Chado query HOWTO: InterPro <-> FlyBase gene

[Josh Goodman]

This query demonstrates how to generate a list of InterPro IDs and their corresponding FlyBase gene. Here is the SQL

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select dbx.accession as INTERPRO_ID, dbx.description as INTERPRO_DOMAIN, f.uniquename as FLYBASE_ID, f.name as FLYBASE_SYMBOL
        from feature f, feature_dbxref fdbx, dbxref dbx, db, cvterm cvt
        where db.name='INTERPRO' and fdbx.is_current=true and cvt.name='gene' and f.is_obsolete=false
              and db.db_id=dbx.db_id and dbx.dbxref_id=fdbx.dbxref_id
              and fdbx.feature_id=f.feature_id and f.type_id=cvt.cvterm_id;


The output produced will contain 4 columns. The first column is the InterPro ID, the second is the InterPro domain name, and the last two are the FlyBase ID and ASCII symbol for the gene corresponding to the InterPro ID. One way to run this query on our database and save the results is by using the PostgreSQL client. Save the above query to a file and use this command.

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psql -h flybase.org -U flybase -f query -o interpro_fbgn.txt flybase


Be sure to substitute 'query' for the file containing the saved query.