Gene Ontology Annotations

Gene Ontology provides annotations linking genes to GO terms describing molecular functions, biological processes, and cellular components.

Data is downloaded from: http://current.geneontology.org/annotations/

Species Included

• Human (NCBITaxon:9606)
• Mouse (NCBITaxon:10090)
• Rat (NCBITaxon:10116)
• Dog (NCBITaxon:9615)
• Pig (NCBITaxon:9823)
• Cow (NCBITaxon:9913)
• Chicken (NCBITaxon:9031)
• Zebrafish (NCBITaxon:7955)
• Fruit fly (NCBITaxon:7227)
• Baker's yeast (NCBITaxon:4932)
• Fission yeast (NCBITaxon:4896)
• C. elegans (NCBITaxon:6239)
• Dictyostelium (NCBITaxon:44689)

Gene to GO Term Associations

This ingest uses GAF (Gene Association Format) files, one per species, to produce gene-to-GO term associations. The GO aspect determines the association type:

• Molecular Activity (Aspect F) — MacromolecularMachineToMolecularActivityAssociation
• Biological Process (Aspect P) — MacromolecularMachineToBiologicalProcessAssociation
• Cellular Component (Aspect C) — MacromolecularMachineToCellularComponentAssociation

Predicate Mapping

The predicate is determined by the GO qualifier column. Default predicates by aspect:

Aspect	Default Predicate
F (Molecular Function)	biolink:enables
P (Biological Process)	biolink:actively_involved_in
C (Cellular Component)	biolink:is_active_in

Qualifiers in the GAF file override these defaults (e.g. contributes_to, acts_upstream_of, part_of, located_in, colocalizes_with, acts_upstream_of_or_within, etc.). Annotations with "NOT" qualifiers are captured with negated: true.

Biolink Captured

• biolink:MacromolecularMachineToMolecularActivityAssociation / ...ToBiologicalProcessAssociation / ...ToCellularComponentAssociation
  • id (UUID)
  • subject (gene ID)
  • predicate (mapped from qualifier, see above)
  • negated (true when qualifier starts with "NOT")
  • object (GO term ID)
  • has_evidence (ECO term)
  • publications (from GAF reference column)
  • species_context_qualifier (NCBITaxon ID)
  • primary_knowledge_source (derived from GAF Assigned_By column)
  • aggregator_knowledge_source (["infores:monarchinitiative"])
  • knowledge_level (knowledge_assertion)
  • agent_type (manual_agent)

Citation

Ashburner et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000 May;25(1):25-9. The Gene Ontology Consortium. The Gene Ontology knowledgebase in 2023. Genetics. 2023 May 4;224(1):iyad031

License

MIT