[GUSDEV] Re: PsiPred view

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

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
>
>