Re: [GUSDEV] Regarding comment tables in the DoTS

[Jian Lu <jl...@vb...>]

Thank you all.

By using dots.nafeaturecomment table, how could you tell the comments 
from GenBank file or curators or other results?

Jian

Bindu Gajria wrote:

> 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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>