From 4eee77162bffb5215cc7fe4fcf5e89efaed627c6 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Mon, 10 May 2021 11:11:58 +0200 Subject: [PATCH 1/2] Update gorule-0000023.md --- metadata/rules/gorule-0000023.md | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/metadata/rules/gorule-0000023.md b/metadata/rules/gorule-0000023.md index 6b8f00b6..85095280 100644 --- a/metadata/rules/gorule-0000023.md +++ b/metadata/rules/gorule-0000023.md @@ -3,7 +3,7 @@ layout: rule id: GORULE:0000023 title: "Materialize annotations for inter-branch links in the GO" type: report -status: proposed +status: implemented contact: "cjmungall@lbl.gov" implementations: - language: java @@ -18,18 +18,23 @@ Annotations will be propagated from MF to BP over part_of, or from BP to CC over ## Background -Historically GO treated MF, BP and CC as distinct ontologies. They are now better regarded as branchers or sub-hierarchies within a single ontology, cross-linked via a variety of relations. Annotators used to make manual duplicate annotations. +MF, BP and CC aspects of the GO can be regarded as branches or sub-hierarchies within a single ontology, cross-linked via a variety of relations. Therefore, annotations can be inferred from their relationships with terms from other aspects. ## Procedure - * Any asserted or inferred annotation to MF, where MF part-of BP, will generate an involved-in to that BP - * Any asserted or inferred annotation to BP, where BP occurs-in CC, will generate a part-of annotation to that CC + * Any asserted or inferred annotation to a MF, where MF part-of BP, will generate an `involved-in` to that BP + * Asserted or inferred annotation to a BP using the `involved-in` relation, where BP occurs-in CC, will generate a `part-of` annotation to that CC + ### Evidence and provenance - * Evidence, references, publications, date are retained - * Assigned_by is GOC + * ECO (GAF2.2 Column 7/GAPD1.1 Column 6): IEA + * "with/from" (GAF2.2 Column 8/GAPD1.1 Column 7): the GO term from which the anontation is propagated + * Reference: GO_REF:0000108 (https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-0000108.md) + * Date (GAF2.2 Column 14/GAPD1.1 Column 9): the date the script was run + * Assigned_by (GAF2.2 Column 15/GAPD1.1 Column 10): GOC ## TBD -Should this pipeline filter annotations based on some redundancy criteria? +* Should this pipeline filter annotations based on some redundancy criteria? +* goref-0000108.md mentions other evidence codes (not 3-letter); those should be fixed From 9e2e17cc32f73923eafa954b78f34033d194814d Mon Sep 17 00:00:00 2001 From: pgaudet Date: Mon, 10 May 2021 09:12:19 +0000 Subject: [PATCH 2/2] refreshing goref and rules README.md files --- metadata/rules/README.md | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/metadata/rules/README.md b/metadata/rules/README.md index 80e5ec50..b3125a5e 100644 --- a/metadata/rules/README.md +++ b/metadata/rules/README.md @@ -524,7 +524,7 @@ please see: https://github.com/geneontology/go-annotation/issues/1479 ## Materialize annotations for inter-branch links in the GO * id: [GORULE:0000023](https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000023.md) - * status: proposed + * status: implemented @@ -532,21 +532,26 @@ Annotations will be propagated from MF to BP over part_of, or from BP to CC over ## Background -Historically GO treated MF, BP and CC as distinct ontologies. They are now better regarded as branchers or sub-hierarchies within a single ontology, cross-linked via a variety of relations. Annotators used to make manual duplicate annotations. +MF, BP and CC aspects of the GO can be regarded as branches or sub-hierarchies within a single ontology, cross-linked via a variety of relations. Therefore, annotations can be inferred from their relationships with terms from other aspects. ## Procedure - * Any asserted or inferred annotation to MF, where MF part-of BP, will generate an involved-in to that BP - * Any asserted or inferred annotation to BP, where BP occurs-in CC, will generate a part-of annotation to that CC + * Any asserted or inferred annotation to a MF, where MF part-of BP, will generate an `involved-in` to that BP + * Asserted or inferred annotation to a BP using the `involved-in` relation, where BP occurs-in CC, will generate a `part-of` annotation to that CC + ### Evidence and provenance - * Evidence, references, publications, date are retained - * Assigned_by is GOC + * ECO (GAF2.2 Column 7/GAPD1.1 Column 6): IEA + * "with/from" (GAF2.2 Column 8/GAPD1.1 Column 7): the GO term from which the anontation is propagated + * Reference: GO_REF:0000108 (https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-0000108.md) + * Date (GAF2.2 Column 14/GAPD1.1 Column 9): the date the script was run + * Assigned_by (GAF2.2 Column 15/GAPD1.1 Column 10): GOC ## TBD -Should this pipeline filter annotations based on some redundancy criteria? +* Should this pipeline filter annotations based on some redundancy criteria? +* goref-0000108.md mentions other evidence codes (not 3-letter); those should be fixed