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gorule-0000002.md

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layout id title contact status fail_mode implementations
rule
GORULE:0000002
No 'NOT' annotations to 'protein binding ; GO:0005515'
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, 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 association.is_not='1' AND term.acc = 'GO:0005515'
SQL
code language source
/^(.*?\t){3}not\tGO:0005515\t/i
regex

Even if an identifier is available in the 'with' column, a qualifier only informs on the GO term, it cannot instruct users to restrict the annotation to just the protein identified in the 'with', therefore an annotation applying protein binding ; GO:0005515 with the not qualifier implies that the annotated protein cannot bind anything.

This is such a wide-reaching statement that few curators would want to make.

This rule only applies to GO:0005515; children of this term can be qualified with not, as further information on the type of binding is then supplied in the GO term; e.g. not + NFAT4 protein binding ; GO:0051529 would be fine, as the negative binding statement only applies to the NFAT4 protein.

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