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gorule-0000008.md

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Raw
layout id title contact status fail_mode implementations
rule
GORULE:0000008
No annotations should be made to uninformative high level 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, db.name AS assigned_by FROM association INNER JOIN gene_product ON association.gene_product_id = gene_product.id INNER JOIN term ON association.term_id = term.id INNER JOIN db ON association.source_db_id=db.id INNER JOIN dbxref AS gpx ON gene_product.dbxref_id = gpx.id WHERE term.acc IN ( 'GO:0050896', 'GO:0007610', 'GO:0051716', 'GO:0009628', 'GO:0009607', 'GO:0042221', 'GO:0009719', 'GO:0009605', 'GO:0006950', 'GO:0048585', 'GO:0048584', 'GO:0048583', 'GO:0001071', 'GO:0000988')
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 oboinowl: <http://www.geneontology.org/formats/oboInOwl#> PREFIX go: <http://purl.obolibrary.org/obo/go#> PREFIX metago: <http://geneontology.org/> PREFIX owl: <http://www.w3.org/2002/07/owl#> SELECT ?s ?p ?o ?too_high ?gaf WHERE { VALUES ?dont_annotate { go:gocheck_do_not_manually_annotate go:gocheck_do_not_annotate } ?too_high oboinowl:inSubset ?dont_annotate . GRAPH ?gaf { # ?gaf metago:graphType metago:gafCam . ?s ?p ?o . ?b owl:annotatedSource ?s ; owl:annotatedTarget ?o ; owl:annotatedProperty ?p . ?b <http://geneontology.org/lego/evidence> ?e . ?o a ?too_high . } }

Some terms are too high-level to provide useful information when used for annotation, regardless of the evidence code used.

We provide and maintain the list of too high-level terms as two subsets in the ontology:

  • gocheck_do_not_annotate "Term not to be used for direct annotation"
  • gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"

Both subsets denote high level terms, not to be used for any manual annotation.

For inferred electronic annotations (IEAs), we allow the use of terms from the gocheck_do_not_manually_annotate subset. These terms may still offer some general information, but a human curator should always be able to find a more specific annotation.