Merge pull request #2034 from geneontology/pgaudet-patch-85

Update gorule-0000020.md
geneontology · Jul 13, 2023 · 30abbc1 · 30abbc1
2 parents c46e551 + 3ccd5e9
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diff --git a/metadata/rules/README.md b/metadata/rules/README.md
@@ -493,11 +493,14 @@ reasoner such as HermiT.
  * status: implemented
 
 
-There should be no annotations to obsolete terms or to an alternate ID. Obsolete terms that have a `replaced_by` tag and
-terms annotated to one of their alternative IDs (merged terms; `alt_id` in the .obo files) will automatically be repaired to the valid term id.
+There should be no annotations to obsolete terms or to an alternate ID (Column 5 of GAF, Column 4 of GPAD). As well, GO terms present in annotations also should be repaired if possible: 
+* with/from: Column 8 of GAF, Column 7 of GPAD
+* extensions, Column 16 of GAF, Column 11 of GPAD 
+
+Obsolete terms that have a `replaced_by` tag and terms annotated to one of their alternative IDs (merged terms; `alt_id` in the .obo files) will automatically be repaired to the valid term id.
 If no replacement is found, the annotation will be filtered.
 
-Other GO terms present in annotations (with/from column, etc) also should be repaired if possible.
+
 
 <a name="gorule0000021"/>
 

diff --git a/metadata/rules/gorule-0000020.md b/metadata/rules/gorule-0000020.md
@@ -16,8 +16,11 @@ examples:
       input: "FB	FBgn0033449	CG1663		GO:1902361	FB:FBrf0202953|GO_REF:0000024	ISS	UniProtKB:Q05516	F			protein	taxon:7227	20171127	FlyBase"
       output: "FB	FBgn0033449	CG1663		GO:0006850	FB:FBrf0202953|GO_REF:0000024	ISS	UniProtKB:Q05516	F			protein	taxon:7227	20171127	FlyBase"
 ---
-There should be no annotations to obsolete terms or to an alternate ID. Obsolete terms that have a `replaced_by` tag and
-terms annotated to one of their alternative IDs (merged terms; `alt_id` in the .obo files) will automatically be repaired to the valid term id.
+There should be no annotations to obsolete terms or to an alternate ID (Column 5 of GAF, Column 4 of GPAD). As well, GO terms present in annotations also should be repaired if possible: 
+* with/from: Column 8 of GAF, Column 7 of GPAD
+* extensions, Column 16 of GAF, Column 11 of GPAD 
+
+Obsolete terms that have a `replaced_by` tag and terms annotated to one of their alternative IDs (merged terms; `alt_id` in the .obo files) will automatically be repaired to the valid term id.
 If no replacement is found, the annotation will be filtered.
 
-Other GO terms present in annotations (with/from column, etc) also should be repaired if possible.
+