Package org.biopax.paxtools.model.level3

Interface Evidence

All Superinterfaces:
BioPAXElement, Cloneable, Level3Element, Serializable, UtilityClass, XReferrable
All Known Implementing Classes:
EvidenceImpl
public interface Evidence extends UtilityClass, XReferrable
Definition: The support for a particular assertion, such as the existence of an interaction or pathway. Usage: At least one of confidence, evidenceCode, or experimentalForm must be instantiated when creating an evidence instance. XREF may reference a publication describing the experimental evidence using a publicationXref or may store a description of the experiment in an experimental description database using a unificationXref (if the referenced experiment is the same) or relationshipXref (if it is not identical, but similar in some way e.g. similar in protocol). Evidence is meant to provide more information than just an xref to the source paper. Examples: A description of a molecular binding assay that was used to detect a protein-protein interaction.

  • Method Details

    • getConfidence

      Set<Score> getConfidence()
      Confidence in the containing instance. Usually a statistical measure.
      Returns:
      a set of scores representing confidence

    • addConfidence

      void addConfidence(Score confidence)
      Confidence in the containing instance. Usually a statistical measure.
      Parameters:
      confidence - a new confidence measure to add

    • removeConfidence

      void removeConfidence(Score confidence)
      Confidence in the containing instance. Usually a statistical measure.
      Parameters:
      confidence - a confidence measure to be removed.

    • getEvidenceCode

      Set<EvidenceCodeVocabulary> getEvidenceCode()
      A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'. Contents of this set should not be modified. Use add/remove methods instead.
      Returns:
      a set of evidence codes for this evidence type.

    • addEvidenceCode

      void addEvidenceCode(EvidenceCodeVocabulary evidenceCode)
      A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
      Parameters:
      evidenceCode - a new evidence code for this evidence.

    • removeEvidenceCode

      void removeEvidenceCode(EvidenceCodeVocabulary evidenceCode)
      A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
      Parameters:
      evidenceCode - to be removed

    • getExperimentalForm

      Set<ExperimentalForm> getExperimentalForm()
      Contents of this set should not be modified. Use add/remove methods instead.
      Returns:
      The experimental forms associated with an evidence instance.

    • addExperimentalForm

      void addExperimentalForm(ExperimentalForm experimentalForm)
      Adds an experimental form.
      Parameters:
      experimentalForm - associated with an evidence instance.

    • removeExperimentalForm

      void removeExperimentalForm(ExperimentalForm experimentalForm)
      Removes an experimental form.
      Parameters:
      experimentalForm - associated with an evidence instance.