Mapping gene to clone IDs in chado

[an-13]

Hello,

I apologize if I am posting to the wrong forum.  I am new to Chado/Gmod and haven't found a way to do the following for drosophila melanogaster:

Using flybase's postgres installation; for a given gene name simply retrieve a list of clone ID(s) from any of the drosophila genome libraries from Berkeley.  For example given the gene symbol  'nito'  retrieve 'GH11110' or given 'Rpn1' retrieve 'LD21723'

Thanks in advance

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[David Emmert]

Hi,

>> I apologize if I am posting to the wrong forum.  I am new to Chado/Gmod and
>> haven't found a way to do the following for drosophila melanogaster:

For more general questions about chado, querying the gmod-schema list is
appropriate, but in cases where you have questions about FlyBase's specific
implementation of chado, it would probably be best to contact
flybase-help[at]morgan.harvard.edu.

>> Using flybase's postgres installation; for a given gene name simply retrieve
>> a list of clone ID(s) from any of the drosophila genome libraries from
>> Berkeley.  For example given the gene symbol  'nito'  retrieve 'GH11110' or
>> given 'Rpn1' retrieve 'LD21723'

Give this query a shot:

SELECT f.feature_id, f.uniquename, f.name, frtp.name, c.feature_id, c.uniquename, c.name, db.name
from feature f, feature_relationship fr, feature c, cvterm ctp, cvterm frtp,
        cvterm ftp, feature_dbxref fd, dbxref dx, db

where f.feature_id = object_id
        and f.type_id = ftp.cvterm_id
        and ftp.name = 'gene'

        and fr.type_id = frtp.cvterm_id
        and frtp.name = 'derived_assoc_cdna_clone'

        and subject_id = c.feature_id
        and c.type_id = ctp.cvterm_id
        and ctp.name = 'cDNA_clone'

        and c.feature_id = fd.feature_id
        and fd.dbxref_id = dx.dbxref_id
        and dx.db_id = db.db_id
        and db.name = 'dgrc'

-- and f.name = 'Rpn1'
        and f.name = 'nito'

        and exists (select * from feature_relationship fr2, cvterm fr2tp, feature p, cvterm ptp where object_id = c.feature_id and fr2.type_id = fr2tp.cvterm_id and fr2tp.name = 'partof' and subject_id = p.feature_id and p.type_id = ptp.cvterm_id and ptp.name = 'cDNA')
;

Best,

-Dave
 (for FlyBase)

>From gmod-schema-bounces@... Thu Aug 14 21:43:34 2008
>> To: gmod-schema@...
>> Subject: [Gmod-schema] Mapping gene to clone IDs in chado
>>
>> Hello,
>>
>> I apologize if I am posting to the wrong forum.  I am new to Chado/Gmod and
>> haven't found a way to do the following for drosophila melanogaster:
>>
>> Using flybase's postgres installation; for a given gene name simply retrieve
>> a list of clone ID(s) from any of the drosophila genome libraries from
>> Berkeley.  For example given the gene symbol  'nito'  retrieve 'GH11110' or
>> given 'Rpn1' retrieve 'LD21723'
>>
>> Thanks in advance
>>

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_______________________________________________
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[an-13]

David,

That seems to be exactly what I was asking for.  Many thanks for the quick and accurate response!

an

On Fri, Aug 15, 2008 at 9:45 AM, David Emmert <emmert@...> wrote:

Hi,

>> I apologize if I am posting to the wrong forum.  I am new to Chado/Gmod and
>> haven't found a way to do the following for drosophila melanogaster:

For more general questions about chado, querying the gmod-schema list is
appropriate, but in cases where you have questions about FlyBase's specific
implementation of chado, it would probably be best to contact
flybase-help[at]morgan.harvard.edu.

>> Using flybase's postgres installation; for a given gene name simply retrieve
>> a list of clone ID(s) from any of the drosophila genome libraries from
>> Berkeley.  For example given the gene symbol  'nito'  retrieve 'GH11110' or
>> given 'Rpn1' retrieve 'LD21723'

Give this query a shot:

SELECT f.feature_id, f.uniquename, f.name, frtp.name, c.feature_id, c.uniquename, c.name, db.name
from feature f, feature_relationship fr, feature c, cvterm ctp, cvterm frtp,
       cvterm ftp, feature_dbxref fd, dbxref dx, db

where f.feature_id = object_id
       and f.type_id = ftp.cvterm_id
       and ftp.name = 'gene'

       and fr.type_id = frtp.cvterm_id
       and frtp.name = 'derived_assoc_cdna_clone'

       and subject_id = c.feature_id
       and c.type_id = ctp.cvterm_id
       and ctp.name = 'cDNA_clone'

       and c.feature_id = fd.feature_id
       and fd.dbxref_id = dx.dbxref_id
       and dx.db_id = db.db_id
       and db.name = 'dgrc'

--      and f.name = 'Rpn1'
       and f.name = 'nito'

       and exists (select * from feature_relationship fr2, cvterm fr2tp, feature p, cvterm ptp where object_id = c.feature_id and fr2.type_id = fr2tp.cvterm_id and fr2tp.name = 'partof' and subject_id = p.feature_id and p.type_id = ptp.cvterm_id and ptp.name = 'cDNA')
;

Best,

-Dave
 (for FlyBase)

>From gmod-schema-bounces@... Thu Aug 14 21:43:34 2008
>> To: gmod-schema@...
>> Subject: [Gmod-schema] Mapping gene to clone IDs in chado

>>
>> Hello,
>>
>> I apologize if I am posting to the wrong forum.  I am new to Chado/Gmod and
>> haven't found a way to do the following for drosophila melanogaster:
>>
>> Using flybase's postgres installation; for a given gene name simply retrieve
>> a list of clone ID(s) from any of the drosophila genome libraries from
>> Berkeley.  For example given the gene symbol  'nito'  retrieve 'GH11110' or
>> given 'Rpn1' retrieve 'LD21723'
>>
>> Thanks in advance
>>

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http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
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