Procedure for unmaintained annotations

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Procedure to deal with unmaintained annotations

  • GOC becomes responsible for maintaining annotations for groups no longer maintaining their annotations. This means that:
  1.  GOC/EBI runs QC checks
  2.  GOC becomes an editor of the annotations
  3.  Annotations will be rolled into the main GAF file

Procedure done by EBI to clean up annotations

Unmapped identifiers

  • Annotations are removed
  • We need to be able to map to a UniProt accession (or RNAcentral or ComplexPortal ID) in order to be able to import annotations.

Annotations to obsolete GO terms for which no replacement is available

  • Annotations are removed

Annotations to GO terms that are flagged as do_not_(manually_)annotate

  • Annotations are removed

Annotations with an invalid combination of evidence code and with/from

  • Annotations are removed

As governed by the rules in https://github.com/geneontology/go-site/blob/master/metadata/eco-usage-constraints.yaml

ISA/ISS Pfam/TIGRFAM

Should be subjected to the 1-year expiration date rule. We probably want to remove old 'ISA-like' annotation: TIGR_TIGRFAMS identifier in their with/from. The type of the entities supplied by these two databases is not compatible - according to the rules in eco-usage-constraints.yaml - with the ISS evidence code (strictly, not compatible with ECO:0000250); however, it is compatible with ECO:0000247 (ISA)

Special cases

For bacterial species

Replace:

  • GO:0001539 cilium or flagellum-dependent cell motility -> GO:0071973 bacterial-type flagellum-dependent cell motility for all bacterial annotations
  • GO:0000910 cytokinesis -> GO:0043093 FtsZ-dependent cytokinesis