01:02:2008 12:16 rhee evidence_code2.obo evidence_code2.obo This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi evidence_code evidence_code2.obo 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. ECO:go http://purl.org/obo/owl/ECO#ECO_go IC evidence_code2.obo inferred from direct assay 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. GO:IDA http://purl.org/obo/owl/GO#GO_IDA IDA evidence_code2.obo inferred from reconstitution assay evidence_code2.obo inferred from 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: cell fractionation evidence_code2.obo inferred from enzyme assay Used when an annotation is made based on assays that determine the catalytic activity of enzymes. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: enzyme assays evidence_code2.obo inferred from sequence alignment ISA evidence_code2.obo inferred from experiment 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. GOC:ecd http://purl.org/obo/owl/GOC#GOC_ecd EXP evidence_code2.obo inferred from sequence orthology ISO evidence_code2.obo inferred from sequence model ISM evidence_code2.obo inferred from electronic annotation 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. GO:IEA http://purl.org/obo/owl/GO#GO_IEA IEA evidence_code2.obo inferred from 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: immunofluorescence evidence_code2.obo inferred from expression pattern IEP evidence_code2.obo inferred from transcript expression evidence_code2.obo inferred from protein expression evidence_code2.obo inferred from genetic interaction IGI evidence_code2.obo TAIR:TED:0000006 http://purl.org/obo/owl/TAIR#TAIR_TED:0000006 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IGI: functional complementation evidence_code2.obo inferred from transgenic rescue evidence_code2.obo inferred from mutant phenotype 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. GO:IMP http://purl.org/obo/owl/GO#GO_IMP IMP evidence_code2.obo inferred from loss-of-function mutant phenotype evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IMP: analysis of overexpression/ectopic expression phenotype evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IMP: anti-sense experiments evidence_code2.obo inferred from RNAi experiment 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IMP: RNAi experiments evidence_code2.obo inferred from specific protein inhibition evidence_code2.obo 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. GO:IPI http://purl.org/obo/owl/GO#GO_IPI IPI evidence_code2.obo inferred from co-purification Used in component annotations when a subunit is isolated as part of purification of its larger complex. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IPI: co-purification evidence_code2.obo inferred from ligand binding evidence_code2.obo inferred from protein binding evidence_code2.obo inferred from hybrid interaction evidence_code2.obo inferred from nucleic acid hybridization evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED ISS: structural similarity evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED ISS: recognized domains evidence_code2.obo inferred from InterPro motif similarity evidence_code2.obo inferred from curated BLAST match evidence_code2.obo inferred from curated BLAST match to protein evidence_code2.obo inferred from curated BLAST match to nucleic acid evidence_code2.obo 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. GO:TAS http://purl.org/obo/owl/GO#GO_TAS TAS evidence_code2.obo 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. GO:NAS http://purl.org/obo/owl/GO#GO_NAS NAS evidence_code2.obo 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. GO:ND http://purl.org/obo/owl/GO#GO_ND ND evidence_code2.obo 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. GO:NR http://purl.org/obo/owl/GO#GO_NR NR evidence_code2.obo inferred from transient rescue evidence_code2.obo inferred from protein assay evidence_code2.obo inferred from immunological assay evidence_code2.obo inferred from similarity Used when attributes or qualities are compared. PhenoScape:IS http://purl.org/obo/owl/PhenoScape#PhenoScape_IS IS evidence_code2.obo inferred from gain-of-function mutant phenotype evidence_code2.obo inferred from in-silico analysis evidence_code2.obo ECO:0000036 TAIR:TED:0000004 http://purl.org/obo/owl/TAIR#TAIR_TED:0000004 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED evidence_code2.obo inferred from spatial pattern of protein expression evidence_code2.obo inferred from level of protein expression evidence_code2.obo inferred from spatial pattern of transcript expression evidence_code2.obo inferred from level of transcript expression evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: expression of a reporter gene evidence_code2.obo inferred from voucher specimen 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. Phenoscape:DOA http://purl.org/obo/owl/Phenoscape#Phenoscape_DOA IVS evidence_code2.obo inferred from genetic similarity Used when comparing organisms, in whole or in part, based on genotypes (markers, polymorphisms, alleles) irrespective of their expression. PhenoScape:IGTS http://purl.org/obo/owl/PhenoScape#PhenoScape_IGTS IGTS evidence_code2.obo inferred from supressor/enhancer interaction IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals) evidence_code2.obo TAIR:TED:0000063 http://purl.org/obo/owl/TAIR#TAIR_TED:0000063 inferred from reviewed computational analysis 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. ECO:go http://purl.org/obo/owl/ECO#ECO_go RCA evidence_code2.obo inferred from 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. TAIT:TED http://purl.org/obo/owl/TAIT#TAIT_TED IGI: double mutant analysis evidence_code2.obo inferred from array experiment evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IGI: epistatic interactions evidence_code2.obo inferred from phenotypic similarity Used when comparing organisms, in whole or in part, based on the outcomes of expressions of genotypes in their environments. PhenoScape:IPTS http://purl.org/obo/owl/PhenoScape#PhenoScape_IPTS IPTS evidence_code2.obo inferred from expression microarray experiment evidence_code2.obo inferred from phenotype evidence_code2.obo ECO:0000014 inferred from positional similarity Used when an annotation is made based on the similarity of the location and or arrangement of structures. PhenoScape:IPS http://purl.org/obo/owl/PhenoScape#PhenoScape_IPS IPS evidence_code2.obo 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. TAIR:tn http://purl.org/obo/owl/TAIR#TAIR_tn IGI: quantitative trait analysis evidence_code2.obo inferred from genomic microarray experiment evidence_code2.obo inferred from compositional similarity Used when an annotation is made based on the similarity of the histological makeup of structures. PhenoScape:ICS http://purl.org/obo/owl/PhenoScape#PhenoScape_ICS ICS evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IGI: functional complementation in heterologous system evidence_code2.obo inferred from CpG island microarray experiment evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IPI: yeast one-hybrid assay evidence_code2.obo inferred from developmental similarity Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures. PhenoScape:IDS http://purl.org/obo/owl/PhenoScape#PhenoScape_IDS IDS evidence_code2.obo inferred from yeast 2-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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IPI: yeast two-hybrid assay evidence_code2.obo inferred from differential methylation hybridization evidence_code2.obo inferred from 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IPI: co-immunoprecipitation evidence_code2.obo inferred from morphological similarity Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures. PhenoScape:IMS http://purl.org/obo/owl/PhenoScape#PhenoScape_IMS IMS evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IPI: Sos-recruitment assay evidence_code2.obo inferred from genomic analysis evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IPI: split-ubiquitin assay evidence_code2.obo inferred from gene expression similarity Used when an annotation is made based on the similarity of expression of genes in structures. PhenoScape:IGES http://purl.org/obo/owl/PhenoScape#PhenoScape_IGES IGES evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IPI: far-Western analysis evidence_code2.obo inferred from methylation-specific PCR evidence_code2.obo inferred from Southern blot hybridization 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED ISS: Southern blotting evidence_code2.obo inferred from 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: affinity chromatography evidence_code2.obo 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. PhenoScape:IP http://purl.org/obo/owl/PhenoScape#PhenoScape_IP IP evidence_code2.obo inferred from 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED ISS: targeting sequence prediction evidence_code2.obo inferred from PCR experiment evidence_code2.obo inferred from 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED ISS: transmembrane domain prediction evidence_code2.obo inferred from immunoprecipitation Used when an annotation is made based on a method that precipitates a multivalent antigen by a bivalent antibody. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: immunoprecipitation evidence_code2.obo inferred from amplification of intermethylated sites evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: immunolocalization evidence_code2.obo inferred from restriction landmark genomic scanning evidence_code2.obo inferred from 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: immunogold labelling evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: immunolocalization of epitope-tagged protein evidence_code2.obo inferred from oligonucleotide microarray evidence_code2.obo inferred from bioassay Used when an annotation is made based on assays using living organisms to measure the effect of a substance, factor, or condition. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: bioassay evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: electrophoretic mobility shift assay evidence_code2.obo inferred from cDNA microarray evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: in situ hybridization evidence_code2.obo inferred from fractionation evidence_code2.obo inferred from Affymetrix array evidence_code2.obo inferred from co-fractionation Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: co-fractionation evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: transcript levels (e.g. microarray data) evidence_code2.obo inferred from Nimblegen array evidence_code2.obo inferred from level of transcript expression determined by Northern assay Used when an annotation is made based on levels of RNA expression determined by a Northern blot experiment. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: transcript levels (e.g. Northerns) evidence_code2.obo 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). TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: transcript levels (e.g. RT-PCR) evidence_code2.obo inferred from RT-PCR experiment evidence_code2.obo inferred from RNA protection assay Used when an annotation is made based on levels of RNA expression determined by an RNA protection assay. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: RNA protection assay evidence_code2.obo inferred from Western blot assay Used when an annotation is made based on levels of protein expression determined by a Western blot assay. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: protein levels (e.g. Western blots) evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: expression library screening evidence_code2.obo inferred from 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: differential hybridization evidence_code2.obo inferred from 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: subtractive hybridization evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IMP: analysis of overexpression/ectopic expression phenotype evidence_code2.obo inferred from protein localization evidence_code2.obo inferred from localization of fusion protein evidence_code2.obo inferred from localization of GFP fusion protein IDA: localization of GFP/YFP fusion protein evidence_code2.obo inferred from localization of YFP fusion protein IDA: localization of GFP/YFP fusion protein evidence_code2.obo inferred from localiztion of GUS fusion protein IDA: localization of GUS fusion protein evidence_code2.obo inferred from localization of lacZ fusion protein evidence_code2.obo inferred from transport assay IDA: transport assay evidence_code2.obo inferred from nucleic acid binding assay evidence_code2.obo inferred from ribohomopolymer binding assay IDA: ribohomopolymer binding assay evidence_code2.obo inferred from thin layer chromatographic assay IDA: thin layer chromatography evidence_code2.obo inferred from protein:ion binding assay evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: Southwestern analysis evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: Northwestern analysis evidence_code2.obo inferred from in vitro binding assay IDA: in vitro binding assay evidence_code2.obo inferred from in vitro transcription reconstitution assay IDA: in vitro reconstitution assay with recombinant protein evidence_code2.obo inferred from in vitro transcription reconstitution assay with recombinant protein IDA: in vitro reconstitution assay with recombinant protein evidence_code2.obo inferred from protein expression in heterologous system IDA: protein expression in heterologous system evidence_code2.obo inferred from protein separation evidence_code2.obo inferred from protein separation followed by direct sequencing IDA: protein separation and direct sequencing evidence_code2.obo inferred from protein separation followed by fragment identification IDA: protein separation and fragment identification evidence_code2.obo inferred from uptake assay in a 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: uptake assay in heterologous system evidence_code2.obo inferred from electrophysiological experiment evidence_code2.obo inferred from two-electrode voltage clamp technique IDA: two-electrode voltage clamp technique evidence_code2.obo inferred from transcription assay evidence_code2.obo inferred from transcriptional activation assay Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: transcriptional activation assay evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IMP: analysis of biochemical trait evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IMP: analysis of physiological response evidence_code2.obo 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. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IMP: analysis of visible trait evidence_code2.obo 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. ECO:go http://purl.org/obo/owl/ECO#ECO_go IGC evidence_code2.obo Inferred from in vivo assay evidence_code2.obo inferred from animal model system evidence_code2.obo inferred from clinical study evidence_code2.obo inferred from in vitro assay evidence_code2.obo inferred from in vitro culture assay ex vivo assay evidence_code2.obo inferred from cell-free assay in vitro assay evidence_code2.obo inferred from enzyme inhibition evidence_code2.obo