Anthony Bretaudeau

Chris Mungall

Damion Dooley

David Osumi-Sutherland

diatomsRcool

James A. Overton

Jim Balhoff

Matthew Brush

Melissa Haendel

Scott Cain

2017-05-29 Release

commit https://github.com/oborel/obo-relations/commit/dd541eb02d08ab6e8a72c2c7fbcbe5db237fe444
Author: Chris Mungall cjm@berkeleybop.org
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 cjm@berkeleybop.org
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 damion.dooley@bccdc.ca
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 damion.dooley@bccdc.ca
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 dosumis@gmail.com
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 dosumis@gmail.com
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 dosumis@gmail.com
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")
 ||      <http://purl.obolibrary.org/obo/RO

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oborel/obo-relations: 2017-04-11 release

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