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Gene Ontology (GO)

The Gene Ontology (GO) project provides a set of hierarchical controlled vocabulary split into 3 categories:

  • Biological process
  • Molecular function
  • Cellular component

UniProtKB lists selected terms derived from the GO project. The GO terms derived from the ‘Biological process’ and Molecular function' categories are listed in the ‘Function’ section; the GO terms derived from the ‘Cellular component’ category are listed in the ‘Subcellular location’ section.

GO terms can be manually or electronically assigned to a UniProtKB entry:

  • Manually assigned GO terms found in UniProtKB/Swiss-Prot are associated with one of 15 GO evidence codes, as well as with a link to the relevant publication, when available. These GO annotations are tagged with a yellow source/evidence label.
  • Electronically assigned GO terms are found in UniProtKB/TrEMBL, but to some extent also in UniProtKB/Swiss-Prot, and are associated with the GO evidence code ‘IEA’, which means ‘inferred from electronic annotation’. These GO annotations are tagged with a blue source/evidence label.

Note that many UniProtKB keywords are manually mapped to GO terms (see document 'Controlled vocabulary of keywords), but the resulting GO annotations in UniProtKB appear with a blue label as “inferred from electronic annotation”.

List of GO evidence codes found in UniProtKB

  • EXP: Inferred from Experiment

Used when experimental results indicate a gene product’s function, process involvement or subcellular location.

  • IBA: Inferred from Biological Aspect of Ancestor

Used when an aspect of a descendent is inferred through the characterization of an aspect of a ancestral gene.

  • IC: Inferred by Curator

Used when annotation is not supported by any evidence, but can be reasonably inferred by a curator from other GO annotations for which evidence is available.

  • IDA: Inferred from Direct Assay

Used when a direct assay for the function, process or component indicated by the GO term is available.

  • HDA: High-throughput Direct Assay
  • IEA: Inferred from Electronic Annotation

Used when annotation derives from computation or automated transfer from a database. These annotations have not been manually checked.

  • IEP: Inferred from Expression Pattern

Used when annotation is inferred from the timing or site of expression of a gene.

  • HEP: High-throughput Expression Pattern
  • IGC: Inferred from Genomic Context

Used when information about the genomic context of a gene product forms part of the evidence for a particular annotation. Genomic context includes, but is not limited to, such things as identity of neighboring genes (i.e. synteny), operon structure, and phylogenetic or other whole genome analysis.

  • IGI: Inferred from Genetic Interaction

Used to describe “traditional” genetic interactions, such as suppressors and synthetic lethals, as well as other techniques, such as functional complementation, rescue experiments, or inferences about a gene drawn from the phenotype of a mutation in a different gene.

  • HGI: High-throughput Genetic Interaction
  • IMP: Inferred from Mutant Phenotype

Used to describe the observations of variations or changes in a gene product, such as mutations or abnormal levels. This includes techniques, such as knockouts, overexpression, anti-sense experiments and use of specific protein inhibitors.

  • HMP: High-throughput Mutant Phenotype
  • IPI: Inferred from Physical Interaction

Used to cover physical interactions between the gene product of interest and another molecule (ion, complex, etc.).

  • ISA: Inferred from Sequence Alignment

Used when the primary piece of evidence is a pairwise or multiple sequence alignment.

  • ISM: Inferred from Sequence Model

Used when any kind of sequence modeling method (e.g. Hidden Markov Models) is the primary piece of evidence

  • ISO: Inferred from Sequence Orthology

Used when the assertion of orthology between the gene product and an experimentally characterized gene product in another organism is the main basis of the annotation

  • ISS: Inferred from Sequence or Structural Similarity

Used for any analysis based on sequence alignment, structure comparison, or evaluation of sequence features, such as composition.

  • NAS: Non-traceable Author Statement

Used for statements found in a published article that cannot be traced back to another publication.

  • TAS: Traceable Author Statement

Used for information obtained from published articles, mostly reviews, as well as text books or dictionaries, where the original experiments are traceable.

Additional information: GO evidence codes

Related documents

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Main funding by: National Institutes of Health

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