Package ubic.gemma.model.association

Enum GOEvidenceCode

java.lang.Object
java.lang.Enum<GOEvidenceCode>
ubic.gemma.model.association.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
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static GOEvidenceCode
    valueOf(String name)
    Returns the enum constant of this type with the specified name.
    static GOEvidenceCode[]
    values()
    Returns an array containing the constants of this enum type, in the order they are declared.

    Methods inherited from class java.lang.Enum

    clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

    Methods inherited from class java.lang.Object

    getClass, notify, notifyAll, wait, wait, wait

  • Enum Constant Details

    • IC

      public static final GOEvidenceCode IC

    • IDA

      public static final GOEvidenceCode IDA

    • IEA

      public static final GOEvidenceCode IEA

    • IEP

      public static final GOEvidenceCode IEP

    • IGI

      public static final GOEvidenceCode IGI

    • IMP

      public static final GOEvidenceCode IMP

    • IPI

      public static final GOEvidenceCode IPI

    • ISS

      public static final GOEvidenceCode ISS

    • NAS

      public static final GOEvidenceCode NAS

    • ND

      public static final GOEvidenceCode ND

    • RCA

      public static final GOEvidenceCode RCA

    • TAS

      public static final GOEvidenceCode TAS

    • NR

      public static final GOEvidenceCode NR

    • EXP

      public static final GOEvidenceCode EXP

    • ISA

      public static final GOEvidenceCode ISA

    • ISM

      public static final GOEvidenceCode ISM

    • 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."

    • ISO

      public static final GOEvidenceCode ISO

    • 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 Details

    • values

      public static GOEvidenceCode[] values()
      Returns an array containing the constants of this enum type, in the order they are declared.
      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