[Gusdev-gusdev] [Fwd: Re: proposed modifications to GO Schema for GUS3.0]

[Arnaud K. <ax...@sa...>]

  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