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

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

Hi Sharon

I was away last week but Matt has replied to you regarding the comment 
field.
Also re. the population of the GO terms into GUS, will the plugin be 
generic enough to be used for others ontologies such as Sequence 
Ontology or the Parasite Life Cycle Ontology which we are planning to use ?

cheers
Arnaud

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
>>