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gorule-0000011.md

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layout id title contact status fail_mode implementations
rule
GORULE:0000011
ND annotations to root nodes only
Proposed
soft
code language source
SELECT gene_product.symbol, CONCAT(gpx.xref_dbname, ':', gpx.xref_key), IF(association.is_not = 1, "NOT", "") AS 'not', term.acc, term.name, evidence.code, CONCAT(dbxref.xref_dbname, ':', dbxref.xref_key) AS evxref, db.name AS assigned_by FROM association INNER JOIN evidence ON association.id = evidence.association_id INNER JOIN gene_product ON association.gene_product_id = gene_product.id INNER JOIN term ON association.term_id = term.id INNER JOIN dbxref ON evidence.dbxref_id = dbxref.id INNER JOIN dbxref AS gpx ON gpx.id = gene_product.dbxref_id INNER JOIN db ON association.source_db_id = db.id WHERE ( evidence.code = 'ND' AND term.acc NOT IN ( 'GO:0005575', 'GO:0003674', 'GO:0008150' ) ) OR ( NOT(evidence.code = 'ND') AND term.acc IN ( 'GO:0005575', 'GO:0003674', 'GO:0008150' ) ) OR ( evidence.code = 'ND' AND ( CONCAT(dbxref.xref_dbname, ':', dbxref.xref_key) NOT IN ( 'GO_REF:0000015', 'FB:FBrf0159398', 'ZFIN:ZDB-PUB-031118-1', 'dictyBase_REF:9851', 'MGI:MGI:2156816', 'SGD_REF:S000069584', 'CGD_REF:CAL0125086', 'RGD:1598407', 'TAIR:Communication:1345790', 'AspGD_REF:ASPL0000111607' ) ) )
SQL

The No Data (ND) evidence code should be used for annotations to the root nodes only and should be accompanied with GO_REF:0000015 or an internal reference. PMIDs cannot be used for annotations made with ND.

  • if you are using an internal reference, that reference ID should be listed as an external accession for GO_REF:0000015. Please add (or email) your internal reference ID for GO_REF:0000015.
  • All ND annotations made with a reference other than GO_REF:0000015 (or an equivalent internal reference that is listed as external accession for GO_REF:0000015) should be filtered out of the GAF.

The SQL code identifies all ND annotations that do not use GO_REF:0000015 or one of the alternative internal references listed for it in the GO references file.