From fea2f1913e25fab4de0c38c4ed7123a40f145aae Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 29 May 2017 12:08:37 -0700 Subject: [PATCH] new release --- CHANGES.md | 323 ++++++++++++++++++++++ core.owl | 39 ++- ro.obo | 119 +++++++- ro.owl | 202 ++++++++++++-- src/ontology/ro.obo | 119 +++++++- src/ontology/ro.owl | 202 ++++++++++++-- src/ontology/subsets/ro-causal.obo | 76 ++++- src/ontology/subsets/ro-causal.owl | 118 +++++++- src/ontology/subsets/ro-chado.obo | 79 +++++- src/ontology/subsets/ro-developmental.obo | 76 ++++- src/ontology/subsets/ro-developmental.owl | 118 +++++++- src/ontology/subsets/ro-eco.obo | 111 +++++++- src/ontology/subsets/ro-eco.owl | 184 +++++++++++- src/ontology/subsets/ro-interaction.obo | 76 ++++- src/ontology/subsets/ro-interaction.owl | 118 +++++++- src/ontology/subsets/ro-mereotopology.obo | 76 ++++- src/ontology/subsets/ro-mereotopology.owl | 118 +++++++- src/ontology/subsets/ro-sequence.obo | 76 ++++- src/ontology/subsets/ro-sequence.owl | 118 +++++++- src/ontology/subsets/ro-time-interval.obo | 76 ++++- src/ontology/subsets/ro-time-interval.owl | 118 +++++++- subsets/ro-causal.obo | 76 ++++- subsets/ro-causal.owl | 118 +++++++- subsets/ro-chado.obo | 79 +++++- subsets/ro-developmental.obo | 76 ++++- subsets/ro-developmental.owl | 118 +++++++- subsets/ro-eco.obo | 111 +++++++- subsets/ro-eco.owl | 184 +++++++++++- subsets/ro-interaction.obo | 76 ++++- subsets/ro-interaction.owl | 118 +++++++- subsets/ro-mereotopology.obo | 76 ++++- subsets/ro-mereotopology.owl | 118 +++++++- subsets/ro-sequence.obo | 76 ++++- subsets/ro-sequence.owl | 118 +++++++- subsets/ro-time-interval.obo | 76 ++++- subsets/ro-time-interval.owl | 118 +++++++- 36 files changed, 3805 insertions(+), 275 deletions(-) create mode 100644 CHANGES.md diff --git a/CHANGES.md b/CHANGES.md new file mode 100644 index 00000000..cd797637 --- /dev/null +++ b/CHANGES.md @@ -0,0 +1,323 @@ +* 2017-05-29 Release + +commit https://github.com/oborel/obo-relations/commit/dd541eb02d08ab6e8a72c2c7fbcbe5db237fe444 +Author: Chris Mungall +Date: 2017-05-29 11:26:56 -0700 + + Temporarily weakening domain of has-developmental-contribution-from to be an IC. + While this can be justified, it leads to violations across most AOs including Uberon + right now. + We can explore adding in future, this may involve distinguishing between true + developmental lineages (continuity of cells) and a weaker sense of tracing + continuity between parts of ICs in general (eg one lumen forming from two predecessors + when a membrane disappears) + + See https://github.com/obophenotype/uberon/issues/1324 + + Inn this commit I also strengthen the grouping relation to only + apply between continuants + +commit https://github.com/oborel/obo-relations/commit/64f00b3cfce967ac2334ec70412f9a00cb363b28 +Merge: a7f710f 8a322a5 +Author: Chris Mungall +Date: 2017-05-29 11:17:56 -0700 + + Merge pull request #162 from oborel/mf_reg_component_relations + + First draft of reg component relations for GO MF refactoring + +commit https://github.com/oborel/obo-relations/commit/0c26411ac08e4d8828bf3c65c2f377bb6f839c2c +Author: Damion Dooley +Date: 2017-05-26 19:23:56 -0700 + + definition change, added 1 relation + + substance removed definition change; + has primary substance added relation + +commit https://github.com/oborel/obo-relations/commit/ebe9c8536aa334cc151556a41e5116f4e5ded427 +Author: Damion Dooley +Date: 2017-05-26 16:25:27 -0700 + + foodon relations + + Adding relations: has consumer, immersed in, has substance added, has + primary substance added. + +commit https://github.com/oborel/obo-relations/commit/8a322a5445e91f530ea2700f4604cca7ce81073f +Author: David Osumi-Sutherland +Date: 2017-05-24 11:59:32 +0100 + + First draft of reg component relations for GO MF refactoring + +commit https://github.com/oborel/obo-relations/commit/4696eb550162787916d34005d49d8359827491de +Author: David Osumi-Sutherland +Date: 2017-05-11 11:27:23 +0100 + + Fixed erroneous typing of RO_0002222 and BFO_0000063 as APs + and removed subAP assertion connecting them. Not clear where this came from. + +commit https://github.com/oborel/obo-relations/commit/70aa2792ff6e0a58ee2f6868ea533199aae5d23c +Author: David Osumi-Sutherland +Date: 2017-05-10 14:04:15 +0100 + + New, more readable relation definitions for regulates releations in RO + + +``` + || Diffing: ro.owl + -- OntologyID(OntologyIRI() VersionIRI()) + ++ OntologyID(OntologyIRI() VersionIRI()) + || + || subject: http://purl.obolibrary.org/obo/BFO_0000063 + -- SubAnnotationPropertyOf(obo:BFO_0000063 obo:RO_0002222) + || BFO_0000063 SubPropertyOf RO_0002222 + ++ SubObjectPropertyOf(obo:BFO_0000063 obo:RO_0002222) + || BFO_0000063 SubPropertyOf RO_0002222 + || + || subject: http://purl.obolibrary.org/obo/GO_0005634 + ++ Declaration(Class(obo:GO_0005634)) + || Class: GO_0005634 + || + || subject: http://purl.obolibrary.org/obo/R0_0009004 + ++ AnnotationAssertion(obo:IAO_0000114 obo:R0_0009004 obo:IAO_0000428) + || IAO_0000114 + ++ AnnotationAssertion(obo:IAO_0000115 obo:R0_0009004 "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect."@en) + || IAO_0000115 "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect."@en + ++ AnnotationAssertion(obo:IAO_0000117 obo:R0_0009004 "Damion Dooley") + || IAO_0000117 "Damion Dooley" + ++ AnnotationAssertion(rdfs:label obo:R0_0009004 "has consumer"@en) + || label "has consumer"@en + ++ AnnotationAssertion(obo:IAO_0000112 obo:R0_0009004 "sardine has consumer some homo sapiens"@en) + || IAO_0000112 "sardine has consumer some homo sapiens"@en + ++ Declaration(ObjectProperty(obo:R0_0009004)) + || ObjectProperty: has consumer + || + || subject: http://purl.obolibrary.org/obo/RO_0002013 + ++ AnnotationAssertion(oboInOwl:created_by obo:RO_0002013 "dos"^^xsd:string) + || created_by "dos"^^string + ++ AnnotationAssertion(oboInOwl:creation_date obo:RO_0002013 "2017-05-24T09:30:46Z"^^xsd:dateTime) + || creation_date "2017-05-24T09:30:46Z"^^dateTime + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002013 "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") + || IAO_0000115 "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." + ++ AnnotationAssertion(rdfs:label obo:RO_0002013 "has regulatory component activity") + || label "has regulatory component activity" + ++ Declaration(ObjectProperty(obo:RO_0002013)) + || ObjectProperty: has regulatory component activity + ++ SubObjectPropertyOf(obo:RO_0002013 obo:RO_0002017) + || has regulatory component activity SubPropertyOf has component activity + ++ SubObjectPropertyOf(obo:RO_0002013 obo:RO_0002334) + || has regulatory component activity SubPropertyOf regulated by + || + || subject: http://purl.obolibrary.org/obo/RO_0002014 + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002014 "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") + || IAO_0000115 "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." + ++ AnnotationAssertion(oboInOwl:created_by obo:RO_0002014 "dos"^^xsd:string) + || created_by "dos"^^string + ++ SubObjectPropertyOf(obo:RO_0002014 obo:RO_0002335) + || has negative regulatory component activity SubPropertyOf negatively regulated by + ++ AnnotationAssertion(rdfs:label obo:RO_0002014 "has negative regulatory component activity") + || label "has negative regulatory component activity" + ++ SubObjectPropertyOf(obo:RO_0002014 obo:RO_0002013) + || has negative regulatory component activity SubPropertyOf has regulatory component activity + ++ AnnotationAssertion(oboInOwl:creation_date obo:RO_0002014 "2017-05-24T09:31:01Z"^^xsd:dateTime) + || creation_date "2017-05-24T09:31:01Z"^^dateTime + ++ AnnotationAssertion(rdfs:comment obo:RO_0002014 "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") + || comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." + ++ Declaration(ObjectProperty(obo:RO_0002014)) + || ObjectProperty: has negative regulatory component activity + || + || subject: http://purl.obolibrary.org/obo/RO_0002015 + ++ AnnotationAssertion(rdfs:label obo:RO_0002015 "has positive regulatory component activity") + || label "has positive regulatory component activity" + ++ Declaration(ObjectProperty(obo:RO_0002015)) + || ObjectProperty: has positive regulatory component activity + ++ SubObjectPropertyOf(obo:RO_0002015 obo:RO_0002013) + || has positive regulatory component activity SubPropertyOf has regulatory component activity + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002015 "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") + || IAO_0000115 "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." + ++ AnnotationAssertion(oboInOwl:creation_date obo:RO_0002015 "2017-05-24T09:31:17Z"^^xsd:dateTime) + || creation_date "2017-05-24T09:31:17Z"^^dateTime + ++ AnnotationAssertion(oboInOwl:created_by obo:RO_0002015 "dos"^^xsd:string) + || created_by "dos"^^string + ++ AnnotationAssertion(rdfs:comment obo:RO_0002015 "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") + || comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." + ++ SubObjectPropertyOf(obo:RO_0002015 obo:RO_0002336) + || has positive regulatory component activity SubPropertyOf positively regulated by + || + || subject: http://purl.obolibrary.org/obo/RO_0002016 + ++ AnnotationAssertion(oboInOwl:created_by obo:RO_0002016 "dos"^^xsd:string) + || created_by "dos"^^string + ++ SubObjectPropertyOf(obo:RO_0002016 obo:RO_0002336) + || has necessary component activity SubPropertyOf positively regulated by + ++ AnnotationAssertion(rdfs:label obo:RO_0002016 "has necessary component activity") + || label "has necessary component activity" + ++ AnnotationAssertion(rdfs:comment obo:RO_0002016 "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.") + || comment "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." + ++ SubObjectPropertyOf(obo:RO_0002016 obo:RO_0002017) + || has necessary component activity SubPropertyOf has component activity + ++ Declaration(ObjectProperty(obo:RO_0002016)) + || ObjectProperty: has necessary component activity + ++ AnnotationAssertion(oboInOwl:creation_date obo:RO_0002016 "2017-05-24T09:36:08Z"^^xsd:dateTime) + || creation_date "2017-05-24T09:36:08Z"^^dateTime + || + || subject: http://purl.obolibrary.org/obo/RO_0002017 + ++ AnnotationAssertion(rdfs:label obo:RO_0002017 "has component activity") + || label "has component activity" + ++ SubObjectPropertyOf(obo:RO_0002017 obo:RO_0002018) + || has component activity SubPropertyOf has component process + ++ AnnotationAssertion(oboInOwl:creation_date obo:RO_0002017 "2017-05-24T09:44:33Z"^^xsd:dateTime) + || creation_date "2017-05-24T09:44:33Z"^^dateTime + ++ AnnotationAssertion(rdfs:comment obo:RO_0002017 "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") + || comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." + ++ AnnotationAssertion(oboInOwl:created_by obo:RO_0002017 "dos"^^xsd:string) + || created_by "dos"^^string + ++ Declaration(ObjectProperty(obo:RO_0002017)) + || ObjectProperty: has component activity + || + || subject: http://purl.obolibrary.org/obo/RO_0002018 + ++ Declaration(ObjectProperty(obo:RO_0002018)) + || ObjectProperty: has component process + ++ AnnotationAssertion(rdfs:label obo:RO_0002018 "has component process") + || label "has component process" + ++ SubObjectPropertyOf(obo:RO_0002018 obo:RO_0002180) + || has component process SubPropertyOf has component + ++ AnnotationAssertion(oboInOwl:creation_date obo:RO_0002018 "2017-05-24T09:49:21Z"^^xsd:dateTime) + || creation_date "2017-05-24T09:49:21Z"^^dateTime + ++ AnnotationAssertion(oboInOwl:created_by obo:RO_0002018 "dos"^^xsd:string) + || created_by "dos"^^string + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002018 "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") + || IAO_0000115 "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + || + || subject: http://purl.obolibrary.org/obo/RO_0002211 + -- AnnotationAssertion(obo:IAO_0000115 obo:RO_0002211 "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y") + || IAO_0000115 "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002211 "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.") + || IAO_0000115 "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." + || + || subject: http://purl.obolibrary.org/obo/RO_0002212 + -- AnnotationAssertion(obo:IAO_0000115 obo:RO_0002212 "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y") + || IAO_0000115 "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002212 "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.") + || IAO_0000115 "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." + || + || subject: http://purl.obolibrary.org/obo/RO_0002213 + -- AnnotationAssertion(obo:IAO_0000115 obo:RO_0002213 "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y") + || IAO_0000115 "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002213 "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.") + || IAO_0000115 "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." + || + || subject: http://purl.obolibrary.org/obo/RO_0002222 + ++ Declaration(ObjectProperty(obo:RO_0002222)) + || ObjectProperty: RO_0002222 + || + || subject: http://purl.obolibrary.org/obo/RO_0002254 + -- ObjectPropertyDomain(obo:RO_0002254 obo:CARO_0000003) + || has developmental contribution from Domain anatomical structure + ++ ObjectPropertyDomain(obo:RO_0002254 obo:BFO_0000004) + || has developmental contribution from Domain BFO_0000004 + || + || subject: http://purl.obolibrary.org/obo/RO_0002258 + ++ ObjectPropertyDomain(obo:RO_0002258 obo:BFO_0000002) + || developmentally preceded by Domain BFO_0000002 + ++ ObjectPropertyRange(obo:RO_0002258 obo:BFO_0000002) + || developmentally preceded by Range BFO_0000002 + || + || subject: http://purl.obolibrary.org/obo/RO_0002578 + -- AnnotationAssertion(obo:IAO_0000115 obo:RO_0002578 "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p") + || IAO_0000115 "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002578 "Proceess(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.") + || IAO_0000115 "Proceess(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." + || + || subject: http://purl.obolibrary.org/obo/RO_0002629 + -- AnnotationAssertion(obo:IAO_0000115 obo:RO_0002629 "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p") + || IAO_0000115 "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002629 "Proceess(P1) directly 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.") + || IAO_0000115 "Proceess(P1) directly 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." + || + || subject: http://purl.obolibrary.org/obo/RO_0002630 + -- AnnotationAssertion(obo:IAO_0000115 obo:RO_0002630 "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p") + || IAO_0000115 "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002630 "Proceess(P1) directly 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.") + || IAO_0000115 "Proceess(P1) directly 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." + || + || subject: http://purl.obolibrary.org/obo/RO_0009001 + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0009001 "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time."@en) + || IAO_0000115 "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time."@en + ++ IrreflexiveObjectProperty(obo:RO_0009001) + || Irreflexive: has substance added + ++ AnnotationAssertion(obo:IAO_0000116 obo:RO_0009001 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients."@en) + || IAO_0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients."@en + ++ Declaration(ObjectProperty(obo:RO_0009001)) + || ObjectProperty: has substance added + ++ AnnotationAssertion(obo:IAO_0000117 obo:RO_0009001 "Damion Dooley") + || IAO_0000117 "Damion Dooley" + ++ AnnotationAssertion(obo:IAO_0000114 obo:RO_0009001 obo:IAO_0000428) + || IAO_0000114 + ++ AnnotationAssertion(obo:IAO_0000112 obo:RO_0009001 "muffin 'has substance added' some 'baking soda'"@en) + || IAO_0000112 "muffin 'has substance added' some 'baking soda'"@en + ++ AnnotationAssertion(rdfs:label obo:RO_0009001 "has substance added"@en) + || label "has substance added"@en + || + || subject: http://purl.obolibrary.org/obo/RO_0009002 + ++ AnnotationAssertion(obo:IAO_0000112 obo:RO_0009002 "'egg white' 'has substance removed' some 'egg yolk'"@en) + || IAO_0000112 "'egg white' 'has substance removed' some 'egg yolk'"@en + ++ Declaration(ObjectProperty(obo:RO_0009002)) + || ObjectProperty: has substance removed + ++ AnnotationAssertion(obo:IAO_0000114 obo:RO_0009002 obo:IAO_0000428) + || IAO_0000114 + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0009002 "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time."@en) + || IAO_0000115 "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time."@en + ++ AnnotationAssertion(obo:IAO_0000117 obo:RO_0009002 "Damion Dooley"@en) + || IAO_0000117 "Damion Dooley"@en + ++ AnnotationAssertion(rdfs:label obo:RO_0009002 "has substance removed"@en) + || label "has substance removed"@en + ++ IrreflexiveObjectProperty(obo:RO_0009002) + || Irreflexive: has substance removed + || + || subject: http://purl.obolibrary.org/obo/RO_0009003 + ++ AnnotationAssertion(obo:IAO_0000117 obo:RO_0009003 "Damion Dooley") + || IAO_0000117 "Damion Dooley" + ++ AnnotationAssertion(obo:IAO_0000114 obo:RO_0009003 obo:IAO_0000428) + || IAO_0000114 + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0009003 "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance."@en) + || IAO_0000115 "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance."@en + ++ AnnotationAssertion(rdfs:label obo:RO_0009003 "immersed in"@en) + || label "immersed in"@en + ++ Declaration(ObjectProperty(obo:RO_0009003)) + || ObjectProperty: immersed in + ++ IrreflexiveObjectProperty(obo:RO_0009003) + || Irreflexive: immersed in + ++ AnnotationAssertion(obo:IAO_0000112 obo:RO_0009003 "sardines 'immersed in' some 'oil and mustard'"@en) + || IAO_0000112 "sardines 'immersed in' some 'oil and mustard'"@en + || + || subject: http://purl.obolibrary.org/obo/RO_0009005 + ++ Declaration(ObjectProperty(obo:RO_0009005)) + || ObjectProperty: has primary substance added + ++ SubObjectPropertyOf(obo:RO_0009005 obo:RO_0009001) + || has primary substance added SubPropertyOf has substance added + ++ AnnotationAssertion(rdfs:label obo:RO_0009005 "has primary substance added"@en) + || label "has primary substance added"@en + ++ AnnotationAssertion(obo:IAO_0000112 obo:RO_0009005 "bread 'has primary substance added' some 'flour'"@en) + || IAO_0000112 "bread 'has primary substance added' some 'flour'"@en + ++ AnnotationAssertion(obo:IAO_0000115 obo:RO_0009005 "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance."@en) + || IAO_0000115 "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance."@en + ++ AnnotationAssertion(obo:IAO_0000117 obo:RO_0009005 "Damion Dooley") + || IAO_0000117 "Damion Dooley" + ++ AnnotationAssertion(obo:IAO_0000114 obo:RO_0009005 obo:IAO_0000428) + || IAO_0000114 + ++ IrreflexiveObjectProperty(obo:RO_0009005) + || Irreflexive: has primary substance added + || + || subject: http://www.geneontology.org/formats/oboInOwl#created_by + ++ Declaration(AnnotationProperty(oboInOwl:created_by)) + || AnnotationProperty: created_by + || + || subject: http://www.geneontology.org/formats/oboInOwl#creation_date + ++ Declaration(AnnotationProperty(oboInOwl:creation_date)) + || AnnotationProperty: creation_date + || + || subject: NO_SUBJECT + ++ SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0002327 obo:RO_0002017) obo:RO_0002327) + || enables o has component activity SubPropertyOf enables +``` diff --git a/core.owl b/core.owl index 2702475b..d55ca19d 100644 --- a/core.owl +++ b/core.owl @@ -481,9 +481,46 @@ A continuant cannot have an occurrent as part: use 'participates in'. has member + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + diff --git a/ro.obo b/ro.obo index a1a1b5c9..72a8fa55 100644 --- a/ro.obo +++ b/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2017-04-11 +data-version: releases/2017-05-29 subsetdef: ro-eco "" subsetdef: RO:0002259 "" remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] @@ -7,7 +7,7 @@ remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 276 Logical Axioms: 56] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 278 Logical Axioms: 58] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14] @@ -20,7 +20,7 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/source http://obofoundry.org/ro property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n############################\n# Classes\n############################\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) [Term] id: BFO:0000002 @@ -582,6 +582,14 @@ comment: Paraphrase of definition: a relation between an independent continuant property_value: IAO:0000111 "site of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Typedef] +id: R0:0009004 +name: has consumer +def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] +property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + [Typedef] id: RO:0000052 name: inheres in @@ -999,6 +1007,60 @@ range: BFO:0000003 ! occurrent is_a: BFO:0000050 ! part of is_a: RO:0002418 ! causally upstream of or within +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002016 +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +is_a: RO:0002017 ! has component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: RO:0002081 name: before or simultaneous with @@ -1715,7 +1777,7 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1737,7 +1799,7 @@ inverse_of: RO:0002334 ! regulated by [Typedef] id: RO:0002212 name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1751,7 +1813,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string @@ -2107,7 +2169,7 @@ def: "x has developmental contribution from y iff x has some part z such that z property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 ! anatomical structure +domain: BFO:0000004 ! independent continuant range: CARO:0000003 ! anatomical structure holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by @@ -2160,6 +2222,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to inverse_of: RO:0002286 ! developmentally succeeded by @@ -2404,6 +2468,7 @@ property_value: IAO:0000232 "This relation differs from the parent relation 'cap property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by +transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 @@ -4195,7 +4260,7 @@ is_a: BFO:0000050 ! part of [Typedef] id: RO:0002578 name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string @@ -4434,7 +4499,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string is_a: RO:0002213 ! positively regulates @@ -4443,7 +4508,7 @@ is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string is_a: RO:0002212 ! negatively regulates @@ -4670,6 +4735,40 @@ name: has eggs laid on by def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] is_a: RO:0002619 ! visited by +[Typedef] +id: RO:0009001 +name: has substance added +def: "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." [] +property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009002 +name: has substance removed +def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] +property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009003 +name: immersed in +def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] +property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009005 +name: has primary substance added +def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] +property_value: IAO:0000112 "bread 'has primary substance added' some 'flour'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string +is_a: RO:0009001 ! has substance added + [Typedef] id: RO:HOM0000000 name: in similarity relationship with diff --git a/ro.owl b/ro.owl index ce15b163..af4ec76d 100644 --- a/ro.owl +++ b/ro.owl @@ -15,7 +15,7 @@ xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"> - + @@ -26,8 +26,8 @@ The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - https://github.com/oborel/obo-relations/ Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] + https://github.com/oborel/obo-relations/ Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] OBO Relations Ontology @@ -669,6 +669,18 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -741,6 +753,18 @@ Where we have an annotation assertion + + + + sardine has consumer some homo sapiens + + 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. + Damion Dooley + has consumer + + + + @@ -1165,6 +1189,84 @@ AND t has_input y + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + @@ -2309,7 +2411,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -2336,7 +2438,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -2360,7 +2462,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -2524,12 +2626,12 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - + @@ -2861,7 +2963,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -2934,6 +3036,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -3434,6 +3538,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes @@ -6255,7 +6363,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -6648,7 +6756,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) directly positively regulates @@ -6661,7 +6769,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) directly negatively regulates @@ -7022,6 +7130,60 @@ Environments include natural environments or exposures, experimentally applied c + + + + + muffin 'has substance added' some 'baking soda' + + "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. + The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. + Damion Dooley + has substance added + + + + + + + + + 'egg white' 'has substance removed' some 'egg yolk' + + "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. + Damion Dooley + has substance removed + + + + + + + + + sardines 'immersed in' some 'oil and mustard' + + "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. + Damion Dooley + immersed in + + + + + + + + + + bread 'has primary substance added' some 'flour' + + 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. + Damion Dooley + has primary substance added + + + + @@ -7207,6 +7369,12 @@ Environments include natural environments or exposures, experimentally applied c + + + + + + @@ -7614,9 +7782,9 @@ Environments include natural environments or exposures, experimentally applied c - - - + + + @@ -7625,9 +7793,9 @@ Environments include natural environments or exposures, experimentally applied c - - - + + + diff --git a/src/ontology/ro.obo b/src/ontology/ro.obo index a1a1b5c9..72a8fa55 100644 --- a/src/ontology/ro.obo +++ b/src/ontology/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2017-04-11 +data-version: releases/2017-05-29 subsetdef: ro-eco "" subsetdef: RO:0002259 "" remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] @@ -7,7 +7,7 @@ remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 276 Logical Axioms: 56] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 278 Logical Axioms: 58] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14] @@ -20,7 +20,7 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/source http://obofoundry.org/ro property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n############################\n# Classes\n############################\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) [Term] id: BFO:0000002 @@ -582,6 +582,14 @@ comment: Paraphrase of definition: a relation between an independent continuant property_value: IAO:0000111 "site of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Typedef] +id: R0:0009004 +name: has consumer +def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] +property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + [Typedef] id: RO:0000052 name: inheres in @@ -999,6 +1007,60 @@ range: BFO:0000003 ! occurrent is_a: BFO:0000050 ! part of is_a: RO:0002418 ! causally upstream of or within +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002016 +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +is_a: RO:0002017 ! has component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: RO:0002081 name: before or simultaneous with @@ -1715,7 +1777,7 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1737,7 +1799,7 @@ inverse_of: RO:0002334 ! regulated by [Typedef] id: RO:0002212 name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1751,7 +1813,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string @@ -2107,7 +2169,7 @@ def: "x has developmental contribution from y iff x has some part z such that z property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 ! anatomical structure +domain: BFO:0000004 ! independent continuant range: CARO:0000003 ! anatomical structure holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by @@ -2160,6 +2222,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to inverse_of: RO:0002286 ! developmentally succeeded by @@ -2404,6 +2468,7 @@ property_value: IAO:0000232 "This relation differs from the parent relation 'cap property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by +transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 @@ -4195,7 +4260,7 @@ is_a: BFO:0000050 ! part of [Typedef] id: RO:0002578 name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string @@ -4434,7 +4499,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string is_a: RO:0002213 ! positively regulates @@ -4443,7 +4508,7 @@ is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string is_a: RO:0002212 ! negatively regulates @@ -4670,6 +4735,40 @@ name: has eggs laid on by def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] is_a: RO:0002619 ! visited by +[Typedef] +id: RO:0009001 +name: has substance added +def: "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." [] +property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009002 +name: has substance removed +def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] +property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009003 +name: immersed in +def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] +property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009005 +name: has primary substance added +def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] +property_value: IAO:0000112 "bread 'has primary substance added' some 'flour'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string +is_a: RO:0009001 ! has substance added + [Typedef] id: RO:HOM0000000 name: in similarity relationship with diff --git a/src/ontology/ro.owl b/src/ontology/ro.owl index ce15b163..af4ec76d 100644 --- a/src/ontology/ro.owl +++ b/src/ontology/ro.owl @@ -15,7 +15,7 @@ xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"> - + @@ -26,8 +26,8 @@ The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - https://github.com/oborel/obo-relations/ Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] + https://github.com/oborel/obo-relations/ Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] OBO Relations Ontology @@ -669,6 +669,18 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -741,6 +753,18 @@ Where we have an annotation assertion + + + + sardine has consumer some homo sapiens + + 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. + Damion Dooley + has consumer + + + + @@ -1165,6 +1189,84 @@ AND t has_input y + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + @@ -2309,7 +2411,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -2336,7 +2438,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -2360,7 +2462,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -2524,12 +2626,12 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - + @@ -2861,7 +2963,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -2934,6 +3036,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -3434,6 +3538,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes @@ -6255,7 +6363,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -6648,7 +6756,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) directly positively regulates @@ -6661,7 +6769,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) directly negatively regulates @@ -7022,6 +7130,60 @@ Environments include natural environments or exposures, experimentally applied c + + + + + muffin 'has substance added' some 'baking soda' + + "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. + The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. + Damion Dooley + has substance added + + + + + + + + + 'egg white' 'has substance removed' some 'egg yolk' + + "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. + Damion Dooley + has substance removed + + + + + + + + + sardines 'immersed in' some 'oil and mustard' + + "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. + Damion Dooley + immersed in + + + + + + + + + + bread 'has primary substance added' some 'flour' + + 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. + Damion Dooley + has primary substance added + + + + @@ -7207,6 +7369,12 @@ Environments include natural environments or exposures, experimentally applied c + + + + + + @@ -7614,9 +7782,9 @@ Environments include natural environments or exposures, experimentally applied c - - - + + + @@ -7625,9 +7793,9 @@ Environments include natural environments or exposures, experimentally applied c - - - + + + diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index 154cd430..515896ac 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -755,6 +755,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 +range: BFO:0000002 is_a: developmentally_related_to ! developmentally related to inverse_of: developmentally_succeeded_by ! developmentally succeeded by @@ -889,7 +891,7 @@ is_a: directly_negatively_regulates ! directly negatively regulates [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string @@ -899,7 +901,7 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string @@ -922,7 +924,7 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: directly_regulates name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] xref: RO:0002578 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1192,6 +1194,24 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_component_activity +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +xref: RO:0002017 +is_a: has_component_process ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: has_component_process +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +xref: RO:0002018 +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: has_connecting_branch name: has connecting branch @@ -1216,7 +1236,7 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 +domain: BFO:0000004 range: CARO:0000003 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1445,6 +1465,27 @@ property_value: seeAlso http://dbpedia.org/property/origin is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to +[Typedef] +id: has_necessary_component_activity +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +xref: RO:0002016 +is_a: has_component_activity ! has component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + [Typedef] id: has_output name: has output @@ -1507,6 +1548,17 @@ property_value: RO:0001900 RO:0001901 is_a: has_part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] +[Typedef] +id: has_positive_regulatory_component_activity +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +xref: RO:0002015 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + [Typedef] id: has_postsynaptic_terminal_in name: has postsynaptic terminal in @@ -1569,6 +1621,16 @@ property_value: RO:0001900 RO:0001901 is_a: has_synaptic_terminal_in ! has synaptic terminal in expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: has_component_activity ! has component activity +is_a: regulated_by ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + [Typedef] id: has_skeleton name: has skeleton @@ -2260,7 +2322,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002212 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2492,7 +2554,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2598,7 +2660,7 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002211 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index 058cd2cd..8cb7d8b1 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -146,6 +146,18 @@ + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630 diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo index 05629225..6217b927 100644 --- a/src/ontology/subsets/ro-chado.obo +++ b/src/ontology/subsets/ro-chado.obo @@ -6,7 +6,7 @@ remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 276 Logical Axioms: 56] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 278 Logical Axioms: 58] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14] @@ -83,6 +83,11 @@ id: BFO:0000067 name: contains_process def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +[Typedef] +id: R0:0009004 +name: has_consumer +def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] + [Typedef] id: RO:0000052 name: inheres_in @@ -328,6 +333,44 @@ def: "A part of relation that applies only between occurents." [] is_a: BFO:0000050 ! part of is_a: RO:0002418 ! causally upstream of or within +[Typedef] +id: RO:0002013 +name: has_regulatory_component_activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002014 +name: has_negative_regulatory_component_activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002015 +name: has_positive_regulatory_component_activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002016 +name: has_necessary_component_activity +is_a: RO:0002017 ! has component activity +is_a: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002017 +name: has_component_activity +is_a: RO:0002018 ! has component process + +[Typedef] +id: RO:0002018 +name: has_component_process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +is_a: RO:0002180 ! has component + [Typedef] id: RO:0002081 name: before_or_simultaneous_with @@ -743,7 +786,7 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] holds_over_chain: RO:0002230 RO:0002211 holds_over_chain: RO:0002578 RO:0002578 is_transitive: true @@ -753,7 +796,7 @@ inverse_of: RO:0002334 ! regulated by [Typedef] id: RO:0002212 name: negatively_regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] holds_over_chain: RO:0002230 RO:0002212 is_transitive: true is_a: RO:0002211 ! regulates @@ -763,7 +806,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively_regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] holds_over_chain: RO:0002212 RO:0002212 holds_over_chain: RO:0002230 RO:0002213 is_transitive: true @@ -1200,6 +1243,7 @@ id: RO:0002327 name: enables is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by +transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 @@ -2402,7 +2446,7 @@ is_a: BFO:0000050 ! part of [Typedef] id: RO:0002578 name: directly_regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] is_a: RO:0002211 ! regulates is_a: RO:0002412 ! immediately causally upstream of @@ -2606,14 +2650,14 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly_positively_regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly_negatively_regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -2803,6 +2847,27 @@ name: has_eggs_laid_on_by def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] is_a: RO:0002619 ! visited by +[Typedef] +id: RO:0009001 +name: has_substance_added +def: "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." [] + +[Typedef] +id: RO:0009002 +name: has_substance_removed +def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] + +[Typedef] +id: RO:0009003 +name: immersed_in +def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] + +[Typedef] +id: RO:0009005 +name: has_primary_substance_added +def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] +is_a: RO:0009001 ! has substance added + [Typedef] id: RO:HOM0000000 name: in_similarity_relationship_with diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index ab6a2357..96124ea9 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -755,6 +755,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 +range: BFO:0000002 is_a: developmentally_related_to ! developmentally related to inverse_of: developmentally_succeeded_by ! developmentally succeeded by @@ -889,7 +891,7 @@ is_a: directly_negatively_regulates ! directly negatively regulates [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string @@ -899,7 +901,7 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string @@ -922,7 +924,7 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: directly_regulates name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] xref: RO:0002578 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1192,6 +1194,24 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_component_activity +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +xref: RO:0002017 +is_a: has_component_process ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: has_component_process +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +xref: RO:0002018 +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: has_connecting_branch name: has connecting branch @@ -1216,7 +1236,7 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 +domain: BFO:0000004 range: CARO:0000003 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1445,6 +1465,27 @@ property_value: seeAlso http://dbpedia.org/property/origin is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to +[Typedef] +id: has_necessary_component_activity +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +xref: RO:0002016 +is_a: has_component_activity ! has component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + [Typedef] id: has_output name: has output @@ -1507,6 +1548,17 @@ property_value: RO:0001900 RO:0001901 is_a: has_part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] +[Typedef] +id: has_positive_regulatory_component_activity +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +xref: RO:0002015 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + [Typedef] id: has_postsynaptic_terminal_in name: has postsynaptic terminal in @@ -1569,6 +1621,16 @@ property_value: RO:0001900 RO:0001901 is_a: has_synaptic_terminal_in ! has synaptic terminal in expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: has_component_activity ! has component activity +is_a: regulated_by ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + [Typedef] id: has_skeleton name: has skeleton @@ -2260,7 +2322,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002212 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2492,7 +2554,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2598,7 +2660,7 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002211 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index 61b1d295..dfa23233 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -146,6 +146,18 @@ + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630 diff --git a/src/ontology/subsets/ro-eco.obo b/src/ontology/subsets/ro-eco.obo index 013b6686..29ef2dbe 100644 --- a/src/ontology/subsets/ro-eco.obo +++ b/src/ontology/subsets/ro-eco.obo @@ -3,7 +3,7 @@ data-version: ro/ro-edit.owl/subsets/ro-eco.owl subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: ro/subsets/ro-eco -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) [Typedef] id: BFO:0000050 @@ -23,6 +23,14 @@ holds_over_chain: BFO:0000050 BFO:0000063 holds_over_chain: RO:0002092 BFO:0000063 is_a: RO:0002222 +[Typedef] +id: R0:0009004 +name: has consumer +def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] +property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + [Typedef] id: RO:0000300 name: in neural circuit with @@ -196,6 +204,60 @@ def: "A part of relation that applies only between occurents." [] is_a: BFO:0000050 is_a: RO:0002418 ! causally upstream of or within +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002016 +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +is_a: RO:0002017 ! has component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: RO:0002082 subset: ro-eco @@ -788,7 +850,7 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -808,7 +870,7 @@ inverse_of: RO:0002334 ! regulated by [Typedef] id: RO:0002212 name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -822,7 +884,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string @@ -1410,6 +1472,7 @@ property_value: IAO:0000232 "This relation differs from the parent relation 'cap property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by +transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 @@ -3124,7 +3187,7 @@ is_a: BFO:0000050 [Typedef] id: RO:0002578 name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string @@ -3358,7 +3421,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string is_a: RO:0002213 ! positively regulates @@ -3367,7 +3430,7 @@ is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string is_a: RO:0002212 ! negatively regulates @@ -3590,6 +3653,40 @@ name: has eggs laid on by def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] is_a: RO:0002619 ! visited by +[Typedef] +id: RO:0009001 +name: has substance added +def: "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." [] +property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009002 +name: has substance removed +def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] +property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009003 +name: immersed in +def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] +property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009005 +name: has primary substance added +def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] +property_value: IAO:0000112 "bread 'has primary substance added' some 'flour'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string +is_a: RO:0009001 ! has substance added + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of diff --git a/src/ontology/subsets/ro-eco.owl b/src/ontology/subsets/ro-eco.owl index 1a7a951f..18fc42ab 100644 --- a/src/ontology/subsets/ro-eco.owl +++ b/src/ontology/subsets/ro-eco.owl @@ -732,6 +732,18 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -814,6 +826,18 @@ Where we have an annotation assertion + + + + sardine has consumer some homo sapiens + + 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. + Damion Dooley + has consumer + + + + @@ -1157,6 +1181,84 @@ AND t has_input y + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + @@ -2129,7 +2231,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -2156,7 +2258,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -2180,7 +2282,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -3185,6 +3287,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes @@ -5899,7 +6005,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -6284,7 +6390,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) directly positively regulates @@ -6297,7 +6403,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) directly negatively regulates @@ -6648,6 +6754,60 @@ Environments include natural environments or exposures, experimentally applied c + + + + + muffin 'has substance added' some 'baking soda' + + "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. + The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. + Damion Dooley + has substance added + + + + + + + + + 'egg white' 'has substance removed' some 'egg yolk' + + "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. + Damion Dooley + has substance removed + + + + + + + + + sardines 'immersed in' some 'oil and mustard' + + "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. + Damion Dooley + immersed in + + + + + + + + + + bread 'has primary substance added' some 'flour' + + 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. + Damion Dooley + has primary substance added + + + + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630 diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index 43ad3a04..bac46403 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -755,6 +755,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 +range: BFO:0000002 is_a: developmentally_related_to ! developmentally related to inverse_of: developmentally_succeeded_by ! developmentally succeeded by @@ -889,7 +891,7 @@ is_a: directly_negatively_regulates ! directly negatively regulates [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string @@ -899,7 +901,7 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string @@ -922,7 +924,7 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: directly_regulates name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] xref: RO:0002578 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1192,6 +1194,24 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_component_activity +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +xref: RO:0002017 +is_a: has_component_process ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: has_component_process +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +xref: RO:0002018 +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: has_connecting_branch name: has connecting branch @@ -1216,7 +1236,7 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 +domain: BFO:0000004 range: CARO:0000003 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1445,6 +1465,27 @@ property_value: seeAlso http://dbpedia.org/property/origin is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to +[Typedef] +id: has_necessary_component_activity +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +xref: RO:0002016 +is_a: has_component_activity ! has component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + [Typedef] id: has_output name: has output @@ -1507,6 +1548,17 @@ property_value: RO:0001900 RO:0001901 is_a: has_part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] +[Typedef] +id: has_positive_regulatory_component_activity +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +xref: RO:0002015 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + [Typedef] id: has_postsynaptic_terminal_in name: has postsynaptic terminal in @@ -1569,6 +1621,16 @@ property_value: RO:0001900 RO:0001901 is_a: has_synaptic_terminal_in ! has synaptic terminal in expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: has_component_activity ! has component activity +is_a: regulated_by ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + [Typedef] id: has_skeleton name: has skeleton @@ -2260,7 +2322,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002212 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2492,7 +2554,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2598,7 +2660,7 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002211 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index 6d5acf7d..240d0c52 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -146,6 +146,18 @@ + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630 diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index 310b95c0..2908ceea 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -755,6 +755,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 +range: BFO:0000002 is_a: developmentally_related_to ! developmentally related to inverse_of: developmentally_succeeded_by ! developmentally succeeded by @@ -889,7 +891,7 @@ is_a: directly_negatively_regulates ! directly negatively regulates [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string @@ -899,7 +901,7 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string @@ -922,7 +924,7 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: directly_regulates name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] xref: RO:0002578 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1192,6 +1194,24 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_component_activity +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +xref: RO:0002017 +is_a: has_component_process ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: has_component_process +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +xref: RO:0002018 +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: has_connecting_branch name: has connecting branch @@ -1216,7 +1236,7 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 +domain: BFO:0000004 range: CARO:0000003 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1445,6 +1465,27 @@ property_value: seeAlso http://dbpedia.org/property/origin is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to +[Typedef] +id: has_necessary_component_activity +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +xref: RO:0002016 +is_a: has_component_activity ! has component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + [Typedef] id: has_output name: has output @@ -1507,6 +1548,17 @@ property_value: RO:0001900 RO:0001901 is_a: has_part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] +[Typedef] +id: has_positive_regulatory_component_activity +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +xref: RO:0002015 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + [Typedef] id: has_postsynaptic_terminal_in name: has postsynaptic terminal in @@ -1569,6 +1621,16 @@ property_value: RO:0001900 RO:0001901 is_a: has_synaptic_terminal_in ! has synaptic terminal in expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: has_component_activity ! has component activity +is_a: regulated_by ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + [Typedef] id: has_skeleton name: has skeleton @@ -2260,7 +2322,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002212 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2492,7 +2554,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2598,7 +2660,7 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002211 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index 24413b5d..81e79c66 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -146,6 +146,18 @@ + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630 diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index 3a21abdd..83936a63 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -755,6 +755,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 +range: BFO:0000002 is_a: developmentally_related_to ! developmentally related to inverse_of: developmentally_succeeded_by ! developmentally succeeded by @@ -889,7 +891,7 @@ is_a: directly_negatively_regulates ! directly negatively regulates [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string @@ -899,7 +901,7 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string @@ -922,7 +924,7 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: directly_regulates name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] xref: RO:0002578 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1192,6 +1194,24 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_component_activity +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +xref: RO:0002017 +is_a: has_component_process ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: has_component_process +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +xref: RO:0002018 +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: has_connecting_branch name: has connecting branch @@ -1216,7 +1236,7 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 +domain: BFO:0000004 range: CARO:0000003 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1445,6 +1465,27 @@ property_value: seeAlso http://dbpedia.org/property/origin is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to +[Typedef] +id: has_necessary_component_activity +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +xref: RO:0002016 +is_a: has_component_activity ! has component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + [Typedef] id: has_output name: has output @@ -1507,6 +1548,17 @@ property_value: RO:0001900 RO:0001901 is_a: has_part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] +[Typedef] +id: has_positive_regulatory_component_activity +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +xref: RO:0002015 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + [Typedef] id: has_postsynaptic_terminal_in name: has postsynaptic terminal in @@ -1569,6 +1621,16 @@ property_value: RO:0001900 RO:0001901 is_a: has_synaptic_terminal_in ! has synaptic terminal in expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: has_component_activity ! has component activity +is_a: regulated_by ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + [Typedef] id: has_skeleton name: has skeleton @@ -2260,7 +2322,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002212 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2492,7 +2554,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2598,7 +2660,7 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002211 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index d218307e..2ac89f0f 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -146,6 +146,18 @@ + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630 diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index 154cd430..515896ac 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -755,6 +755,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 +range: BFO:0000002 is_a: developmentally_related_to ! developmentally related to inverse_of: developmentally_succeeded_by ! developmentally succeeded by @@ -889,7 +891,7 @@ is_a: directly_negatively_regulates ! directly negatively regulates [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string @@ -899,7 +901,7 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string @@ -922,7 +924,7 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: directly_regulates name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] xref: RO:0002578 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1192,6 +1194,24 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_component_activity +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +xref: RO:0002017 +is_a: has_component_process ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: has_component_process +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +xref: RO:0002018 +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: has_connecting_branch name: has connecting branch @@ -1216,7 +1236,7 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 +domain: BFO:0000004 range: CARO:0000003 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1445,6 +1465,27 @@ property_value: seeAlso http://dbpedia.org/property/origin is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to +[Typedef] +id: has_necessary_component_activity +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +xref: RO:0002016 +is_a: has_component_activity ! has component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + [Typedef] id: has_output name: has output @@ -1507,6 +1548,17 @@ property_value: RO:0001900 RO:0001901 is_a: has_part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] +[Typedef] +id: has_positive_regulatory_component_activity +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +xref: RO:0002015 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + [Typedef] id: has_postsynaptic_terminal_in name: has postsynaptic terminal in @@ -1569,6 +1621,16 @@ property_value: RO:0001900 RO:0001901 is_a: has_synaptic_terminal_in ! has synaptic terminal in expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: has_component_activity ! has component activity +is_a: regulated_by ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + [Typedef] id: has_skeleton name: has skeleton @@ -2260,7 +2322,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002212 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2492,7 +2554,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2598,7 +2660,7 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002211 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index 058cd2cd..8cb7d8b1 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -146,6 +146,18 @@ + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630 diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index 05629225..6217b927 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -6,7 +6,7 @@ remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 276 Logical Axioms: 56] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 278 Logical Axioms: 58] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14] @@ -83,6 +83,11 @@ id: BFO:0000067 name: contains_process def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +[Typedef] +id: R0:0009004 +name: has_consumer +def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] + [Typedef] id: RO:0000052 name: inheres_in @@ -328,6 +333,44 @@ def: "A part of relation that applies only between occurents." [] is_a: BFO:0000050 ! part of is_a: RO:0002418 ! causally upstream of or within +[Typedef] +id: RO:0002013 +name: has_regulatory_component_activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002014 +name: has_negative_regulatory_component_activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002015 +name: has_positive_regulatory_component_activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002016 +name: has_necessary_component_activity +is_a: RO:0002017 ! has component activity +is_a: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002017 +name: has_component_activity +is_a: RO:0002018 ! has component process + +[Typedef] +id: RO:0002018 +name: has_component_process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +is_a: RO:0002180 ! has component + [Typedef] id: RO:0002081 name: before_or_simultaneous_with @@ -743,7 +786,7 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] holds_over_chain: RO:0002230 RO:0002211 holds_over_chain: RO:0002578 RO:0002578 is_transitive: true @@ -753,7 +796,7 @@ inverse_of: RO:0002334 ! regulated by [Typedef] id: RO:0002212 name: negatively_regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] holds_over_chain: RO:0002230 RO:0002212 is_transitive: true is_a: RO:0002211 ! regulates @@ -763,7 +806,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively_regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] holds_over_chain: RO:0002212 RO:0002212 holds_over_chain: RO:0002230 RO:0002213 is_transitive: true @@ -1200,6 +1243,7 @@ id: RO:0002327 name: enables is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by +transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 @@ -2402,7 +2446,7 @@ is_a: BFO:0000050 ! part of [Typedef] id: RO:0002578 name: directly_regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] is_a: RO:0002211 ! regulates is_a: RO:0002412 ! immediately causally upstream of @@ -2606,14 +2650,14 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly_positively_regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly_negatively_regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -2803,6 +2847,27 @@ name: has_eggs_laid_on_by def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] is_a: RO:0002619 ! visited by +[Typedef] +id: RO:0009001 +name: has_substance_added +def: "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." [] + +[Typedef] +id: RO:0009002 +name: has_substance_removed +def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] + +[Typedef] +id: RO:0009003 +name: immersed_in +def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] + +[Typedef] +id: RO:0009005 +name: has_primary_substance_added +def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] +is_a: RO:0009001 ! has substance added + [Typedef] id: RO:HOM0000000 name: in_similarity_relationship_with diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index ab6a2357..96124ea9 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -755,6 +755,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 +range: BFO:0000002 is_a: developmentally_related_to ! developmentally related to inverse_of: developmentally_succeeded_by ! developmentally succeeded by @@ -889,7 +891,7 @@ is_a: directly_negatively_regulates ! directly negatively regulates [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string @@ -899,7 +901,7 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string @@ -922,7 +924,7 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: directly_regulates name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] xref: RO:0002578 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1192,6 +1194,24 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_component_activity +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +xref: RO:0002017 +is_a: has_component_process ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: has_component_process +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +xref: RO:0002018 +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: has_connecting_branch name: has connecting branch @@ -1216,7 +1236,7 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 +domain: BFO:0000004 range: CARO:0000003 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1445,6 +1465,27 @@ property_value: seeAlso http://dbpedia.org/property/origin is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to +[Typedef] +id: has_necessary_component_activity +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +xref: RO:0002016 +is_a: has_component_activity ! has component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + [Typedef] id: has_output name: has output @@ -1507,6 +1548,17 @@ property_value: RO:0001900 RO:0001901 is_a: has_part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] +[Typedef] +id: has_positive_regulatory_component_activity +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +xref: RO:0002015 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + [Typedef] id: has_postsynaptic_terminal_in name: has postsynaptic terminal in @@ -1569,6 +1621,16 @@ property_value: RO:0001900 RO:0001901 is_a: has_synaptic_terminal_in ! has synaptic terminal in expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: has_component_activity ! has component activity +is_a: regulated_by ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + [Typedef] id: has_skeleton name: has skeleton @@ -2260,7 +2322,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002212 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2492,7 +2554,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2598,7 +2660,7 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002211 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index 61b1d295..dfa23233 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -146,6 +146,18 @@ + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630 diff --git a/subsets/ro-eco.obo b/subsets/ro-eco.obo index 013b6686..29ef2dbe 100644 --- a/subsets/ro-eco.obo +++ b/subsets/ro-eco.obo @@ -3,7 +3,7 @@ data-version: ro/ro-edit.owl/subsets/ro-eco.owl subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: ro/subsets/ro-eco -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) [Typedef] id: BFO:0000050 @@ -23,6 +23,14 @@ holds_over_chain: BFO:0000050 BFO:0000063 holds_over_chain: RO:0002092 BFO:0000063 is_a: RO:0002222 +[Typedef] +id: R0:0009004 +name: has consumer +def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] +property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + [Typedef] id: RO:0000300 name: in neural circuit with @@ -196,6 +204,60 @@ def: "A part of relation that applies only between occurents." [] is_a: BFO:0000050 is_a: RO:0002418 ! causally upstream of or within +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002016 +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +is_a: RO:0002017 ! has component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: RO:0002082 subset: ro-eco @@ -788,7 +850,7 @@ is_a: RO:0002203 ! develops into [Typedef] id: RO:0002211 name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -808,7 +870,7 @@ inverse_of: RO:0002334 ! regulated by [Typedef] id: RO:0002212 name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -822,7 +884,7 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string @@ -1410,6 +1472,7 @@ property_value: IAO:0000232 "This relation differs from the parent relation 'cap property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by +transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 @@ -3124,7 +3187,7 @@ is_a: BFO:0000050 [Typedef] id: RO:0002578 name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string @@ -3358,7 +3421,7 @@ is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002629 name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string is_a: RO:0002213 ! positively regulates @@ -3367,7 +3430,7 @@ is_a: RO:0002578 ! directly regulates [Typedef] id: RO:0002630 name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string is_a: RO:0002212 ! negatively regulates @@ -3590,6 +3653,40 @@ name: has eggs laid on by def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] is_a: RO:0002619 ! visited by +[Typedef] +id: RO:0009001 +name: has substance added +def: "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." [] +property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009002 +name: has substance removed +def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] +property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009003 +name: immersed in +def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] +property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Typedef] +id: RO:0009005 +name: has primary substance added +def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] +property_value: IAO:0000112 "bread 'has primary substance added' some 'flour'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Damion Dooley" xsd:string +is_a: RO:0009001 ! has substance added + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of diff --git a/subsets/ro-eco.owl b/subsets/ro-eco.owl index 1a7a951f..18fc42ab 100644 --- a/subsets/ro-eco.owl +++ b/subsets/ro-eco.owl @@ -732,6 +732,18 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -814,6 +826,18 @@ Where we have an annotation assertion + + + + sardine has consumer some homo sapiens + + 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. + Damion Dooley + has consumer + + + + @@ -1157,6 +1181,84 @@ AND t has_input y + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + @@ -2129,7 +2231,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -2156,7 +2258,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -2180,7 +2282,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -3185,6 +3287,10 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes @@ -5899,7 +6005,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -6284,7 +6390,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) directly positively regulates @@ -6297,7 +6403,7 @@ the a supports either the existence of b, or the truth value of b. - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) directly negatively regulates @@ -6648,6 +6754,60 @@ Environments include natural environments or exposures, experimentally applied c + + + + + muffin 'has substance added' some 'baking soda' + + "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. + The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. + Damion Dooley + has substance added + + + + + + + + + 'egg white' 'has substance removed' some 'egg yolk' + + "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. + Damion Dooley + has substance removed + + + + + + + + + sardines 'immersed in' some 'oil and mustard' + + "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. + Damion Dooley + immersed in + + + + + + + + + + bread 'has primary substance added' some 'flour' + + 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. + Damion Dooley + has primary substance added + + + + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630 diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index 43ad3a04..bac46403 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -755,6 +755,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 +range: BFO:0000002 is_a: developmentally_related_to ! developmentally related to inverse_of: developmentally_succeeded_by ! developmentally succeeded by @@ -889,7 +891,7 @@ is_a: directly_negatively_regulates ! directly negatively regulates [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string @@ -899,7 +901,7 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string @@ -922,7 +924,7 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: directly_regulates name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] xref: RO:0002578 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1192,6 +1194,24 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_component_activity +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +xref: RO:0002017 +is_a: has_component_process ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: has_component_process +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +xref: RO:0002018 +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: has_connecting_branch name: has connecting branch @@ -1216,7 +1236,7 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 +domain: BFO:0000004 range: CARO:0000003 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1445,6 +1465,27 @@ property_value: seeAlso http://dbpedia.org/property/origin is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to +[Typedef] +id: has_necessary_component_activity +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +xref: RO:0002016 +is_a: has_component_activity ! has component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + [Typedef] id: has_output name: has output @@ -1507,6 +1548,17 @@ property_value: RO:0001900 RO:0001901 is_a: has_part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] +[Typedef] +id: has_positive_regulatory_component_activity +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +xref: RO:0002015 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + [Typedef] id: has_postsynaptic_terminal_in name: has postsynaptic terminal in @@ -1569,6 +1621,16 @@ property_value: RO:0001900 RO:0001901 is_a: has_synaptic_terminal_in ! has synaptic terminal in expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: has_component_activity ! has component activity +is_a: regulated_by ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + [Typedef] id: has_skeleton name: has skeleton @@ -2260,7 +2322,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002212 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2492,7 +2554,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2598,7 +2660,7 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002211 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 6d5acf7d..240d0c52 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -146,6 +146,18 @@ + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630 diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index 310b95c0..2908ceea 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -755,6 +755,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 +range: BFO:0000002 is_a: developmentally_related_to ! developmentally related to inverse_of: developmentally_succeeded_by ! developmentally succeeded by @@ -889,7 +891,7 @@ is_a: directly_negatively_regulates ! directly negatively regulates [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string @@ -899,7 +901,7 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string @@ -922,7 +924,7 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: directly_regulates name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] xref: RO:0002578 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1192,6 +1194,24 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_component_activity +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +xref: RO:0002017 +is_a: has_component_process ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: has_component_process +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +xref: RO:0002018 +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: has_connecting_branch name: has connecting branch @@ -1216,7 +1236,7 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 +domain: BFO:0000004 range: CARO:0000003 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1445,6 +1465,27 @@ property_value: seeAlso http://dbpedia.org/property/origin is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to +[Typedef] +id: has_necessary_component_activity +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +xref: RO:0002016 +is_a: has_component_activity ! has component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + [Typedef] id: has_output name: has output @@ -1507,6 +1548,17 @@ property_value: RO:0001900 RO:0001901 is_a: has_part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] +[Typedef] +id: has_positive_regulatory_component_activity +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +xref: RO:0002015 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + [Typedef] id: has_postsynaptic_terminal_in name: has postsynaptic terminal in @@ -1569,6 +1621,16 @@ property_value: RO:0001900 RO:0001901 is_a: has_synaptic_terminal_in ! has synaptic terminal in expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: has_component_activity ! has component activity +is_a: regulated_by ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + [Typedef] id: has_skeleton name: has skeleton @@ -2260,7 +2322,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002212 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2492,7 +2554,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2598,7 +2660,7 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002211 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index 24413b5d..81e79c66 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -146,6 +146,18 @@ + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630 diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index 3a21abdd..83936a63 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -755,6 +755,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 +range: BFO:0000002 is_a: developmentally_related_to ! developmentally related to inverse_of: developmentally_succeeded_by ! developmentally succeeded by @@ -889,7 +891,7 @@ is_a: directly_negatively_regulates ! directly negatively regulates [Typedef] id: directly_negatively_regulates name: directly negatively regulates -def: "p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002630 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string @@ -899,7 +901,7 @@ is_a: negatively_regulates ! negatively regulates [Typedef] id: directly_positively_regulates name: directly positively regulates -def: "p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p" [] +def: "Proceess(P1) directly 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." [] xref: RO:0002629 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string @@ -922,7 +924,7 @@ is_a: transitively_provides_input_for ! transitively provides input for [Typedef] id: directly_regulates name: directly regulates -def: "p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p" [] +def: "Proceess(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." [] xref: RO:0002578 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -1192,6 +1194,24 @@ property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part +[Typedef] +id: has_component_activity +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +xref: RO:0002017 +is_a: has_component_process ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: has_component_process +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +xref: RO:0002018 +is_a: has_component ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + [Typedef] id: has_connecting_branch name: has connecting branch @@ -1216,7 +1236,7 @@ xref: RO:0002254 property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000003 +domain: BFO:0000004 range: CARO:0000003 is_a: developmentally_preceded_by ! developmentally preceded by inverse_of: developmentally_contributes_to ! developmentally contributes to @@ -1445,6 +1465,27 @@ property_value: seeAlso http://dbpedia.org/property/origin is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to +[Typedef] +id: has_necessary_component_activity +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +xref: RO:0002016 +is_a: has_component_activity ! has component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: has_negative_regulatory_component_activity +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +xref: RO:0002014 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: negatively_regulated_by ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + [Typedef] id: has_output name: has output @@ -1507,6 +1548,17 @@ property_value: RO:0001900 RO:0001901 is_a: has_part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] +[Typedef] +id: has_positive_regulatory_component_activity +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +xref: RO:0002015 +is_a: has_regulatory_component_activity ! has regulatory component activity +is_a: positively_regulated_by ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + [Typedef] id: has_postsynaptic_terminal_in name: has postsynaptic terminal in @@ -1569,6 +1621,16 @@ property_value: RO:0001900 RO:0001901 is_a: has_synaptic_terminal_in ! has synaptic terminal in expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] +[Typedef] +id: has_regulatory_component_activity +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +xref: RO:0002013 +is_a: has_component_activity ! has component activity +is_a: regulated_by ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + [Typedef] id: has_skeleton name: has skeleton @@ -2260,7 +2322,7 @@ is_a: regulated_by ! regulated by [Typedef] id: negatively_regulates name: negatively regulates -def: "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002212 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2492,7 +2554,7 @@ is_a: regulated_by ! regulated by [Typedef] id: positively_regulates name: positively regulates -def: "x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002213 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations @@ -2598,7 +2660,7 @@ is_a: causally_downstream_of_or_within ! causally downstream of or within [Typedef] id: regulates name: regulates -def: "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y" [] +def: "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." [] xref: RO:0002211 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "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" xsd:string diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index d218307e..2ac89f0f 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -146,6 +146,18 @@ + + + + + + + + + + + + @@ -456,6 +468,96 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + RO:0002013 + has_regulatory_component_activity + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + RO:0002014 + has_negative_regulatory_component_activity + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + RO:0002015 + has_positive_regulatory_component_activity + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + RO:0002016 + has_necessary_component_activity + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + RO:0002017 + has_component_activity + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + RO:0002018 + has_component_process + has component process + + + + @@ -1077,7 +1179,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + 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. 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 Chris Mungall David Hill @@ -1102,7 +1204,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + 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. Chris Mungall negatively regulates (process to process) @@ -1120,7 +1222,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + 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. Chris Mungall positively regulates (process to process) @@ -1575,7 +1677,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] @@ -1648,6 +1750,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false @@ -4432,7 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + Proceess(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. Chris Mungall directly regulates (processual) @@ -4817,7 +4921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly positively regulates (process to process) RO:0002629 @@ -4832,7 +4936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p + Proceess(P1) directly 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. directly negatively regulates (process to process) RO:0002630