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

David Osumi-Sutherland djs93 at gen.cam.ac.uk
Wed May 8 02:27:45 PDT 2013


Hi Erick,

It is important that the xref to the RO id stays in place though.  It is used by the OBO to OWL converter (https://code.google.com/p/oboformat/) to ensure that the relation gets the correct URI in the OWL version

e.g.

>> xref: RO:0002092

->
 http://purl.obolibrary.org/obo/RO_0002092
label: happens_during

Ultimately it would probably be better to use the RO IDs directly in the OBO versions,  but tooling issues make this problematic right now.

David
 



On 8 May 2013, at 8/May/2013 10:09:17, Jane Lomax wrote:

> 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> 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
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> go-discuss mailing list
>> >> go-discuss at lists.stanford.edu
>> >> https://mailman.stanford.edu/mailman/listinfo/go-discuss
>> >>
>> >
>> >
>> > _______________________________________________
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>> > https://mailman.stanford.edu/mailman/listinfo/go-discuss
>> >
> 
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David Osumi-Sutherland, PhD
Ontologist at FlyBase & Virtual Fly Brain
Department of Genetics, University of Cambridge,
Downing Street, Cambridge, CB2 3EH, UK
Tel: +44 (0)1223 333 963, Fax: +44 (0)1223 766 732
http://www.virtualflybrain.org



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