Re: [GUSDEV] Regarding comment tables in the DoTS

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

dots.nafeaturecomment table has the field na_feature_id, which is a 
foreign key. plasmodium gene features are stored in dots.genefeature, 
whose primary key is na_feature_id. so, one can identify the comment in 
the nafeaturecomment table to a particular gene.

bindu

On Apr 26, 2005, at 11:45 AM, Jian Lu wrote:

> 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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>>
>