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

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

Sharon Diskin wrote:

> 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.  

Re. the Sequence Ontology I can only see a SequenceOntology table. Would 
it be possible to have the same design for SO (or for any others) than 
for GO, I mean not only store SO terms but also their relationships ?

>
> 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 l
>>>>et 
>>>>>&
>>>>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
>>>>
>>>>        
>>>>
>>
>