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[go-friends] [go-discuss] Announcement: three new relationship types to be added to core GO file

Phillip Lord phillip.lord at newcastle.ac.uk
Fri May 10 03:17:13 PDT 2013



Like "Wearing long trousers" happens_during "puberty", but is not
part_of it.

Phil


Chris Mungall <cjmungall at lbl.gov> writes:
> We're currently separating out cell cycle phases from biological processes
> proper. We don't consider the processes to be part of the stage. We would use
> the happens_during relation to connect processes to stages.
>
> This is all consistent with release 2 of the Basic Formal Ontology (BFO), the
> relation can be defined in terms of a chain of the ''occupies spatiotemporal
> region' relation with part_of between occurrents.
>
> On May 7, 2013, at 9:14 AM, Alan Ruttenberg wrote:
>
>> How does happens_during differ from part_of?
>> 
>> Thanks,
>> Alan
>> 
>> 
>> On Tue, May 7, 2013 at 8:50 AM, Jane Lomax <jane at ebi.ac.uk> wrote:
>> Dear GO friends - we will be adding three new relationships to this core GO file:
>> 
>> go.obo     http://purl.obolibrary.org/obo/go.obo          
>> go.owl     http://purl.obolibrary.org/obo/go.owl
>> 
>> For more information about the content of these and other files, please see our beta ontology downloads page:
>> 
>> http://beta.geneontology.org/page/download-ontology
>> 
>> Note that this file is equivalent to these legacy files:
>> 
>> ftp://ftp.geneontology.org/pub/go/ontology/obo_format_1_2/gene_ontology.1_2.obo
>> ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo
>> 
>> so these files will be affected too.
>> 
>> The relationships are starts_with, ends_with and happens_during. Their
>> definitions from the OBO relations ontology are listed below.
>> 
>> We'll start adding these to the file in 2 weeks, 21 May 2013. Let us know if you have any questions.
>> 
>> many thanks,
>> 
>> GO ontology editors
>> 
>> 
>> 
>> From: http://code.google.com/p/obo-relations/ 
>> [Typedef]
>> id: RO:0002224
>> name: starts with
>> def: "x starts with y if and only if x has part y and the time point at
>> which x starts is equivalent to the time point at which y starts. Formally:
>> ?(y) = ?(x) ? ?(y) < ?(x), where ? is a function that maps a process to a
>> start point, and ? is a function that maps a process to an end point." []
>> property_value: IAO:0000112 "Every insulin receptor signaling pathway starts
>> with the binding of a ligand to the insulin receptor" xsd:string
>> property_value: IAO:0000114 IAO:0000125
>> property_value: IAO:0000118 "started by" xsd:string
>> is_transitive: true
>> is_a: BFO:0000051 ! has part
>> is_a: RO:0002222 ! temporally related to
>> inverse_of: RO:0002223 ! starts
>> 
>> [Typedef]
>> id: RO:0002230
>> name: ends with
>> def: "x ends with y if and only if x has part y and the time point at which
>> x ends is equivalent to the time point at which y ends. Formally: ?(y) >
>> ?(x) ? ?(y) = ?(x), where ? is a function that maps a process to a start
>> point, and ? is a function that maps a process to an end point." []
>> property_value: IAO:0000114 IAO:0000125
>> property_value: IAO:0000118 "finished by" xsd:string
>> is_transitive: true
>> is_a: BFO:0000051 ! has part
>> is_a: RO:0002222 ! temporally related to
>> 
>> [Typedef]
>> id: RO:0002092
>> name: happens_during
>> comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with
>> start(X)) AND (end(X) before_or_simultaneous_with end(Y))
>> property_value: IAO:0000118 "d" xsd:string
>> property_value: IAO:0000118 "during" xsd:string
>> is_transitive: true
>> is_a: BFO:0000050 ! part of
>> is_a: RO:0002093 ! ends_during
>> 
>> 
>> 
>> 
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>> https://mailman.stanford.edu/mailman/listinfo/go-discuss
>> 
>> 
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>
>
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-- 
Phillip Lord,                           Phone: +44 (0) 191 222 7827
Lecturer in Bioinformatics,             Email: phillip.lord at newcastle.ac.uk
School of Computing Science,            http://homepages.cs.ncl.ac.uk/phillip.lord
Room 914 Claremont Tower,               skype: russet_apples
Newcastle University,                   twitter: phillord
NE1 7RU                                 


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