Table 5.
GO evidence codes + reference combinations. Users should consider both the type of evidence and the review level. GO internal references (starting with GO_REF:) describe specific annotation methods and are available at https://github.com/geneontology/go-site/tree/master/metadata/gorefs/README.md.
| Evidence code | Reference | Evidence-type description | Review-level description |
|---|---|---|---|
| Inferred from direct assay (IDA) | Scientific publication providing experimental data | Experimental, most direct evidence for function | Individually expert-reviewed |
| Inferred from mutant phenotype (IMP) | Scientific publication providing experimental data | Experimental, from a perturbation in the normal function | Individually expert-reviewed |
| Inferred from genetic interaction (IGI) | Scientific publication providing experimental data | Experimental, from perturbations in normal functions of more than one gene | Individually expert-reviewed |
| Inferred from expression pattern (IEP) | Scientific publication providing experimental data | Experimental, used only for biological process annotations, from comparison with genes of known function | Individually expert-reviewed |
| Inferred from protein interaction (IPI) | Scientific publication providing experimental data | Experimental, used only for annotations to protein binding terms | Individually expert-reviewed |
| Inferred from high throughput direct assay (HDA) | Scientific publication providing experimental data | Experimental (high throughput), direct | Not individually reviewed; expert review methodology to exclude high false positive rate observations |
| Inferred from high throughput mutant phenotype (HMP) | Scientific publication providing experimental data | Experimental (high throughput), mutant phenotype | Not individually reviewed; expert review to exclude high false positive rate observations |
| Inferred from high throughput genetic interaction (HGI) | Scientific publication providing experimental data | Experimental (high throughput), genetic interaction | Not individually reviewed; expert review to exclude high false positive rate observations |
| Inferred from high throughput expression pattern (HEP) | Scientific publication providing experimental data | Experimental (high throughput), expression pattern | Not individually reviewed; expert review to exclude high false positive rate observations |
| Inferred from biological ancestor (IBA) | (Gaudet et al. 2011) | Homology, from experimental evidence propagated through a phylogenetic tree and/or from direct experimental evidence | Individually expert-reviewed in the context of all experimental annotations for related genes |
| Inferred from sequence similarity (ISS) | Scientific publication providing sequence similarity evidence | Homology, from experimental evidence propagated from one gene to one related gene, asserted in the publication | Individually expert-reviewed in the context of all experimental annotations for related genes |
| Inferred from sequence similarity (ISS) | GO_REF:0000024 | Homology, from experimental evidence propagated from one gene to one related gene, asserted by a biocurator | Individually expert-reviewed |
| Inferred from sequence orthology (ISO) | Scientific publication providing orthology evidence | Homology, from experimental evidence propagated from one gene to one orthologous gene | Individually expert-reviewed |
| Inferred from sequence Orthology | GO_REF:0000008 | Homology, from experimental evidence propagated from one mammalian gene to one orthologous mouse gene | Individually expert-reviewed |
| ISO, Inferred from Sequence orthology (ISO) | GO_REF:0000024 | Homology, from experimental evidence propagated from one gene to one orthologous gene | Individually expert-reviewed |
| Inferred from sequence orthology (ISO) | GO_REF:0000096 | Homology, from experimental evidence propagated from one gene to one orthologous gene among human, mouse, and rat orthologs | Not individually reviewed; orthology manually reviewed |
| Inferred from sequence orthology (ISO) | GO_REF:0000101 | Homology, from experimental evidence propagated from one gene to one orthologous gene | Not individually reviewed; orthology computed using OrthoMCL |
| Inferred from electronic annotation (IEA) | GO_REF:0000107 | Homology, from experimental evidence propagated from one gene to one orthologous gene | Not individually reviewed; one-to-one orthology computed using Ensembl Compara phylogenetic trees |
| Inferred from electronic annotation (IEA) | GO_REF:0000002 | Homology, from a hit to an InterPro signature | Not individually reviewed; expert review of annotations of signatures to ensure low or no false positives |
| Inferred from electronic annotation (IEA) | GO_REF:0000003 | Imported from another resource, from mapping an EC number assigned in UniProt | Not individually reviewed; expert review of mappings; EC assignments are manually reviewed for Swiss-Prot and computationally inferred for TrEMBL |
| Inferred from electronic annotation (IEA) | GO_REF:0000004 | Imported from another resource, from mapping a manually assigned Swiss-Prot keyword | Not individually reviewed; expert review of keywords and mappings |
| Inferred from electronic annotation (IEA) | GO_REF:0000104 | Homology, from manually curated UniRule | Not individually reviewed; expert curation of UniRules to ensure low or no false positives |
| Inferred from electronic annotation (IEA) | GO_REF:0000108 | Logical assertion using the ontology, from asserted relation between different aspects of GO | Not individually reviewed; expert curation of ontology links |
| Inferred from electronic annotation (IEA) | GO_REF:0000117 | Computational, from machine learning | Not individually reviewed; assigned by machine learning from curated training sets |
| Traceable author statement (TAS) | Scientific publication citing original data | From a published statement referencing experimental evidence in a different paper | Individually reviewed |
| Nontraceable author statement (NAS) | Scientific publication with general biological knowledge statement | From an unreferenced published statement | Individually reviewed |