adding gorule-0000059 text

metadata/rules/gorule-0000059.md

@@ -0,0 +1,21 @@
+---
+layout: rule
+id: GORULE:0000059
+title: "GAF Version 2.1 should have Qualifiers upgraded based on the GO Term"
+type: repair
+fail_mode: soft
+status: proposed
+tags: []
+contact: "go-quality@mailman.stanford.edu"
+---
+
+When processing GAF version 2.1, if the qualifier field (column 4) does not have a relation
+a relation should be computed based on the following rule:
+* If the annotation GO Term is in `molecular function` then the relation should be `RO:0002327 "enables"`
+* If the annotation GO Term is in `biological process` then the relation should be `RO:0002264 "acts upstream or within"`
+* If the annotation GO Term is in `cellular component` then
+    * If the GO Term is a subclass of `"GO:0032991 "protein-containing complex"` then the relation should be `"BFO:0000050 "part of"`
+    * Otherwise the relation should be `RO:0001025 "located in"`
+
+This is due to the other annotation formats having a richer set of Relations available to them. In order to interoperate between GAF 2.1
+and other formats as other formats have a richer set of allowed relations, this will be a process to provide basic compatibility.