---
layout: rule
id: GORULE:0000023
title: "Materialize annotations for inter-branch links in the GO"
type: report
status: proposed
contact: "cjmungall@lbl.gov"
implementations:
  - language: java
    source: https://github.com/owlcollab/owltools/blob/master/OWLTools-Annotation/src/main/java/owltools/gaf/inference/BasicAnnotationPropagator.java
issues:
  - https://github.com/geneontology/go-annotation/issues/1544
fail_mode: soft

---

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.

## Procedure

 * Any asserted or inferred annotation to MF (excluding annotations with a NOT qualifier), where MF part-of BP, will generate an involved-in to that BP
 * Any asserted or inferred annotation to BP (excluding annotations with a NOT qualifier), 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

## TBD

Should this pipeline filter annotations based on some redundancy criteria?