Enum GOEvidenceCode

  • All Implemented Interfaces:
    Serializable, Comparable<GOEvidenceCode>

    public enum GOEvidenceCode
    extends Enum<GOEvidenceCode>
    This enumeration was originally based on GO, but is used for all entities that have evidenciary aspects; Thus it has been expanded to include: Terms from RGD (rat genome database)
    • IED = Inferred from experimental data
    • IAGP = Inferred from association of genotype and phenotype
    • IPM = Inferred from phenotype manipulation
    • QTM = Quantitative Trait Measurement
    And our own custom code IIA which means Inferred from Imported Annotation to distinguish IEAs that we ourselves have computed See https://geneontology.org/docs/guide-go-evidence-codes/ for documentation of GO evidence codes.
    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description
      EXP  
      HDA
      Inferred from High Throughput Direct Assay (HDA)
      HEP
      Inferred from High Throughput Expression Pattern (HEP)
      HGI
      Inferred from High Throughput Genetic Interaction (HGI)
      HMP
      Inferred from High Throughput Mutant Phenotype (HMP)
      HTP
      Inferred from High Throughput Experiment (HTP)
      IAGP
      Inferred from association of genotype and phenotype (RGD code)
      IBA
      A type of phylogenetic evidence whereby an aspect of a descendant is inferred through the characterization of an aspect of a ancestral gene.
      IBD
      A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
      IC  
      IDA  
      IEA  
      IED
      Inferred from experimental data (RGD code)
      IEP  
      IGC
      Inferred from Genomic Context; This evidence code can be used whenever information about the genomic context of a gene product forms part of the evidence for a particular annotation.
      IGI  
      IIA
      Added by Gemma: Inferred from Imported Annotation.
      IKR
      A type of phylogenetic evidence characterized by the loss of key sequence residues.
      IMP  
      IMR
      Inferred from Missing Residues.
      IPI  
      IPM
      Inferred from phenotype manipulation (RGD code)
      IRD
      Inferred from Rapid Divergence.
      ISA  
      ISM  
      ISO  
      ISS  
      NAS  
      ND  
      NR  
      OTHER
      Unsupported/unknown GO evidence code are mapped to this value.
      QTM
      Quantitative Trait Measurement (RGD code)
      RCA  
      TAS  
    • Enum Constant Detail

      • IGC

        public static final GOEvidenceCode IGC
        Inferred from Genomic Context; This evidence code can be used whenever information about the genomic context of a gene product forms part of the evidence for a particular annotation. Genomic context includes, but is not limited to, such things as identity of the genes neighboring the gene product in question (i.e. synteny), operon structure, and phylogenetic or other whole genome analysis. "We recommend making an entry in the with/from column when using this evidence code. In cases where operon structure or synteny are the compelling evidence, include identifier(s) for the neighboring genes in the with/from column. In casees where metabolic reconstruction is the compelling evidence, and there is an identifier for the pathway or system, that should be entered in the with/from column. When multiple entries are placed in the with/from field, they are separated by pipes."
      • IIA

        public static final GOEvidenceCode IIA
        Added by Gemma: Inferred from Imported Annotation. To be distinguished from IEA or IC, represents annotations that were present in imported data, and which have unknown evidence in the original source (though generally put there manually).
      • IBA

        public static final GOEvidenceCode IBA
        A type of phylogenetic evidence whereby an aspect of a descendant is inferred through the characterization of an aspect of a ancestral gene.
      • IBD

        public static final GOEvidenceCode IBD
        A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
      • IKR

        public static final GOEvidenceCode IKR
        A type of phylogenetic evidence characterized by the loss of key sequence residues. Annotating with this evidence codes implies a NOT annotation. This evidence code is also referred to as IMR (inferred from Missing Residues).
      • IRD

        public static final GOEvidenceCode IRD
        Inferred from Rapid Divergence. A type of phylogenetic evidence characterized by rapid divergence from ancestral sequence. Annotating with this evidence codes implies a NOT annotation.
      • IMR

        public static final GOEvidenceCode IMR
        Inferred from Missing Residues. Represents a NOT association. IMR is a synonym of IKR.
      • IED

        public static final GOEvidenceCode IED
        Inferred from experimental data (RGD code)
      • IAGP

        public static final GOEvidenceCode IAGP
        Inferred from association of genotype and phenotype (RGD code)
      • IPM

        public static final GOEvidenceCode IPM
        Inferred from phenotype manipulation (RGD code)
      • QTM

        public static final GOEvidenceCode QTM
        Quantitative Trait Measurement (RGD code)
      • HDA

        public static final GOEvidenceCode HDA
        Inferred from High Throughput Direct Assay (HDA)
      • HEP

        public static final GOEvidenceCode HEP
        Inferred from High Throughput Expression Pattern (HEP)
      • HGI

        public static final GOEvidenceCode HGI
        Inferred from High Throughput Genetic Interaction (HGI)
      • HMP

        public static final GOEvidenceCode HMP
        Inferred from High Throughput Mutant Phenotype (HMP)
      • HTP

        public static final GOEvidenceCode HTP
        Inferred from High Throughput Experiment (HTP)
      • OTHER

        public static final GOEvidenceCode OTHER
        Unsupported/unknown GO evidence code are mapped to this value.
    • Method Detail

      • values

        public static GOEvidenceCode[] values()
        Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
        for (GOEvidenceCode c : GOEvidenceCode.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static GOEvidenceCode valueOf​(String name)
        Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
        Parameters:
        name - the name of the enum constant to be returned.
        Returns:
        the enum constant with the specified name
        Throws:
        IllegalArgumentException - if this enum type has no constant with the specified name
        NullPointerException - if the argument is null