diff --git a/metadata/rules/README.md b/metadata/rules/README.md index 0eb5da48..217210c1 100644 --- a/metadata/rules/README.md +++ b/metadata/rules/README.md @@ -66,6 +66,7 @@ For more details for GOC members on how to create rules, see [SOP.md](SOP.md) * GORULE:0000062 Infer annotations on molecular function via has_part * GORULE:0000063 Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column) * GORULE:0000064 TreeGrafter IEAs should be filtered for GO reference species + * GORULE:0000065 Annotations to term that are candidates for obsoletion should be removed @@ -1087,3 +1088,16 @@ Noting that ISM is not covered by this rule yet. If an annotation has GO_REF:0000118 (GAF column 6, GPAD column 5) and the taxon (GAF column 13, GPI column 7) is present in the GO reference species list (i.e 143 Panther species; [go-reference-species.yaml](https://github.com/geneontology/go-site/blob/master/metadata/go-reference-species.yaml)), then the annotation should be filter out. Note that this is not a line-by-line check in GPAD since it required both the GPAD and the GPI files. + + + +## Annotations to term that are candidates for obsoletion should be removed + + * id: [GORULE:0000065](https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000065.md) + * status: implemented + + +Terms scheduled for obsoletion are identified by the subset gocheck_obsoletion_candidate. +New annotations should not be made to these terms, and existing annotations should be removed or replaced. + +Error report: .report.md diff --git a/metadata/rules/gorule-0000065.md b/metadata/rules/gorule-0000065.md new file mode 100644 index 00000000..a0d5c9d4 --- /dev/null +++ b/metadata/rules/gorule-0000065.md @@ -0,0 +1,26 @@ +--- +layout: rule +id: GORULE:0000065 +title: "Annotations to term that are candidates for obsoletion should be removed" +type: report +fail_mode: soft +status: implemented +contact: "go-quality@lists.stanford.edu" +implementations: + - language: python + source: https://github.com/biolink/ontobio/blob/master/ontobio/io/qc.py +examples: + fail: + - comment: fails because GO:0007190 is in the subset gocheck_obsoletion_candidate + format: gaf + input: "UniProtKB P04049 RAF1 involved_in GO:0007190 PMID:15385642 IDA P protein taxon:9606 20171206 BHF-UCL" + pass: + - comment: Should pass + format: gaf + input: "UniProtKB A0A0H3GM48 dacA enables GO:0004016 PMID:23716572 IDA F protein taxon:393133 20160304 UniProt" + +--- +Terms scheduled for obsoletion are identified by the subset gocheck_obsoletion_candidate. +New annotations should not be made to these terms, and existing annotations should be removed or replaced. + +Error report: .report.md