Chado query HOWTO: FBal ID -> Annotation ID

[Josh Goodman]

This query returns a 5 column list containing the current values of the allele ID and symbol, the corresponding gene ID and symbol, and the gene annotation ID. Instructions for connecting to our public Chado database can be found here.

Code: Select all

select allele.uniquename as allele_id, allele.name as allele_symbol,
       gene.uniquename as gene_id, gene.name as gene_symbol, dbx.accession as annotation_id
        from feature allele, feature gene, feature_relationship fr, feature_dbxref fdbx, dbxref dbx, db,
             cvterm fr_type
        where allele.uniquename ~ '^FBal[0-9]+$' and allele.is_obsolete=false and allele.is_analysis=false and
              gene.is_obsolete=false and gene.is_analysis=false and upper(db.name) = 'FLYBASE ANNOTATION IDS' and
              fdbx.is_current=true and fr_type.name='alleleof' and
              allele.feature_id=fr.subject_id and fr.type_id=fr_type.cvterm_id and fr.object_id=gene.feature_id and
              gene.feature_id=fdbx.feature_id and fdbx.dbxref_id=dbx.dbxref_id and dbx.db_id=db.db_id;