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

Jane Lomax jane at ebi.ac.uk
Tue May 7 07:43:55 PDT 2013


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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