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

Pankaj Jaiswal (OSU) jaiswalp at science.oregonstate.edu
Thu May 9 14:35:23 PDT 2013


Shouldn't these 'cell cycle phases' be a class of of Cell(type) ontology.

Pankaj

On 5/9/2013 2:16 PM, Alan Ruttenberg wrote:
> Hi,
> Thanks.
>
> There are three words you use here. Phases stages and processes. I
> can  look up biological process. Can you tell me where I can find the
> other two please?
>
> -Alan
>
> On Thursday, May 9, 2013, Chris Mungall wrote:
>
>     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/
>>         <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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>>         https://mailman.stanford.edu/mailman/listinfo/go-discuss
>>
>>
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>
>
>
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