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Releases: oborel/obo-relations

2017-05-29 release

29 May 19:11
@cmungall cmungall
v2017-05-29
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2017-05-29 release
  • 2017-05-29 Release

commit dd541eb
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 64f00b3
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 0c26411
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 ebe9c85
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 8a322a5
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 4696eb5
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 70aa279
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(<http://purl.obolibrary.org/obo/ro.owl>) VersionIRI(<http://purl.obolibrary.org/obo/ro/releases/2017-04-11/ro.owl>))
 ++  OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro.owl>) VersionIRI(<http://purl.obolibrary.org/obo/ro/releases/2017-05-29/ro.owl>))
 ||   
 ||  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)
 ||      <http://purl.obolibrary.org/obo/R0_0009004> IAO_0000114 <http://purl.obolibrary.org/obo/IAO_0000428>
 ++  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)
 ||      <http://purl.obolibrary.org/obo/R0_0009004> 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")
 ||      <http://purl.obolibrary.org/obo/R0_0009004> IAO_0000117 "Damion Dooley"
 ++  AnnotationAssertion(rdfs:label obo:R0_0009004 "has consumer"@en)
 ||      <http://purl.obolibrary.org/obo/R0_0009004> label "has consumer"@en
 ++  AnnotationAssertion(obo:IAO_0000112 obo:R0_0009004 "sardine has consumer some homo sapiens"@en)
 ||      <http://purl.obolibrary.org/obo/R0_0009004> 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)
 ||      <http://purl.obolibrary.org/obo/RO_0002013> created_by "dos"^^string
 ++  AnnotationAssertion(oboInOwl:creation_date obo:RO_0002013 "2017-05-24T09:30:46Z"^^xsd:dateTime)
 ||      <http://purl.obolibrary.org/obo/RO_0002013> 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.")
 ||      <http://purl.obolibrary.org/obo/RO_0002013> 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")
 ||      <http://purl.obolibrary.org/obo/RO_0002013> 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.")
 ||      <http://purl.obolibrary.org/obo/RO_0002014> 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)
 ||      <http://purl.obolibrary.org/obo/RO_0002014> 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")
 ||      <http://purl.obolibrary.org/obo/RO_0002014> 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)
 ||      <http://purl.obolibrary.org/obo/RO_0002014> 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'.")
 ||      <http://purl.obolibrary.org/obo/RO_0002014> 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")
 ||      <http://purl.obolibrary.org/obo/RO_0002015> 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.")
 ||      <http://purl.obolibrary.org/obo/RO_0002015> 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 formal...
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2017-04-11 release

11 Apr 19:08
@cmungall cmungall
v2017-04-11
76aaa19
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2017-04-11 release
  • Separate out GO imports, #157
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2017-03-23 release

23 Mar 20:36
@cmungall cmungall
v2017-03-23
07db785
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2017-03-23 release
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2016-10-28 release

28 Oct 21:07
@cmungall cmungall
v2016-10-28
fe0e7ec
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2016-10-28 release
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2016-10-24 release

24 Oct 15:52
@cmungall cmungall
v2016-10-24
2a033e6
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2016-10-24 release
  • NR: + and - versions of causally upstream of. #124
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2016-09-02 release

02 Sep 11:28
@cmungall cmungall
v2016-09-02
da40a60
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2016-09-02 release
  • Removed OBO_REL:is_a from ro-chado. Fixes #115
  • New shortcut/chain relations linking continuants to downstream occurrents. Fixes #123
  • Added missing definitions
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2016-08-24 release

25 Aug 02:57
@cmungall cmungall
v2016-08-24
fc42248
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2016-08-24 release 
v2016-08-24

new release
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2016-06-15 release

15 Jun 23:03
@cmungall cmungall
v2016-06-15
350bcf7
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2016-06-15 release 
v2016-06-15

ro chado, see #68 #95
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2016-05-13 release

14 May 21:23
@cmungall cmungall
v2016-05-13
3fd4a78
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2016-05-13 release 
new release, featuring NRs for allergic and autoimmune triggers, and …

…exposure relations
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2016-02-24 release

25 Feb 07:06
@cmungall cmungall
v2016-02-24
ea49df9
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2016-02-24 release 
v2016-02-24

new release
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