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Update gorule-0000061.md
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improved formulation gorule-0000061
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pgaudet authored Sep 14, 2023
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Expand Up @@ -19,7 +19,7 @@ GAF2.2 files require a gene product to term (gp2term) relation in Column 4. Allo
* For `GO:0005575 "cellular component"`
* If the annotation is to the root term `"cellular_component"`, then the gp2term relation should be `RO:0002432 "is_active_in"`; else, it is repaired to `RO:0002432 "is_active_in"`.
* If the annotation is to `"GO:0032991 "protein-containing complex"` or a subclass descendant of, then the gp2term relation should be `"BFO:0000050 "part of"`; else, it is repaired to `"BFO:0000050 "part of"`.
* If the annotation is to `GO:0110165 "cellular anatomical entity"` or to `GO:0044423 "virion component"` or a descendant, then the allowed gp2term relations are `RO:0001025 "located in"` and `RO:0002432 "is_active_in"`, and `RO_0002325 "colocalizes_with"`; else it is repaired to `RO:0001025 "located in"`.
* If the annotation is to `GO:0110165 "cellular anatomical entity"` or to `GO:0044423 "virion component"` or a descendant of either of these terms, then the allowed gp2term relations are `RO:0001025 "located in"` and `RO:0002432 "is_active_in"`, and `RO_0002325 "colocalizes_with"`; else it is repaired to `RO:0001025 "located in"`.

* If an annotation has a negation (`NOT`), is is kept as a pipe-separated value with the gp2term relation.

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