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Update gorule-0000023.md #1683

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4eee771
Update gorule-0000023.md
pgaudet May 10, 2021
9e2e17c
refreshing goref and rules README.md files
pgaudet May 10, 2021
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19 changes: 12 additions & 7 deletions metadata/rules/README.md
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Expand Up @@ -524,29 +524,34 @@ 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



Annotations will be propagated from MF to BP over part_of, or from BP to CC over occurs_in.

## 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

<a name="gorule0000024"/>

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19 changes: 12 additions & 7 deletions metadata/rules/gorule-0000023.md
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Expand Up @@ -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: "[email protected]"
implementations:
- language: java
Expand All @@ -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