Package ubic.gemma.model.expression.biomaterial

Class BioMaterial

  • All Implemented Interfaces:
    gemma.gsec.model.Securable, gemma.gsec.model.SecuredChild, Serializable, Describable, Identifiable
    @Indexed
public class BioMaterial
extends AbstractDescribable
implements gemma.gsec.model.SecuredChild, Serializable
    In MAGE, BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... In MAGE, Biomaterial subclasses such as BioSample and BioSource can be related to other biomaterial through a directed acyclic graph (represented by treatment(s)). In our implementation, we don't care so much about the experimental procedures and we just lump all of the BioMaterial into one class.
    See Also:
    Serialized Form

    • Constructor Detail

      • BioMaterial

        public BioMaterial()

    • Method Detail

      • getName

        @Field
public String getName()
        Description copied from interface: Describable
        Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.
        Specified by:
        getName in interface Describable
        Overrides:
        getName in class AbstractDescribable

      • getBioAssaysUsedIn

        @ContainedIn
public Set<BioAssay> getBioAssaysUsedIn()

      • setBioAssaysUsedIn

        public void setBioAssaysUsedIn​(Set<BioAssay> bioAssaysUsedIn)

      • getCharacteristics

        @IndexedEmbedded
public Set<Characteristic> getCharacteristics()

      • setCharacteristics

        public void setCharacteristics​(Set<Characteristic> characteristics)

      • getExternalAccession

        @IndexedEmbedded
public DatabaseEntry getExternalAccession()
        Returns:
        An optional external reference for this BioMaterial. In many cases this is the same as the accession for the related BioAssay. We store the information here to help make the data easier to trace. Note that more than one BioMaterial may reference a given external accession.

      • setExternalAccession

        public void setExternalAccession​(DatabaseEntry externalAccession)

      • getFactorValues

        @IndexedEmbedded
public Set<FactorValue> getFactorValues()
        Returns:
        The values that this BioAssay is associated with for the experiment.

      • setFactorValues

        public void setFactorValues​(Set<FactorValue> factorValues)

      • getSecurityOwner

        public gemma.gsec.model.Securable getSecurityOwner()
        Specified by:
        getSecurityOwner in interface gemma.gsec.model.SecuredChild

      • getSourceTaxon

        public Taxon getSourceTaxon()

      • setSourceTaxon

        public void setSourceTaxon​(Taxon sourceTaxon)

      • setTreatments

        public void setTreatments​(Set<Treatment> treatments)