Re: [GUSDEV] Regarding comment tables in the DoTS

[Bindu G. <bi...@pc...>]

hi Jian -
appending to Ed's reply:
to help in curation, we have set up a mechanism in PlasmoDB to allow 
for the user community to submit (and view) comments on genes. and for 
this, PlasmoDB uses dots.nafeaturecomment table. will be glad to 
provide specifics on how this table, or the others are used.

Bindu


On Apr 26, 2005, at 10:09 AM, Ed Robinson wrote:

> Curation is something we are still/constantly incorporating
> into GUS.  If you can give us more information about your
> specific curatorial needs, a number of people here can point
> you to the best places to locate that information.
>
> Generally, the comment fields you are talking about are not
> used for curatorial purposes, but are used for capturing
> annotations loaded from input files such as GenBank.  For
> instance,  a comment in the header of a GenBank file would
> likely go in the comment section, a commnet or note in a gene
> feature would go in an NAComment and a comment or note in a
> CDS feature would go in an AAComment.  Of course, the tables
> you mention AAFeatureImp and NAFeatureImp are not themselves
> tables you would use directly.  Rather, you would use specific
> feature views of these tables, such as GeneFeature, Transcript
> and TranslatedAAFeature.
>
> Of course, none of this should stop you from using these
> tables in the ways that seem best for your data.  If you want
> to add free-form notes to features, these tables are are
> likely one of the better places.
>
> In general, curatorial information is found in the SRes
> tables, so you should look at those closely also.
>
> Also, you should dig around in the documentation section of
> gusdb.org.  There are some papers that discuss the schema
> buried somewhere in there.
>
> -ed
>
>
>
> ---- Original message ----
>> Date: Mon, 25 Apr 2005 12:11:28 -0400
>> From: Jian Lu <jl...@vb...>
>> Subject: [GUSDEV] Regarding comment tables in the DoTS
>> To: gus...@li...
>>
>> Hi GUS folks,
>>
>> I am new in GUS schema. This might not be a new question, but I just
>> want to understand more about GUS. It would be great  if someone 
>> already
>> has had answers.
>>
>> I realize that there are different comment tables at DoTS:
>>
>> COMMENTS (COMMENTS_ID, COMMENT_STRING, REVIEW_STATUS_ID, ...)
>>
>> AACOMMENT (AA_COMMENT_ID, AA_SEQUENCE_ID, COMMENT_NAME_ID,
>> COMMENT_STRING, ...)
>>
>> NACOMMENT (NA_COMMENT_ID, NA_SEQUENCE_ID, COMMENT_STRING, ...)
>>
>> They have all common attributes (comment_id and comment_string), and 
>> AA
>> and NA groups have their associated sequence_ids. However, the
>> differences are obvious that REVIEW_STATUS_ID only at the COMMENTS
>> table, and COMMENT_NAME_ID only exists at the AACOMMENT table.
>>
>> Also, there is a NAFEATURECOMMENT table associated with NAFEATUREIMP
>> table. But there is no such table for AAFEATUREIMP.
>> If there would be comments on a feature, where should they go?
>>
>> The reason I brought this issue is we are considering to use comment
>> tables to store curation evidence and knowledge content, and we want 
>> to
>> make our development consistent.
>>
>> Thanks,
>>
>> Jian Lu
>> VBI
>>
>>
>>
>>
>>
>>
>>
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> -----------------
> Ed Robinson
> Center for Tropical and Emerging Global Diseases
> University of Georgia, Athens, GA 30602
> ero...@ug.../(706)542.1447/254.8883
>
>
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