Taxon

CaCORE::CaBIO::Taxon - Perl extension for Taxon.

Abstract

The CaCORE::CaBIO::Taxon is a Perl object representation of the caBIO Taxon object.

Description

An object representing the various names (scientific, common, abbreviated, etc.) for a species associated with a specific instance of a Gene, Chromosome, Pathway, Protein, or Tissue.

Attributes of Taxon

The following are all the attributes of the Taxon object and their data types:

scientificName

data type: string

ethnicityStrain

data type: string

abbreviation

data type: string

commonName

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Taxon

The following are all the objects that are associated with the Taxon:

Gene:

One to many assoication, use getGeneCollection to get a collection of associated Gene.

Protein:

One to many assoication, use getProteinCollection to get a collection of associated Protein.

Pathway:

One to many assoication, use getPathwayCollection to get a collection of associated Pathway.

Tissue:

One to many assoication, use getTissueCollection to get a collection of associated Tissue.

Chromosome:

One to many assoication, use getChromosomeCollection to get a collection of associated Chromosome.

Clone:

One to many assoication, use getCloneCollection to get a collection of associated Clone.

  End Associations and related methods


Agent

CaCORE::CaBIO::Agent - Perl extension for Agent.

Abstract

The CaCORE::CaBIO::Agent is a Perl object representation of the caBIO Agent object.

Description

A therapeutic agent (drug, intervention therapy) used in a clinical trail protocol.

Attributes of Agent

The following are all the attributes of the Agent object and their data types:

isCMAPAgent

data type: boolean

comment

data type: string

source

data type: string

NSCNumber

data type: long

name

data type: string

EVSId

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Agent

The following are all the objects that are associated with the Agent:

Target:

One to many assoication, use getTargetCollection to get a collection of associated Target.

ClinicalTrialProtocol:

One to many assoication, use getClinicalTrialProtocolCollection to get a collection of associated ClinicalTrialProtocol.

  End Associations and related methods


Chromosome

CaCORE::CaBIO::Chromosome - Perl extension for Chromosome.

Abstract

The CaCORE::CaBIO::Chromosome is a Perl object representation of the caBIO Chromosome object.

Description

An object representing a specific chromosome for a specific taxon; provides access to all known genes contained in the chromosome and to the taxon.

Attributes of Chromosome

The following are all the attributes of the Chromosome object and their data types:

id

data type: long

number

data type: string

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Chromosome

The following are all the objects that are associated with the Chromosome:

Taxon:

Many to one assoication, use getTaxon to get the associated Taxon.

Gene:

One to many assoication, use getGeneCollection to get a collection of associated Gene.

Location:

One to many assoication, use getLocationCollection to get a collection of associated Location.

  End Associations and related methods


Gene

CaCORE::CaBIO::Gene - Perl extension for Gene.

Abstract

The CaCORE::CaBIO::Gene is a Perl object representation of the caBIO Gene object.

Description

Gene objects are the effective portal to most of the genomic information provided by the caBIO data services; organs, diseases, chromosomes, pathways, sequence data, and expression experiments are among the many objects accessible via a gene.

Attributes of Gene

The following are all the attributes of the Gene object and their data types:

id

data type: long

clusterId

data type: long

symbol

data type: string

fullName

data type: string

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Gene

The following are all the objects that are associated with the Gene:

GeneOntology:

One to many assoication, use getGeneOntologyCollection to get a collection of associated GeneOntology.

GeneAlias:

One to many assoication, use getGeneAliasCollection to get a collection of associated GeneAlias.

Protein:

One to many assoication, use getProteinCollection to get a collection of associated Protein.

ExpressionFeature:

One to many assoication, use getExpressionFeatureCollection to get a collection of associated ExpressionFeature.

Pathway:

One to many assoication, use getPathwayCollection to get a collection of associated Pathway.

OrganOntology:

One to many assoication, use getOrganOntologyCollection to get a collection of associated OrganOntology.

Taxon:

Many to one assoication, use getTaxon to get the associated Taxon.

Library:

One to many assoication, use getLibraryCollection to get a collection of associated Library.

GeneRelativeLocation:

One to many assoication, use getGeneRelativeLocationCollection to get a collection of associated GeneRelativeLocation.

Chromosome:

Many to one assoication, use getChromosome to get the associated Chromosome.

DatabaseCrossReference:

One to many assoication, use getDatabaseCrossReferenceCollection to get a collection of associated DatabaseCrossReference.

GenericReporter:

One to many assoication, use getGenericReporterCollection to get a collection of associated GenericReporter.

Target:

One to many assoication, use getTargetCollection to get a collection of associated Target.

Histopathology:

One to many assoication, use getHistopathologyCollection to get a collection of associated Histopathology.

Location:

One to many assoication, use getLocationCollection to get a collection of associated Location.

NucleicAcidSequence:

One to many assoication, use getNucleicAcidSequenceCollection to get a collection of associated NucleicAcidSequence.

HomologousAssociation:

One to many assoication, use getHomologousAssociationCollection to get a collection of associated HomologousAssociation.

  End Associations and related methods


Vocabulary

CaCORE::CaBIO::Vocabulary - Perl extension for Vocabulary.

Abstract

The CaCORE::CaBIO::Vocabulary is a Perl object representation of the caBIO Vocabulary object.

Description

The object describes the vocabulary.

Attributes of Vocabulary

The following are all the attributes of the Vocabulary object and their data types:

generalTerm

data type: string

coreTerm

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Vocabulary

The following are all the objects that are associated with the Vocabulary:

Anomaly:

One to many assoication, use getAnomalyCollection to get a collection of associated Anomaly.

  End Associations and related methods


Protocol

CaCORE::CaBIO::Protocol - Perl extension for Protocol.

Abstract

The CaCORE::CaBIO::Protocol is a Perl object representation of the caBIO Protocol object.

Description

An object representation of the protocol used in assembling a clone library.

Attributes of Protocol

The following are all the attributes of the Protocol object and their data types:

type

data type: string

description

data type: string

name

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Protocol

The following are all the objects that are associated with the Protocol:

Library:

One to many assoication, use getLibraryCollection to get a collection of associated Library.

Tissue:

One to many assoication, use getTissueCollection to get a collection of associated Tissue.

  End Associations and related methods


Tissue

CaCORE::CaBIO::Tissue - Perl extension for Tissue.

Abstract

The CaCORE::CaBIO::Tissue is a Perl object representation of the caBIO Tissue object.

Description

A group of similar cells united to perform a specific function.

Attributes of Tissue

The following are all the attributes of the Tissue object and their data types:

type

data type: string

cellType

data type: string

histology

data type: string

id

data type: long

sex

data type: string

cellLine

data type: string

supplier

data type: string

developmentalStage

data type: string

description

data type: string

organ

data type: string

name

data type: string

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Tissue

The following are all the objects that are associated with the Tissue:

Protocol:

Many to one assoication, use getProtocol to get the associated Protocol.

Taxon:

Many to one assoication, use getTaxon to get the associated Taxon.

Library:

One to many assoication, use getLibraryCollection to get a collection of associated Library.

  End Associations and related methods


SNP

CaCORE::CaBIO::SNP - Perl extension for SNP.

Abstract

The CaCORE::CaBIO::SNP is a Perl object representation of the caBIO SNP object.

Description

An object representing a Single Nucleotide Polymorphism; provides access to the clones and the trace files from which it was identified, the two most common substitutions at that position, the offset of the SNP in the parent sequence, and a confidence score.

Attributes of SNP

The following are all the attributes of the SNP object and their data types:

alleleA

data type: string

validationStatus

data type: string

alleleB

data type: string

DBSNPID

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of SNP

The following are all the objects that are associated with the SNP:

DatabaseCrossReference:

One to many assoication, use getDatabaseCrossReferenceCollection to get a collection of associated DatabaseCrossReference.

PopulationFrequency:

One to many assoication, use getPopulationFrequencyCollection to get a collection of associated PopulationFrequency.

Location:

One to many assoication, use getLocationCollection to get a collection of associated Location.

GeneRelativeLocation:

One to many assoication, use getGeneRelativeLocationCollection to get a collection of associated GeneRelativeLocation.

  End Associations and related methods


GeneAlias

CaCORE::CaBIO::GeneAlias - Perl extension for GeneAlias.

Abstract

The CaCORE::CaBIO::GeneAlias is a Perl object representation of the caBIO GeneAlias object.

Description

This object describes the gene alias.

Attributes of GeneAlias

The following are all the attributes of the GeneAlias object and their data types:

name

data type: string

type

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of GeneAlias

The following are all the objects that are associated with the GeneAlias:

Gene:

One to many assoication, use getGeneCollection to get a collection of associated Gene.

  End Associations and related methods


Library

CaCORE::CaBIO::Library - Perl extension for Library.

Abstract

The CaCORE::CaBIO::Library is a Perl object representation of the caBIO Library object.

Description

An object representing a CGAP library; provides access to information about: the tissue sample and its method of preparation, the library protocol that was used, the clones contained in the library, and the sequence information derived from the library.

Attributes of Library

The following are all the attributes of the Library object and their data types:

type

data type: string

rsite1

data type: string

creationDate

data type: dateTime

labHost

data type: string

cloneVector

data type: string

id

data type: long

clonesToDate

data type: long

sequencesToDate

data type: long

keyword

data type: string

description

data type: string

cloneProducer

data type: string

rsite2

data type: string

cloneVectorType

data type: string

uniGeneId

data type: long

name

data type: string

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Library

The following are all the objects that are associated with the Library:

Protocol:

Many to one assoication, use getProtocol to get the associated Protocol.

Gene:

One to many assoication, use getGeneCollection to get a collection of associated Gene.

Clone:

One to many assoication, use getCloneCollection to get a collection of associated Clone.

Tissue:

Many to one assoication, use getTissue to get the associated Tissue.

Histopathology:

One to many assoication, use getHistopathologyCollection to get a collection of associated Histopathology.

  End Associations and related methods


Clone

CaCORE::CaBIO::Clone - Perl extension for Clone.

Abstract

The CaCORE::CaBIO::Clone is a Perl object representation of the caBIO Clone object.

Description

An object used to hold information pertaining to I.M.A.G.E. clones; provides access to sequence information, associated trace files, and the clone's library.

Attributes of Clone

The following are all the attributes of the Clone object and their data types:

type

data type: string

insertSize

data type: long

name

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Clone

The following are all the objects that are associated with the Clone:

Taxon:

One to many assoication, use getTaxonCollection to get a collection of associated Taxon.

CloneRelativeLocation:

One to many assoication, use getCloneRelativeLocationCollection to get a collection of associated CloneRelativeLocation.

Library:

Many to one assoication, use getLibrary to get the associated Library.

NucleicAcidSequence:

One to many assoication, use getNucleicAcidSequenceCollection to get a collection of associated NucleicAcidSequence.

  End Associations and related methods


Target

CaCORE::CaBIO::Target - Perl extension for Target.

Abstract

The CaCORE::CaBIO::Target is a Perl object representation of the caBIO Target object.

Description

A gene thought to be at the root of a disease etiology, and which is targeted for therapeutic intervention in a clinical trial.

Attributes of Target

The following are all the attributes of the Target object and their data types:

type

data type: string

name

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Target

The following are all the objects that are associated with the Target:

Gene:

One to many assoication, use getGeneCollection to get a collection of associated Gene.

Agent:

One to many assoication, use getAgentCollection to get a collection of associated Agent.

Anomaly:

One to many assoication, use getAnomalyCollection to get a collection of associated Anomaly.

  End Associations and related methods


Location

CaCORE::CaBIO::Location - Perl extension for Location.

Abstract

The CaCORE::CaBIO::Location is a Perl object representation of the caBIO Location object.

Description

Attributes of Location

The following are all the attributes of the Location object and their data types:

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Location

The following are all the objects that are associated with the Location:

SNP:

Many to one assoication, use getSNP to get the associated SNP.

Gene:

Many to one assoication, use getGene to get the associated Gene.

NucleicAcidSequence:

Many to one assoication, use getNucleicAcidSequence to get the associated NucleicAcidSequence.

Chromosome:

Many to one assoication, use getChromosome to get the associated Chromosome.

  End Associations and related methods


CloneRelativeLocation

CaCORE::CaBIO::CloneRelativeLocation - Perl extension for CloneRelativeLocation.

Abstract

The CaCORE::CaBIO::CloneRelativeLocation is a Perl object representation of the caBIO CloneRelativeLocation object.

Description

Attributes of CloneRelativeLocation

The following are all the attributes of the CloneRelativeLocation object and their data types:

type

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of CloneRelativeLocation

The following are all the objects that are associated with the CloneRelativeLocation:

Clone:

Many to one assoication, use getClone to get the associated Clone.

NucleicAcidSequence:

Many to one assoication, use getNucleicAcidSequence to get the associated NucleicAcidSequence.

  End Associations and related methods


NucleicAcidSequence

CaCORE::CaBIO::NucleicAcidSequence - Perl extension for NucleicAcidSequence.

Abstract

The CaCORE::CaBIO::NucleicAcidSequence is a Perl object representation of the caBIO NucleicAcidSequence object.

Description

An object representation of a nucleic acid sequence; provides access to the clones from which it was derived.

Attributes of NucleicAcidSequence

The following are all the attributes of the NucleicAcidSequence object and their data types:

value

data type: string

type

data type: string

length

data type: long

accessionNumber

data type: string

id

data type: long

accessionNumberVersion

data type: string

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of NucleicAcidSequence

The following are all the objects that are associated with the NucleicAcidSequence:

Gene:

One to many assoication, use getGeneCollection to get a collection of associated Gene.

DatabaseCrossReference:

One to many assoication, use getDatabaseCrossReferenceCollection to get a collection of associated DatabaseCrossReference.

Location:

Many to one assoication, use getLocation to get the associated Location.

CloneRelativeLocation:

Many to one assoication, use getCloneRelativeLocation to get the associated CloneRelativeLocation.

  End Associations and related methods


DiseaseOntology

CaCORE::CaBIO::DiseaseOntology - Perl extension for DiseaseOntology.

Abstract

The CaCORE::CaBIO::DiseaseOntology is a Perl object representation of the caBIO DiseaseOntology object.

Description

Disease objects specify a disease name and ID; disease objects also provide access to: ontological relations to other diseases; clinical trial protocols treating the disease; and specific histologies associated with instances of the disease.

Attributes of DiseaseOntology

The following are all the attributes of the DiseaseOntology object and their data types:

name

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of DiseaseOntology

The following are all the objects that are associated with the DiseaseOntology:

ParentDiseaseOntologyRelationship:

One to many assoication, use getParentDiseaseOntologyRelationshipCollection to get a collection of associated ParentDiseaseOntologyRelationship.

ChildDiseaseOntologyRelationship:

One to many assoication, use getChildDiseaseOntologyRelationshipCollection to get a collection of associated ChildDiseaseOntologyRelationship.

Histopathology:

One to many assoication, use getHistopathologyCollection to get a collection of associated Histopathology.

ClinicalTrialProtocol:

One to many assoication, use getClinicalTrialProtocolCollection to get a collection of associated ClinicalTrialProtocol.

  End Associations and related methods


ClinicalTrialProtocol

CaCORE::CaBIO::ClinicalTrialProtocol - Perl extension for ClinicalTrialProtocol.

Abstract

The CaCORE::CaBIO::ClinicalTrialProtocol is a Perl object representation of the caBIO ClinicalTrialProtocol object.

Description

The protocol associated with a clinical trial; organizes administrative information about the trial such as Organization ID, participants, phase, etc., and provides access to the administered Agents.

Attributes of ClinicalTrialProtocol

The following are all the attributes of the ClinicalTrialProtocol object and their data types:

currentStatus

data type: string

participationType

data type: string

treatmentFlag

data type: string

leadOrganizationId

data type: string

NIHAdminCode

data type: string

title

data type: string

id

data type: long

PDQIdentifier

data type: string

documentNumber

data type: string

leadOrganizationName

data type: string

phase

data type: string

PIName

data type: string

currentStatusDate

data type: dateTime

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of ClinicalTrialProtocol

The following are all the objects that are associated with the ClinicalTrialProtocol:

Agent:

One to many assoication, use getAgentCollection to get a collection of associated Agent.

ProtocolAssociation:

One to many assoication, use getProtocolAssociationCollection to get a collection of associated ProtocolAssociation.

DiseaseOntology:

One to many assoication, use getDiseaseOntologyCollection to get a collection of associated DiseaseOntology.

Histopathology:

One to many assoication, use getHistopathologyCollection to get a collection of associated Histopathology.

  End Associations and related methods


ProtocolAssociation

CaCORE::CaBIO::ProtocolAssociation - Perl extension for ProtocolAssociation.

Abstract

The CaCORE::CaBIO::ProtocolAssociation is a Perl object representation of the caBIO ProtocolAssociation object.

Description

An association class relating between Clinical Trial Protocols to Diseases.

Attributes of ProtocolAssociation

The following are all the attributes of the ProtocolAssociation object and their data types:

diseaseSubCategory

data type: string

CTEPNAME

data type: string

IMTCODE

data type: long

id

data type: long

diseaseCategory

data type: string

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of ProtocolAssociation

The following are all the objects that are associated with the ProtocolAssociation:

DiseaseOntology:

Many to one assoication, use getDiseaseOntology to get the associated DiseaseOntology.

ClinicalTrialProtocol:

Many to one assoication, use getClinicalTrialProtocol to get the associated ClinicalTrialProtocol.

  End Associations and related methods


Pathway

CaCORE::CaBIO::Pathway - Perl extension for Pathway.

Abstract

The CaCORE::CaBIO::Pathway is a Perl object representation of the caBIO Pathway object.

Description

An object representation of a molecular/cellular pathway compiled by BioCarta. Pathways are associated with specific Taxon objects, and contain multiple Gene objects, which may be Targets for treatment.

Attributes of Pathway

The following are all the attributes of the Pathway object and their data types:

description

data type: string

diagram

data type: string

name

data type: string

id

data type: long

displayValue

data type: string

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Pathway

The following are all the objects that are associated with the Pathway:

Gene:

One to many assoication, use getGeneCollection to get a collection of associated Gene.

Histopathology:

One to many assoication, use getHistopathologyCollection to get a collection of associated Histopathology.

Taxon:

Many to one assoication, use getTaxon to get the associated Taxon.

  End Associations and related methods


OrganOntology

CaCORE::CaBIO::OrganOntology - Perl extension for OrganOntology.

Abstract

The CaCORE::CaBIO::OrganOntology is a Perl object representation of the caBIO OrganOntology object.

Description

A representation of an organ whose name occurs in a controlled vocabulary; provides access to any Histopathology objects for the organ, and, because it is $quot;ontolog-able,$quot; provides access to its ancestral and descendant terms in the vocabulary.

Attributes of OrganOntology

The following are all the attributes of the OrganOntology object and their data types:

name

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of OrganOntology

The following are all the objects that are associated with the OrganOntology:

ParentOrganOntologyRelationship:

One to many assoication, use getParentOrganOntologyRelationshipCollection to get a collection of associated ParentOrganOntologyRelationship.

Gene:

One to many assoication, use getGeneCollection to get a collection of associated Gene.

ExpressionFeature:

One to many assoication, use getExpressionFeatureCollection to get a collection of associated ExpressionFeature.

Histopathology:

One to many assoication, use getHistopathologyCollection to get a collection of associated Histopathology.

ChildOrganOntologyRelationship:

One to many assoication, use getChildOrganOntologyRelationshipCollection to get a collection of associated ChildOrganOntologyRelationship.

Anomaly:

One to many assoication, use getAnomalyCollection to get a collection of associated Anomaly.

  End Associations and related methods


OrganOntologyRelationship

CaCORE::CaBIO::OrganOntologyRelationship - Perl extension for OrganOntologyRelationship.

Abstract

The CaCORE::CaBIO::OrganOntologyRelationship is a Perl object representation of the caBIO OrganOntologyRelationship object.

Description

Organ relationship object describes relationships among organs.

Attributes of OrganOntologyRelationship

The following are all the attributes of the OrganOntologyRelationship object and their data types:

type

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of OrganOntologyRelationship

The following are all the objects that are associated with the OrganOntologyRelationship:

ChildOrganOntology:

Many to one assoication, use getChildOrganOntology to get the associated ChildOrganOntology.

ParentOrganOntology:

Many to one assoication, use getParentOrganOntology to get the associated ParentOrganOntology.

  End Associations and related methods


Histopathology

CaCORE::CaBIO::Histopathology - Perl extension for Histopathology.

Abstract

The CaCORE::CaBIO::Histopathology is a Perl object representation of the caBIO Histopathology object.

Description

An object representing anatomical changes in a diseased tissue sample associated with an expression experiment; captures the relationship between organ and disease.

Attributes of Histopathology

The following are all the attributes of the Histopathology object and their data types:

comments

data type: string

relationalOperation

data type: string

tumorIncidenceRate

data type: float

ageOfOnset

data type: string

id

data type: long

microscopicDescription

data type: string

grossDescription

data type: string

survivalInfo

data type: string

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Histopathology

The following are all the objects that are associated with the Histopathology:

Metastasis:

One to many assoication, use getMetastasisCollection to get a collection of associated Metastasis.

Gene:

One to many assoication, use getGeneCollection to get a collection of associated Gene.

Library:

One to many assoication, use getLibraryCollection to get a collection of associated Library.

DiseaseOntology:

Many to one assoication, use getDiseaseOntology to get the associated DiseaseOntology.

OrganOntology:

Many to one assoication, use getOrganOntology to get the associated OrganOntology.

ClinicalTrialProtocol:

One to many assoication, use getClinicalTrialProtocolCollection to get a collection of associated ClinicalTrialProtocol.

Anomaly:

One to many assoication, use getAnomalyCollection to get a collection of associated Anomaly.

  End Associations and related methods


GeneOntology

CaCORE::CaBIO::GeneOntology - Perl extension for GeneOntology.

Abstract

The CaCORE::CaBIO::GeneOntology is a Perl object representation of the caBIO GeneOntology object.

Description

An object providing entry to a Gene object's position in the Gene Ontology Consortium's controlled vocabularies, as recorded by LocusLink; provides access to gene objects corresponding to the ontological term, as well as to ancestor and descendant terms in the ontology tree.

Attributes of GeneOntology

The following are all the attributes of the GeneOntology object and their data types:

name

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of GeneOntology

The following are all the objects that are associated with the GeneOntology:

ChildGeneOntologyRelationship:

One to many assoication, use getChildGeneOntologyRelationshipCollection to get a collection of associated ChildGeneOntologyRelationship.

Gene:

One to many assoication, use getGeneCollection to get a collection of associated Gene.

ParentGeneOntologyRelationship:

One to many assoication, use getParentGeneOntologyRelationshipCollection to get a collection of associated ParentGeneOntologyRelationship.

  End Associations and related methods


GeneOntologyRelationship

CaCORE::CaBIO::GeneOntologyRelationship - Perl extension for GeneOntologyRelationship.

Abstract

The CaCORE::CaBIO::GeneOntologyRelationship is a Perl object representation of the caBIO GeneOntologyRelationship object.

Description

This object specifies GoOntologyrRelationship.

Attributes of GeneOntologyRelationship

The following are all the attributes of the GeneOntologyRelationship object and their data types:

relationshipType

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of GeneOntologyRelationship

The following are all the objects that are associated with the GeneOntologyRelationship:

ParentGeneOntology:

Many to one assoication, use getParentGeneOntology to get the associated ParentGeneOntology.

ChildGeneOntology:

Many to one assoication, use getChildGeneOntology to get the associated ChildGeneOntology.

  End Associations and related methods


DiseaseOntologyRelationship

CaCORE::CaBIO::DiseaseOntologyRelationship - Perl extension for DiseaseOntologyRelationship.

Abstract

The CaCORE::CaBIO::DiseaseOntologyRelationship is a Perl object representation of the caBIO DiseaseOntologyRelationship object.

Description

The diseaser relationship specifies the relationship among diseases.

Attributes of DiseaseOntologyRelationship

The following are all the attributes of the DiseaseOntologyRelationship object and their data types:

type

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of DiseaseOntologyRelationship

The following are all the objects that are associated with the DiseaseOntologyRelationship:

ChildDiseaseOntology:

Many to one assoication, use getChildDiseaseOntology to get the associated ChildDiseaseOntology.

ParentDiseaseOntology:

Many to one assoication, use getParentDiseaseOntology to get the associated ParentDiseaseOntology.

  End Associations and related methods


Anomaly

CaCORE::CaBIO::Anomaly - Perl extension for Anomaly.

Abstract

The CaCORE::CaBIO::Anomaly is a Perl object representation of the caBIO Anomaly object.

Description

An irregularity in either the expression of a gene or its structure (i.e., a mutation).

Attributes of Anomaly

The following are all the attributes of the Anomaly object and their data types:

description

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Anomaly

The following are all the objects that are associated with the Anomaly:

OrganOntology:

One to many assoication, use getOrganOntologyCollection to get a collection of associated OrganOntology.

Histopathology:

Many to one assoication, use getHistopathology to get the associated Histopathology.

Vocabulary:

One to many assoication, use getVocabularyCollection to get a collection of associated Vocabulary.

  End Associations and related methods


PopulationFrequency

CaCORE::CaBIO::PopulationFrequency - Perl extension for PopulationFrequency.

Abstract

The CaCORE::CaBIO::PopulationFrequency is a Perl object representation of the caBIO PopulationFrequency object.

Description

Attributes of PopulationFrequency

The following are all the attributes of the PopulationFrequency object and their data types:

majorFrequency

data type: double

type

data type: string

minorAllele

data type: string

ethnicity

data type: string

minorFrequency

data type: double

majorAllele

data type: string

id

data type: long

  End Attributes
  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of PopulationFrequency

The following are all the objects that are associated with the PopulationFrequency:

SNP:

Many to one assoication, use getSNP to get the associated SNP.

  End Associations and related methods


ProteinSequence

CaCORE::CaBIO::ProteinSequence - Perl extension for ProteinSequence.

Abstract

The CaCORE::CaBIO::ProteinSequence is a Perl object representation of the caBIO ProteinSequence object.

Description

Attributes of ProteinSequence

The following are all the attributes of the ProteinSequence object and their data types:

checkSum

data type: string

value

data type: string

molecularWeightInDaltons

data type: double

length

data type: long

id

data type: long

  End Attributes

  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of ProteinSequence

The following are all the objects that are associated with the ProteinSequence:

Protein:

Many to one assoication, use getProtein to get the associated Protein.

  End Associations and related methods


Protein

CaCORE::CaBIO::Protein - Perl extension for Protein.

Abstract

The CaCORE::CaBIO::Protein is a Perl object representation of the caBIO Protein object.

Description

Attributes of Protein

The following are all the attributes of the Protein object and their data types:

copyrightStatement

data type: string

primaryAccession

data type: string

name

data type: string

uniProtCode

data type: string

id

data type: long

  End Attributes

  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Protein

The following are all the objects that are associated with the Protein:

Taxon:

One to many assoication, use getTaxonCollection to get a collection of associated Taxon.

Gene:

One to many assoication, use getGeneCollection to get a collection of associated Gene.

SecondaryAccession:

One to many assoication, use getSecondaryAccessionCollection to get a collection of associated SecondaryAccession.

Keywords:

One to many assoication, use getKeywordsCollection to get a collection of associated Keywords.

ProteinSequence:

Many to one assoication, use getProteinSequence to get the associated ProteinSequence.

ProteinAlias:

One to many assoication, use getProteinAliasCollection to get a collection of associated ProteinAlias.

  End Associations and related methods


ProteinAlias

CaCORE::CaBIO::ProteinAlias - Perl extension for ProteinAlias.

Abstract

The CaCORE::CaBIO::ProteinAlias is a Perl object representation of the caBIO ProteinAlias object.

Description

Attributes of ProteinAlias

The following are all the attributes of the ProteinAlias object and their data types:

name

data type: string

id

data type: long

  End Attributes

  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of ProteinAlias

The following are all the objects that are associated with the ProteinAlias:

Protein:

One to many assoication, use getProteinCollection to get a collection of associated Protein.

  End Associations and related methods


HomologousAssociation

CaCORE::CaBIO::HomologousAssociation - Perl extension for HomologousAssociation.

Abstract

The CaCORE::CaBIO::HomologousAssociation is a Perl object representation of the caBIO HomologousAssociation object.

Description

Attributes of HomologousAssociation

The following are all the attributes of the HomologousAssociation object and their data types:

similarityPercentage

data type: float

homologousId

data type: long

id

data type: long

  End Attributes

  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of HomologousAssociation

The following are all the objects that are associated with the HomologousAssociation:

HomologousGene:

Many to one assoication, use getHomologousGene to get the associated HomologousGene.

  End Associations and related methods


PhysicalLocation

CaCORE::CaBIO::PhysicalLocation - Perl extension for PhysicalLocation.

Abstract

The CaCORE::CaBIO::PhysicalLocation is a Perl object representation of the caBIO PhysicalLocation object.

Description

Attributes of PhysicalLocation

The following are all the attributes of the PhysicalLocation object and their data types:

chromosomalStartPosition

data type: long

chromosomalEndPosition

data type: long

  End Attributes

  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of PhysicalLocation

The following are all the objects that are associated with the PhysicalLocation:

Cytoband:

One to many assoication, use getCytobandCollection to get a collection of associated Cytoband.

  End Associations and related methods


Cytoband

CaCORE::CaBIO::Cytoband - Perl extension for Cytoband.

Abstract

The CaCORE::CaBIO::Cytoband is a Perl object representation of the caBIO Cytoband object.

Description

Attributes of Cytoband

The following are all the attributes of the Cytoband object and their data types:

name

data type: string

id

data type: long

  End Attributes

  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of Cytoband

The following are all the objects that are associated with the Cytoband:

PhysicalLocation:

Many to one assoication, use getPhysicalLocation to get the associated PhysicalLocation.

  End Associations and related methods


CytogeneticLocation

CaCORE::CaBIO::CytogeneticLocation - Perl extension for CytogeneticLocation.

Abstract

The CaCORE::CaBIO::CytogeneticLocation is a Perl object representation of the caBIO CytogeneticLocation object.

Description

Attributes of CytogeneticLocation

The following are all the attributes of the CytogeneticLocation object and their data types:

  End Attributes

  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of CytogeneticLocation

The following are all the objects that are associated with the CytogeneticLocation:

StartCytoband:

Many to one assoication, use getStartCytoband to get the associated StartCytoband.

EndCytoband:

Many to one assoication, use getEndCytoband to get the associated EndCytoband.

  End Associations and related methods


GeneRelativeLocation

CaCORE::CaBIO::GeneRelativeLocation - Perl extension for GeneRelativeLocation.

Abstract

The CaCORE::CaBIO::GeneRelativeLocation is a Perl object representation of the caBIO GeneRelativeLocation object.

Description

Attributes of GeneRelativeLocation

The following are all the attributes of the GeneRelativeLocation object and their data types:

type

data type: string

id

data type: long

  End Attributes

  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of GeneRelativeLocation

The following are all the objects that are associated with the GeneRelativeLocation:

  End Associations and related methods


GenericReporter

CaCORE::CaBIO::GenericReporter - Perl extension for GenericReporter.

Abstract

The CaCORE::CaBIO::GenericReporter is a Perl object representation of the caBIO GenericReporter object.

Description

Attributes of GenericReporter

The following are all the attributes of the GenericReporter object and their data types:

name

data type: string

type

data type: string

id

data type: long

  End Attributes

  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of GenericReporter

The following are all the objects that are associated with the GenericReporter:

GenericArray:

One to many assoication, use getGenericArrayCollection to get a collection of associated GenericArray.

  End Associations and related methods


GenericArray

CaCORE::CaBIO::GenericArray - Perl extension for GenericArray.

Abstract

The CaCORE::CaBIO::GenericArray is a Perl object representation of the caBIO GenericArray object.

Description

Attributes of GenericArray

The following are all the attributes of the GenericArray object and their data types:

arrayName

data type: string

platform

data type: string

type

data type: string

id

data type: long

  End Attributes

  Note: Although you can also use the corresponding setter methods to set the
  attribute values, it is not recommended to do so unless you absolutely have
  to change the object's attributes.

Associations of GenericArray

The following are all the objects that are associated with the GenericArray:

GenericReporter:

One to many assoication, use getGenericReporterCollection to get a collection of associated GenericReporter.

  End Associations and related methods