evidence_code
type: Class
has OBO namespace: evidence_code2.obo

inferred by curator
type: Class
subclass of: evidence_code
has OBO namespace: evidence_code2.obo
has related synonym: IC
has definition: 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.
  type: Definition
  has db xref: ECO:go
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_go

inferred from direct assay
type: Class
subclass of: inferred from experiment
has OBO namespace: evidence_code2.obo
has related synonym: IDA
has definition: Definition
  label: 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.
  has db xref: GO:IDA
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_IDA

inferred from reconstitution assay
type: Class
subclass of: inferred from direct assay
has OBO namespace: evidence_code2.obo

inferred from cell fractionation
type: Class
subclass of: inferred from fractionation
has OBO namespace: evidence_code2.obo
has related synonym: IDA: cell fractionation
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from enzyme assay
type: Class
subclass of: inferred from protein assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: enzyme assays
has definition: Used when an annotation is made based on assays that determine the catalytic activity of enzymes.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from sequence alignment
type: Class
subclass of: inferred from sequence similarity
has OBO namespace: evidence_code2.obo
has related synonym: ISA

inferred from experiment
type: Class
subclass of: evidence_code
has OBO namespace: evidence_code2.obo
has exact synonym: EXP
has definition: Definition
  label: 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.
  has db xref: GOC:ecd
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_ecd

inferred from sequence orthology
type: Class
subclass of: inferred from sequence alignment
has OBO namespace: evidence_code2.obo
has related synonym: ISO

inferred from sequence model
type: Class
subclass of: inferred from genetic similarity
has OBO namespace: evidence_code2.obo
has related synonym: ISM

inferred from electronic annotation
type: Class
subclass of: inferred from in-silico analysis
has OBO namespace: evidence_code2.obo
has related synonym: IEA
has definition: Definition
  label: 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.
  has db xref: GO:IEA
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_IEA

inferred from immunofluorescence
type: Class
subclass of: inferred from immunological assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: immunofluorescence
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from expression pattern
type: Class
subclass of: inferred from experiment
has OBO namespace: evidence_code2.obo
has definition: Definition
has related synonym: IEP

inferred from transcript expression
type: Class
subclass of: inferred from expression pattern
has OBO namespace: evidence_code2.obo

inferred from protein expression
type: Class
subclass of: inferred from expression pattern
subclass of: inferred from protein assay
has OBO namespace: evidence_code2.obo

inferred from genetic interaction
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has db xref: TAIR:TED:0000006
  type: DbXref
  has URI: http://purl.org/obo/owl/TAIR#TAIR_TED:0000006
has related synonym: IGI

inferred from functional complementation
type: Class
subclass of: inferred from genetic interaction
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IGI: functional complementation

inferred from transgenic rescue
type: Class
subclass of: inferred from functional complementation
has OBO namespace: evidence_code2.obo

inferred from mutant phenotype
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has exact synonym: IMP
has definition: Definition
  label: 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.
  has db xref: GO:IMP
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_IMP

inferred from loss-of-function mutant phenotype
type: Class
subclass of: inferred from mutant phenotype
has OBO namespace: evidence_code2.obo

inferred from ectopic expression
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IMP: analysis of overexpression/ectopic expression phenotype

inferred from anti-sense experiment
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IMP: anti-sense experiments

inferred from RNAi experiment
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has related synonym: IMP: RNAi experiments
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from specific protein inhibition
type: Class
subclass of: inferred from protein assay
has OBO namespace: evidence_code2.obo

inferred from physical interaction
type: Class
subclass of: inferred from experiment
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: GO:IPI
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_IPI
has related synonym: IPI

inferred from co-purification
type: Class
subclass of: inferred from physical interaction
has OBO namespace: evidence_code2.obo
has definition: Used in component annotations when a subunit is isolated as part of purification of its larger complex.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IPI: co-purification

inferred from ligand binding
type: Class
subclass of: inferred from physical interaction
has OBO namespace: evidence_code2.obo

inferred from protein binding
type: Class
subclass of: inferred from ligand binding
subclass of: inferred from protein assay
has OBO namespace: evidence_code2.obo

inferred from hybrid interaction
type: Class
subclass of: inferred from ligand binding
has OBO namespace: evidence_code2.obo

inferred from nucleic acid hybridization
type: Class
subclass of: inferred from genomic analysis
has OBO namespace: evidence_code2.obo

inferred from structural similarity
type: Class
subclass of: inferred from genetic similarity
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: ISS: structural similarity

inferred from motif similarity
type: Class
subclass of: inferred from sequence similarity
has OBO namespace: evidence_code2.obo
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: ISS: recognized domains

inferred from InterPro motif similarity
type: Class
subclass of: inferred from motif similarity
has OBO namespace: evidence_code2.obo

inferred from curated BLAST match
type: Class
subclass of: inferred from sequence alignment
has OBO namespace: evidence_code2.obo

inferred from curated BLAST match to protein
type: Class
subclass of: inferred from curated BLAST match
has OBO namespace: evidence_code2.obo

inferred from curated BLAST match to nucleic acid
type: Class
subclass of: inferred from curated BLAST match
has OBO namespace: evidence_code2.obo

traceable author statement
type: Class
subclass of: evidence_code
subclass of: inferred from in-silico analysis
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: GO:TAS
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_TAS
has related synonym: TAS

non-traceable author statement
type: Class
subclass of: evidence_code
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: GO:NAS
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_NAS
has related synonym: NAS

no biological data
type: Class
subclass of: evidence_code
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: GO:ND
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ND
has related synonym: ND

not_recorded
type: Class
subclass of: evidence_code
has OBO namespace: evidence_code2.obo
has definition: Used for annotations done before curators began tracking evidence types (appears in some legacy annotations). It may not be used for new annotations.
  type: Definition
  has db xref: GO:NR
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_NR
has related synonym: NR

inferred from transient rescue
type: Class
subclass of: inferred from functional complementation
has OBO namespace: evidence_code2.obo

inferred from protein assay
type: Class
subclass of: inferred from direct assay
has OBO namespace: evidence_code2.obo

inferred from immunological assay
type: Class
subclass of: inferred from ligand binding
subclass of: inferred from protein assay
has OBO namespace: evidence_code2.obo

inferred from similarity
type: Class
subclass of: evidence_code
has OBO namespace: evidence_code2.obo
has definition: Used when attributes or qualities are compared.
  type: Definition
  has db xref: PhenoScape:IS
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IS
has exact synonym: IS

inferred from gain-of-function mutant phenotype
type: Class
subclass of: inferred from mutant phenotype
has OBO namespace: evidence_code2.obo

inferred from in-silico analysis
type: Class
subclass of: evidence_code
has alternative id: ECO:0000036
has OBO namespace: evidence_code2.obo
has db xref: TAIR:TED:0000004
  type: DbXref
  has URI: http://purl.org/obo/owl/TAIR#TAIR_TED:0000004

inferred from sequence similarity
type: Class
subclass of: inferred from genetic similarity
has OBO namespace: evidence_code2.obo
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from spatial pattern of protein expression
type: Class
subclass of: inferred from protein expression
has OBO namespace: evidence_code2.obo

inferred from level of protein expression
type: Class
subclass of: inferred from protein expression
has OBO namespace: evidence_code2.obo

inferred from spatial pattern of transcript expression
type: Class
subclass of: inferred from transcript expression
has OBO namespace: evidence_code2.obo

inferred from level of transcript expression
type: Class
subclass of: inferred from transcript expression
has OBO namespace: evidence_code2.obo

inferred from reporter gene assay
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IEP: expression of a reporter gene

inferred from voucher specimen
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has exact synonym: IVS
has definition: Definition
  label: 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.
  has db xref: Phenoscape:DOA
    type: DbXref
    has URI: http://purl.org/obo/owl/Phenoscape#Phenoscape_DOA

inferred from genetic similarity
type: Class
subclass of: inferred from similarity
has OBO namespace: evidence_code2.obo
has exact synonym: IGTS
has definition: Used when comparing organisms, in whole or in part, based on genotypes (markers, polymorphisms, alleles) irrespective of their expression.
  type: Definition
  has db xref: PhenoScape:IGTS
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IGTS

inferred from supressor/enhancer interaction
type: Class
subclass of: inferred from genetic interaction
has OBO namespace: evidence_code2.obo
has db xref: TAIR:TED:0000063
  type: DbXref
  has URI: http://purl.org/obo/owl/TAIR#TAIR_TED:0000063
has related synonym: IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)

inferred from reviewed computational analysis
type: Class
subclass of: inferred from in-silico analysis
has OBO namespace: evidence_code2.obo
has related synonym: RCA
has definition: Definition
  label: 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.
  has db xref: ECO:go
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_go

inferred from double mutant analysis
type: Class
subclass of: inferred from genetic interaction
has OBO namespace: evidence_code2.obo
has related synonym: IGI: double mutant analysis
has definition: 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.
  type: Definition
  has db xref: TAIT:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIT#TAIT_TED

inferred from array experiment
type: Class
subclass of: inferred from expression pattern
has OBO namespace: evidence_code2.obo

inferred from epistatic interaction
type: Class
subclass of: inferred from genetic interaction
has OBO namespace: evidence_code2.obo
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IGI: epistatic interactions

inferred from phenotypic similarity
type: Class
subclass of: inferred from similarity
has OBO namespace: evidence_code2.obo
has definition: Used when comparing organisms, in whole or in part, based on the outcomes of expressions of genotypes in their environments.
  type: Definition
  has db xref: PhenoScape:IPTS
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IPTS
has exact synonym: IPTS

inferred from expression microarray experiment
type: Class
subclass of: inferred from array experiment
has OBO namespace: evidence_code2.obo

inferred from phenotype
type: Class
subclass of: inferred from experiment
has OBO namespace: evidence_code2.obo
has alternative id: ECO:0000014

inferred from positional similarity
type: Class
subclass of: inferred from phenotypic similarity
has OBO namespace: evidence_code2.obo
has exact synonym: IPS
has definition: Used when an annotation is made based on the similarity of the location and or arrangement of structures.
  type: Definition
  has db xref: PhenoScape:IPS
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IPS

inferred from quantitative trait analysis
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has definition: Used when an annotation is made for a gene product that has not been cloned but is associated with a quantitative trait locus.
  type: Definition
  has db xref: TAIR:tn
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_tn
has related synonym: IGI: quantitative trait analysis

inferred from genomic microarray experiment
type: Class
subclass of: inferred from array experiment
has OBO namespace: evidence_code2.obo

inferred from compositional similarity
type: Class
subclass of: inferred from phenotypic similarity
has OBO namespace: evidence_code2.obo
has definition: Used when an annotation is made based on the similarity of the histological makeup of structures.
  type: Definition
  has db xref: PhenoScape:ICS
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_ICS
has exact synonym: ICS

inferred from functional complemtation in heterologous system
type: Class
subclass of: inferred from functional complementation
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IGI: functional complementation in heterologous system

inferred from CpG island microarray experiment
type: Class
subclass of: inferred from array experiment
has OBO namespace: evidence_code2.obo

inferred from yeast one-hybrid assay
type: Class
subclass of: inferred from hybrid interaction
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IPI: yeast one-hybrid assay

inferred from developmental similarity
type: Class
subclass of: inferred from phenotypic similarity
has OBO namespace: evidence_code2.obo
has definition: Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures.
  type: Definition
  has db xref: PhenoScape:IDS
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IDS
has exact synonym: IDS

inferred from yeast 2-hybrid assay
type: Class
subclass of: inferred from hybrid interaction
has OBO namespace: evidence_code2.obo
has related synonym: IPI: yeast two-hybrid assay
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from differential methylation hybridization
type: Class
subclass of: inferred from nucleic acid hybridization
has OBO namespace: evidence_code2.obo

inferred from co-immunoprecipitation
type: Class
subclass of: inferred from immunoprecipitation
has OBO namespace: evidence_code2.obo
has related synonym: IPI: co-immunoprecipitation
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from morphological similarity
type: Class
subclass of: inferred from phenotypic similarity
has OBO namespace: evidence_code2.obo
has exact synonym: IMS
has definition: Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures.
  type: Definition
  has db xref: PhenoScape:IMS
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IMS

inferred from Sos-recruitment assay
type: Class
subclass of: inferred from physical interaction
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IPI: Sos-recruitment assay

inferred from genomic analysis
type: Class
subclass of: inferred from experiment
has OBO namespace: evidence_code2.obo

inferred from split-ubiquitin assay
type: Class
subclass of: inferred from physical interaction
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IPI: split-ubiquitin assay

inferred from gene expression similarity
type: Class
subclass of: inferred from phenotypic similarity
has OBO namespace: evidence_code2.obo
has exact synonym: IGES
has definition: Used when an annotation is made based on the similarity of expression of genes in structures.
  type: Definition
  has db xref: PhenoScape:IGES
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IGES

inferred from far-Western assay
type: Class
subclass of: inferred from physical interaction
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IPI: far-Western analysis

inferred from methylation-specific PCR
type: Class
subclass of: inferred from PCR experiment
has OBO namespace: evidence_code2.obo

inferred from Southern blot hybridization
type: Class
subclass of: inferred from nucleic acid hybridization
has OBO namespace: evidence_code2.obo
has related synonym: ISS: Southern blotting
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from affinity chromatography
type: Class
subclass of: inferred from ligand binding
has OBO namespace: evidence_code2.obo
has related synonym: IDA: affinity chromatography
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from phylogeny
type: Class
subclass of: inferred from reviewed computational analysis
has OBO namespace: evidence_code2.obo
has exact synonym: IP
has definition: Definition
  label: 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.
  has db xref: PhenoScape:IP
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IP

inferred from targeting sequence prediction
type: Class
subclass of: inferred from motif similarity
has OBO namespace: evidence_code2.obo
has related synonym: ISS: targeting sequence prediction
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from PCR experiment
type: Class
subclass of: inferred from genomic analysis
has OBO namespace: evidence_code2.obo

inferred from transmembrane domain prediction
type: Class
subclass of: inferred from motif similarity
has OBO namespace: evidence_code2.obo
has related synonym: ISS: transmembrane domain prediction
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from immunoprecipitation
type: Class
subclass of: inferred from immunological assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: immunoprecipitation
has definition: Used when an annotation is made based on a method that precipitates a multivalent antigen by a bivalent antibody.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from amplification of intermethylated sites
type: Class
subclass of: inferred from genomic analysis
has OBO namespace: evidence_code2.obo

inferred from immunolocalization
type: Class
subclass of: inferred from immunological assay
subclass of: inferred from protein localization
has OBO namespace: evidence_code2.obo
has definition: Used when an annotation is made based on methods that detect the presence of macromolecules, proteins, and compounds by the use of antibodies.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IDA: immunolocalization

inferred from restriction landmark genomic scanning
type: Class
subclass of: inferred from genomic analysis
has OBO namespace: evidence_code2.obo

inferred from immunogold labelling
type: Class
subclass of: inferred from immunological assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: immunogold labelling
has definition: Used when an annotation is made based on immunolocalization method that detects an antigen in cytological preparations by using a gold-labeled secondary antibody.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from immunolocalization of epitope-tagged protein
type: Class
subclass of: inferred from immunolocalization
has OBO namespace: evidence_code2.obo
has definition: Used when an annotation is made based on immunolocalization of recombinant proteins fused with epitopes that are recognized by antibodies.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IDA: immunolocalization of epitope-tagged protein

inferred from oligonucleotide microarray
type: Class
subclass of: inferred from array experiment
has OBO namespace: evidence_code2.obo

inferred from bioassay
type: Class
subclass of: inferred from direct assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: bioassay
has definition: Used when an annotation is made based on assays using living organisms to measure the effect of a substance, factor, or condition.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from electrophoretic mobility shift assay
type: Class
subclass of: inferred from direct assay
has OBO namespace: evidence_code2.obo
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IDA: electrophoretic mobility shift assay

inferred from cDNA microarray
type: Class
subclass of: inferred from array experiment
has OBO namespace: evidence_code2.obo

inferred from in situ hybridization
type: Class
subclass of: inferred from nucleic acid hybridization
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IDA: in situ hybridization

inferred from fractionation
type: Class
subclass of: inferred from direct assay
has OBO namespace: evidence_code2.obo

inferred from Affymetrix array
type: Class
subclass of: inferred from array experiment
has OBO namespace: evidence_code2.obo

inferred from co-fractionation
type: Class
subclass of: inferred from fractionation
has OBO namespace: evidence_code2.obo
has related synonym: IDA: co-fractionation
has definition: Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from level of transcript expression determined by microarray analysis
type: Class
subclass of: inferred from level of transcript expression
subclass of: inferred from expression microarray experiment
has OBO namespace: evidence_code2.obo
has definition: Used when an annotation is made based on levels of RNA expression determined by microarray experiment.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IEP: transcript levels (e.g. microarray data)

inferred from Nimblegen array
type: Class
subclass of: inferred from array experiment
has OBO namespace: evidence_code2.obo

inferred from level of transcript expression determined by Northern assay
type: Class
subclass of: inferred from level of transcript expression
has OBO namespace: evidence_code2.obo
has related synonym: IEP: transcript levels (e.g. Northerns)
has definition: Used when an annotation is made based on levels of RNA expression determined by a Northern blot experiment.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from level of transcript expression determined by RT-PCR
type: Class
subclass of: inferred from level of transcript expression
subclass of: inferred from RT-PCR experiment
has OBO namespace: evidence_code2.obo
has definition: Used when an annotation is made based on levels of RNA expression determined by an RT-PCR experiment (quantitative or otherwise).
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IEP: transcript levels (e.g. RT-PCR)

inferred from RT-PCR experiment
type: Class
subclass of: inferred from PCR experiment
has OBO namespace: evidence_code2.obo

inferred from RNA protection assay
type: Class
subclass of: inferred from transcript expression
has OBO namespace: evidence_code2.obo
has related synonym: IEP: RNA protection assay
has definition: Used when an annotation is made based on levels of RNA expression determined by an RNA protection assay.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from Western blot assay
type: Class
subclass of: inferred from level of protein expression
has OBO namespace: evidence_code2.obo
has related synonym: IEP: protein levels (e.g. Western blots)
has definition: Used when an annotation is made based on levels of protein expression determined by a Western blot assay.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from expression library screening
type: Class
subclass of: inferred from protein expression
subclass of: inferred from immunological assay
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IEP: expression library screening

inferred from differential hybridization
type: Class
subclass of: inferred from transcript expression
subclass of: inferred from nucleic acid hybridization
has OBO namespace: evidence_code2.obo
has related synonym: IEP: differential hybridization
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from subtractive hybridization
type: Class
subclass of: inferred from transcript expression
subclass of: inferred from nucleic acid hybridization
has OBO namespace: evidence_code2.obo
has related synonym: IEP: subtractive hybridization
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from over expression
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has related synonym: IMP: analysis of overexpression/ectopic expression phenotype
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from protein localization
type: Class
subclass of: inferred from protein assay
has OBO namespace: evidence_code2.obo

inferred from localization of fusion protein
type: Class
subclass of: inferred from protein localization
has OBO namespace: evidence_code2.obo

inferred from localization of GFP fusion protein
type: Class
subclass of: inferred from localization of fusion protein
has OBO namespace: evidence_code2.obo
has related synonym: IDA: localization of GFP/YFP fusion protein

inferred from localization of YFP fusion protein
type: Class
subclass of: inferred from localization of fusion protein
has OBO namespace: evidence_code2.obo
has related synonym: IDA: localization of GFP/YFP fusion protein

inferred from localiztion of GUS fusion protein
type: Class
subclass of: inferred from localization of fusion protein
has OBO namespace: evidence_code2.obo
has related synonym: IDA: localization of GUS fusion protein

inferred from localization of lacZ fusion protein
type: Class
subclass of: inferred from localization of fusion protein
has OBO namespace: evidence_code2.obo

inferred from transport assay
type: Class
subclass of: inferred from direct assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: transport assay

inferred from nucleic acid binding assay
type: Class
subclass of: inferred from ligand binding
has OBO namespace: evidence_code2.obo

inferred from ribohomopolymer binding assay
type: Class
subclass of: inferred from nucleic acid binding assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: ribohomopolymer binding assay

inferred from thin layer chromatographic assay
type: Class
subclass of: inferred from direct assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: thin layer chromatography

inferred from protein:ion binding assay
type: Class
subclass of: inferred from protein binding
has OBO namespace: evidence_code2.obo

inferred from Southwestern analysis
type: Class
subclass of: inferred from nucleic acid binding assay
has OBO namespace: evidence_code2.obo
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IDA: Southwestern analysis

inferred from Northwestern analysis
type: Class
subclass of: inferred from nucleic acid binding assay
has OBO namespace: evidence_code2.obo
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IDA: Northwestern analysis

inferred from in vitro binding assay
type: Class
subclass of: inferred from physical interaction
has OBO namespace: evidence_code2.obo
has related synonym: IDA: in vitro binding assay

inferred from in vitro transcription reconstitution assay
type: Class
subclass of: inferred from reconstitution assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: in vitro reconstitution assay with recombinant protein

inferred from in vitro transcription reconstitution assay with recombinant protein
type: Class
subclass of: inferred from in vitro transcription reconstitution assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: in vitro reconstitution assay with recombinant protein

inferred from protein expression in heterologous system
type: Class
subclass of: inferred from protein expression
has OBO namespace: evidence_code2.obo
has related synonym: IDA: protein expression in heterologous system

inferred from protein separation
type: Class
subclass of: inferred from fractionation
has OBO namespace: evidence_code2.obo

inferred from protein separation followed by direct sequencing
type: Class
subclass of: inferred from protein separation
has OBO namespace: evidence_code2.obo
has related synonym: IDA: protein separation and direct sequencing

inferred from protein separation followed by fragment identification
type: Class
subclass of: inferred from protein separation
has OBO namespace: evidence_code2.obo
has related synonym: IDA: protein separation and fragment identification

inferred from uptake assay in a heterologous system
type: Class
subclass of: inferred from transport assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: uptake assay in heterologous system
has definition: Used when an annotation is made based on small molecule update assays carried out in a heterologous system that contains a recombinant protein.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from electrophysiological experiment
type: Class
subclass of: inferred from direct assay
has OBO namespace: evidence_code2.obo

inferred from two-electrode voltage clamp technique
type: Class
subclass of: inferred from electrophysiological experiment
has OBO namespace: evidence_code2.obo
has related synonym: IDA: two-electrode voltage clamp technique

inferred from transcription assay
type: Class
subclass of: inferred from direct assay
has OBO namespace: evidence_code2.obo

inferred from transcriptional activation assay
type: Class
subclass of: inferred from transcription assay
has OBO namespace: evidence_code2.obo
has related synonym: IDA: transcriptional activation assay
has definition: Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

inferred from biochemical trait
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has definition: 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.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IMP: analysis of biochemical trait

inferred from physiological response
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IMP: analysis of physiological response

inferred from visible phenotype
type: Class
subclass of: inferred from phenotype
has OBO namespace: evidence_code2.obo
has definition: Used when an annotation is made based on the visual examination of a mutant phenotype; for example, abnormalities in organism morphology.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
has related synonym: IMP: analysis of visible trait

inferred from genomic context
type: Class
subclass of: evidence_code
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: 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.
  has db xref: ECO:go
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_go
has related synonym: IGC

Inferred from in vivo assay
type: Class
subclass of: inferred from bioassay
has OBO namespace: evidence_code2.obo

inferred from animal model system
type: Class
subclass of: Inferred from in vivo assay
has OBO namespace: evidence_code2.obo

inferred from clinical study
type: Class
subclass of: Inferred from in vivo assay
has OBO namespace: evidence_code2.obo

inferred from in vitro assay
type: Class
subclass of: inferred from bioassay
has OBO namespace: evidence_code2.obo

inferred from in vitro culture assay
type: Class
subclass of: inferred from in vitro assay
has OBO namespace: evidence_code2.obo
has related synonym: ex vivo assay

inferred from cell-free assay
type: Class
subclass of: inferred from in vitro assay
has OBO namespace: evidence_code2.obo
has related synonym: in vitro assay

inferred from enzyme inhibition
type: Class
subclass of: inferred from enzyme assay
subclass of: inferred from specific protein inhibition
has OBO namespace: evidence_code2.obo