Hi Sharon
I forward you an example of a GO comment given by Matt.
cheers
Arnaud
-------- Original Message --------
Subject: Re: proposed modifications to GO Schema for GUS3.0
Date: Tue, 16 Jul 2002 13:19:51 +0100
From: Matt Berriman <mb...@sa...>
To: Arnaud Kerhornou <ax...@sa...>
References:
<Pin...@sn...>
<3D2...@sa...> <3D2...@pc...>
<3D2...@sa...> <3D2...@pc...>
<3D3...@sa...>
Here's a complete entry from the GO database:
term: C-terminal protein farnesylation
goid: GO:0006503
definition: The covalent or non-covalent attachment of a farnesyl moiety
to the carboxy terminus of a protein. OBSOLETE.
definition_reference: GO:jl
comment: This term was made obsolete because the process is not exclusive to the carboxy terminus
of a protein. Consider instead the biological process term 'protein amino acid farnesylation ;
GO:0018347'.
cheers
Matt
Arnaud Kerhornou wrote:
> Sharon Diskin wrote:
>
>>
>>> Also re. the GOTerm table, would it be possible to add a comment
>>> field ?
>>
>>
>>
>> I do not have a problem with this. Does anyone else have an opinion
>> on this? What type of information would you put in the comment field?
>
>
> Matt,
>
> Do you have an example of comment you want to store ?
>
> I should mention than the GO database design allows to store several
> comments (one to many relationship), one comment field might be enough
> though and would keep the design simple.
>
> cheers
> Arnaud
>
>>
>> Cheers,
>> Sharon
>>
>> p.s. I will be out of town until Monday July 22nd.
>>
>>>
>>> cheers
>>> Arnaud
>>>
>>> Sharon Diskin wrote:
>>>
>>>> Hi Arnaud,
>>>>
>>>> I've attached the new GO schema and documentation that Jonathan
>>>> Schug and I have come up. We believe that this new schema addresses
>>>> your concern about the association date and also provides a better
>>>> way of tracking multiple instances/sources of the same association
>>>> (see description of GOAssociationInstance table).
>>>>
>>>>
>>>> Regarding your other question concerning the 'DB:Ref' and 'from or
>>>> with', we see these being tracked using the generic Evidence
>>>> table. The 'from or with' would be Evidence for the
>>>> GOAssocInstEvidCode entry as it is connected to a specific evidence
>>>> code that is assigned to the association. The 'DB:Ref' (such as in
>>>> the PubMed example you mentioned) would be Evidence for the
>>>> GOAssociationInstance entry as it is _not_ connected to a specific
>>>> evidence code, but rather the association as a whole. More details
>>>> can be found in the attached documentation.
>>>>
>>>>
>>>> Any feedback is welcome. Also, if any of this is unclear, just let
>>>> us know.
>>>>
>>>> Cheers,
>>>> Sharon
>>>>
>>>>
>>>
>>
>
>
>
--
Dr Matthew Berriman
Senior Computer Biologist - Pathogen Sequencing Unit -
The Wellcome Trust Sanger Institute
Tel +44 (0)1223 494817 - Fax +44 (0)1223 494919
http://www.sanger.ac.uk
--
Arnaud Kerhornou
The Wellcome Trust Sanger Institute
The Pathogen Sequencing Unit
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Work: +44 (0) 1223 494955
Fax: +44 (0) 1223 494919
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