Re: [GUSDEV] Loading Prosite DB

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

Aaron,

We are also working on InterProScan and other analysis tools. But we=20
haven't got a plugin yet. If your plugin is ready, I would like to play=20
it. Here is the view that we created for InterProScan. Please comment=20
it. Thanks.

--
-- VIEW DOTS.INTERPROSCAN
-- used to store outputs from InterProScan
-- June 29, 2005
--=20
-- For GUS 3.0
CREATE VIEW DOTS.INTERPROSCAN 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 AS INTERPROSCAN_ID,
    PREDICTION_ALGORITHM_ID,
    IS_PREDICTED,
    REVIEW_STATUS_ID,
    INT1 AS PVALUE_EXP,
    FLOAT1  as PVALUE_MANT,
    FLOAT2  as SCORE,
    STRING1 AS MEMBER_ID,
    STRING2 AS MEMBER_DESCRIPTION,
    MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE,=20
OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID,=20
ROW_ALG_INVOCATION_ID
    FROM DOTS.AAFEATUREIMP
    WHERE SUBCLASS_VIEW=3D'InterProScan';

-- For GUS 3.5
CREATE VIEW DOTS.INTERPROSCAN 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 AS INTERPROSCAN_ID,
    PREDICTION_ALGORITHM_ID,
    IS_PREDICTED,
    REVIEW_STATUS_ID,
    NUMBER1 as PVALUE_EXP,
    FLOAT1  as PVALUE_MANT,
    FLOAT2  as SCORE,
    STRING1 as MEMBER_ID,
    STRING2 as MEMBER_DESCRIPTION,
    MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE,=20
OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID,=20
ROW_ALG_INVOCATION_ID
    FROM DOTS.AAFEATUREIMP
    WHERE SUBCLASS_VIEW=3D'InterProScan';

Aaron J. Mackey wrote:

> FYI, we are currently developing a plugin to load such data from =20
> InterProScan ... we're happy to collaborate with interested parties.
>
> -Aaron
>
> On Aug 2, 2005, at 11:21 AM, Chris Stoeckert wrote:
>
>> Hi Sanjeev,
>> I don't think we have a loader at CBIL for Prosite. We load Prodom =20
>> and CDD (pfam, SMART).
>> Cheers,
>> Chris
>>
>> On Aug 1, 2005, at 4:49 PM, Kumar, Sanjeev (Contr) wrote:
>>
>>
>>> Hi,
>>>   Do we have Plugin to load PrositeDB data related to Protein =20
>>> motif? The data is available
>>>   at url address : http://ca.expasy.org/prosite/
>>>
>>> Thanks
>>> Sanjeev
>>>
>>>
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>>
>>
>>
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>
> --=20
> Aaron J. Mackey, Ph.D.
> Project Manager, ApiDB Bioinformatics Resource Center
> Penn Genomics Institute, University of Pennsylvania
> email:  am...@pc...
> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
> fax:    215-746-6697
> postal: Penn Genomics Institute
>         Goddard Labs 212
>         415 S. University Avenue
>         Philadelphia, PA  19104-6017
>
>
>
>
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