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

Jane Lomax jane at ebi.ac.uk
Wed May 8 02:09:17 PDT 2013


Hi Erick - yes we will be following our normal strategy and adding the 
relation to gene_ontology_ext.obo without an RO id, as you describe. I'm 
just making a test file which will contain the new relations so yo can 
take a look...

Jane

On 08/05/2013 09:21, Erick Antezana wrote:
> Hi,
>
> does it mean that the gene_ontology_ext.obo will include in its header 
> something like:
>
>   import: RO
>
> Why don't you follow the "current strategy": add the new relationship 
> (as it happened with "regulates" --  which was already in RO) with an 
> xref to its counterpart in RO:
>
> [Typedef]
> id: regulates
> name: regulates
> xref: RO:0002211
> holds_over_chain: results_in regulates
> transitive_over: part_of ! part_of
>
> then, we could have for instance:
>
> [Typedef]
> id: happens_during
> 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))
> xref: RO:0002092
> property_value: IAO:0000118 "d" xsd:string
> property_value: IAO:0000118 "during" xsd:string
> is_transitive: true
> is_a: part_of ! part_of
> is_a: ends_during ! ends_during
>
> instead of:
>
> [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
>
>
> I think some consistency is needed here...
>
> cheers,
> Erick
>
>
>
> On 7 May 2013 18:14, Alan Ruttenberg <alanruttenberg at gmail.com 
> <mailto:alanruttenberg at gmail.com>> 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 
> <mailto: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
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> go-discuss mailing list
> >> go-discuss at lists.stanford.edu <mailto:go-discuss at lists.stanford.edu>
> >> https://mailman.stanford.edu/mailman/listinfo/go-discuss
> >>
> >
> >
> > _______________________________________________
> > go-discuss mailing list
> > go-discuss at lists.stanford.edu <mailto:go-discuss at lists.stanford.edu>
> > https://mailman.stanford.edu/mailman/listinfo/go-discuss
> >

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