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

Chris Mungall cjmungall at lbl.gov
Thu May 9 14:09:24 PDT 2013


Hi Alan,

We're currently separating out cell cycle phases from biological processes proper. We don't consider the processes to be part of the stage. We would use the happens_during relation to connect processes to stages.

This is all consistent with release 2 of the Basic Formal Ontology (BFO), the relation can be defined in terms of a chain of the ''occupies spatiotemporal region' relation with part_of between occurrents.

On May 7, 2013, at 9:14 AM, Alan Ruttenberg 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
> 
> 
> 
> 
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> 
> 
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