution from @@ -1072,6 +1120,8 @@ inverse_of: RO:0002255 ! developmentally contributes to [Typedef] id: RO:0002255 name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002203 BFO:0000050 @@ -1115,6 +1165,21 @@ property_value: IAO:0000232 "In general you should not use this relation to make 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)" [] + +[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)" [] + +[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)" [] + [Typedef] id: RO:0002285 name: developmentally replaces @@ -1164,6 +1229,7 @@ is_a: RO:0002330 ! genomically related to 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 "Chris Mungall" xsd:string is_a: RO:0002292 ! expresses @@ -1280,7 +1346,7 @@ is_a: RO:0002329 ! part of structure that is capable of [Typedef] id: RO:0002327 -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string @@ -1347,6 +1413,7 @@ is_a: RO:0002328 ! functionally related to id: RO:0002334 name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string is_transitive: true @@ -1355,12 +1422,16 @@ is_a: RO:0002427 ! causally downstream of or within [Typedef] id: RO:0002335 name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002334 ! regulated by [Typedef] id: RO:0002336 name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO:0002334 ! regulated by @@ -1447,14 +1518,18 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: RO:0002352 name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: RO: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 "Chris Mungall" xsd:string is_a: RO:0002328 ! functionally related to @@ -1538,10 +1613,13 @@ is_a: RO:0002320 ! evolutionarily related to [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: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png is_a: BFO:0000050 is_a: RO:0002323 ! mereotopologically related to @@ -1550,12 +1628,12 @@ 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 {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 @@ -1568,8 +1646,9 @@ is_a: RO:0002375 ! in branching relationship with 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 {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -1871,6 +1950,8 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true @@ -2007,7 +2088,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -2175,7 +2256,9 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string @@ -2532,7 +2615,9 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: RO:0002566 ! causally influences @@ -2559,6 +2644,8 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to @@ -2618,6 +2705,7 @@ inverse_of: RO:0002517 ! is start sequence of id: RO:0002517 name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "starts" xsd:string @@ -2642,6 +2730,7 @@ inverse_of: RO:0002519 ! is end sequence of id: RO:0002519 name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "ends" xsd:string @@ -2684,6 +2773,7 @@ inverse_of: RO:0002523 ! is bound by sequence of id: RO:0002523 name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string is_transitive: true @@ -2706,6 +2796,7 @@ inverse_of: RO:0002525 ! is subsequence of id: RO:0002525 name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "contained by" xsd:string @@ -2808,7 +2899,9 @@ inverse_of: RO:0002554 ! hyperparasitized by [Typedef] id: RO:0002554 name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002445 RO:0002445 is_a: RO:0002453 ! host of @@ -2841,8 +2934,10 @@ 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 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/25052702 is_a: RO:0002616 ! related via evidence or inference to @@ -2873,7 +2968,7 @@ 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2905,7 +3000,9 @@ 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 "Chris Mungall" xsd:string is_a: RO:0002375 ! in branching relationship with @@ -2956,6 +3053,8 @@ 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 "Chris Mungall" xsd:string is_a: BFO:0000050 @@ -3222,6 +3321,8 @@ 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] @@ -3247,6 +3348,8 @@ 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] @@ -3260,6 +3363,8 @@ 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] @@ -3273,6 +3378,8 @@ 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] diff --git a/subsets/ro-eco.owl b/subsets/ro-eco.owl index 8a9d2014..32c492aa 100644 --- a/subsets/ro-eco.owl +++ b/subsets/ro-eco.owl @@ -29,6 +29,14 @@ + + + + + + + + @@ -209,6 +217,26 @@ + + + + Chris Mungall + 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. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + + + + + + + + defined by inverse + + + + + @@ -689,12 +717,6 @@ Where we have an annotation assertion - - - - - - @@ -727,12 +749,6 @@ Where we have an annotation assertion - - - - - - @@ -801,7 +817,6 @@ Where we have an annotation assertion - @@ -810,7 +825,6 @@ Where we have an annotation assertion - @@ -963,6 +977,7 @@ range: spatial region or site (immaterial continuant) + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. is allergic trigger for @@ -974,12 +989,34 @@ range: spatial region or site (immaterial continuant) + 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. is autoimmune trigger for + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + has allergic trigger + + + + + + + + + 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. + has autoimmune trigger + + + + @@ -1121,12 +1158,6 @@ AND t has_input y regulates transport of - - - - A relationship that holds between a process that regulates a transport process and the entity transported by that process. - GOC:dos - @@ -1138,12 +1169,6 @@ AND t has_input y A part of relation that applies only between occurents. occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -1660,12 +1685,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -1712,6 +1731,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of derived by descent from + has derived by descendant @@ -1956,7 +1977,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of has phenotype Chris Mungall + phenotype of @@ -1989,9 +2012,11 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan + develops into @@ -2077,13 +2102,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite that kills or sterilizes its host parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -2091,6 +2109,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of parasitoid of + has parasitoid @@ -2101,7 +2121,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of directly develops from developmental precursor of + directly develops into @@ -2316,24 +2338,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of surrounded by Chris Mungall + surrounds - - - - Chris Mungall - 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. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - - - - @@ -2390,12 +2403,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -2406,12 +2413,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -2505,12 +2506,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -2521,12 +2516,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -2537,12 +2526,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.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. hemiparasite of - - - - 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. - - @@ -2618,6 +2601,52 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + has active substance + has active pharmaceutical ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + + active ingredient in' + + + + + + + + + + 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. + connecting branch of + + + + + + + + + inverse of connecting branch of + + has connecting branch + + + + @@ -2642,7 +2671,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + inverse of has developmental contribution from Chris Mungall + developmentally contributes to @@ -2697,6 +2728,33 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + has biological role + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + has application role + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + has chemical role + + + + @@ -2772,6 +2830,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of ubiquiotously expressed in Chris Mungall + ubiquitously expresses @@ -3073,12 +3132,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables - - - - enables - http://www.arabidopsis.org/ - @@ -3187,6 +3240,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates Chris Mungall regulated by (processual) + regulated by @@ -3196,7 +3250,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall + negatively regulated by @@ -3206,7 +3262,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall + positively regulated by @@ -3346,7 +3404,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall + input of @@ -3357,7 +3417,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall + output of @@ -3483,9 +3545,12 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -3511,24 +3576,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -3544,14 +3591,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati distributary channel of http://en.wikipedia.org/wiki/Distributary + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -4026,8 +4068,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall + causally downstream of or within @@ -4244,12 +4288,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -4536,9 +4574,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with + preyed upon by http://eol.org/schema/terms/HasPredator @@ -5139,8 +5179,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of determined by Chris Mungall determines (material entity to system) + determines @@ -5190,8 +5232,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of transcribed from Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 + transcribed to @@ -5278,6 +5322,7 @@ the a supports either the existence of b, or the truth value of b.starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 + is start sequence of @@ -5310,6 +5355,7 @@ the a supports either the existence of b, or the truth value of b.ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 + is end sequence of @@ -5366,6 +5412,7 @@ the a supports either the existence of b, or the truth value of b.inverse of bounds sequence of Chris Mungall + is bound by sequence of @@ -5399,6 +5446,7 @@ the a supports either the existence of b, or the truth value of b.Chris Mungall contained by + is subsequence of @@ -5547,10 +5595,12 @@ the a supports either the existence of b, or the truth value of b. + inverse of hyperparasite of Chris Mungall has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized by @@ -5598,8 +5648,10 @@ the a supports either the existence of b, or the truth value of b. + inverse of is evidence for Chris Mungall + 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. has evidence @@ -5650,12 +5702,6 @@ the a supports either the existence of b, or the truth value of b. results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -5710,7 +5756,9 @@ the a supports either the existence of b, or the truth value of b. + inverse of branching part of Chris Mungall + has branching part @@ -5785,7 +5833,9 @@ the a supports either the existence of b, or the truth value of b. + inverse of has skeleton Chris Mungall + skeleton of @@ -6218,6 +6268,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of ectoparasite of + has ectoparasite @@ -6260,6 +6312,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of mesoparasite of + has mesoparasite @@ -6281,6 +6335,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of intercellular endoparasite of + has intercellular endoparasite @@ -6302,6 +6358,8 @@ the a supports either the existence of b, or the truth value of b. + inverse of intracellular endoparasite of + has intracellular endoparasite @@ -6457,6 +6515,9 @@ Environments include natural environments or exposures, experimentally applied c /////////////////////////////////////////////////////////////////////////////////////// --> + + + curation status specification @@ -6481,6 +6542,10 @@ Environments include natural environments or exposures, experimentally applied c term replaced by + + inverse of has disposition + + 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. diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index 5d86046f..b017cccd 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index 10492968..63235031 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index eadc4459..4c1103da 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 7f065cf0..c3942036 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index 71715c8e..7844559e 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index 832a9f45..c332c69d 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index f29f5321..f985cbf2 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -17,6 +17,14 @@ property_value: IAO:0000232 "Intended to be used when the target of the relation is_a: trophically_interacts_with ! trophically interacts with inverse_of: provides_nutrients_for ! provides nutrients for +[Typedef] +id: active_ingredient_in' +name: active ingredient in' +def: "inverse of has active ingredient" [] +subset: RO:0002259 +xref: RO:0002249 +is_a: part_of + [Typedef] id: actively_participates_in name: actively participates in @@ -308,6 +316,8 @@ inverse_of: causally_upstream_of ! causally upstream of [Typedef] id: causally_downstream_of_or_within name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 xref: RO:0002427 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -495,6 +505,14 @@ property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: connecting_branch_of +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." [] +xref: RO:0002252 +is_a: in_branching_relationship_with ! in branching relationship with +inverse_of: has_connecting_branch ! has connecting branch + [Typedef] id: connects name: connects @@ -516,7 +534,7 @@ xref: RO:0002150 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string 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 {http://purl.org/dc/elements/1.1/source="RO:cjm"} +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 @@ -632,7 +650,9 @@ is_a: overlaps ! overlaps [Typedef] id: determines name: determines +def: "inverse of determined by" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002508 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "determines (material entity to system)" xsd:string @@ -641,6 +661,8 @@ is_a: causally_influences ! causally influences [Typedef] id: developmentally_contributes_to name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 xref: RO:0002255 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -758,6 +780,8 @@ is_a: developmentally_preceded_by ! developmentally preceded by [Typedef] id: develops_into name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 xref: RO:0002203 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -798,6 +822,8 @@ inverse_of: directly_develops_into ! directly develops into [Typedef] id: directly_develops_into name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 xref: RO:0002210 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "developmental precursor of" xsd:string @@ -862,9 +888,10 @@ is_a: regulates ! regulates id: distributary_of 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 xref: RO:0002377 -property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "branch of" xsd:string @@ -929,7 +956,7 @@ is_a: functionally_related_to ! functionally related to [Typedef] id: enables -name: enables {http://purl.org/dc/elements/1.1/contributor="http://www.arabidopsis.org/"} +name: enables xref: RO:0002327 property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -986,7 +1013,7 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: facultative_parasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] xref: RO:0002228 is_a: parasite_of ! parasite of @@ -1036,6 +1063,15 @@ xref: RO:0002002 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_a: mereotopologically_related_to ! mereotopologically related to +[Typedef] +id: has_active_ingredient +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." [] +xref: RO:0002248 +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +is_a: has_part +inverse_of: active_ingredient_in' ! active ingredient in' + [Typedef] id: has_active_participant name: has active participant @@ -1049,10 +1085,29 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: has_participant +[Typedef] +id: has_allergic_trigger +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." [] +xref: RO:0001022 +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + +[Typedef] +id: has_autoimmune_trigger +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." [] +xref: RO:0001023 +range: BFO:0000040 +is_a: causes_or_contributes_to_condition ! causes or contributes to condition + [Typedef] id: has_branching_part name: has branching part +def: "inverse of branching part of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: in_branching_relationship_with ! in branching relationship with @@ -1078,6 +1133,14 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_connecting_branch +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +xref: RO:0002253 +is_a: in_branching_relationship_with ! in branching relationship with + [Typedef] id: has_dendrite_location name: has dendrite location @@ -1123,6 +1186,8 @@ is_a: has_input ! has input [Typedef] id: has_ectoparasite name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 xref: RO:0002633 is_a: parasitized_by ! parasitized by @@ -1243,6 +1308,8 @@ inverse_of: input_of ! input of [Typedef] id: has_intercellular_endoparasite name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002639 is_a: has_endoparasite ! has endoparasite @@ -1260,12 +1327,16 @@ is_a: has_participant [Typedef] id: has_intracellular_endoparasite name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 xref: RO:0002641 is_a: has_endoparasite ! has endoparasite [Typedef] id: has_mesoparasite name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 xref: RO:0002637 is_a: parasitized_by ! parasitized by @@ -1315,6 +1386,8 @@ inverse_of: output_of ! output of [Typedef] id: has_parasitoid name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 xref: RO:0002209 is_a: parasitized_by ! parasitized by @@ -1523,7 +1596,7 @@ is_a: is_vector_for ! is vector for [Typedef] id: hemiparasite_of 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." [https://en.wikipedia.org/wiki/Parasitic_plant] +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." [] xref: RO:0002237 is_a: parasite_of ! parasite of @@ -1552,7 +1625,9 @@ inverse_of: hyperparasitized_by ! hyperparasitized by [Typedef] id: hyperparasitized_by name: hyperparasitized by +def: "inverse of hyperparasite of" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002554 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: host_of ! host of @@ -1611,11 +1686,14 @@ is_a: transports_or_maintains_localization_of ! transports or maintains localiza [Typedef] id: in_branching_relationship_with 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." [] xref: RO:0002375 property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/issues/170 xsd:anyURI property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving 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: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -1654,7 +1732,9 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: input_of name: input of +def: "inverse of has input" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -1756,6 +1836,7 @@ xref: RO:0001020 property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_allergic_trigger ! has allergic trigger [Typedef] id: is_autoimmune_trigger_for @@ -1764,11 +1845,13 @@ def: "A relation between a material entity and a condition (a phenotype or disea xref: RO:0001021 domain: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +inverse_of: has_autoimmune_trigger ! has autoimmune trigger [Typedef] id: is_bound_by_sequence_of name: is bound by sequence of def: "inverse of bounds sequence of" [] +subset: RO:0002259 xref: RO:0002523 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1811,6 +1894,7 @@ is_a: trophically_interacts_with ! trophically interacts with id: is_end_sequence_of name: is end sequence of def: "inverse of has end sequence" [] +subset: RO:0002259 xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1879,6 +1963,7 @@ is_a: sequentially_related_to ! sequentially related to id: is_start_sequence_of name: is start sequence of def: "inverse of has start sequence" [] +subset: RO:0002259 xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1891,6 +1976,7 @@ is_a: is_subsequence_of ! is subsequence of id: is_subsequence_of name: is subsequence of def: "inverse of has subsequence" [] +subset: RO:0002259 xref: RO:0002525 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2049,6 +2135,8 @@ is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] id: negatively_regulated_by name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 xref: RO:0002335 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2068,7 +2156,7 @@ inverse_of: negatively_regulated_by ! negatively regulated by [Typedef] id: obligate_parasite_of name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] xref: RO:0002227 is_a: parasite_of ! parasite of @@ -2085,7 +2173,7 @@ is_obsolete: true [Typedef] id: occurent_part_of name: occurent part of -def: "A part of relation that applies only between occurents." [GOC:dos] +def: "A part of relation that applies only between occurents." [] xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 @@ -2095,7 +2183,9 @@ is_a: part_of [Typedef] id: output_of name: output of +def: "inverse of has output" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: functionally_related_to ! functionally related to @@ -2152,7 +2242,7 @@ is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite [Typedef] id: parasitoid_of name: parasitoid of -def: "A parasite that kills or sterilizes its host" [https://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions, https://github.com/oborel/obo-relations/issues/81] +def: "A parasite that kills or sterilizes its host" [] xref: RO:0002208 is_a: parasite_of ! parasite of inverse_of: has_parasitoid ! has parasitoid @@ -2272,6 +2362,8 @@ inverse_of: pollinated_by ! pollinated by [Typedef] id: positively_regulated_by name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 xref: RO:0002336 property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: regulated_by ! regulated by @@ -2301,7 +2393,9 @@ is_a: temporally_related_to [Typedef] id: preyed_upon_by name: preyed upon by +def: "inverse of preys on" [] subset: ro-eco +subset: RO:0002259 xref: RO:0002458 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has predator" xsd:string @@ -2369,6 +2463,7 @@ inverse_of: sends_output_to ! sends output to id: regulated_by name: regulated by def: "inverse of regulates" [] +subset: RO:0002259 xref: RO:0002334 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000589 "regulated by (processual)" xsd:string @@ -2632,7 +2727,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres [Typedef] id: results_in_movement_of 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" [GOC:mtg_berkeley_2013] +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] xref: RO:0002565 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string @@ -2705,7 +2800,7 @@ is_a: related_via_localization_to ! related via localization to [Typedef] id: root_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] xref: RO:0002236 is_a: parasite_of ! parasite of @@ -2746,6 +2841,8 @@ range: RO:0002532 [Typedef] id: skeleton_of name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 xref: RO:0002576 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: CARO:0000003 @@ -2795,7 +2892,7 @@ is_a: has_part [Typedef] id: stem_parasite_of 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)" [https://en.wikipedia.org/wiki/Parasitic_plant] +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] xref: RO:0002235 is_a: parasite_of ! parasite of @@ -2830,6 +2927,8 @@ inverse_of: surrounds ! surrounds [Typedef] id: surrounds name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 xref: RO:0002221 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2844,7 +2943,7 @@ subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 "Chris Mungall" xsd:string 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 {http://purl.org/dc/elements/1.1/source="http://www.ncbi.nlm.nih.gov/pubmed/19278549"} +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string property_value: RO:0002561 GO:0044403 is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -2916,12 +3015,12 @@ 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 xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string {http://purl.org/dc/elements/1.1/source="GAZ"} -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string {http://purl.org/dc/elements/1.1/source="FMA"} +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 "Chris Mungall" xsd:string property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string {http://purl.org/dc/elements/1.1/source="http://dbpedia.org/ontology/drainsTo"} +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 diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index 304a8939..d240aba1 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -128,12 +128,6 @@ - - - - - - @@ -273,6 +267,7 @@ + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. @@ -287,6 +282,7 @@ + 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. RO:0001021 @@ -296,6 +292,33 @@ + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + 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. + RO:0001022 + has_allergic_trigger + has allergic trigger + + + + + + + + + + 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. + RO:0001023 + has_autoimmune_trigger + has autoimmune trigger + + + + @@ -430,12 +453,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 occurent_part_of occurent part of - - - - A part of relation that applies only between occurents. - GOC:dos - @@ -771,12 +788,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 continuous with FMA:85972 - - - - 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) - RO:cjm - @@ -968,10 +979,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 + develops_into develops into @@ -1024,13 +1037,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 parasitoid_of parasitoid of - - - - A parasite that kills or sterilizes its host - - - @@ -1038,7 +1044,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of parasitoid of RO:0002209 + has_parasitoid has parasitoid @@ -1050,8 +1058,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of directly develops from developmental precursor of RO:0002210 + directly_develops_into directly develops into @@ -1241,9 +1251,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of surrounded by Chris Mungall RO:0002221 + surrounds surrounds @@ -1327,12 +1339,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 obligate_parasite_of obligate parasite of - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - - @@ -1345,12 +1351,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 facultative_parasite_of facultative parasite of - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - - @@ -1421,12 +1421,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 stem_parasite_of stem parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - - @@ -1439,12 +1433,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 root_parasite_of root parasite of - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - - @@ -1457,12 +1445,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 hemiparasite_of hemiparasite of - - - - 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. - - @@ -1529,6 +1511,61 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + 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. + RO:0002248 + has active substance + has active pharmaceutical ingredient + has_active_ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + RO:0002249 + + active_ingredient_in' + active ingredient in' + + + + + + + + + + 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. + RO:0002252 + connecting_branch_of + connecting branch of + + + + + + + + + inverse of connecting branch of + RO:0002253 + + has_connecting_branch + has connecting branch + + + + @@ -1553,8 +1590,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + inverse of has developmental contribution from Chris Mungall RO:0002255 + developmentally_contributes_to developmentally contributes to @@ -1958,12 +1997,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati enables enables - - - - enables - http://www.arabidopsis.org/ - @@ -2053,6 +2086,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Chris Mungall regulated by (processual) RO:0002334 + regulated_by regulated by @@ -2063,8 +2097,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of negatively regulates Chris Mungall RO:0002335 + negatively_regulated_by negatively regulated by @@ -2075,8 +2111,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of positively regulates Chris Mungall RO:0002336 + positively_regulated_by positively regulated by @@ -2237,8 +2275,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has input Chris Mungall RO:0002352 + input_of input of @@ -2251,8 +2291,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of has output Chris Mungall RO:0002353 + output_of output of @@ -2383,11 +2425,14 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + 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. Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships 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) RO:0002375 in_branching_relationship_with in branching relationship with + https://github.com/obophenotype/uberon/issues/170 @@ -2415,24 +2460,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati http://en.wikipedia.org/wiki/Tributary - - - - Deschutes River tributary_of Columbia River - GAZ - - - - - inferior epigastric vein tributary_of external iliac vein - FMA - - - - - drains to - - @@ -2450,14 +2477,9 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002377 distributary_of + 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 distributary of - - - - Deschutes River distributary_of Little Lava Lake - GAZ - @@ -2888,9 +2910,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of causally upstream of or within Chris Mungall RO:0002427 + causally_downstream_of_or_within causally downstream of or within @@ -3107,12 +3131,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different symbiotically_interacts_with symbiotically interacts with - - - - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - @@ -3372,10 +3390,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of preys on Chris Mungall has predator is target of predation interaction with RO:0002458 + preyed_upon_by preyed upon by @@ -3720,9 +3740,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of determined by Chris Mungall determines (material entity to system) RO:0002508 + determines determines @@ -3813,6 +3835,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 + is_start_sequence_of is start sequence of @@ -3849,6 +3872,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 + is_end_sequence_of is end sequence of @@ -3913,6 +3937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall RO:0002523 + is_bound_by_sequence_of is bound by sequence of @@ -3951,6 +3976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different contained by RO:0002525 + is_subsequence_of is subsequence of @@ -4108,11 +4134,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of hyperparasite of Chris Mungall RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by + hyperparasitized_by hyperparasitized by @@ -4190,12 +4218,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different results_in_movement_of results in movement of - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - GOC:mtg_berkeley_2013 - @@ -4246,8 +4268,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of branching part of Chris Mungall RO:0002569 + has_branching_part has branching part @@ -4324,8 +4348,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of has skeleton Chris Mungall RO:0002576 + skeleton_of skeleton of @@ -4765,7 +4791,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of ectoparasite of RO:0002633 + has_ectoparasite has ectoparasite @@ -4815,7 +4843,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of mesoparasite of RO:0002637 + has_mesoparasite has mesoparasite @@ -4840,7 +4870,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intercellular endoparasite of RO:0002639 + has_intercellular_endoparasite has intercellular endoparasite @@ -4865,7 +4897,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + inverse of intracellular endoparasite of RO:0002641 + has_intracellular_endoparasite has intracellular endoparasite