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

[Matt B. <mb...@sa...>]

That should be sufficient.  In the GO database, there is only ever one 
comment per GO term.

cheers
Matt

Sharon Diskin wrote:

> Okay, thanks.   Does this mean that a single comment field added to 
> the GOTerm table is sufficient in your view?  
>
> Alternatively, we could use the DoTS.Comments table to store comments, 
> these can then be associated through the Evidence table to any row in 
> GUS.  So, another option would be to use the Comments table to store 
> the text, and link it to the GOTerm entry through the Evidence table. 
>  If this is not an appropriate use of the Evidence table, then we 
> could just create a GOTermComments linking table.  
>
> cheers,
> sharon
>
> Arnaud Kerhornou wrote:
>
>> 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 
>>exa
>>mple 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 
>>>>>
>>> (s
>>ee 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 
>>>>>&g
>>t; 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
>>
>>
>>
>>
>>
>

-- 

  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