used_in
type: ObjectProperty
has OBO namespace: evidence_code2.obo

evidence
type: Class
has OBO namespace: evidence_code2.obo
has definition: A type of information that is used to support an assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has related synonym: evidence code
has related synonym: evidence_code

inference from background scientific knowledge
type: Class
subclass of: curator inference
has OBO namespace: evidence_code2.obo
has exact synonym: IC
  type: Synonym
  has db xref: GO:IC
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_IC
has definition: A curator inference that links the current annotation to a different evidence-based annotation via background knowledge of the curator.
  type: Definition
  has db xref: ECO:go
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_go
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: inferred by curator
  type: Synonym
  has db xref: GO:IC
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_IC

direct assay evidence
type: Class
subclass of: experimental evidence
has OBO namespace: evidence_code2.obo
has definition: Experimental evidence that is based on direct measurement of some aspect of a biological feature.
  type: Definition
  has db xref: GO:IDA
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_IDA
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

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

cell fractionation evidence
type: Class
subclass of: fractionation evidence
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

enzyme assay evidence
type: Class
subclass of: protein assay evidence
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

experimental evidence
type: Class
subclass of: evidence
has OBO namespace: evidence_code2.obo
has exact synonym: EXP
  type: Synonym
  has db xref: GO:EXP
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_EXP
has exact synonym: inferred from experiment
  type: Synonym
  has db xref: GO:EXP
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_EXP
has definition: An evidence type that is based on the results of a laboratory assay.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
  has db xref: GOC:ecd
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_ecd

immunofluorescence evidence
type: Class
subclass of: immunological assay evidence
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

expression pattern evidence
type: Class
subclass of: experimental evidence
comment: Use this evidence type when the annotation is inferred from the timing or location of expression of a gene. It may be difficult to determine whether the expression pattern truly indicates that a gene plays a role in a given process.
has OBO namespace: evidence_code2.obo
has definition: Experimental evidence that is based on characterization of gene expression.
  type: Definition
  has db xref: GO:IEP
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_IEP
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: IEP
  type: Synonym
  has db xref: GO:IEP
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_IEP
has exact synonym: inferred from expression pattern
  type: Synonym
  has db xref: GO:IEP
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_IEP

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

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

genetic interaction evidence
type: Class
subclass of: experimental phenotypic evidence
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

functional complementation evidence
type: Class
subclass of: genetic interaction evidence
has OBO namespace: evidence_code2.obo
has related synonym: IGI: functional complementation
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

transgenic rescue experiment evidence
type: Class
subclass of: functional complementation evidence
has OBO namespace: evidence_code2.obo

mutant phenotype evidence
type: Class
subclass of: experimental phenotypic evidence
has OBO namespace: evidence_code2.obo
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

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

ectopic expression evidence
type: Class
subclass of: experimental phenotypic evidence
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

anti-sense experiment evidence
type: Class
subclass of: experimental phenotypic evidence
has OBO namespace: evidence_code2.obo
has related synonym: IMP: anti-sense experiments
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

RNAi evidence
type: Class
subclass of: experimental phenotypic evidence
has OBO namespace: evidence_code2.obo
has related synonym: IMP: RNAi experiment
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

specific protein inhibition experiment evidence
type: Class
subclass of: protein assay evidence
has OBO namespace: evidence_code2.obo

physical interaction evidence
type: Class
subclass of: experimental evidence
comment: Molecules interacted with might include protein, nucleic acid, ion, or complex.
has OBO namespace: evidence_code2.obo
has related synonym: IPI
  type: Synonym
  has db xref: GOECO:IPI
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IPI
has definition: Experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has related synonym: inferred from physical interaction
  type: Synonym
  has db xref: GOECO:IPI
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IPI
has db xref: GOECO:IPI
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IPI

co-purification evidence
type: Class
subclass of: physical interaction evidence
has OBO namespace: evidence_code2.obo
has related synonym: IPI: co-purification
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

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

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

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

nucleic acid hybridization evidence
type: Class
subclass of: experimental genomic evidence
has OBO namespace: evidence_code2.obo

structural similarity evidence
type: Class
subclass of: phenotypic similarity evidence
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 or 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 broad synonym: inferred from sequence or structural similarity
  type: Synonym
  has db xref: GO:ISS
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ISS
has broad synonym: ISS
  type: Synonym
  has db xref: GO:ISS
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ISS

motif similarity evidence
type: Class
subclass of: sequence similarity evidence
has OBO namespace: evidence_code2.obo
has related synonym: ISS: recognized domains
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

match to InterPro signature evidence
type: Class
subclass of: match to sequence model evidence
has OBO namespace: evidence_code2.obo

BLAST evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: BLAST evidence
has OBO namespace: evidence_code2.obo
has related synonym: curated BLAST analysis
has definition: A type of BLAST evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

protein BLAST evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: protein BLAST evidence
has OBO namespace: evidence_code2.obo
has related synonym: curated protein BLAST analysis
has db xref: GO_REF:0000027
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000027
has db xref: GO_REF:0000018
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000018
has db xref: GO_REF:0000012
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000012
has definition: Protein BLAST evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

nucleotide BLAST evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: nucleotide BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: nucleotide BLAST evidence
has OBO namespace: evidence_code2.obo
has definition: Nucleotide BLAST evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has related synonym: curated nucleic acid BLAST analysis

traceable author statement
type: Class
subclass of: author statement
comment: The traceable author statement (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 OBO namespace: evidence_code2.obo
has definition: An author statement that is based on a cited reference.
  type: Definition
  has db xref: GO:TAS
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_TAS
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

non-traceable author statement
type: Class
subclass of: author statement
comment: The non-traceable author statement evidence code should be used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation. The source of the information may be peer reviewed papers, textbooks, database records or vouchered specimens.
has OBO namespace: evidence_code2.obo
has definition: An author statement that is not associated with results presented or a cited reference.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

no biological data found
type: Class
subclass of: curator inference
has OBO namespace: evidence_code2.obo
has exact synonym: ND
  type: Synonym
  has db xref: GO:ND
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ND
has exact synonym: no biological data available
  type: Synonym
  has db xref: GO:ND
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ND
has definition: A curator inference that states that a search found no information about a biological feature.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
  has db xref: GO:ND
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ND

not_recorded
type: Class
subclass of: ObsoleteClass
comment: The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations.
has OBO namespace: evidence_code2.obo
has definition: An evidence that reflects an annotation was made before curators began tracking evidence types.
  type: Definition
  has db xref: GO:NR
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_NR
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: NR
  type: Synonym
  has db xref: GO:NR
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_NR
has exact synonym: not recorded
  type: Synonym
  has db xref: GO:NR
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_NR

transient rescue experiment evidence
type: Class
subclass of: functional complementation evidence
has OBO namespace: evidence_code2.obo

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

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

similarity evidence
type: Class
subclass of: evidence
has OBO namespace: evidence_code2.obo
has exact synonym: IS
has definition: An evidence type that is based on comparing likeness of distinct biological entities.
  type: Definition
  has db xref: PhenoScape:IS
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IS
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has related synonym: inferred from similarity

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

sequence similarity evidence
type: Class
subclass of: similarity evidence
comment: A sequence similarity analysis may involve a gene or a gene product, and it could be based on similarity to a single other gene or to a group of other genes.
has OBO namespace: evidence_code2.obo
has broad synonym: inferred from sequence or structural similarity
  type: Synonym
  has db xref: GO:ISS
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ISS
has broad synonym: ISS
  type: Synonym
  has db xref: GO:ISS
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ISS
has exact synonym: inferred from sequence similarity
has definition: A type of similarity based on biomolecular sequence.
  type: Definition
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

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

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

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

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

reporter gene assay evidence
type: Class
subclass of: experimental phenotypic evidence
has OBO namespace: evidence_code2.obo
has related synonym: IEP: expression of a reporter gene
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

voucher specimen analysis evidence
type: Class
subclass of: experimental phenotypic evidence
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 description for a species or higher level group that given by an author who explicitly references an observation of a voucher specimen(s). Voucher specimens are defined 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

genetic similarity evidence
type: Class
subclass of: similarity evidence
comment: A genetic similarity analysis might consider genetic markers, polymorphisms, alleles, or other characteristics sometimes considered as part of the field of traditional genetics. Although an attempt has been made to treat as distinct the concepts of "genetic", "genotypic", "genomic", and "sequence", there is considerable overlap in usage throughout the field of biology.
has OBO namespace: evidence_code2.obo
has exact synonym: IGTS
has definition: A type of similarity based on genotype without respect to expression.
  type: Definition
  has db xref: PhenoScape:IGTS
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IGTS
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has related synonym: inferred from genetic similarity

suppressor/enhancer interaction evidence
type: Class
subclass of: genetic interaction evidence
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)

computational combinatorial evidence
type: Class
subclass of: combinatorial evidence
comment: Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
has OBO namespace: evidence_code2.obo
has definition: A type of combinatorial analysis where data are combined and evaluated by an algorithm.
  type: Definition
  has db xref: ECO:go
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_go
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has db xref: TAIR:TED:0000004
  type: DbXref
  has URI: http://purl.org/obo/owl/TAIR#TAIR_TED:0000004

double mutant phenotype evidence
type: Class
subclass of: genetic interaction evidence
has OBO namespace: evidence_code2.obo
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
has related synonym: IGI: double mutant analysis

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

epistatic interaction evidence
type: Class
subclass of: genetic interaction evidence
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

phenotypic similarity evidence
type: Class
subclass of: similarity evidence
comment: Phenotype is defined as the outcome of the expression of a genotype in a given environment. A comparison might involve whole organisms or sub-parts of organisms.
has OBO namespace: evidence_code2.obo
has related synonym: inferred from phenotypic similarity
has definition: A type of similarity based on the expression of a genotype in an environment.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
  has db xref: PhenoScape:IPTS
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IPTS
has exact synonym: IPTS

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

experimental phenotypic evidence
type: Class
subclass of: experimental evidence
has OBO namespace: evidence_code2.obo
has alternative id: ECO:0000014
has related synonym: inferred from phenotype
has definition: Experimental evidence that is based on the expression of a genotype in an environment.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

positional similarity evidence
type: Class
subclass of: phenotypic similarity evidence
has OBO namespace: evidence_code2.obo
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
has exact synonym: IPS

quantitative trait analysis evidence
type: Class
subclass of: experimental phenotypic evidence
has OBO namespace: evidence_code2.obo
has related synonym: IGI: quantitative trait analysis
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

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

compositional similarity evidence
type: Class
subclass of: phenotypic similarity evidence
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

functional complementation in heterologous system evidence
type: Class
subclass of: functional complementation evidence
has OBO namespace: evidence_code2.obo
has related synonym: IGI: functional complementation in heterologous system
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

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

yeast one-hybrid evidence
type: Class
subclass of: hybrid interaction evidence
has OBO namespace: evidence_code2.obo
has related synonym: IPI: yeast one-hybrid assay
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

developmental similarity evidence
type: Class
subclass of: phenotypic similarity evidence
has OBO namespace: evidence_code2.obo
has exact synonym: IDS
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

yeast 2-hybrid evidence
type: Class
subclass of: hybrid interaction evidence
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

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

co-immunoprecipitation evidence
type: Class
subclass of: immunoprecipitation evidence
has OBO namespace: evidence_code2.obo
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
has related synonym: IPI: co-immunoprecipitation

morphological similarity evidence
type: Class
subclass of: phenotypic similarity evidence
has OBO namespace: evidence_code2.obo
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
has exact synonym: IMS

Sos-recruitment assay evidence
type: Class
subclass of: physical interaction evidence
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

experimental genomic evidence
type: Class
subclass of: experimental evidence
has OBO namespace: evidence_code2.obo
has definition: Experimental evidence that characterizes an attribute of the genome underlying a gene product.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: inferred from genomic analysis

split-ubiquitin assay evidence
type: Class
subclass of: physical interaction evidence
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

gene expression similarity evidence
type: Class
subclass of: phenotypic similarity evidence
has OBO namespace: evidence_code2.obo
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
has exact synonym: IGES

far-Western evidence
type: Class
subclass of: physical interaction evidence
has OBO namespace: evidence_code2.obo
has related synonym: IPI: far-Western analysis
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

methylation-specific polymerase chain reaction evidence
type: Class
subclass of: polymerase chain reaction evidence
has OBO namespace: evidence_code2.obo
has exact synonym: methylation-specific PCR evidence

Southern hybridization evidence
type: Class
subclass of: nucleic acid hybridization evidence
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

affinity chromatography evidence
type: Class
subclass of: ligand binding evidence
comment: "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" (from original definition by TAIR:TED). Types of highly specific interaction might include those of antigen and antibody, enzyme and substrate, or receptor and ligand.
has OBO namespace: evidence_code2.obo
has related synonym: IDA: affinity chromatography
has definition: Definition
  label: A type of ligand binding evidence resulting from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound.
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

phylogenetic evidence
type: Class
subclass of: similarity evidence
has OBO namespace: evidence_code2.obo
has exact synonym: IP
  type: Synonym
  has db xref: PhenoScape:IP
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IP
has definition: A type of similarity that indicates common ancestry.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
  has db xref: PhenoScape:IP
    type: DbXref
    has URI: http://purl.org/obo/owl/PhenoScape#PhenoScape_IP

targeting sequence prediction evidence
type: Class
subclass of: motif similarity evidence
has OBO namespace: evidence_code2.obo
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
has related synonym: ISS: targeting sequence prediction

polymerase chain reaction evidence
type: Class
subclass of: experimental genomic evidence
has OBO namespace: evidence_code2.obo
has exact synonym: PCR evidence

transmembrane domain prediction evidence
type: Class
subclass of: motif similarity evidence
has OBO namespace: evidence_code2.obo
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
has related synonym: ISS: transmembrane domain prediction

gene neighbors evidence
type: Class
subclass of: genomic context evidence
comment: Genomic cluster analyses include synteny and operon structure.
has OBO namespace: evidence_code2.obo
has related synonym: ICL
has exact synonym: inferred from genome cluster
has db xref: GO_REF:0000025
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000025
has definition: Evidence that supports the identity of a gene product on the basis of the identity of neighboring genes.
  type: Definition
  has db xref: GOC:mg
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_mg
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

immunoprecipitation evidence
type: Class
subclass of: immunological assay evidence
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

intermethylated site amplification evidence
type: Class
subclass of: experimental genomic evidence
has OBO namespace: evidence_code2.obo

immunolocalization evidence
type: Class
subclass of: immunological assay evidence
subclass of: protein localization evidence
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

biological system reconstruction
type: Class
subclass of: evidence
comment: The biological system in question might be a multi-step process or a physical complex comprising several components. A common basis for system reconstruction is orthology, where all of the components of an experimentally characterized complex exist in one organism; if a second organism contains orthologs of all components, then the existence of the complex is inferred. In the case of a genome-wide analysis, a gene product is said to fulfill a necessary function for a pathway or complex when, with all of the other necessary functions or components also present, the pathway or complex is reconstructed.
has OBO namespace: evidence_code2.obo
has related synonym: ISR
has related synonym: inferred from system reconstruction
has definition: Evidence based on reconstruction of a biological system that is based on an existing experimentally supported model of that biological system.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
  has db xref: GOC:mg
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_mg

restriction landmark genomic scanning evidence
type: Class
subclass of: experimental genomic evidence
has OBO namespace: evidence_code2.obo
has exact synonym: RLGS evidence

immunogold labelling evidence
type: Class
subclass of: immunological assay evidence
has OBO namespace: evidence_code2.obo
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
has related synonym: IDA: immunogold labelling

epitope-tagged protein immunolocalization evidence
type: Class
subclass of: immunolocalization evidence
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

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

biological assay evidence
type: Class
subclass of: direct assay evidence
has OBO namespace: evidence_code2.obo
has related synonym: IDA: bioassay
has definition: Direct assay evidence that is derived by using a living organism to measure the effect of a substance, factor, or condition.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
  has db xref: TAIR:TED
    type: DbXref
    has URI: http://purl.org/obo/owl/TAIR#TAIR_TED

electrophoretic mobility shift assay evidence
type: Class
subclass of: direct assay evidence
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

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

in situ hybridization evidence
type: Class
subclass of: nucleic acid hybridization evidence
has OBO namespace: evidence_code2.obo
has related synonym: IDA: in situ hybridization
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

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

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

co-fractionation evidence
type: Class
subclass of: fractionation evidence
has OBO namespace: evidence_code2.obo
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
has related synonym: IDA: co-fractionation

microarray RNA expression level evidence
type: Class
subclass of: transcript expression level evidence
subclass of: expression microarray evidence
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)

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

Northern assay evidence
type: Class
subclass of: transcript expression level evidence
has OBO namespace: evidence_code2.obo
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
has related synonym: IEP: transcript levels (e.g. Northerns)

reverse transcription polymerase chain reaction transcription evidence
type: Class
subclass of: transcript expression level evidence
subclass of: reverse transcription polymerase chain reaction evidence
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)
has exact synonym: RT-PCR transcription evidence

reverse transcription polymerase chain reaction evidence
type: Class
subclass of: polymerase chain reaction evidence
has OBO namespace: evidence_code2.obo
has exact synonym: RT-PCR evidence

RNA protection assay evidence
type: Class
subclass of: transcript expression evidence
has OBO namespace: evidence_code2.obo
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
has related synonym: IEP: RNA protection assay

Western blot evidence
type: Class
subclass of: protein expression level evidence
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

expression library screen evidence
type: Class
subclass of: protein expression evidence
subclass of: immunological assay evidence
has OBO namespace: evidence_code2.obo
has related synonym: IEP: expression library screening
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

differential hybridization evidence
type: Class
subclass of: transcript expression evidence
subclass of: nucleic acid hybridization evidence
has OBO namespace: evidence_code2.obo
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
has related synonym: IEP: differential hybridization

subtractive hybridization evidence
type: Class
subclass of: transcript expression evidence
subclass of: nucleic acid hybridization evidence
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

over expression analysis evidence
type: Class
subclass of: experimental phenotypic evidence
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

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

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

green fluorescent protein fusion protein localization evidence
type: Class
subclass of: fusion protein localization evidence
has OBO namespace: evidence_code2.obo
has exact synonym: GFP fusion protein localization evidence
has related synonym: IDA: localization of GFP/YFP fusion protein

yellow fluorescent protein fusion protein localization evidence
type: Class
subclass of: fusion protein localization evidence
has OBO namespace: evidence_code2.obo
has exact synonym: YFP fusion protein localization evidence
has related synonym: IDA: localization of GFP/YFP fusion protein

beta-glucuronidase fusion protein localization evidence
type: Class
subclass of: fusion protein localization evidence
has OBO namespace: evidence_code2.obo
has exact synonym: GUS fusion protein localization evidence
has related synonym: IDA: localization of GUS fusion protein
has narrow synonym: GUS staining evidence

beta-galactosidase fusion protein localization evidence
type: Class
subclass of: fusion protein localization evidence
has OBO namespace: evidence_code2.obo
has exact synonym: LacZ fusion protein localization evidence

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

nucleic acid binding evidence
type: Class
subclass of: ligand binding evidence
has OBO namespace: evidence_code2.obo

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

thin layer chromatography evidence
type: Class
subclass of: chromatography evidence
has OBO namespace: evidence_code2.obo
has related synonym: IDA: thin layer chromatography
has exact synonym: TLC evidence
has definition: A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

protein:ion binding evidence
type: Class
subclass of: protein binding evidence
has OBO namespace: evidence_code2.obo

Southwestern blot evidence
type: Class
subclass of: nucleic acid binding evidence
has OBO namespace: evidence_code2.obo
has related synonym: IDA: Southwestern analysis
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

Northwestern blot evidence
type: Class
subclass of: nucleic acid binding evidence
has OBO namespace: evidence_code2.obo
has related synonym: IDA: Northwestern analysis
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

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

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

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

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

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

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

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

heterologous system uptake evidence
type: Class
subclass of: transport assay evidence
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

electrophysiology assay evidence
type: Class
subclass of: direct assay evidence
has OBO namespace: evidence_code2.obo

two-electrode voltage clamp experiment evidence
type: Class
subclass of: electrophysiology assay evidence
has OBO namespace: evidence_code2.obo
has related synonym: IDA: two-electrode voltage clamp technique

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

transcriptional activation assay
type: Class
subclass of: transcription assay
has OBO namespace: evidence_code2.obo
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
has related synonym: IDA: transcriptional activation assay

biochemical trait analysis evidence
type: Class
subclass of: experimental phenotypic evidence
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

mutant physiological response evidence
type: Class
subclass of: experimental phenotypic evidence
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

mutant visible phenotype evidence
type: Class
subclass of: experimental phenotypic evidence
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

genomic context evidence
type: Class
subclass of: evidence
comment: This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis.
has OBO namespace: evidence_code2.obo
has definition: An evidence type that is based on the location of a gene, which gives rise to a gene product, within the genome.
  type: Definition
  has db xref: ECO:go
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_go
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

in vivo assay evidence
type: Class
subclass of: biological assay evidence
has OBO namespace: evidence_code2.obo

animal model system study evidence
type: Class
subclass of: experimental evidence
has OBO namespace: evidence_code2.obo
has definition: A type of experimental evidence arising from the investigation of an animal model system.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

clinical study evidence
type: Class
subclass of: experimental evidence
has OBO namespace: evidence_code2.obo
has definition: A type of experimental evidence arising from a controlled investigation that uses human subjects.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

in vitro assay evidence
type: Class
subclass of: biological assay evidence
has OBO namespace: evidence_code2.obo

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

cell-free assay evidence
type: Class
subclass of: in vitro assay evidence
has OBO namespace: evidence_code2.obo
has broad synonym: in vitro assay

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

sequence alignment evidence
type: Class
subclass of: sequence similarity evidence
has alternative id: ECO:00000057
has OBO namespace: evidence_code2.obo
has exact synonym: inferred from sequence alignment
  type: Synonym
  has db xref: GO:ISA
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ISA
has definition: Definition
  label: Used when a sequence alignment is the basis for making an annotation, but only when the alignment has been manually reviewed; or if the information is in a published paper, the authors have manually reviewed the evidence. Such alignments may be pairwise alignments or multiple alignments. BLAST produces pairwise alignments and any annotations based solely on the evaluation of BLAST results should use this code.
  has db xref: url:http://www.geneontology.org/GO.evidence.shtml
    type: DbXref
    has URI: http://purl.org/obo/owl/url#url_http://www.geneontology.org/GO.evidence.shtml
has exact synonym: ISA
  type: Synonym
  has db xref: GO:ISA
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ISA

sequence orthology evidence
type: Class
subclass of: sequence similarity evidence
has OBO namespace: evidence_code2.obo
has alternative id: ECO:00000060
has definition: Definition
  label: Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. Orthology is established by multiple criteria generally including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors.
  has db xref: url:http://www.geneontology.org/GO.evidence.shtml
    type: DbXref
    has URI: http://purl.org/obo/owl/url#url_http://www.geneontology.org/GO.evidence.shtml
has exact synonym: inferred from sequence orthology
  type: Synonym
  has db xref: GO:ISO
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ISO
has exact synonym: ISO
  type: Synonym
  has db xref: GO:ISO
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ISO
has related synonym: ortholog evidence

match to sequence model evidence
type: Class
subclass of: sequence similarity evidence
comment: Used when evidence from any kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Examples of relevant evidence are: Hidden Markov Models, PROSITE motifs, and tools such as tRNASCAN.
has OBO namespace: evidence_code2.obo
has alternative id: ECO:00000063
has exact synonym: ISM
  type: Synonym
  has db xref: GO:ISM
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ISM
has definition: Sequence similarity evidence that is based on a sequence-based statistical model that predicts the function of a gene product.
  type: Definition
  has db xref: url:http://www.geneontology.org/GO.evidence.shtml
    type: DbXref
    has URI: http://purl.org/obo/owl/url#url_http://www.geneontology.org/GO.evidence.shtml
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: inferred from sequence model
  type: Synonym
  has db xref: GO:ISM
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_ISM

automatic assertion
type: Class
subclass of: assertion method
comment: An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically.
has OBO namespace: evidence_code2.obo
has alternative id: ECO:00000067
has exact synonym: IEA
  type: Synonym
  has db xref: GOECO:IEA
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IEA
has exact synonym: inferred from electronic annotation
  type: Synonym
  has db xref: GOECO:IEA
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IEA
has db xref: GO_REF:0000023
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000023
has db xref: GO_REF:0000004
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000004
has definition: An assertion method that does not involve human review.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has db xref: GOECO:IEA
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IEA

author statement
type: Class
subclass of: evidence
has OBO namespace: evidence_code2.obo
has definition: An evidence type that is based on an assertion by the author of a paper, which is read by a curator.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

curator inference
type: Class
subclass of: evidence
has OBO namespace: evidence_code2.obo
has definition: An evidence type that is based on conclusions drawn by a curator.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

BLAST evidence
type: Class
subclass of: sequence alignment evidence
has OBO namespace: evidence_code2.obo
has definition: A type of sequence alignment evidence obtained with basic local alignment search tool (BLAST).
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

nucleotide BLAST evidence
type: Class
subclass of: BLAST evidence
has OBO namespace: evidence_code2.obo
has definition: BLAST evidence from aligning nucleotide sequence with nucleotide sequence.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

protein BLAST evidence
type: Class
subclass of: BLAST evidence
has OBO namespace: evidence_code2.obo
has definition: BLAST evidence from aligning amino acid or translated nucleotide sequence with amino acid or translated nucleotide sequence.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

BLAST evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: BLAST evidence
has OBO namespace: evidence_code2.obo
has definition: A type of BLAST evidence that is used in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

nucleotide BLAST evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: nucleotide BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: nucleotide BLAST evidence
has OBO namespace: evidence_code2.obo
has definition: Nucleotide BLAST evidence that is used in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

protein BLAST evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: protein BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: protein BLAST evidence
has OBO namespace: evidence_code2.obo
has definition: Protein BLAST evidence that is used in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

combinatorial evidence
type: Class
subclass of: evidence
comment: A key aspect of this type of evidence is that two or more pieces of information are combined to generate an emergent type of evidence not possible with the constituent pieces of evidence alone. A combinatorial analysis typically involves incorporation of different types of evidence.
has alternative id: ECO:0000043
has alternative id: ECO:0000036
has OBO namespace: evidence_code2.obo
has related synonym: inferred from in-silico analysis
has definition: A type of evidence that arises out of the integration of more than one line of evidence.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

combinatorial evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: combinatorial evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: combinatorial evidence
comment: Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
has OBO namespace: evidence_code2.obo
has definition: A type of combinatorial analysis that is used in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

biological aspect of descendant evidence
type: Class
subclass of: phylogenetic evidence
comment: This type of evidence can be used in support of both positive and "not" GO annotations. It should be used to annotate ancestral genes but not extant ones.
has OBO namespace: evidence_code2.obo
has definition: A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

rapid divergence from ancestral sequence evidence
type: Class
subclass of: phylogenetic evidence
comment: Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence.
has OBO namespace: evidence_code2.obo
has definition: A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

phylogenetic determination of loss of key residues evidence
type: Class
subclass of: phylogenetic evidence
comment: The loss of certain residues important for function can indicate that a sequence lacks a particular function.
has OBO namespace: evidence_code2.obo
has definition: A type of phylogenetic evidence characterized by the absence of key sequence residues.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

assertion method
type: Class
has OBO namespace: evidence_code2.obo
has definition: A means by which a statement is made about an entity.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

manual assertion
type: Class
subclass of: assertion method
comment: A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information.
has OBO namespace: evidence_code2.obo
has definition: An assertion method that involves human review.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

nucleotide sequencing assay evidence
type: Class
subclass of: sequencing assay evidence
has OBO namespace: evidence_code2.obo
has related synonym: DNA sequencing
  type: Synonym
  has db xref: OBI:0000626
    type: DbXref
    has URI: http://purl.org/obo/owl/OBI#OBI_0000626
has definition: A sequencing assay result for a biopolymer that comprises nucleotides.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

sequencing assay evidence
type: Class
subclass of: experimental evidence
has OBO namespace: evidence_code2.obo
has definition: A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
  type: Definition
  has db xref: OBI:0600047
    type: DbXref
    has URI: http://purl.org/obo/owl/OBI#OBI_0600047
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

high throughput nucleotide sequencing assay evidence
type: Class
subclass of: nucleotide sequencing assay evidence
comment: Typically thousands to millions of reads are produced in parallel.
has OBO namespace: evidence_code2.obo
has definition: A nucleotide sequencing assay result that is derived from a parallelized sequencing technique.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

Illumina sequencing evidence
type: Class
subclass of: high throughput nucleotide sequencing assay evidence
comment: In Illumina sequencing technology, adapters are ligated onto the ends of randomly fragmented DNA. After single-stranded fragments are bound to the inside surface of a flow cell channel, they undergo in-place bridge PCR amplification. To begin the sequencing cycle, labeled reversible terminators, primers and DNA polymerase are added, followed by laser excitation of the fluorescent label and high resolution scanning. After non-incorporated nucleotides are washed away and the dye is chemically removed, the next cycle repeats with four labeled reversible terminators, primers and DNA polymerase, again followed by imaging.
has OBO namespace: evidence_code2.obo
has definition: A high throughput nucleotide sequencing result derived by Illumina (Solexa) sequencing technology.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has related synonym: Solexa sequencing result
  type: Synonym
  has db xref: OBI:0000724
    type: DbXref
    has URI: http://purl.org/obo/owl/OBI#OBI_0000724

454 pyrosequencing evidence
type: Class
subclass of: high throughput nucleotide sequencing assay evidence
comment: 454 pyrosequencing technology amplifies individual DNA fragments inside water droplets within an oil solution (emulsion PCR). Within each droplet, a single DNA template is attached to a single primer-coated bead. Each bead is subsequently captured in a picolitre well within the sequencing machine. A luciferase-based readout system is used to identify individual nucleotides added to the nascent DNA.
has OBO namespace: evidence_code2.obo
has broad synonym: pyrosequencing
  type: Synonym
  has db xref: OBI:0000730
    type: DbXref
    has URI: http://purl.org/obo/owl/OBI#OBI_0000730
has definition: A high throughput nucleotide sequencing result derived by 454 pyrosequencing technology.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

SOLiD sequencing evidence
type: Class
subclass of: high throughput nucleotide sequencing assay evidence
comment: SOLiD sequencing technology is based on sequencing by ligation. After library preparation, emulsion PCR and bead enrichment are performed, including 3' modification of templates on selected beads to allow covalent bonding to a slide. 3' modified beads are attached to a glass slide and primers are added. Four fluorescently labeled di-base probes are added and multiple cycles of ligation, detection and cleavage are performed. The number of cycles determines read length. After a number of ligation cycles, the extension product is removed and another round of ligation cycles is performed with a new primer complimentary to the n-1 position of the template. Five rounds of primer reset are performed for each sequence tag.
has OBO namespace: evidence_code2.obo
has definition: A high throughput nucleotide sequencing result derived by SOLiD sequencing technology.
  type: Definition
  has db xref: OBI:0000706
    type: DbXref
    has URI: http://purl.org/obo/owl/OBI#OBI_0000706
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

chain termination sequencing evidence
type: Class
subclass of: nucleotide sequencing assay evidence
comment: Chain termination sequencing, also called Sanger sequencing after its developer, uses dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. Single-stranded DNA template, DNA primer, DNA polymerase, fluorescently or radioactively labeled nucleotides, and one of four ddNTPs are added together in each of four separate sequencing reactions. The synthesized and labeled DNA fragments from each of the four reactions are denatured, separated by size by gel electrophoresis, and visualized by autoradiography or UV light.
has OBO namespace: evidence_code2.obo
has exact synonym: Sanger sequencing
has exact synonym: dye terminator sequencing
has definition: A nucleotide sequencing assay result derived by the chain termination sequencing method.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
  has db xref: OBI:0000695
    type: DbXref
    has URI: http://purl.org/obo/owl/OBI#OBI_0000695

chromatin immunoprecipitation evidence
type: Class
subclass of: immunoprecipitation evidence
comment: Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq).
has OBO namespace: evidence_code2.obo
has exact synonym: ChIP evidence
has definition: An immunoprecipitation experiment that is used to identify a protein binding site on a genomic DNA sequence.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

chromatin immunoprecipitation-PCR evidence
type: Class
subclass of: chromatin immunoprecipitation evidence
has OBO namespace: evidence_code2.obo
has exact synonym: ChIP-PCR evidence
has definition: A chromatin immunoprecipitation (ChIP) experiment that uses polymerase chain reaction (PCR) for DNA detection.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

chromatin immunoprecipitation-qPCR evidence
type: Class
subclass of: chromatin immunoprecipitation evidence
has OBO namespace: evidence_code2.obo
has exact synonym: ChIP-qPCR evidence
has definition: A chromatin immunoprecipitation (ChIP) experiment that uses quantitative polymerase chain reaction (qPCR) for DNA detection.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

chromatin immunoprecipitation-seq evidence
type: Class
subclass of: chromatin immunoprecipitation evidence
has OBO namespace: evidence_code2.obo
has definition: A chromatin immunoprecipitation (ChIP) experiment that uses high-throughput sequencing for DNA detection.
  type: Definition
  has db xref: OBI:0000716
    type: DbXref
    has URI: http://purl.org/obo/owl/OBI#OBI_0000716
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: ChIP-SEQ evidence
  type: Synonym
  has db xref: OBI:0000716
    type: DbXref
    has URI: http://purl.org/obo/owl/OBI#OBI_0000716
has exact synonym: ChIP-seq evidence

chromatin immunoprecipitation-chip evidence
type: Class
subclass of: chromatin immunoprecipitation evidence
has OBO namespace: evidence_code2.obo
has exact synonym: ChIP-on-chip evidence
has exact synonym: ChIP-chip evidence
has definition: A chromatin immunoprecipitation (ChIP) experiment that uses a tiling microarray for DNA detection.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

quantitative polymerase chain reaction evidence
type: Class
subclass of: polymerase chain reaction evidence
comment: Quantitative PCR enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
has OBO namespace: evidence_code2.obo
has definition: A polymerase chain reaction experiment where the reaction product is quantified in real-time across cycles by means of fluorescent dyes.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: qRT-PCR evidence
has exact synonym: quantitative PCR evidence
has exact synonym: real-time PCR evidence
has exact synonym: real-time polymerase chain reaction evidence
has exact synonym: Q-PCR evidence

chromosome conformation capture-based evidence
type: Class
subclass of: experimental genomic evidence
comment: Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C.
has OBO namespace: evidence_code2.obo
has narrow synonym: chromosome conformation capture
has narrow synonym: 3C
has definition: Definition
  label: A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, and DNA processing and quantitation.
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

chromosome conformation capture evidence
type: Class
subclass of: chromosome conformation capture-based evidence
comment: 3C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C differs only in the fifth step, which involves performing either standard polymerase chain reaction (PCR) or quantitative PCR (qPCR) for product quantitation.
has OBO namespace: evidence_code2.obo
has exact synonym: 3C
has definition: A type of chromosome conformation capture-based evidence that is derived by performing a type of polymerase chain reaction (PCR) in the final product quantitation step.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

circularized chromosome conformation capture evidence
type: Class
subclass of: chromosome conformation capture-based evidence
comment: 4C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 4C differs only in the fifth step, which involves inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation.
has OBO namespace: evidence_code2.obo
has exact synonym: circularized 3C
has exact synonym: chromosome conformation capture on chip
has exact synonym: 4C
has definition: Definition
  label: A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray.
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

carbon-copy chromosome conformation capture evidence
type: Class
subclass of: chromosome conformation capture-based evidence
comment: 5C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 5C differs only in the fifth step, which involves ligation-mediated amplification (LMA) followed by product quantitation.
has OBO namespace: evidence_code2.obo
has exact synonym: 5C
has exact synonym: carbon-copy 3C
has definition: A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

chromosome conformation capture-PCR evidence
type: Class
subclass of: chromosome conformation capture evidence
has OBO namespace: evidence_code2.obo
has exact synonym: 3C-PCR
has broad synonym: 3C
has definition: A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

chromosome conformation capture-qPCR evidence
type: Class
subclass of: chromosome conformation capture evidence
has OBO namespace: evidence_code2.obo
has exact synonym: 3C-quantitative PCR
has exact synonym: 3C-qPCR
has definition: A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: 3C-real-time PCR

Hi-C evidence
type: Class
subclass of: chromosome conformation capture-based evidence
comment: Hi-C is used to study the structural properties and spatial organization of chromosomes inside cells. Hi-C is similar to other types of chromosome conformation capture technology, but involves the addition of biotinylated nucleotides during the second or fourth step and enrichment for ligated fragments using immunoprecipitation after the fourth step.
has OBO namespace: evidence_code2.obo
has definition: A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

chromosome conformation capture sequencing evidence
type: Class
subclass of: chromosome conformation capture-based evidence
comment: 3C-seq is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C-seq differs only in the fifth step, which involves inverse polymerase chain reaction (PCR) on a circularized 3C library prior to product quantitation.
has OBO namespace: evidence_code2.obo
has exact synonym: circularized 3C-seq
has exact synonym: circularized 3C sequencing
has exact synonym: 4C-seq
has definition: Definition
  label: A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with high-throughput (HT) sequencing.
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: 4C sequencing
has exact synonym: 3C-seq
has exact synonym: 3C sequencing

anatomical perturbation evidence
type: Class
subclass of: experimental phenotypic evidence
has OBO namespace: evidence_code2.obo
has definition: Experimental phenotypic evidence where a structural feature of an organism is disrupted.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

environmental perturbation evidence
type: Class
subclass of: experimental phenotypic evidence
comment: Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth.
has OBO namespace: evidence_code2.obo
has definition: Experimental phenotypic evidence where the extra-organismal context of an organism is modified.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has related synonym: mechanical constraint evidence

tissue ablation evidence
type: Class
subclass of: anatomical perturbation evidence
comment: A tissue ablation experiment involves observing the phenotype of an entity whose tissues have been disrupted through genetic or biochemical manipulation, physical destruction, or some other means.
has OBO namespace: evidence_code2.obo
has exact synonym: ablated tissue evidence
has definition: A type of anatomical perturbation that is based on disruption of tissue.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

tissue grafting evidence
type: Class
subclass of: anatomical perturbation evidence
has OBO namespace: evidence_code2.obo
has definition: A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

combinatorial evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: combinatorial evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: combinatorial evidence
comment: Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
has OBO namespace: evidence_code2.obo
has definition: A type of combinatorial analysis that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

computational combinatorial evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: computational combinatorial evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: computational combinatorial evidence
has OBO namespace: evidence_code2.obo
has exact synonym: inferred from reviewed computational analysis
  type: Synonym
  has db xref: GOECO:RCA
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_RCA
has exact synonym: RCA
  type: Synonym
  has db xref: GOECO:RCA
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_RCA
has db xref: GOECO:RCA
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_RCA
has definition: A type of computational combinatorial analysis that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

computational combinatorial evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: computational combinatorial evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: computational combinatorial evidence
has OBO namespace: evidence_code2.obo
has definition: A type of computational combinatorial analysis that is used in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

sequence alignment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: sequence alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: sequence alignment evidence
has OBO namespace: evidence_code2.obo
has definition: Sequence alignment evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has db xref: GOECO:ISA
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_ISA
has exact synonym: inferred from sequence alignment
  type: Synonym
  has db xref: GOECO:ISA
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_ISA
has exact synonym: ISA
  type: Synonym
  has db xref: GOECO:ISA
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_ISA

sequence alignment evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: sequence alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: sequence alignment evidence
has OBO namespace: evidence_code2.obo
has definition: Sequence alignment evidence that is used in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

sequence similarity evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: sequence similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: sequence similarity evidence
has OBO namespace: evidence_code2.obo
has definition: Sequence similarity evidence that is used in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

sequence similarity evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: sequence similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: sequence similarity evidence
has OBO namespace: evidence_code2.obo
has db xref: GOECO:ISS
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_ISS
has definition: Sequence similarity evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

similarity evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: similarity evidence
has OBO namespace: evidence_code2.obo
has definition: Similarity evidence that is used in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

similarity evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: similarity evidence
has OBO namespace: evidence_code2.obo
has definition: Similarity evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

genetic similarity evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genetic similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: genetic similarity evidence
has OBO namespace: evidence_code2.obo
has definition: Genetic similarity evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

genetic similarity evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: genetic similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: genetic similarity evidence
has OBO namespace: evidence_code2.obo
has definition: Genetic similarity evidence that is used in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

match to sequence model evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: match to sequence model evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: match to sequence model evidence
has OBO namespace: evidence_code2.obo
has db xref: GO_REF:0000011
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000011
has db xref: GOECO:ISM
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_ISM
has definition: A match to sequence model evidence that is employed in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

match to sequence model evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: match to sequence model evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: match to sequence model evidence
has OBO namespace: evidence_code2.obo
has db xref: GO_REF:0000019
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000019
has db xref: GO_REF:0000002
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000002
has definition: A match to sequence model evidence that is employed in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

motif similarity evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: motif similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: motif similarity evidence
has OBO namespace: evidence_code2.obo
has definition: Motif similarity evidence that is employed in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

motif similarity evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: motif similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: motif similarity evidence
has OBO namespace: evidence_code2.obo
has definition: Motif similarity evidence that is employed in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

match to InterPro signature evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: match to InterPro signature evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: match to InterPro signature evidence
has OBO namespace: evidence_code2.obo
has definition: A match to InterPro signature evidence that is employed in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

match to InterPro signature evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: match to InterPro signature evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: match to InterPro signature evidence
has OBO namespace: evidence_code2.obo
has definition: A match to InterPro signature evidence that is employed in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

targeting sequence prediction evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: targeting sequence prediction evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: targeting sequence prediction evidence
has OBO namespace: evidence_code2.obo
has definition: A targeting sequence prediction that is employed in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

targeting sequence prediction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: targeting sequence prediction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: targeting sequence prediction evidence
has OBO namespace: evidence_code2.obo
has definition: A targeting sequence prediction that is employed in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

transmembrane domain prediction evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: transmembrane domain prediction evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: transmembrane domain prediction evidence
has OBO namespace: evidence_code2.obo
has definition: Transmembrane domain prediction that is employed in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

transmembrane domain prediction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: transmembrane domain prediction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: transmembrane domain prediction evidence
has OBO namespace: evidence_code2.obo
has definition: Transmembrane domain prediction that is employed in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

sequence orthology evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: sequence orthology evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: sequence orthology evidence
has OBO namespace: evidence_code2.obo
has definition: Sequence orthology evidence that is employed in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has db xref: GO_REF:0000003
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000003
has db xref: GO_REF:0000019
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000019
has db xref: GO_REF:0000035
  type: DbXref
  has URI: http://purl.org/obo/owl/GO_REF#GO_REF_0000035
has related synonym: Ortholog evidence

sequence orthology evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: sequence orthology evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: sequence orthology evidence
has OBO namespace: evidence_code2.obo
has related synonym: Ortholog evidence
has db xref: GOECO:ISO
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_ISO
has definition: Sequence orthology evidence that is employed in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

enzyme-linked immunoabsorbent assay evidence
type: Class
subclass of: immunological assay evidence
has OBO namespace: evidence_code2.obo
has exact synonym: enzyme-linked immunosorbent assay
has exact synonym: ELISA
has definition: An immunological assay that binds an antigen to a substrate and utilizes an antibody directly or indirectly linked to an enzyme to determine the amount of bound antigen.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

flow cytometry evidence
type: Class
subclass of: direct assay evidence
has OBO namespace: evidence_code2.obo
has exact synonym: FCM
has definition: A direct assay that passes a stream of cells or particles past a light source, followed by using a detector to monitor light scatter or fluorochrome excitation to characterize the cells or particles.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

experimental evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: experimental evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence
has OBO namespace: evidence_code2.obo
has db xref: GOECO:EXP
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_EXP
has definition: A type of experimental evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: expression pattern evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence
has OBO namespace: evidence_code2.obo
has definition: A type of expression pattern evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has db xref: GOECO:IEP
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IEP

array experiment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: array experiment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: array experiment evidence
has OBO namespace: evidence_code2.obo
has definition: A type of array experiment evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

Affymetrix array experiment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Affymetrix array experiment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: Affymetrix array experiment evidence
has OBO namespace: evidence_code2.obo
has definition: A type of Affymetrix array experiment evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

cDNA microarray evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cDNA microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: cDNA microarray evidence
has OBO namespace: evidence_code2.obo
has definition: A type of evidence arising from a cDNA microarray experiment that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

CpG island microarray evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: CpG island microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: CpG island microarray evidence
has OBO namespace: evidence_code2.obo
has definition: A type of evidence arising from a CpG island microarray experiment that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

expression microarray evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: expression microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression microarray evidence
has OBO namespace: evidence_code2.obo
has definition: A type of expression microarray evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

genomic microarray evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genomic microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: genomic microarray evidence
has OBO namespace: evidence_code2.obo
has definition: A type of evidence arising from a genomic microarray experiment that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

Nimblegen array evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Nimblegen array evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: Nimblegen array evidence
has OBO namespace: evidence_code2.obo
has definition: A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

oligonucleotide microarray evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: oligonucleotide microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: oligonucleotide microarray evidence
has OBO namespace: evidence_code2.obo
has definition: A type of evidence arising from an oligonucleotide microarray experiment that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

Western blot evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Western blot evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: Western blot evidence
has OBO namespace: evidence_code2.obo
has definition: A type of Western blot assay that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

protein expression level evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein expression level evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: protein expression level evidence
has OBO namespace: evidence_code2.obo
has definition: A type of protein expression level analysis that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

expression library screen evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: expression library screen evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression library screen evidence
has OBO namespace: evidence_code2.obo
has definition: A type of expression library screen data that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

heterologous protein expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: heterologous protein expression evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: heterologous protein expression evidence
has OBO namespace: evidence_code2.obo
has definition: A type of heterologous protein expression analysis that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

spatial pattern of protein expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: spatial pattern of protein expression evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: spatial pattern of protein expression evidence
has OBO namespace: evidence_code2.obo
has definition: A type of protein expression spatial pattern analysis that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

protein expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein expression evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: protein expression evidence
has OBO namespace: evidence_code2.obo
has definition: A type of protein expression analysis that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

microarray RNA expression level evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: microarray RNA expression level evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: microarray RNA expression level evidence
has OBO namespace: evidence_code2.obo
has definition: A type of microarray RNA expression level data that is used in manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

transcript expression level used in manual assertion
type: Class
equivalent class: Class
  intersection of: transcript expression level evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: transcript expression level evidence
has OBO namespace: evidence_code2.obo
has definition: A type of transcript expression level data that is used in manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

differential hybridization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: differential hybridization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: differential hybridization evidence
has OBO namespace: evidence_code2.obo
has definition: A type of differential hybridization experiment that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

RNA protection assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: RNA protection assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: RNA protection assay evidence
has OBO namespace: evidence_code2.obo
has definition: A type of RNA protection assay that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

spatial pattern of transcript expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: spatial pattern of transcript expression evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: spatial pattern of transcript expression evidence
has OBO namespace: evidence_code2.obo
has definition: A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

subtractive hybridization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: subtractive hybridization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: subtractive hybridization evidence
has OBO namespace: evidence_code2.obo
has definition: A type of subtractive hybridization experiment that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

transcript expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: transcript expression evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: transcript expression evidence
has OBO namespace: evidence_code2.obo
has definition: A type of transcript expression evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

morpholino experiment evidence
type: Class
subclass of: experimental phenotypic evidence
comment: Morpholino oligonucleotides modify gene expression by blocking access of other molecules to specific, approximately 25-base-long regions of the base-pairing surfaces of ribonucleic acid (RNA). To achieve this anti-sense knockdown technique, delivery of the morpholino can be achieved via microinjection, electroporation, or another method.
has OBO namespace: evidence_code2.obo
has broad synonym: anti-sense
has definition: A type of experimental phenotypic evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

systematic evolution of ligands by exponential amplification evidence
type: Class
subclass of: physical interaction evidence
comment: SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein.
has OBO namespace: evidence_code2.obo
has definition: A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
  has db xref: url:http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment
    type: DbXref
    has URI: http://purl.org/obo/owl/url#url_http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment
has exact synonym: in vitro selection evidence
has exact synonym: SELEX evidence
has related synonym: in vitro evolution evidence

bacterial one-hybrid evidence
type: Class
subclass of: hybrid interaction evidence
comment: Bacterial one-hybrid assay is a method for screening a library of candidate proteins (prey plasmid) for the ability to bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to reporter genes (bait plasmid). Transformation of a bacterial host with two different plasmids is required: One is designed to express the "bait". The other plasmid contains a "prey" which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes.
has OBO namespace: evidence_code2.obo
has exact synonym: B1H evidence
has definition: Definition
  label: A type of evidence arising from a hybrid interaction experiment that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

RNA-seq evidence
type: Class
subclass of: transcript expression evidence
comment: Total RNA is isolated from cells and mRNA is purified by targeting the 3' polyadenylated (poly(A)) tail with poly(T) oligos covalently attached to a substrate. Next, cDNA fragments are generated either by hydrolysis of RNA into 200-300 base oligonucleotides, preceded by reverse transcription, or by reverse transcription initiated by random primers. The cDNA second strand is synthesized, fragments are adapter ligated and high-throughput sequencing is performed by Roche 454, Illumina, ABI-SOLiD, or another HT sequencing technology. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
has OBO namespace: evidence_code2.obo
has exact synonym: whole transcriptome shotgun sequencing
  type: Synonym
  has db xref: PMID:18611170
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_18611170
has exact synonym: WTSS
has definition: A type of transcript expression evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has related synonym: RNA sequencing

green fluorescent protein transcript localization evidence
type: Class
subclass of: transcriptional activation assay
comment: This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of green fluorescent protein".
has OBO namespace: evidence_code2.obo
has definition: A transcriptional activation assay that uses a green fluorescent protein (GFP) reporter gene.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: localization of GFP transcript

LacZ transcript localization evidence
type: Class
subclass of: transcriptional activation assay
comment: This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of LacZ protein".
has OBO namespace: evidence_code2.obo
has definition: A transcriptional activation assay that uses a LacZ reporter gene.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

cleavage arrested development evidence
type: Class
subclass of: experimental phenotypic evidence
comment: In the embryos of some organisms, inhibition of cytokinesis blocks neither the cell cycle nor the unfolding of the developmental program. As such, embryonic morphology can be frozen, allowing analysis of the developmental fate of each cell present at the time of cleavage arrest.
has OBO namespace: evidence_code2.obo
has definition: A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

cytochalasin experiment evidence
type: Class
subclass of: cleavage arrested development evidence
comment: Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments.
has OBO namespace: evidence_code2.obo
has definition: A type of cleavage arrested development that arises after treatment with cytochalasin.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

green fluorescent protein immunolocalization evidence
type: Class
subclass of: immunolocalization evidence
comment: This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript".
has OBO namespace: evidence_code2.obo
has definition: A type of immunolocalization experiment data that was generated using green fluorescent protein (GFP) as a marker.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: GFP immunolocalization evidence

beta-galactosidase protein immunolocalization evidence
type: Class
subclass of: immunolocalization evidence
comment: This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript".
has OBO namespace: evidence_code2.obo
has definition: A type of immunolocalization experiment data that was generated using LacZ protein as a marker.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: LacZ protein immunolocalization evidence

author statement used in manual assertion
type: Class
equivalent class: Class
  intersection of: author statement
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: author statement
has OBO namespace: evidence_code2.obo
has definition: A type of author statement that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

non-traceable author statement used in manual assertion
type: Class
equivalent class: Class
  intersection of: non-traceable author statement
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: non-traceable author statement
has OBO namespace: evidence_code2.obo
has db xref: GOECO:NAS
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_NAS
has definition: A type of non-traceable author statement that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: non-traceable author statement
  type: Synonym
  has db xref: GOECO:NAS
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_NAS
has exact synonym: NAS
  type: Synonym
  has db xref: GOECO:NAS
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_NAS

traceable author statement used in manual assertion
type: Class
equivalent class: Class
  intersection of: traceable author statement
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: traceable author statement
has OBO namespace: evidence_code2.obo
has exact synonym: traceable author statement
  type: Synonym
  has db xref: GOECO:TAS
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_TAS
has definition: A type of traceable author statement that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has db xref: GOECO:TAS
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_TAS
has exact synonym: TAS
  type: Synonym
  has db xref: GOECO:TAS
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_TAS

curator inference used in manual assertion
type: Class
equivalent class: Class
  intersection of: curator inference
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: curator inference
has OBO namespace: evidence_code2.obo
has db xref: GOECO:IC
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IC
has definition: A type of curator inference that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

inference from background scientific knowledge used in manual assertion
type: Class
equivalent class: Class
  intersection of: inference from background scientific knowledge
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: inference from background scientific knowledge
has OBO namespace: evidence_code2.obo
has definition: A type of inference from background scientific knowledge that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

no biological data found used in manual assertion
type: Class
equivalent class: Class
  intersection of: no biological data found
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: no biological data found
has OBO namespace: evidence_code2.obo
has db xref: GOECO:ND
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_ND
has definition: A type of no biological data found that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

biological aspect of ancestor evidence
type: Class
subclass of: phylogenetic evidence
comment: First, a characteristic of the most recent common ancestor (MRCA) is inferred from experimental evidence in descendants; this is followed by inferring a characteristic of a descendant of the MRCA. This type of evidence can be used in support of both positive and "not" GO annotations.
has OBO namespace: evidence_code2.obo
has definition: A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

cap analysis of gene expression evidence
type: Class
subclass of: transcript expression evidence
comment: cDNA is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
has OBO namespace: evidence_code2.obo
has exact synonym: CAGE
  type: Synonym
  has db xref: PMID:16489339
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_16489339
has definition: A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

nano-cap analysis of gene expression evidence
type: Class
subclass of: transcript expression evidence
comment: NanoCAGE captures the 5' ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5' full length cDNAs is extended upon hybridization of the riboguanosine-tailed template switching oligonucleotides to these extra cytosines. In semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers, which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template switching, semisuppressive PCR, and EcoP151 cleavage, 25-bp tags are ligated to bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA.
has OBO namespace: evidence_code2.obo
has definition: A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has related synonym: nanoCAGE
  type: Synonym
  has db xref: PMID:20543846
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_20543846

imported information
type: Class
subclass of: evidence
has OBO namespace: evidence_code2.obo
has definition: An evidence type that is based on work performed by a person or group prior to a use by different person or group.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

imported information used in manual assertion
type: Class
equivalent class: Class
  intersection of: imported information
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: imported information
has OBO namespace: evidence_code2.obo
has definition: A type of imported information that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

imported information used in automatic assertion
type: Class
equivalent class: Class
  intersection of: imported information
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: imported information
has OBO namespace: evidence_code2.obo
has definition: A type of imported information that is used in an automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

direct assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: direct assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence
has OBO namespace: evidence_code2.obo
has definition: A type of direct assay evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has db xref: GOECO:IDA
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IDA
has related synonym: IDA
  type: Synonym
  has db xref: GOECO:IDA
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IDA
has exact synonym: inferred from direct assay
  type: Synonym
  has db xref: GOECO:IDA
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IDA

mutant phenotype evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: mutant phenotype evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mutant phenotype evidence
has OBO namespace: evidence_code2.obo
has definition: A type of mutant phenotype evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has db xref: GOECO:IMP
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IMP
has related synonym: IMP
  type: Synonym
  has db xref: GOECO:IMP
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IMP
has related synonym: inferred from mutant phenotype
  type: Synonym
  has db xref: GOECO:IMP
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IMP

genetic interaction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genetic interaction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: genetic interaction evidence
has OBO namespace: evidence_code2.obo
has db xref: GOECO:IGI
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IGI
has exact synonym: IGI
  type: Synonym
  has db xref: GOECO:IGI
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IGI
has exact synonym: inferred from genetic interaction
  type: Synonym
  has db xref: GOECO:IGI
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IGI
has definition: A type of genetic interaction experiment evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

genomic context evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genomic context evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: genomic context evidence
has OBO namespace: evidence_code2.obo
has db xref: GOECO:IGC
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IGC
has related synonym: IGC
  type: Synonym
  has db xref: GOECO:IGC
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IGC
has exact synonym: inferred from genomic context
  type: Synonym
  has db xref: GOECO:IGC
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IGC
has definition: A type of genomic context evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

biological aspect of ancestor evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: biological aspect of ancestor evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: biological aspect of ancestor evidence
has OBO namespace: evidence_code2.obo
has exact synonym: inferred from biological aspect of ancestor
  type: Synonym
  has db xref: GOECO:IBA
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IBA
has exact synonym: IBA
  type: Synonym
  has db xref: GOECO:IBA
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IBA
has definition: A type of biological aspect of ancestor evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has db xref: GOECO:IBA
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IBA

biological aspect of descendant evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: biological aspect of descendant evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: biological aspect of descendant evidence
has OBO namespace: evidence_code2.obo
has db xref: GOECO:IBD
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IBD
has exact synonym: IBD
  type: Synonym
  has db xref: GOECO:IBD
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IBD
has definition: A type of biological aspect of descendant evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: inferred from biological aspect of descendant
  type: Synonym
  has db xref: GOECO:IBD
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IBD

phylogenetic determination of loss of key residues evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: phylogenetic determination of loss of key residues evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: phylogenetic determination of loss of key residues evidence
has OBO namespace: evidence_code2.obo
has exact synonym: inferred from key residues
  type: Synonym
  has db xref: GOECO:IKR
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IKR
has db xref: GOECO:IMR
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IMR
has db xref: GOECO:IKR
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IKR
has exact synonym: inferred from missing residues
  type: Synonym
  has db xref: GOECO:IKR
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IKR
has definition: A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: IMR
  type: Synonym
  has db xref: GOECO:IKR
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IKR
has exact synonym: IKR
  type: Synonym
  has db xref: GOECO:IKR
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IKR

rapid divergence from ancestral sequence evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: rapid divergence from ancestral sequence evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: rapid divergence from ancestral sequence evidence
has OBO namespace: evidence_code2.obo
has definition: A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: IRD
  type: Synonym
  has db xref: GOECO:IRD
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IRD
has db xref: GOECO:IRD
  type: DbXref
  has URI: http://purl.org/obo/owl/GOECO#GOECO_IRD
has exact synonym: inferred from rapid divergence
  type: Synonym
  has db xref: GOECO:IRD
    type: DbXref
    has URI: http://purl.org/obo/owl/GOECO#GOECO_IRD

imported manually asserted information used in automatic assertion
type: Class
subclass of: imported information used in automatic assertion
has OBO namespace: evidence_code2.obo
has definition: Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

imported automatically asserted information used in automatic assertion
type: Class
subclass of: imported information used in automatic assertion
has OBO namespace: evidence_code2.obo
has definition: Evidence that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

imaging assay evidence
type: Class
subclass of: direct assay evidence
has OBO namespace: evidence_code2.obo
has definition: Direct assay evidence derived from analysis of an image.
  type: Definition
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC

chromatography evidence
type: Class
subclass of: experimental evidence
has OBO namespace: evidence_code2.obo
has definition: Definition
  label: A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase.
  has db xref: ECO:MCC
    type: DbXref
    has URI: http://purl.org/obo/owl/ECO#ECO_MCC
has exact synonym: chromatographic evidence