Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Rama Balakrishnan ramab at stanford.edu
Tue May 7 08:11:43 PDT 2013


Jane,

Can you please also list provide some examples where these relationships will be used in GO?

Thanks,
Rama

On May 7, 2013, at 7:43 AM, 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
>> 
>> 
>> 
> 
> _______________________________________________
> go-discuss mailing list
> go-discuss at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/go-discuss

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/go-friends/attachments/20130507/26f0d4db/attachment-0001.html>


More information about the go-friends mailing list