wiki:ProteinComplexInventory

Version 1 (modified by vw253, 6 years ago) (diff)

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From Oliver:) or a machine with MySql?

cat generate_complexes.sql | mysql -A --host=mysql-amigo.ebi.ac.uk -u go_select -P 4085 --password=amigo go_latest >GO_complexes

where

generate_complexes.sql is: SELECT

t.acc, t.name, gene_product.symbol, gene_product.full_name, evidence.code, dbxref.xref_dbname

FROM

term AS cc INNER JOIN graph_path AS tcl ON cc.id = tcl.term1_id INNER JOIN graph_path AS acl ON tcl.term2_id = acl.term1_id INNER JOIN term AS t ON t.id=acl.term1_id INNER JOIN association ON association.term_id = acl.term2_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 evidence ON evidence.association_id = association.id INNER JOIN dbxref ON dbxref.id = gene_product.dbxref_id

WHERE

species.genus = 'Schizosaccharomyces' AND species.species = 'pombe' AND cc.name='macromolecular complex';