diff --git a/metadata/rules/gorule-0000027.md b/metadata/rules/gorule-0000027.md index 8fa274dd..f0f51612 100644 --- a/metadata/rules/gorule-0000027.md +++ b/metadata/rules/gorule-0000027.md @@ -10,11 +10,12 @@ implementations: - language: python source: https://github.com/biolink/ontobio/blob/master/ontobio/io/gafparser.py --- -- DB (GAF and GPAD column 1); and all DB abbreviations in 'with' field (GAF column 8; GPAD column 7)and in the annotation extensions (GAF column 16; GPAD column 11) must be in [db-xrefs.yaml](https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml) (see below) -- Noting that for the 'with' field (GAF column 8; GPAD column 7), GO terms are allowed for IC evidence code, i. e. there are values other than DB:identifiers. -- The `assigned_by` field (GAF column 15; GPAD column 10) is checked against [groups.yaml](https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml) +- DB (GAF and GPAD column 1); and all DB abbreviations in 'with' field (GAF column 8; GPAD column 7) and in the annotation extensions (GAF column 16; GPAD column 11) must be in [db-xrefs.yaml](https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml) (see below) - id_syntax information in the [db-xrefs.yaml](https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml) file can be used to validate local identifiers. -- All GO IDs must be extant in current ontology: GO IDs can be present in Columns 5, 8, and 16 of GAF (4, 7, 11 in GPAD). +- The 'with' field can additionally contain GO terms, when the Evidence code is IC. GO terms are checked in GORULE:0000001. +- The `assigned_by` field (GAF column 15; GPAD column 10) is checked against [groups.yaml](https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml) + +- TBC (thy may be GORULE:0000001) All GO IDs must be extant in current ontology: GO IDs can be present in Columns 5, 8, and 16 of GAF (4, 7, 11 in GPAD). ### Additional notes on identifiers