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gorule-0000007.md

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layout id title contact status fail_mode implementations
rule
GORULE:0000007
IPI should not be used with catalytic activity molecular function terms
Proposed
soft
code language source
SELECT gene_product.symbol, CONCAT(gpx.xref_dbname, ':', gpx.xref_key) AS gpxref, IF(association.is_not=1,"NOT","") AS 'not', term.acc, term.name, evidence.code, db.name AS assigned_by FROM term INNER JOIN graph_path ON term.id = graph_path.term2_id INNER JOIN term AS term2 ON graph_path.term1_id = term2.id INNER JOIN association ON graph_path.term2_id = association.term_id INNER JOIN evidence ON association.id = evidence.association_id INNER JOIN gene_product ON association.gene_product_id = gene_product.id INNER JOIN dbxref AS gpx ON gene_product.dbxref_id = gpx.id INNER JOIN db ON association.source_db_id=db.id WHERE term2.acc = 'GO:0003824' AND evidence.code = 'IPI'
SQL
language code
sparql
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX RO: <http://purl.obolibrary.org/obo/RO_> PREFIX hasEvidence: <http://geneontology.org/lego/evidence> PREFIX ECO: <http://purl.obolibrary.org/obo/ECO_> PREFIX GO: <http://purl.obolibrary.org/obo/GO_> PREFIX catalytic_activity: <http://purl.obolibrary.org/obo/GO_0003824> PREFIX IPI: <http://purl.obolibrary.org/obo/ECO_0000353> PREFIX metago: <http://geneontology.org/> SELECT ?subj ?relation ?object ?s ?evidence WHERE { GRAPH ?g { ?g metago:graphType metago:gafCam . ?s hasEvidence: ?evidence . ?evidence a IPI: . ?s owl:annotatedSource ?subj . ?s owl:annotatedProperty ?relation . ?s owl:annotatedTarget ?object . ?subj ?relation ?object . ?subj a ?iclass . ?object a catalytic_activity: . FILTER (?iclass != owl:NamedIndividual) # There should be no results where instances of # 'catalytic_activity molecular function' ; GO:0003824 also have evidences of IPI } } LIMIT 100

The IPI (Inferred from Physical Interaction) evidence code is used where an annotation can be supported from interaction evidence between the gene product of interest and another molecule (see the evidence code documentation). While the IPI evidence code is frequently used to support annotations to terms that are children of binding ; GO:0005488, it is thought unlikely by the Binding working group that enough information can be obtained from a binding interaction to support an annotation to a term that is a chid of catalytic activity ; GO:0003824. Such IPI annotations to child terms of catalytic activity ; GO:0003824 may need to be revisited and corrected.

For more information, see the catalytic activity annotation guide on the GO wiki.