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

Jane Lomax jane at ebi.ac.uk
Tue May 7 08:49:11 PDT 2013


Sure. These are all to be used in the cell cycle branch right now, but 
no doubt they will be used in other places too further down the line. 
They will be used in the logical definitions.

/happens_during/ will be used between biological process and cell cycle 
phases. For example:

'nuclear cell cycle DNA replication'
intersection_of:  'DNA-dependent DNA replication'
intersection_of:  happens_during 'S phase'

and /ends_during/ and /starts_during/ will be used in the logical 
definitions for cell cycle phase transitions, e.g.

'G1/S transition of mitotic cell cycle'
intersection_of: 'cell cycle phase transition'
intersection_of: starts_during 'G1 phase of mitotic cell cycle'
intersection_of: ends_during 'S phase of mitotic cell cycle'

we'll make a test file available for those that want it.

Jane


On 07/05/2013 16:11, Rama Balakrishnan wrote:
> 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
>>>
>>>
>>>
>>
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>

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