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

[Sharon D. <di...@SN...>]

Hi Arnaud,

Welcome back.

I believe Jonathan S. is re-writing the plugin that loads GO, and that 
he is using some sort of generic underlying parser to do this.  If I 
understand correctly,  the parsing code may be generic enough and would 
likely just require writing some small amount of code to do the correct 
mapping.  

Jonathan - is this correct?  

Thanks,
Sharon

Arnaud Kerhornou wrote:

> 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 
>>>>&
>>>gt;>&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
>>>
>