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  • Gene Ontology all descendants SQL (or other solutions)

    Dear GO SQL Experts,

    I would like to create a GO annotation text file which contains the set of genes connected to each GOids and its all descendants (children, grandchildren, etc.).

    Can somebody give me some hints how to do this?
    (I am working with D.melanogaster and FlyBase geneIDs - FBgn)

    I already created an SQl query for this:
    SELECT
    term.acc AS superterm_acc,
    dbxref.xref_key AS gp_acc,
    evidence.code AS code
    FROM term
    INNER JOIN graph_path ON (term.id=graph_path.term1_id)
    INNER JOIN association ON (graph_path.term2_id=association.term_id)
    INNER JOIN evidence ON (association.term_id=evidence.id)
    INNER JOIN gene_product ON (association.gene_product_id=gene_product.id)
    INNER JOIN species ON (gene_product.species_id=species.id)
    INNER JOIN dbxref ON (gene_product.dbxref_id=dbxref.id)
    WHERE
    species.genus = 'Drosophila'
    AND
    species = 'melanogaster';

    But I am not sure if the query is correct since the evidence codes that I get are seems to be imperfect:
    bash$ awk '{print $3}' downloaded_file | sort | uniq -c
    6387 IDA
    921948 IEA
    2911 IEP
    113 IGC
    257 IMP
    123 ISA
    13 ISO
    664 ISS
    904 NAS
    583144 ND
    24598 RCA

    accordnig to this query I got more kinds of evidence codes:
    SELECT evidence.code, count(DISTINCT association.id)
    FROM gene_product
    INNER JOIN dbxref ON (gene_product.dbxref_id=dbxref.id)
    INNER JOIN association ON (gene_product.id=association.gene_product_id)
    INNER JOIN species ON (gene_product.species_id=species.id)
    INNER JOIN evidence ON (association.id=evidence.association_id)
    WHERE dbxref.xref_dbname = 'FB'
    AND
    species.genus = 'Drosophila'
    AND
    species = 'melanogaster'
    GROUP BY evidence.code;
    IBA 1254
    IC 1130
    IDA 11801
    IEA 13541
    IEP 974
    IGC 18
    IGI 2016
    IKR 63
    IMP 18364
    IPI 1889
    IRD 9
    ISA 141
    ISM 1301
    ISO 1
    ISS 14862
    NAS 10277
    ND 6899
    RCA 19
    TAS 4732

    Cheers,
    Eszter Ari
    Institut für Populationsgenetik
    Vetmeduni Vienna
    Veterinärplatz 1
    1210 Wien, Austria

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