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gorule-0000006.md

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layout id title contact status fail_mode implementations
rule
GORULE:0000006
IEP usage is restricted to terms from the Biological Process ontology
Implemented
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, term.term_type, evidence.code, db.name AS assigned_by FROM association 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 term ON association.term_id = term.id INNER JOIN evidence ON association.id = evidence.association_id INNER JOIN db ON association.source_db_id=db.id WHERE evidence.code = 'IEP' AND term.term_type != 'biological_process'
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 has_evidence: <http://geneontology.org/lego/evidence> PREFIX ECO: <http://purl.obolibrary.org/obo/ECO_> PREFIX IEP: <http://purl.obolibrary.org/obo/ECO_0000270> PREFIX GO: <http://purl.obolibrary.org/obo/GO_> PREFIX biological_process: <http://purl.obolibrary.org/obo/GO_0008150> PREFIX metago: <http://geneontology.org/> SELECT ?subj ?subjClass ?relation ?object ?go_term ?s ?evidence WHERE { GRAPH ?g { ?g metago:graphType metago:gafCam . ?s has_evidence: ?evidence . ?evidence a IEP: . ?s owl:annotatedSource ?subj . ?s owl:annotatedProperty ?relation . ?s owl:annotatedTarget ?object . ?subj ?relation ?object . ?subj a ?subjClass . ?object a ?go_term . FILTER (?subjClass != owl:NamedIndividual) FILTER (?go_term != owl:NamedIndividual) FILTER NOT EXISTS { # Filter out all appropriately annotated GO terms (Biological Process) ?object a biological_process: } } } LIMIT 100

The IEP evidence code is used where process involvement is inferred from the timing or location of expression of a gene, particularly when comparing a gene that is not yet characterized with the timing or location of expression of genes known to be involved in a particular process. This type of annotation is only suitable with terms from the Biological Process ontology.

For more information, see the binding guidelines on the GO wiki.