evidence_code
inferred by curator
To be used for those cases where an annotation is not supported by any evidence, but can be reasonably inferred by a curator from other GO annotations, for which evidence is available.
inferred from direct assay
IDA
Used to indicate a direct assay was carried out to determine the function, process, or component indicated by the GO term. Curators therefore need to be careful, because an experiment considered as a direct assay for a term from one ontology may be a different kind of evidence for a term from another of the ontologies. In particular, there are more kinds of direct assays for cellular component than for function or process. For example, a fractionation experiment might provide "direct assay" evidence that a gene product is in the nucleus, but "protein interaction" (IPI) evidence for its function or process.
inferred from reconstitution assay
inferred from cell fractionation
IDA: cell fractionation
Used when an annotation is made based on separation of subcellular components based on their physical properties, such as density in sucrose density gradients. This evidence is used mostly for annotations to the cellular component ontology.
inferred from enzyme assay
IDA: enzyme assays
Used when an annotation is made based on assays that determine the catalytic activity of enzymes.
inferred from sequence alignment
ISA
inferred from experiment
EXP
Used in an annotation to indicate that an experimental assay has been located the cited reference, whose results indicate a gene product's function, process involvement, or subcellular location (indicated by the GO term). The IE code is the parent code for the IDA, IMP, IGI, IEP and IPIexperimental codes. The IE evidence code can be used where any of the assays described for the IDA, IMP, IGI, IPI or IEP evidence codes is reported. However it is highly encouraged that groups should annotate to one of the more granular experimental codes (IDA, IMP, IGI, IPI or IEP ) instead of IE, and all curators directly involved in the GO Reference Genome annotation effort are obliged to use these and not IE. The IE code exists for groups who would like to contribute high-quality GO annotations that are produced from directly associating GO terms to gene products by citing experimental published results, but where the group is unable to fit the appropriate specific experimental GO evidence codes to each annotation.
inferred from sequence orthology
ISO
inferred from sequence model
ISM
inferred from electronic annotation
IEA
Used for annotations that depend directly on computation or automated transfer of annotations from a database, particularly when the analysis is performed internally and not published. A key feature that distinguishes this evidence code from others is that it is not made by a curator; use IEA when no curator has checked the specific annotation to verify its accuracy. The actual method used (BLAST search, Swiss-Prot keyword mapping, etc.) doesn't matter.
inferred from immunofluorescence
IDA: immunofluorescence
Used when an annotation is made based on methods that detect the presence of macromolecules, proteins, and compounds by the use of a fluorescent-labeled antibody.
inferred from expression pattern
IEP
inferred from transcript expression
inferred from protein expression
inferred from genetic interaction
IGI
inferred from functional complementation
Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a mutant background in the organism of the gene's origin or a heterologous organism with a mutation in the homologous gene.
IGI: functional complementation
inferred from transgenic rescue
inferred from mutant phenotype
IMP
The IMP evidence code covers those cases when the function, process or cellular localization of a gene product is inferred based on differences in the function, process, or cellular localization between two different alleles of the corresponding gene. The IMP code is used for cases where one allele may be designated 'wild-type' and another as 'mutant'. It is also used in cases where allelic variation occurs naturally and no specific allele is designated as wild-type or mutant. Caution should be used when making annotations from gain-of-function mutations as it may be difficult to infer a gene's normal function from a gain of function mutation, although it is sometimes possible.
inferred from loss-of-function mutant phenotype
inferred from ectopic expression
Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress or ectopically express the gene product in question.
IMP: analysis of overexpression/ectopic expression phenotype
inferred from anti-sense experiment
Used when an annotation is based on a phenotype observed when expressing an anti-sense version of a gene product in a wild-type (for that gene product) background.
IMP: anti-sense experiments
inferred from RNAi experiment
IMP: RNAi experiments
Inference based on a phenotype observed when expressing an RNAi construct that includes a fragment of the gene product in a wild-type (for that gene product) background. A double-stranded RNA specifically suppresses the expression of the gene bearing its complementary sequence.
inferred from specific protein inhibition
inferred from physical interaction
Covers physical interactions between the gene product of interest and another molecule (such as a protein, ion or complex). IPI can be thought of as a type of IDA, where the actual binding partner or target can be specified, using "with" in the with/from field.
IPI
inferred from co-purification
Used in component annotations when a subunit is isolated as part of purification of its larger complex.
IPI: co-purification
inferred from ligand binding
inferred from protein binding
inferred from hybrid interaction
inferred from nucleic acid hybridization
inferred from structural similarity
Used when an annotation is made based on the structural similarity of the annotated gene/gene product to a single other gene or group of genes. In the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field.
ISS: structural similarity
inferred from motif similarity
Used when an annotation is made based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence.
ISS: recognized domains
inferred from InterPro motif similarity
inferred from curated BLAST match
inferred from curated BLAST match to protein
inferred from curated BLAST match to nucleic acid
traceable author statement
The TAS evidence code covers author statements that are attributed to a cited source. Typically this type of information comes from review articles. Material from the introductions and discussion sections of non-review papers may also be suitable if another reference is cited as the source of experimental work or analysis. When annotating with this code the curator should use caution and be aware that authors often cite papers dealing with experiments that were performed in organisms different from the one being discussed in the paper at hand. Thus a problem with the TAS code is that it may turn out from following up the references in the paper that no experiments were performed on the gene in the organism actually being characterized in the primary paper. For this reason we recommend (when time and resources allow) that curators track down the cited paper and annotate directly from the experimental paper using the appropriate experimental evidence code. When this is not possible and it is necessary to annotate from reviews, the TAS code is the appropriate code to use for statements that are associated with a cited reference. Once an annotation has been made to a given term using an experimental evidence code, we recommend removing any annotations made to the same term using the TAS evidence code.
TAS
non-traceable author statement
The NAS evidence code should be used in allncases where the author makes a statement that a curator wants to capture butnfor which there are neither results presented nor a specific reference citednin the source used to make the annotation. The source of the information maynbe peer reviewed papers, textbooks, database records or vouchered specimens.
NAS
no biological data
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. Use of the ND evidence code indicates that the annotator at the contributing database found no information that allowed making an annotation to any term indicating specific knowledge from the ontology in question (molecular function, biological process, or cellular component) as of the date indicated. This code should be used only for annotations to the root terms, molecular function ; GO:0003674, biological process ; GO:0008150, or cellular component ; GO:0005575, which, when used in annotations, indicate that no knowledge is available about a gene product in that aspect of GO.
not_recorded
Used for annotations done before curators began tracking evidence types (appears in some legacy annotations). It may not be used for new annotations.
inferred from transient rescue
inferred from protein assay
inferred from immunological assay
inferred from similarity
Used when attributes or qualities are compared.
inferred from gain-of-function mutant phenotype
inferred from in-silico analysis
inferred from sequence similarity
Used when an annotation is made based on the sequence similarity of the annotated gene/gene product to a single other gene or group of genes and this evidence has been examined by a curator.
inferred from spatial pattern of protein expression
inferred from level of protein expression
inferred from spatial pattern of transcript expression
inferred from level of transcript expression
inferred from reporter gene assay
Used when an annotation is made on the basis of the expression pattern of a reporter gene. The reporter gene may consist of the native promoter of the gene in question that drives the expression of a readily assayable gene product such as GUS or GFP. The reporter gene may also be a marker of a particular type of physiological response.
IEP: expression of a reporter gene
inferred from voucher specimen
IVS
Used when an annotation is made on the basis of for a phenotype descriptionnfor a species or higher level group that given by an author who explicitlynreferences an observation of a voucher specimen(s). Voucher specimens arendefined as those specimens with permanent museum catalog numbers. Thus it would be possible for a person to examine this particular specimen and observe the annotated phenotype.
inferred from genetic similarity
IGTS
Used when comparing organisms, in whole or in part, based on genotypes (markers, polymorphisms, alleles) irrespective of their expression.
inferred from supressor/enhancer interaction
IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
inferred from reviewed computational analysis
RCA
Used for: Predictions based on large-scale experiments (e.g. genome-wide two-hybrid, genome-wide synthetic interactions); Predictions based on integration of large-scale datasets of several types; Text-based computation (e.g. text mining). This code is used for annotations based on a non-sequence-based computational method, where the results have been reviewed by an author or a curator. IEA should be used for any computational annotations that are not checked for accuracy by a curator (or by the authors of a paper describing such analysis), and sequence comparisons that have been reviewed use ISS. For microarray results alone, IEP is preferred, but RCA is used when microarray results are combined with results of other types of large-scale experiments.
inferred from double mutant analysis
IGI: double mutant analysis
Used when an annotation is made based on the phenotype of double mutant organism that contains a mutation in the gene product of interest in addition to a second mutation at an unrelated locus.
inferred from array experiment
inferred from epistatic interaction
Used when an annotation is based on results of epistatis analysis of an allele of the gene in question and a mutant allele at another locus.
IGI: epistatic interactions
inferred from phenotypic similarity
Used when comparing organisms, in whole or in part, based on the outcomes of expressions of genotypes in their environments.
IPTS
inferred from expression microarray experiment
inferred from phenotype
inferred from positional similarity
IPS
Used when an annotation is made based on the similarity of the location and or arrangement of structures.
inferred from quantitative trait analysis
Used when an annotation is made for a gene product that has not been cloned but is associated with a quantitative trait locus.
IGI: quantitative trait analysis
inferred from genomic microarray experiment
inferred from compositional similarity
Used when an annotation is made based on the similarity of the histological makeup of structures.
ICS
inferred from functional complemtation in heterologous system
Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a heterologous organism with a mutation in the homologous gene.
IGI: functional complementation in heterologous system
inferred from CpG island microarray experiment
inferred from yeast one-hybrid assay
Used when an annotation is based on the interaction of a protein with a DNA fragment in a yeast one-hybrid assay. The assay involves screening a library of candidate proteins for the ability bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to a yeast reporter gene.
IPI: yeast one-hybrid assay
inferred from developmental similarity
Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures.
IDS
inferred from yeast 2-hybrid assay
IPI: yeast two-hybrid assay
Used when an annotation is based on the interaction between two proteins in a yeast two-hybrid assay. The assay involves screening a trap-tagged library with a bait-tagged vector. The library is tagged with a DNA-binding domain (trap) and the bait is tagged with a transcriptional activation domain. Interaction between a library-trap protein and the bait results in activation of a yeast reporter gene whose transcription can be experimentally assayed.
inferred from differential methylation hybridization
inferred from co-immunoprecipitation
IPI: co-immunoprecipitation
Used when an annotation is based on the interaction of one gene product with another in a co-immunoprecipitation assay (two or more proteins are precipitated when treated with an antibody specific to a single protein). The interacting protein is referenced in the evidence_with column.
inferred from morphological similarity
IMS
Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures.
inferred from Sos-recruitment assay
Used when an annotation is based on the interaction of two proteins in a Sos-recruitment assay. The assay is a genetic screening system that detects protein-protein interactions and is not based on a transcriptional readout.
IPI: Sos-recruitment assay
inferred from genomic analysis
inferred from split-ubiquitin assay
Used when an annotation is based on the interaction of two proteins in a split-ubiquitin assay. The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquiting (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough together to reconstitute split-ubiquitin, resulting in the release of the reporter protein by the action of the UBPs.
IPI: split-ubiquitin assay
inferred from gene expression similarity
IGES
Used when an annotation is made based on the similarity of expression of genes in structures.
inferred from far-Western assay
Used when an annotation is based on the interaction of protein with another in a far-Western assay. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody. The interacting protein is referenced in the evidence_with column.
IPI: far-Western analysis
inferred from methylation-specific PCR
inferred from Southern blot hybridization
ISS: Southern blotting
Used when an annotation is based on the hybridization of a probe derived from the gene in question with a gene of known function/process/component. Can also be used when a probe derived from a gene of known function/process/component hybridizes with the gene in question.
inferred from affinity chromatography
IDA: affinity chromatography
Used when an annotation is made based on affinity chromatography, which is a selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent.
inferred from phylogeny
Used when an annotation is made based on the common ancestry of structures on a particular phylogenetic tree. Typically, other evidence (a type of similarity) supports a prior hypothesis of homology for these structures.
inferred from targeting sequence prediction
ISS: targeting sequence prediction
Used when a component annotation is made based on the presence of a targeting sequence in a protein's primary sequence. The presence of the targeting sequence may be detected by computational prediction and/or the author's manual examination of the sequence.
inferred from PCR experiment
inferred from transmembrane domain prediction
ISS: transmembrane domain prediction
Used when a component annotation is made based on the presence of one or more transmembrane domains in a protein's primary sequence. The presence of the transmembrane domains may be detected by computational prediction and/or the author's manual examination of the sequence.
inferred from immunoprecipitation
IDA: immunoprecipitation
Used when an annotation is made based on a method that precipitates a multivalent antigen by a bivalent antibody.
inferred from amplification of intermethylated sites
inferred from immunolocalization
Used when an annotation is made based on methods that detect the presence of macromolecules, proteins, and compounds by the use of antibodies.
IDA: immunolocalization
inferred from restriction landmark genomic scanning
inferred from immunogold labelling
IDA: immunogold labelling
Used when an annotation is made based on immunolocalization method that detects an antigen in cytological preparations by using a gold-labeled secondary antibody.
inferred from immunolocalization of epitope-tagged protein
Used when an annotation is made based on immunolocalization of recombinant proteins fused with epitopes that are recognized by antibodies.
IDA: immunolocalization of epitope-tagged protein
inferred from oligonucleotide microarray
inferred from bioassay
IDA: bioassay
Used when an annotation is made based on assays using living organisms to measure the effect of a substance, factor, or condition.
inferred from electrophoretic mobility shift assay
Used when an annotation is made based on electrophoretic mobility shift of macromolecules, compounds, and proteins. Most commonly used for detecting the binding of protein to DNA.
IDA: electrophoretic mobility shift assay
inferred from cDNA microarray
inferred from in situ hybridization
Used when an annotation is made based on a method that hybridizes a labeled nucleic acid probe to a tissue or cell specimen in which the cellular structures are still intact. Depending on the label and protocol used, the probe may detect complementary DNA or RNA by hybridizing specifically to that gene or sequence.
IDA: in situ hybridization
inferred from fractionation
inferred from Affymetrix array
inferred from co-fractionation
IDA: co-fractionation
Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules.
inferred from level of transcript expression determined by microarray analysis
Used when an annotation is made based on levels of RNA expression determined by microarray experiment.
IEP: transcript levels (e.g. microarray data)
inferred from Nimblegen array
inferred from level of transcript expression determined by Northern assay
IEP: transcript levels (e.g. Northerns)
Used when an annotation is made based on levels of RNA expression determined by a Northern blot experiment.
inferred from level of transcript expression determined by RT-PCR
Used when an annotation is made based on levels of RNA expression determined by an RT-PCR experiment (quantitative or otherwise).
IEP: transcript levels (e.g. RT-PCR)
inferred from RT-PCR experiment
inferred from RNA protection assay
IEP: RNA protection assay
Used when an annotation is made based on levels of RNA expression determined by an RNA protection assay.
inferred from Western blot assay
IEP: protein levels (e.g. Western blots)
Used when an annotation is made based on levels of protein expression determined by a Western blot assay.
inferred from expression library screening
Used when an annotation is made on the basis of a protein expression library screen where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein.
IEP: expression library screening
inferred from differential hybridization
IEP: differential hybridization
Used when an annotation is made based on results of a differential hybridization experiment that demonstrates expression of an RNA under one condition and not another.
inferred from subtractive hybridization
IEP: subtractive hybridization
Used when an annotation is made based on results of a subtractive hybridization experiment that demonstrates expression of an RNA under one condition and not another.
inferred from over expression
Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress the gene product in question.
inferred from protein localization
inferred from localization of fusion protein
inferred from localization of GFP fusion protein
IDA: localization of GFP/YFP fusion protein
inferred from localization of YFP fusion protein
inferred from localiztion of GUS fusion protein
IDA: localization of GUS fusion protein
inferred from localization of lacZ fusion protein
inferred from transport assay
IDA: transport assay
inferred from nucleic acid binding assay
inferred from ribohomopolymer binding assay
IDA: ribohomopolymer binding assay
inferred from thin layer chromatographic assay
IDA: thin layer chromatography
inferred from protein:ion binding assay
inferred from Southwestern analysis
Used when an annotation is made based on a Southwestern blot analysis, which detects DNA binding of proteins using labeled DNA as probe hybridizing to electrophoretically separated proteins.
IDA: Southwestern analysis
inferred from Northwestern analysis
Used when an annotation is made based on a Northwestern blot analysis, which detects RNA binding of proteins using labeled RNA as probe hybridizing to electrophoretically separated proteins.
IDA: Northwestern analysis
inferred from in vitro binding assay
IDA: in vitro binding assay
inferred from in vitro transcription reconstitution assay
IDA: in vitro reconstitution assay with recombinant protein
inferred from in vitro transcription reconstitution assay with recombinant protein
inferred from protein expression in heterologous system
IDA: protein expression in heterologous system
inferred from protein separation
inferred from protein separation followed by direct sequencing
IDA: protein separation and direct sequencing
inferred from protein separation followed by fragment identification
IDA: protein separation and fragment identification
inferred from uptake assay in a heterologous system
IDA: uptake assay in heterologous system
Used when an annotation is made based on small molecule update assays carried out in a heterologous system that contains a recombinant protein.
inferred from electrophysiological experiment
inferred from two-electrode voltage clamp technique
IDA: two-electrode voltage clamp technique
inferred from transcription assay
inferred from transcriptional activation assay
IDA: transcriptional activation assay
Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene.
inferred from biochemical trait
Used when an annotation is made based on the analysis of a biochemical aspect of a mutant phenotype; for example, the accumulation of a biosynthetic intermediate.
IMP: analysis of biochemical trait
inferred from physiological response
Used when an annotation is made based on the physiological response of a mutant to an external stimulus; for example, abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions.
IMP: analysis of physiological response
inferred from visible phenotype
Used when an annotation is made based on the visual examination of a mutant phenotype; for example, abnormalities in organism morphology.
IMP: analysis of visible trait
inferred from genomic context
Used whenever 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 the genes neighboring the gene product in question (i.e. synteny), operon structure, and phylogenetic or other whole genome analysis.
IGC
Inferred from in vivo assay
inferred from animal model system
inferred from clinical study
inferred from in vitro assay
inferred from in vitro culture assay
ex vivo assay
inferred from cell-free assay
in vitro assay
inferred from enzyme inhibition