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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 02:37:43 PDT 2013


The test file is available here:

http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/scratch/gene_ontology_test.obo
http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/scratch/gene_ontology_test.owl



On 07/05/2013 15:43, Jane Lomax wrote:
> Apologies, there was an error in my last email. These 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
>
> are equivalent to go-basic.obo, and so in fact will /not/ be affected 
> by these changes.
>
> This file will be affected:
>
> ftp://ftp.geneontology.org/pub/go/ontology/obo_format_1_2/gene_ontology_ext.obo
>
> as will:
>
> go.obo http://purl.obolibrary.org/obo/go.obo
> go.owl http://purl.obolibrary.org/obo/go.owl
>
> If anyone needs a test file containing the new relations let me know.
>
> Jane
>
>
> On 07/05/2013 13:50, Jane Lomax 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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