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From: Jian Lu <jl...@vb...> - 2006-01-03 14:27:20
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Chris,
Happy New Year!
Sorry for late reply since I was on vacation. We have this view which
has been used for our annotation pipeline. Here is the SQL.
CREATE VIEW DOTS.PSIPRED AS SELECT
AA_FEATURE_ID,
AA_SEQUENCE_ID,
FEATURE_NAME_ID,
PARENT_ID,
NA_FEATURE_ID,
SUBCLASS_VIEW,
SEQUENCE_ONTOLOGY_ID,
DESCRIPTION,
PFAM_ENTRY_ID,
MOTIF_AA_SEQUENCE_ID,
REPEAT_TYPE_ID,
EXTERNAL_DATABASE_RELEASE_ID,
SOURCE_ID,
PREDICTION_ALGORITHM_ID,
IS_PREDICTED,
REVIEW_STATUS_ID,
CLOB1 AS CONFIDENCE,
CLOB2 AS SECONDARY_STRUCTURE,
MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE,
OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID,
ROW_ALG_INVOCATION_ID
FROM DOTS.AAFEATUREIMP
WHERE SUBCLASS_VIEW='PsiPred'
WITH CHECK OPTION;
Thank you.
Jian
Chris Stoeckert wrote:
> Dear Jian,
>
> Awhile back you had requested the addition of two CLOB attributes to
> AAFeatureImp in order to capture ouput from Psipred. I had approved
> that request but learnt from Mike that with the way we are managing
> schema changes to GUS now "the schema representation abstracts the imp
> tables away, so the clobs would be added automatically when used by a
> subclass. Until there's a subclass that's going to have a clob
> column, I can't force them into the imp table."
>
> This simply means that we need to submit a specific view such as for
> Psipred that has clobs as needed. Can you supply that view (or if you
> prefer a more general view) of AAFeatureImp?
>
> Shailesh, where and how are we storing Psipred output you generated
> for PlasmoDB in GUS?
>
> Thanks,
> Chris
>
> Chris Stoeckert, Ph.D.
>
> Research Associate Professor, Dept. of Genetics
>
> 1415 Blockley Hall, Center for Bioinformatics
>
> 423 Guardian Dr., University of Pennsylvania
>
> Philadelphia, PA 19104
>
> Ph: 215-573-4409 FAX: 215-573-3111
>
>
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