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

Erick Antezana erick.antezana at gmail.com
Wed May 8 01:21:10 PDT 2013


Hi,

does it mean that the gene_ontology_ext.obo will include in its header
something like:

  import: RO

Why don't you follow the "current strategy": add the new relationship (as
it happened with "regulates" --  which was already in RO) with an xref to
its counterpart in RO:

[Typedef]
id: regulates
name: regulates
xref: RO:0002211
holds_over_chain: results_in regulates
transitive_over: part_of ! part_of

then, we could have for instance:

[Typedef]
id: happens_during
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))
xref: RO:0002092
property_value: IAO:0000118 "d" xsd:string
property_value: IAO:0000118 "during" xsd:string
is_transitive: true
is_a: part_of ! part_of
is_a: ends_during ! ends_during

instead of:

[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


I think some consistency is needed here...

cheers,
Erick



On 7 May 2013 18:14, Alan Ruttenberg <alanruttenberg at gmail.com> 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
>>
>>
>>
>>
>>
>> _______________________________________________
>> go-discuss mailing list
>> go-discuss at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/go-discuss
>>
>
>
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