Gene Ontology (GO)
Last modified September 9, 2013
This subsection of the ‘Ontologies’ section lists selected terms derived from the Gene Ontology (GO) project.The GO project provides a set of hierarchical controlled vocabulary split into 3 categories:
- Biological process
- Cellular component
- Molecular function
- Manually assigned GO terms found in UniProtKB are associated with one of 11 GO evidence codes, as well as with a link to the relevant publication, when available.
- Electronically assigned GO terms are found in UniProtKB/TrEMBL, when manually assigned GO terms is not available, and are associated with the GO evidence code ‘IEA’, which means ‘inferred from electronic annotation’.
Note that several UniProtKB keywords are manually mapped to GO terms (see document ‘Controlled vocabulary of keywords‘).
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.
- 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.
- 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.
- 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.
- 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.
- IPI: Inferred from Physical Interaction
Used to cover physical interactions between the gene product of interest and another molecule (ion, complex, etc.).
- 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.
- RCA: inferred from Reviewed Computational Analysis
Used for annotations based on a non-sequence-based computational methods where the results have been reviewed by an author or a curator.
- 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