Re: [GUSDEV] Regarding comment tables in the DoTS

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

As Ed mentioned, that dots.nafeaturecomment is also used for storing 
GenBank data comment . If I insert a new comment to 
dots.nafeaturecomment table with the same fk na_feature_id, how could I 
tell which one is which by query? (assuming there has been GenBank comment)

Thanks,
Jian

Bindu Gajria wrote:

> 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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>>