Merge pull request #2204 from geneontology/pgaudet-patch-104

Update gorule-0000027.md
geneontology · Nov 30, 2023 · fbe4127 · fbe4127
2 parents 9a04955 + ec5f3b0
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diff --git a/metadata/rules/README.md b/metadata/rules/README.md
@@ -613,11 +613,12 @@ See also GORULE:0000037
  * status: implemented
 
 
--   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
 

diff --git 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