Table 2.
Evidence code categories, evidence code names and definitions
| Category | Evidence code | Types of evidence | Supporting data |
|---|---|---|---|
| Experimental | Inferred from Experiment (EXP) | Any experimental assay | |
| Inferred from Direct Assay (IDA) | (i) Enzyme assays | ||
| (ii) In vitro reconstitution (e.g. transcription) | |||
| (iii) Immunofluorescence (for cellular component) | |||
| (iv) Cell fractionation (for cellular component) | |||
| (v) Physical interaction/binding assay (sometimes appropriate for cellular component or molecular function) | |||
| Inferred from Physical Interaction (IPI) | (i) Two-hybrid interactions | With column should be filled with Identifier of the interacting protein | |
| (ii) Co-purification | |||
| (iii) Co-immunoprecipitation | |||
| (iv) Ion/protein binding experiments | |||
| Inferred from Mutant Phenotype (IMP) | (i) Mutations, natural or introduced, that result in partial or complete impairment or alteration of the function of that gene | ||
| (ii) Polymorphism or allelic variation (including where no allele is designated wild-type or mutant) | |||
| (iii) Any procedure that disturbs the expression or function of the gene, including RNAi, anti-sense RNAs, antibody depletion, or the use of any molecule or experimental condition that may disturb or affect the normal functioning of the gene, including: inhibitors, blockers, modifiers, any type of antagonists, temperature jumps, changes in pH or ionic strength | |||
| (iv) Overexpression or ectopic expression of wild-type or mutant gene | |||
| Inferred from Genetic Interaction (IGI) | (i) ‘Traditional’ genetic interactions such as suppressors, synthetic lethals, etc. | With column should be filled with identifier of the interacting gene | |
| (ii) Functional complementation | |||
| (iii) Rescue experiments | |||
| (iv) Inference about one gene drawn from the phenotype of a mutation in a different gene | |||
| Inferred from Expression Pattern (IEP) | (i) Transcript levels or timing (e.g. Northerns, microarray data) | ||
| (ii) Protein levels (e.g. Western blots) | |||
| Computational Analysis | Inferred by Sequence Similarity (ISS) | Sequence, structural similarity-based analysis | With column should be filled with identifier of the similar gene/protein |
| Inferred by Sequence Alignment (ISA) | Pairwise or multiple alignment | With column should be filled with identifier of the similar gene/protein | |
| Inferred by Sequence Orthology (ISO) | Assertion of orthology between the gene product and a gene product in another organism | With column should be filled with identifier of the similar gene/protein | |
| Inferred from Sequence Model (ISM) | Prediction methods for noncoding RNA genes such as tRNASCAN-SE, Snoscan, and Rfam | ||
| Inferred from genomic context (IGC) | Information about the genomic context of a gene product forms part of the evidence for a particular annotation. | ||
| (i) operon structure | |||
| (ii) syntenic regions | |||
| (iii) pathway analysis | |||
| (iv) genome scale analysis of processes | |||
| Inferred from Key Residues (IKR) | Sequence analysis, where lack of key sequence residues is used to make a negative (NOT) annotation | Should include NOT qualifier and With column is required if analysis is carried out by a curator and GO_reference:0000047 | |
| Author | Traceable Author Statement (TAS) | Original evidence is referenced in the article and therefore can be traced to another source | |
| Non-traceable Author Statement (NAS) | Statements in articles that cannot be traced to another article or experiment | ||
| Curatorial | No Data (ND) | Used for annotations when information about the molecular function, biological process, or cellular component of the gene or gene product being annotated is not available | Should be used only with root nodes |
| Inferred by Curator (IC) | Annotation reasonably inferred by a curator from other GO annotations, for which direct evidence is available | GO ID should be filled in the from column |
The evidence codes are used to represent the method or type of results used to define the annotation. Annotators should use this table as a quick reference guide and consult the detailed documentation available online (http://www.geneontology.org/GO.evidence.shtml) for specific details (including the do’s and don’ts) on how the method or results are matched to each evidence code.