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Agent

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Agent

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

EVSId

data type: string

NSCNumber

data type: long

bigid

data type: string

comment

data type: string

id

data type: long

isCMAPAgent

data type: boolean

name

data type: string

source

data type: string

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:

Instance of "ClinicalTrialProtocol":

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

Instance of "Target":

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

Anomaly

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Anomaly

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

bigid

data type: string

description

data type: string

id

data type: long

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:

Collection of "Histopathology":

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

Instance of "OrganOntology":

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

Instance of "Vocabulary":

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

Chromosome

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Chromosome

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

bigid

data type: string

id

data type: long

number

data type: string

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:

Instance of "Gene":

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

Instance of "Location":

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

Collection of "Taxon":

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

ClinicalTrialProtocol

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of ClinicalTrialProtocol

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

NIHAdminCode

data type: string

PDQIdentifier

data type: string

PIName

data type: string

bigid

data type: string

currentStatus

data type: string

currentStatusDate

data type: dateTime

documentNumber

data type: string

id

data type: long

leadOrganizationId

data type: string

leadOrganizationName

data type: string

participationType

data type: string

phase

data type: string

title

data type: string

treatmentFlag

data type: string

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:

Instance of "Agent":

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

Instance of "DiseaseOntology":

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

Instance of "Histopathology":

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

Instance of "ProtocolAssociation":

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

Clone

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Clone

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

bigid

data type: string

id

data type: long

insertSize

data type: long

name

data type: string

type

data type: string

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:

Instance of "CloneRelativeLocation":

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

Collection of "Library":

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

Instance of "NucleicAcidSequence":

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

Instance of "Taxon":

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

CloneRelativeLocation

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of CloneRelativeLocation

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

bigid

data type: string

id

data type: long

type

data type: string

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:

Collection of "Clone":

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

Collection of "NucleicAcidSequence":

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

Cytoband

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Cytoband

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

bigid

data type: string

id

data type: long

name

data type: string

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:

Collection of "PhysicalLocation":

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

CytogeneticLocation

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

ABSTRACT

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

CytogeneticLocation extends from domain object "Location".

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of CytogeneticLocation

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

bigid

data type: string

endCytobandLocId

data type: long

startCytobandLocId

data type: long

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:

Collection of "EndCytoband":

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

Collection of "StartCytoband":

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

DiseaseOntology

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of DiseaseOntology

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

bigid

data type: string

id

data type: long

name

data type: string

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:

Instance of "ChildDiseaseOntologyRelationship":

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

Instance of "ClinicalTrialProtocol":

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

Instance of "Histopathology":

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

Instance of "ParentDiseaseOntologyRelationship":

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

DiseaseOntologyRelationship

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of DiseaseOntologyRelationship

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

bigid

data type: string

id

data type: long

type

data type: string

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:

Collection of "ChildDiseaseOntology":

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

Collection of "ParentDiseaseOntology":

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

Gene

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Gene

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

bigid

data type: string

clusterId

data type: long

fullName

data type: string

id

data type: long

symbol

data type: string

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:

Collection of "Chromosome":

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

Instance of "DatabaseCrossReference":

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

Instance of "GeneAlias":

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

Instance of "GeneOntology":

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

Instance of "GeneRelativeLocation":

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

Instance of "GenericReporter":

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

Instance of "Histopathology":

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

Instance of "HomologousAssociation":

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

Instance of "Library":

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

Instance of "Location":

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

Instance of "NucleicAcidSequence":

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

Instance of "OrganOntology":

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

Instance of "Pathway":

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

Instance of "Protein":

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

Instance of "Target":

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

Collection of "Taxon":

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

GeneAlias

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of GeneAlias

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

bigid

data type: string

id

data type: long

name

data type: string

type

data type: string

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:

Instance of "Gene":

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

GeneOntology

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of GeneOntology

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

bigid

data type: string

id

data type: long

name

data type: string

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:

Instance of "ChildGeneOntologyRelationship":

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

Instance of "Gene":

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

Instance of "ParentGeneOntologyRelationship":

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

GeneOntologyRelationship

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of GeneOntologyRelationship

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

bigid

data type: string

id

data type: long

relationshipType

data type: string

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:

Collection of "ChildGeneOntology":

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

Collection of "ParentGeneOntology":

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

GeneRelativeLocation

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of GeneRelativeLocation

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

bigid

data type: string

id

data type: long

type

data type: string

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:

GenericArray

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of GenericArray

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

arrayName

data type: string

bigid

data type: string

id

data type: long

platform

data type: string

type

data type: string

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:

Instance of "GenericReporter":

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

GenericReporter

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of GenericReporter

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

bigid

data type: string

id

data type: long

name

data type: string

type

data type: string

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:

Collection of "Gene":

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

Instance of "GenericArray":

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

Histopathology

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Histopathology

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

ageOfOnset

data type: string

comments

data type: string

grossDescription

data type: string

id

data type: long

microscopicDescription

data type: string

relationalOperation

data type: string

survivalInfo

data type: string

tumorIncidenceRate

data type: float

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:

Instance of "Anomaly":

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

Instance of "ClinicalTrialProtocol":

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

Collection of "DiseaseOntology":

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

Instance of "Gene":

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

Instance of "Library":

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

Instance of "Metastasis":

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

Collection of "OrganOntology":

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

HomologousAssociation

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of HomologousAssociation

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

bigid

data type: string

homologousId

data type: long

id

data type: long

similarityPercentage

data type: float

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:

Collection of "HomologousGene":

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

Library

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Library

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

bigid

data type: string

cloneProducer

data type: string

cloneVector

data type: string

cloneVectorType

data type: string

clonesToDate

data type: long

creationDate

data type: dateTime

description

data type: string

id

data type: long

keyword

data type: string

labHost

data type: string

name

data type: string

rsite1

data type: string

rsite2

data type: string

sequencesToDate

data type: long

type

data type: string

uniGeneId

data type: long

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:

Instance of "Clone":

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

Instance of "Gene":

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

Instance of "Histopathology":

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

Collection of "Protocol":

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

Collection of "Tissue":

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

Location

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Location

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

id

data type: long

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:

Collection of "SNP":

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

Collection of "Chromosome":

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

Collection of "Gene":

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

Collection of "NucleicAcidSequence":

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

NucleicAcidSequence

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of NucleicAcidSequence

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

accessionNumber

data type: string

accessionNumberVersion

data type: string

bigid

data type: string

id

data type: long

length

data type: long

type

data type: string

value

data type: string

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:

Collection of "CloneRelativeLocation":

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

Instance of "DatabaseCrossReference":

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

Instance of "Gene":

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

Instance of "Location":

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

OrganOntology

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of OrganOntology

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

bigid

data type: string

id

data type: long

name

data type: string

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:

Instance of "Anomaly":

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

Instance of "ChildOrganOntologyRelationship":

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

Instance of "Gene":

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

Instance of "Histopathology":

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

Instance of "ParentOrganOntologyRelationship":

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

OrganOntologyRelationship

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of OrganOntologyRelationship

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

bigid

data type: string

id

data type: long

type

data type: string

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:

Collection of "ChildOrganOntology":

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

Collection of "ParentOrganOntology":

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

Pathway

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Pathway

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

bigid

data type: string

description

data type: string

diagram

data type: string

displayValue

data type: string

id

data type: long

name

data type: string

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:

Instance of "Gene":

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

Instance of "Histopathology":

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

Collection of "Taxon":

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

PhysicalLocation

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

ABSTRACT

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

PhysicalLocation extends from domain object "Location".

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of PhysicalLocation

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

chromosomalEndPosition

data type: long

chromosomalStartPosition

data type: long

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:

Instance of "Cytoband":

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

PopulationFrequency

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of PopulationFrequency

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

bigid

data type: string

ethnicity

data type: string

id

data type: long

majorAllele

data type: string

majorFrequency

data type: double

minorAllele

data type: string

minorFrequency

data type: double

type

data type: string

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:

Collection of "SNP":

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

Protein

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Protein

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

bigid

data type: string

copyrightStatement

data type: string

id

data type: long

name

data type: string

primaryAccession

data type: string

uniProtCode

data type: string

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:

Instance of "Gene":

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

Instance of "Keywords":

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

Instance of "ProteinAlias":

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

Collection of "ProteinSequence":

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

Instance of "SecondaryAccession":

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

Instance of "Taxon":

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

ProteinAlias

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of ProteinAlias

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

bigid

data type: string

id

data type: long

name

data type: string

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:

Instance of "Protein":

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

ProteinSequence

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of ProteinSequence

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

bigid

data type: string

checkSum

data type: string

id

data type: long

length

data type: long

molecularWeightInDaltons

data type: double

value

data type: string

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:

Collection of "Protein":

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

Protocol

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Protocol

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

bigid

data type: string

description

data type: string

id

data type: long

name

data type: string

type

data type: string

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:

Instance of "Library":

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

Instance of "Tissue":

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

ProtocolAssociation

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of ProtocolAssociation

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

CTEPNAME

data type: string

IMTCODE

data type: long

bigid

data type: string

diseaseCategory

data type: string

diseaseSubCategory

data type: string

id

data type: long

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:

Collection of "ClinicalTrialProtocol":

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

Collection of "DiseaseOntology":

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

SNP

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of SNP

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

DBSNPID

data type: string

alleleA

data type: string

alleleB

data type: string

bigid

data type: string

id

data type: long

validationStatus

data type: string

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:

Instance of "DatabaseCrossReference":

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

Instance of "GeneRelativeLocation":

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

Instance of "Location":

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

Instance of "PopulationFrequency":

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

Target

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Target

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

bigid

data type: string

id

data type: long

name

data type: string

type

data type: string

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:

Instance of "Agent":

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

Instance of "Anomaly":

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

Instance of "Gene":

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

Taxon

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Taxon

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

abbreviation

data type: string

bigid

data type: string

commonName

data type: string

ethnicityStrain

data type: string

id

data type: long

scientificName

data type: string

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:

Instance of "Chromosome":

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

Instance of "Clone":

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

Instance of "Gene":

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

Instance of "Pathway":

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

Instance of "Protein":

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

Instance of "Tissue":

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

Tissue

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Tissue

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

cellLine

data type: string

cellType

data type: string

description

data type: string

developmentalStage

data type: string

histology

data type: string

id

data type: long

name

data type: string

organ

data type: string

sex

data type: string

supplier

data type: string

type

data type: string

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:

Instance of "Library":

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

Collection of "Protocol":

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

Collection of "Taxon":

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

Vocabulary

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

ABSTRACT

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

SYNOPSIS

See CaCORE::ApplicationService.

DESCRIPTION

ATTRIBUTES of Vocabulary

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

bigid

data type: string

coreTerm

data type: string

generalTerm

data type: string

id

data type: long

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:

Instance of "Anomaly":

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

SUPPORT

Please do not contact author directly. Send email to ncicb@pop.nci.nih.gov to request support or report a bug.

AUTHOR

Shan Jiang <jiangs@mail.nih.gov>

COPYRIGHT AND LICENSE

The CaCORE Software License, Version 1.0

Copyright 2001-2005 SAIC. This software was developed in conjunction with the National Cancer Institute, and so to the extent government employees are co-authors, any rights in such works shall be subject to Title 17 of the United States Code, section 105. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the disclaimer of Article 5, below. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the disclaimer of Article 5 in the documentation and/or other materials provided with the distribution.

  2. The end-user documentation included with the redistribution, if any, must include the following acknowledgment: "This product includes software developed by SAIC and the National Cancer Institute." If no such end-user documentation is to be included, this acknowledgment shall appear in the software itself, wherever such third-party acknowledgments normally appear.

  3. The names "The National Cancer Institute", "NCI" and "SAIC" must not be used to endorse or promote products derived from this software. This license does not authorize the licensee to use any trademarks owned by either NCI or SAIC.

  4. This license does not authorize or prohibit the incorporation of this software into any third party proprietary programs. Licensee is expressly made responsible for obtaining any permission required to incorporate this software into third party proprietary programs and for informing licensee's end-users of their obligation to secure any required permissions before incorporating this software into third party proprietary software programs.

  5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE) ARE DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE, SAIC, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.