Chado query HOWTO: FBgn -> FBal

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Chado query HOWTO: FBgn -> FBal

Postby Josh Goodman » Wed Feb 23, 2011 4:06 pm

This query returns a 6 column list containing the current values of the gene ID and symbol, the corresponding allele ID and symbol, and the genus and species. Instructions for connecting to our public Chado database can be found here.

Code: Select all
select g.uniquename as FBgn, g.name as gsym,
       a.uniquename as FBal, a.name as asym,
       o.genus, o.species
       from feature g left join feature_relationship fr on (g.feature_id=fr.object_id)
                      left join feature a on (fr.subject_id=a.feature_id)
                      left join cvterm cvt on (fr.type_id=cvt.cvterm_id)
                      left join organism o on (g.organism_id=o.organism_id)
       where g.uniquename ~ '^FBgn[0-9]+$'
          and g.is_obsolete=false
          and g.is_analysis=false
          and a.uniquename ~ '^FBal[0-9]+$'
          and a.is_obsolete=false
          and a.is_analysis=false
          and cvt.name='alleleof';
Josh Goodman
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Joined: Mon Nov 26, 2007 2:39 pm

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