Inferred from Electronic Annotation (IEA)

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Overview

The IEA evidence code is used for annotations that are computationally, or automatically, assigned to gene products without further manual, curator review. IEA annotations are derived from several types of pipelines:

  • mappings between classification systems (EC, RHEA, etc) and GO terms that have been manually assessed to be equivalent. Any entry mapped to a classification system (such as an EC number) is automatically annotated the GO terms defined in the mapping.
  • mappings between protein or RNA families or sequence motifs and GO terms representing the conserved function(s) of that family or motif. Any entry belonging to the family or bearing the motif is automatically annotated the GO terms defined in the mapping. Mappings that could results in false positive hits are removed.
  • automatic transfer of annotation to orthologous gene products (Ensembl Compara), in which GO annotations are transferred across genes from orthologous groups of very closely related species.
  • rule-based annotations (UniRule), and machine-learning derive rules (ARBA).

IEA annotations must use a reference from the GO Consortium's collection of GO references to indicate the method by which the IEA annotation was made.

Methods for automated annotation generation

Automated annotation based on mappings controlled vocabularies

One of the primary methods of generating electronic annotations is to manually map GO terms to corresponding concepts in the controlled vocabularies used by the UniProt Knowledgebase or other external resources. The mappings that are currently used by the GO Consortium to produce annotations are:

Method Description Mapping file
Enzyme Commission numbers   Automated annotations from EC  EC2GO
HAMAP  Automated annotations from HAMAP  HAMAP2GO
InterPro domains  Automated annotations from InterPro  InterPro2GO
RHEA reactions   Automated annotations from RHEA  RHEA2GO
UniProt Keywords  Automated annotations from UniProt Keywords  SPKW2GO
UniProt Subcellular locations  Automated annotations from UniProt Subcellular locations  SPSL2GO

Automated annotation by phylogeny

Automated annotation by orthology

Automated annotation by machine-learning derived rules

Annotations from GO Inter-Ontology Links

  • Terms in different aspects of the ontology, e.g. Molecular Function or Biological Process, may be linked with relations from the Relations Ontology (RO).
  • When these relations are transitive, resulting annotations may be made using the IEA evidence code and the GO term of the 'child term' in the With/From field.

Use of the With/From Field for IEA

  • All IEA annotations must include an entry in the With/From Field of the Gene Association File (GAF) to indicate what individual sequences, sequence objects, methods, keyword mapping files, etc. are the basis of the annotation. When multiple entries are placed in the With/From field, they are separated by pipes.
DB Object ID DB Object Symbol GO ID DB:Reference Evidence Code With (or) From
FB:FBgn0261456 hpo GO:0005524 (ATP binding) GO_REF:0000002 IEA InterPro:IPR000719 |InterPro:IPR002290 |InterPro:IPR017441
UniProtKB:P01106 MYC GO:0006366 (transcription by RNA polymerase II) GO_REF:0000108 IEA GO:0001077 (transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding)

Examples where the IEA Evidence Code Should NOT be Used

Quality Control Checks

Evidence and Conclusion Ontology

ECO:0000501 evidence used in automatic assertion

Links

Curator Guide to GO Evidence Codes

Gene Ontology website GO Evidence Codes list

Review Status

Last reviewed: November 4, 2020