From 18451ad285c91ef656dc43d6251caba06889e5e2 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sun, 5 May 2024 15:58:09 +0300 Subject: [PATCH] Updated obographs to 0.3.1 --- CHANGELOG.md | 1 + docs/examples/ro-base.json | 2978 +++++++++++++++++++++--------------- robot-core/pom.xml | 2 +- 3 files changed, 1707 insertions(+), 1274 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e3cde082c..3c1118073 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Updated `duplicate_exact_syonym` [`report`] query to be case-insensitive and ignore synoyms annotated as abbreviation or acronym synonym types [#1179] - Extend `--drop-axiom-annotations` option to support value-specific removal of axiom annotations [#1193] - Add `--enforce-obo-format`, `--exclude-named-classes` and `--include-subclass-of` features to relax command [#1060, #1183] +- Updated obographs to [version 0.3.1](https://github.com/geneontology/obographs/releases/tag/v0.3.1) ### Fixed - '--annotate-with-source true' does not work with extract --method subset [#1160] diff --git a/docs/examples/ro-base.json b/docs/examples/ro-base.json index d9c97ac7b..b2227623c 100644 --- a/docs/examples/ro-base.json +++ b/docs/examples/ro-base.json @@ -139,33 +139,187 @@ } } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000060", - "lbl" : "obsolete preceded by", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/BFO_0000141", + "lbl" : "immaterial entity", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000000", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000003", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000006", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000007", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001001", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001010", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0010000", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000000", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000101", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000540", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0003674", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0004842", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0004872", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0005634", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0008150", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0016301", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/OGMS_0000031", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0000402", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0001199", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0002124", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002310", + "lbl" : "exposure event or process", + "type" : "CLASS", "meta" : { - "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ], - "deprecated" : true + "definition" : { + "val" : "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:55:39Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/173" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000141", - "lbl" : "immaterial entity", + "id" : "http://purl.obolibrary.org/obo/RO_0002532", + "lbl" : "sequentially ordered entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any entity that is ordered in discrete units along a linear axis." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002533", + "lbl" : "sequence atomic unit", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any individual unit of a collection of like units arranged in a linear order" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002534", + "lbl" : "sequence bearer", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any entity that can be divided into parts such that each part is an atomical unit of a sequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002577", + "lbl" : "system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity consisting of multiple components that are causally integrated." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.jbiomedsem.com/content/4/1/43" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UPHENO_0001001", "type" : "CLASS" }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY" + "id" : "http://xmlns.com/foaf/0.1/image", + "type" : "CLASS" }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "id" : "http://purl.obolibrary.org/obo/BFO_0000060", + "lbl" : "obsolete preceded by", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." - } + "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000300", "lbl" : "obsolete in neural circuit with", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons." @@ -190,6 +344,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0000301", "lbl" : "obsolete upstream in neural circuit with", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first." @@ -214,6 +369,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0000302", "lbl" : "obsolete downstream in neural circuit with", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first." @@ -238,6 +394,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0001020", "lbl" : "is allergic trigger for", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -251,6 +408,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0001021", "lbl" : "is autoimmune trigger for", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -260,6 +418,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0001022", "lbl" : "has allergic trigger", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -273,27 +432,17 @@ "id" : "http://purl.obolibrary.org/obo/RO_0001023", "lbl" : "has autoimmune trigger", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." } } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001900", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", "lbl" : "regulates in other organism", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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)." @@ -307,6 +456,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002012", "lbl" : "occurent part of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A part of relation that applies only between occurents." @@ -316,6 +466,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002022", "lbl" : "directly regulated by", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], "basicPropertyValues" : [ { @@ -330,6 +481,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002023", "lbl" : "directly negatively regulated by", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", @@ -347,6 +499,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002024", "lbl" : "directly positively regulated by", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", @@ -361,214 +514,81 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002029", - "lbl" : "has increased age-specific mortality rate", + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.", - "xrefs" : [ "PMID:24138933", "Wikipedia:Infant_mortality" ] + "val" : "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." }, - "comments" : [ "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses." ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-05-22T16:43:28Z" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Hill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Tanya Berardini" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + "val" : "GO" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "?X DisjointWith RO_0002162 some ?Y " + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002171", - "lbl" : "mutually spatially disjoint with", + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B." + "val" : "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "non-overlapping with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "shares no parts with" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002172", - "lbl" : "taxonomic class assertion", + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon." + "val" : "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002173", - "lbl" : "ambiguous for taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]" - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002174", - "lbl" : "dubious for taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T." - }, - "comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", - "lbl" : "regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Hill" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Tanya Berardini" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "false" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", - "lbl" : "negatively regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", - "lbl" : "positively regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" @@ -587,6 +607,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002215", "lbl" : "capable of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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. " @@ -619,6 +640,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002216", "lbl" : "capable of part of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -638,6 +660,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002217", "lbl" : "obsolete actively participates in", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" @@ -659,6 +682,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002218", "lbl" : "obsolete has active participant", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" @@ -679,6 +703,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002240", "lbl" : "has exposure receptor", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." @@ -692,6 +717,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002241", "lbl" : "has exposure stressor", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -705,6 +731,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002242", "lbl" : "has exposure route", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" @@ -718,6 +745,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002243", "lbl" : "has exposure transport path", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." @@ -731,6 +759,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002244", "lbl" : "related via exposure to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "Any relationship between an exposure event or process and any other entity." @@ -740,14 +769,11 @@ "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002259", - "lbl" : "defined by inverse", - "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002263", "lbl" : "acts upstream of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." @@ -765,6 +791,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002264", "lbl" : "acts upstream of or within", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." @@ -786,6 +813,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002302", "lbl" : "is treated by substance", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "Inverse of 'is substance that treats'" @@ -800,6 +828,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002304", "lbl" : "causally upstream of, positive effect", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -815,6 +844,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002305", "lbl" : "causally upstream of, negative effect", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y" ], "basicPropertyValues" : [ { @@ -829,6 +859,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002309", "lbl" : "has exposure stimulus", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." @@ -850,41 +881,11 @@ "val" : "2017-06-05T17:35:04Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002310", - "lbl" : "exposure event or process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-06-05T17:55:39Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/pull/173" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002326", "lbl" : "contributes to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { @@ -914,6 +915,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002327", "lbl" : "enables", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { @@ -949,6 +951,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002331", "lbl" : "involved in", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" @@ -971,6 +974,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002334", "lbl" : "regulated by", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "inverse of regulates" @@ -988,6 +992,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002335", "lbl" : "negatively regulated by", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "inverse of negatively regulates" @@ -1002,6 +1007,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002336", "lbl" : "positively regulated by", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "inverse of positively regulates" @@ -1016,6 +1022,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002401", "lbl" : "obsolete has indirect input", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], "basicPropertyValues" : [ { @@ -1031,6 +1038,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002402", "lbl" : "obsolete has direct output", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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. " @@ -1054,6 +1062,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002403", "lbl" : "obsolete has indirect output", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], "basicPropertyValues" : [ { @@ -1069,6 +1078,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002404", "lbl" : "causally downstream of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "inverse of upstream of" @@ -1085,6 +1095,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002405", "lbl" : "immediately causally downstream of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", @@ -1098,6 +1109,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002406", "lbl" : "directly activates", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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" @@ -1123,6 +1135,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002407", "lbl" : "indirectly activates", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one." @@ -1142,6 +1155,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002408", "lbl" : "directly inhibits", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -1161,6 +1175,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002409", "lbl" : "indirectly inhibits", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", @@ -1180,6 +1195,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002410", "lbl" : "causally related to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "This relation groups causal relations between material entities and causal relations between processes" @@ -1202,6 +1218,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002411", "lbl" : "causally upstream of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" @@ -1219,6 +1236,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002412", "lbl" : "immediately causally upstream of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -1238,6 +1256,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002413", "lbl" : "directly provides input for", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c" @@ -1263,6 +1282,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002414", "lbl" : "transitively provides input for", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "transitive form of directly_provides_input_for" @@ -1281,23 +1301,11 @@ "val" : "transitively provides input for (process to process)" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002416", - "lbl" : "logical macro assertion", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002418", "lbl" : "causally upstream of or within", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -1317,54 +1325,11 @@ "val" : "influences (processual)" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002419", - "lbl" : "annotation property cardinality", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002420", - "lbl" : "logical macro assertion on a class", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A logical macro assertion whose domain is an IRI for a class" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002421", - "lbl" : "logical macro assertion on a property", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A logical macro assertion whose domain is an IRI for a property" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002422", - "lbl" : "logical macro assertion on an object property", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002423", - "lbl" : "logical macro assertion on an annotation property", - "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002427", "lbl" : "causally downstream of or within", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "inverse of causally upstream of or within" @@ -1382,6 +1347,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002428", "lbl" : "involved in regulation of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" @@ -1395,6 +1361,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002429", "lbl" : "involved in positive regulation of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" @@ -1411,6 +1378,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002430", "lbl" : "involved in negative regulation of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" @@ -1427,6 +1395,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002431", "lbl" : "involved in or involved in regulation of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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" @@ -1446,6 +1415,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002448", "lbl" : "directly regulates activity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." @@ -1466,6 +1436,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002449", "lbl" : "directly negatively regulates activity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." @@ -1489,6 +1460,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002450", "lbl" : "directly positively regulates activity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." @@ -1508,51 +1480,11 @@ "val" : "directly activates" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002474", - "lbl" : "dispositional interpretation", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002475", - "lbl" : "has no connections with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "shares no connection with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002483", - "lbl" : "inherited annotation property", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002484", - "lbl" : "curator guidance link", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)" - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002500", "lbl" : "causal agent in process", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" @@ -1566,6 +1498,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002501", "lbl" : "causal relation between processes", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -1581,32 +1514,11 @@ "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002504", - "lbl" : "always present in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "brain always_present_in_taxon 'Vertebrata'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "forelimb always_present_in_taxon Euarchontoglires" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "never lost in" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002506", "lbl" : "causal relation between entities", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -1626,6 +1538,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002507", "lbl" : "determined by", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -1658,6 +1571,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002508", "lbl" : "determines", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "inverse of determined by" @@ -1675,6 +1589,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002509", "lbl" : "determined by part of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { "val" : "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." @@ -1686,757 +1601,1216 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002532", - "lbl" : "sequentially ordered entity", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002559", + "lbl" : "causally influenced by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Any entity that is ordered in discrete units along a linear axis." - }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influenced by (entity-centric)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002533", - "lbl" : "sequence atomic unit", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "lbl" : "causally influences", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Any individual unit of a collection of like units arranged in a linear order" + "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influences (entity-centric)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002534", - "lbl" : "sequence bearer", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002578", + "lbl" : "directly regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Any entity that can be divided into parts such that each part is an atomical unit of a sequence" + "val" : "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002535", - "lbl" : "temporal logical macro assertion on a class", + "id" : "http://purl.obolibrary.org/obo/RO_0002584", + "lbl" : "has part structure that is capable of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { + "definition" : { + "val" : "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" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. " + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002536", - "lbl" : "measurement property has unit", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002537", - "lbl" : "has start time value", + "id" : "http://purl.obolibrary.org/obo/RO_0002595", + "lbl" : "causal relation between material entity and a process", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { + "definition" : { + "val" : "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." + }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002538", - "lbl" : "has end time value", + "id" : "http://purl.obolibrary.org/obo/RO_0002596", + "lbl" : "capable of regulating", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." + }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pyrethroid -> growth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002539", - "lbl" : "start, days post fertilization", + "id" : "http://purl.obolibrary.org/obo/RO_0002597", + "lbl" : "capable of negatively regulating", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property." + "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002540", - "lbl" : "end, days post fertilization", + "id" : "http://purl.obolibrary.org/obo/RO_0002598", + "lbl" : "capable of positively regulating", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property." + "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "renin -> arteriolar smooth muscle contraction" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002541", - "lbl" : "start, years post birth", + "id" : "http://purl.obolibrary.org/obo/RO_0002599", + "lbl" : "capable of inhibiting or preventing pathological process", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1." + "val" : "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." }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pazopanib -> pathological angiogenesis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002542", - "lbl" : "end, years post birth", + "id" : "http://purl.obolibrary.org/obo/RO_0002600", + "lbl" : "capable of upregulating or causing pathological process", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2" + "val" : "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." }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "benzene -> cancer [CHEBI]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "causes disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002543", - "lbl" : "start, months post birth", + "id" : "http://purl.obolibrary.org/obo/RO_0002606", + "lbl" : "is substance that treats", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1." + "val" : "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." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "val" : "https://code.google.com/p/obo-relations/issues/detail?id=46" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002544", - "lbl" : "end, months post birth", + "id" : "http://purl.obolibrary.org/obo/RO_0002608", + "lbl" : "process has causal agent", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2" + "val" : "Inverse of 'causal agent in process'" }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002545", - "lbl" : "month of gestation", + "id" : "http://purl.obolibrary.org/obo/RO_0002609", + "lbl" : "obsolete related via dependence to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. 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"http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:58:43Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317346" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004017", + "lbl" : "realizable has basis in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:01Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002561", - "lbl" : "is symmetric relational form of process class", + "id" : "http://purl.obolibrary.org/obo/RO_0004018", + "lbl" : "is basis for realizable", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p" - }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:29Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002562", - "lbl" : "is relational form of process class", + "id" : "http://purl.obolibrary.org/obo/RO_0004019", + "lbl" : "disease has basis in", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process" - }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:26:47Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002566", - "lbl" : "causally influences", + "id" : "http://purl.obolibrary.org/obo/RO_0004020", + "lbl" : "disease has basis in dysfunction of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." + "val" : "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in dysfunction of (disease to anatomical structure)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:29:32Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002575", - "lbl" : "is direct form of", + "id" : "http://purl.obolibrary.org/obo/RO_0004021", + "lbl" : "disease has basis in disruption of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y" + "val" : "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002423", - "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in disruption of (disease to process)" }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "Chris Mungall" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:37:52Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002577", - "lbl" : "system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0004022", + "lbl" : "disease has basis in feature", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A material entity consisting of multiple components that are causally integrated." + "val" : "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.jbiomedsem.com/content/4/1/43" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:46:07Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002578", - "lbl" : "directly regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0004023", + "lbl" : "causal relationship with disease as subject", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly regulates (processual)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:50:54Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002579", - "lbl" : "is indirect form of", + "id" : "http://purl.obolibrary.org/obo/RO_0004024", + "lbl" : "disease causes disruption of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y" + "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "Chris Mungall" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes disruption of (disease to process)" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:51:09Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002580", - "lbl" : "logical macro assertion on an axiom", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "lbl" : "is a defining property chain axiom", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "lbl" : "is a defining property chain axiom where second argument is reflexive", + "id" : "http://purl.obolibrary.org/obo/RO_0004025", + "lbl" : "disease causes dysfunction of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." - } + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes dysfunction of (disease to anatomical entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:58:20Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002584", - "lbl" : "has part structure that is capable of", + "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "lbl" : "realized in response to stimulus", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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" + "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002594", - "lbl" : "is relational form of a class", + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "lbl" : "disease arises from structure", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis." - } + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002595", - "lbl" : "causal relation between material entity and a process", + "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "lbl" : "acts upstream of or within, positive effect", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "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." - }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:30Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002596", - "lbl" : "capable of regulating", + "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "lbl" : "acts upstream of or within, negative effect", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." - }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pyrethroid -> growth" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:51Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002597", - "lbl" : "capable of negatively regulating", + "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "lbl" : "acts upstream of, positive effect", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." + "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002598", - "lbl" : "capable of positively regulating", + "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "lbl" : "acts upstream of, negative effect", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." + "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "renin -> arteriolar smooth muscle contraction" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002599", - "lbl" : "capable of inhibiting or preventing pathological process", + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "lbl" : "causally upstream of or within, negative effect", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "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." - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pazopanib -> pathological angiogenesis" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "treats" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002600", - "lbl" : "capable of upregulating or causing pathological process", + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "lbl" : "causally upstream of or within, positive effect", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "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." - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "benzene -> cancer [CHEBI]" + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "causes disease" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002601", - "lbl" : "logical macro assertion involving identity", + "id" : "http://purl.obolibrary.org/obo/RO_0004096", + "lbl" : "DEPRECATED inheres in", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A shortcut relationship that holds between two entities based on their identity criteria" - } + "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], + "deprecated" : true } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002602", - "lbl" : "in approximate one to one relationship with", + "id" : "http://purl.obolibrary.org/obo/RO_0004097", + "lbl" : "DEPRECATED bearer of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds." - } + "deprecated" : true } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002603", - "lbl" : "is approximately equivalent to", + "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "lbl" : "realized in response to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y" + "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "triggered by process", + "xrefs" : [ "RO:cjm" ] + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, \"Database D states that x=y\"" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "Austin Meier" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "Marie Angelique Laporte" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002604", - "lbl" : "is opposite of", + "id" : "http://purl.obolibrary.org/obo/RO_0011002", + "lbl" : "regulates activity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + "val" : "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002605", - "lbl" : "is indistinguishable from", + "id" : "http://purl.obolibrary.org/obo/RO_0011003", + "lbl" : "regulates quantity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." - } + "val" : "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002606", - "lbl" : "is substance that treats", + "id" : "http://purl.obolibrary.org/obo/RO_0011004", + "lbl" : "indirectly regulates activity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "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." + "val" : "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "treats" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://code.google.com/p/obo-relations/issues/detail?id=46" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002608", - "lbl" : "process has causal agent", + "id" : "http://purl.obolibrary.org/obo/RO_0011007", + "lbl" : "decreases by repression quantity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Inverse of 'causal agent in process'" + "val" : "The entity A has an activity that down-regulates by repression the quantity of B. 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The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + "val" : "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - } ], - "deprecated" : true + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002611", - "lbl" : "evidential logical macro assertion on an axiom", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002612", - "lbl" : "axiom has evidence", + "id" : "http://purl.obolibrary.org/obo/RO_0011009", + "lbl" : "directly positively regulates quantity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom" + "val" : "The entity A has an activity that directly positively regulates the quantity of B." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002613", - "lbl" : "axiom contradicted by evidence", + "id" : "http://purl.obolibrary.org/obo/RO_0011010", + "lbl" : "directly negatively regulates quantity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom" + "val" : "The entity A has an activity that directly negatively regulates the quantity of B." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002617", - "lbl" : "is representative IRI for equivalence set", + "id" : "http://purl.obolibrary.org/obo/RO_0011013", + "lbl" : "indirectly positively regulates activity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "this property relates an IRI to the xsd boolean value \"True\" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent." + "val" : "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002629", - "lbl" : "directly positively regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0011014", + "lbl" : "destabilizes quantity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." + "val" : "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly positively regulates (process to process)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002630", - "lbl" : "directly negatively regulates", + "id" : "http://purl.obolibrary.org/obo/RO_0011015", + "lbl" : "stabilizes quantity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." + "val" : "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly negatively regulates (process to process)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003002", - "lbl" : "represses expression of", + "id" : "http://purl.obolibrary.org/obo/RO_0011016", + "lbl" : "indirectly negatively regulates activity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." + "val" : "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Vasundra Touré" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003003", - "lbl" : "increases expression of", + "id" : "http://purl.obolibrary.org/obo/RO_0011021", + "lbl" : "directly regulates quantity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." + "val" : "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -2444,954 +2818,903 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003302", - "lbl" : "causes or contributes to condition", + "id" : "http://purl.obolibrary.org/obo/RO_0011022", + "lbl" : "indirectly regulates quantity of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." + "val" : "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." }, - "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). 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These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "comments" : [ "This could be used to record the increased infant morality rate in some population compared to wild-type. 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[PHENOSCPAE:asilomar_mtg]" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:56:06Z" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_410295" + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004013", - "lbl" : "is causal germline mutation in", + "id" : "http://purl.obolibrary.org/obo/RO_0002174", + "lbl" : "dubious for taxon", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." + "val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T." }, + "comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:56:40Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004014", - "lbl" : "is causal somatic mutation in", + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]." + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:57:07Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004015", - "lbl" : "is causal susceptibility factor for", + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "lbl" : "defined by inverse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002416", + "lbl" : "logical macro assertion", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." + "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:57:43Z" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317345" + "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004016", - "lbl" : "is causal germline mutation partially giving rise to", + "id" : "http://purl.obolibrary.org/obo/RO_0002419", + "lbl" : "annotation property cardinality", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]." + "val" : "An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002420", + "lbl" : "logical macro assertion on a class", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a class" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:58:43Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317346" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004017", - "lbl" : "realizable has basis in", + "id" : "http://purl.obolibrary.org/obo/RO_0002421", + "lbl" : "logical macro assertion on a property", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:20:01Z" - } ] + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a property" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004018", - "lbl" : "is basis for realizable", + "id" : "http://purl.obolibrary.org/obo/RO_0002422", + "lbl" : "logical macro assertion on an object property", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:20:29Z" - } ] + "definition" : { + "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004019", - "lbl" : "disease has basis in", + "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "lbl" : "logical macro assertion on an annotation property", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002474", + "lbl" : "dispositional interpretation", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:26:47Z" - } ] + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004020", - "lbl" : "disease has basis in dysfunction of", + "id" : "http://purl.obolibrary.org/obo/RO_0002475", + "lbl" : "has no connections with", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." + "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease has basis in dysfunction of (disease to anatomical structure)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no connection with" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:29:32Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004021", - "lbl" : "disease has basis in disruption of", + "id" : "http://purl.obolibrary.org/obo/RO_0002483", + "lbl" : "inherited annotation property", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002484", + "lbl" : "curator guidance link", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." + "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002504", + "lbl" : "always present in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease has basis in disruption of (disease to process)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brain always_present_in_taxon 'Vertebrata'" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "forelimb always_present_in_taxon Euarchontoglires" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:37:52Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "never lost in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004022", - "lbl" : "disease has basis in feature", + "id" : "http://purl.obolibrary.org/obo/RO_0002535", + "lbl" : "temporal logical macro assertion on a class", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "definition" : { - "val" : "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." - }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:46:07Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. " } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004023", - "lbl" : "causal relationship with disease as subject", + "id" : "http://purl.obolibrary.org/obo/RO_0002536", + "lbl" : "measurement property has unit", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002537", + "lbl" : "has start time value", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:50:54Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004024", - "lbl" : "disease causes disruption of", + "id" : "http://purl.obolibrary.org/obo/RO_0002538", + "lbl" : "has end time value", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "definition" : { - "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process." - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease causes disruption of (disease to process)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:51:09Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004025", - "lbl" : "disease causes dysfunction of", + "id" : "http://purl.obolibrary.org/obo/RO_0002539", + "lbl" : "start, days post fertilization", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease causes dysfunction of (disease to anatomical entity)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:58:20Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004028", - "lbl" : "realized in response to stimulus", + "id" : "http://purl.obolibrary.org/obo/RO_0002540", + "lbl" : "end, days post fertilization", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." + "val" : "Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:45:49Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004030", - "lbl" : "disease arises from structure", + "id" : "http://purl.obolibrary.org/obo/RO_0002541", + "lbl" : "start, years post birth", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." + "val" : "Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:58:44Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004032", - "lbl" : "acts upstream of or within, positive effect", + "id" : "http://purl.obolibrary.org/obo/RO_0002542", + "lbl" : "end, years post birth", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "definition" : { + "val" : "Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:49:30Z" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004033", - "lbl" : "acts upstream of or within, negative effect", + "id" : "http://purl.obolibrary.org/obo/RO_0002543", + "lbl" : "start, months post birth", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "definition" : { + "val" : "Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:49:51Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004034", - "lbl" : "acts upstream of, positive effect", + "id" : "http://purl.obolibrary.org/obo/RO_0002544", + "lbl" : "end, months post birth", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" + "val" : "Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:53:14Z" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004035", - "lbl" : "acts upstream of, negative effect", + "id" : "http://purl.obolibrary.org/obo/RO_0002545", + "lbl" : "month of gestation", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" + "val" : "Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:53:22Z" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004046", - "lbl" : "causally upstream of or within, negative effect", + "id" : "http://purl.obolibrary.org/obo/RO_0002546", + "lbl" : "has developmental stage marker", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { + "definition" : { + "val" : "A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-13T23:55:05Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004047", - "lbl" : "causally upstream of or within, positive effect", + "id" : "http://purl.obolibrary.org/obo/RO_0002547", + "lbl" : "start, days post coitum", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of coitum." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-13T23:55:19Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004048", - "lbl" : "is directional form of", + "id" : "http://purl.obolibrary.org/obo/RO_0002548", + "lbl" : "end, days post coitum", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"" + "val" : "Count of number of days intervening between the end of the stage and the time of coitum." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-13T23:59:29Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004049", - "lbl" : "is positive form of", + "id" : "http://purl.obolibrary.org/obo/RO_0002549", + "lbl" : "start, weeks post birth", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-14T00:03:16Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004050", - "lbl" : "is negative form of", + "id" : "http://purl.obolibrary.org/obo/RO_0002550", + "lbl" : "end, weeks post birth", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-14T00:03:24Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004096", - "lbl" : "DEPRECATED inheres in", + "id" : "http://purl.obolibrary.org/obo/RO_0002560", + "lbl" : "is asymmetric relational form of process class", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], - "deprecated" : true + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004097", - "lbl" : "DEPRECATED bearer of", + "id" : "http://purl.obolibrary.org/obo/RO_0002561", + "lbl" : "is symmetric relational form of process class", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "deprecated" : true + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009501", - "lbl" : "realized in response to", + "id" : "http://purl.obolibrary.org/obo/RO_0002562", + "lbl" : "is relational form of process class", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." + "val" : "R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Austin Meier" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "Marie Angelique Laporte" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011002", - "lbl" : "regulates activity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002575", + "lbl" : "is direct form of", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." + "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002423", + "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011003", - "lbl" : "regulates quantity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002579", + "lbl" : "is indirect form of", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." + "val" : "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "pred" : "http://purl.org/dc/terms/creator", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011004", - "lbl" : "indirectly regulates activity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002580", + "lbl" : "logical macro assertion on an axiom", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002581", + "lbl" : "is a defining property chain axiom", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" - } ] + "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011007", - "lbl" : "decreases by repression quantity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" - } ] + "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011008", - "lbl" : "increases by expression quantity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002594", + "lbl" : "is relational form of a class", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" - } ] + "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011009", - "lbl" : "directly positively regulates quantity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002601", + "lbl" : "logical macro assertion involving identity", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A has an activity that directly positively regulates the quantity of B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" - } ] + "val" : "A shortcut relationship that holds between two entities based on their identity criteria" + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011010", - "lbl" : "directly negatively regulates quantity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002602", + "lbl" : "in approximate one to one relationship with", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A has an activity that directly negatively regulates the quantity of B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" - } ] + "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011013", - "lbl" : "indirectly positively regulates activity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002603", + "lbl" : "is approximately equivalent to", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." + "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly activates" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, \"Database D states that x=y\"" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011014", - "lbl" : "destabilizes quantity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002604", + "lbl" : "is opposite of", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." + "val" : "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" + "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011015", - "lbl" : "stabilizes quantity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002605", + "lbl" : "is indistinguishable from", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" - } ] + "val" : "x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + } } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011016", - "lbl" : "indirectly negatively regulates activity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002611", + "lbl" : "evidential logical macro assertion on an axiom", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002612", + "lbl" : "axiom has evidence", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly inhibits" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011021", - "lbl" : "directly regulates quantity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002613", + "lbl" : "axiom contradicted by evidence", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011022", - "lbl" : "indirectly regulates quantity of", + "id" : "http://purl.obolibrary.org/obo/RO_0002617", + "lbl" : "is representative IRI for equivalence set", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." + "val" : "this property relates an IRI to the xsd boolean value \"True\" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011023", - "lbl" : "indirectly negatively regulates quantity of", + "id" : "http://purl.obolibrary.org/obo/RO_0004048", + "lbl" : "is directional form of", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." + "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:59:29Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011024", - "lbl" : "indirectly positively regulates quantity of", + "id" : "http://purl.obolibrary.org/obo/RO_0004049", + "lbl" : "is positive form of", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "definition" : { - "val" : "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Vasundra Touré" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:16Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0014001", - "lbl" : "disease has infectious agent", + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "definition" : { - "val" : "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." - }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040042", "lbl" : "is homeomorphic for", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C." @@ -3415,6 +3738,7 @@ "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "lbl" : "valid_for_go_annotation_extension", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", @@ -3431,6 +3755,7 @@ "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "lbl" : "valid_for_go_gp2term", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", @@ -3447,6 +3772,7 @@ "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", "lbl" : "valid_for_go_ontology", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", @@ -3463,6 +3789,7 @@ "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", "lbl" : "valid_for_gocam", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", @@ -3479,44 +3806,149 @@ "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "lbl" : "eco subset", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" } ] } + }, { + "id" : "http://purl.org/dc/elements/1.1/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/spar/cito/citesAsAuthority", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#editor_note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "lbl" : "database_cross_reference", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "lbl" : "has_narrow_synonym", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion", "lbl" : "has_obo_format_version", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "lbl" : "has_related_synonym", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#id", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#comment", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://xmlns.com/foaf/0.1/homepage", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "meta" : { diff --git a/robot-core/pom.xml b/robot-core/pom.xml index 9f94fa0b0..4a3f16090 100644 --- a/robot-core/pom.xml +++ b/robot-core/pom.xml @@ -209,7 +209,7 @@ org.geneontology.obographs obographs-owlapi - 0.3.0 + 0.3.1 net.sourceforge.owlapi