Common Sub-Domain::BiologicEntityClassification

: Public Class

Created:	11/11/2008 11:20:43 AM
Modified:	8/26/2017 2:00:31 AM

Project:
Author:
Version:	1.0
Phase:	1.0
Status:
Complexity:	Easy
Difficulty:
Priority:
Multiplicity:
Advanced:
UUID:	{B72F88C3-8F4D-4c4a-A0B6-56403A0BAB4A}
Appears In:	UML-Based Comprehensive BRIDG Model Diagram, View BSP: Biospecimen, View MB: Molecular Biology, View CM: Common, View IM: Imaging, BiologicEntity and Related Classes, DICOM SR TID 1500 BRIDG Class Diagram, Oncology & Imaging View, SDTM 3.1.3 View

DEFINITION: A group within a system of categories distinguished by structure, origin, etc. to which organisms may be assigned. [adapted from http://dictionary.reference.com/browse/classification?s=t] EXAMPLE(S): OTHER NAME(S): NOTE(S):

Attributes
Associations From
Tagged Values

Attribute

Public TN
commonName

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:LSDAMv2.2.3Plus=Organism.commonName

Notes:

DEFINITION: The generally-used term for the organism type. EXAMPLE(S): human is the common name for the species Homo sapiens OTHER NAME(S): NOTE(S):

Public CD
scientificNameCode

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:AE=Organism.species
Map:CTRv1.0=Animal.speciesCode
Map:DICOM=Patient Module - Patient Species Description (0010,2201)
Map:DICOM=TID 1007 SubjectContext,Patient > Subject Species
Map:HCTv1.0=CDE 2787415:Therapies.Specify the ALS, ALG, ATS, ATG animal source:x
Map:HCTv1.0=CDE 2787403:Therapies.Specify the ALS, ALG, ATS, ATG animal source:
Map:HCTv1.0=CDE 2960357:Therapies.What was the source of the preparative regimen medication?
Map:HCTV1.0=CDE 2960362:Therapies.What was the other source of the preparative regimen medication?
Map:HCTV1.0=CDE 2753243:Therapies.Specify the other source of the preparative regimen medication:
Map:HL7SD=Animal.code
Map:HL7SP=Animal.name
Map:LSDAMv2.2.3Plus=Organism.scientificName
Map:PGx v1.0=SB.SBNSPCES
Map:PGx v1.0=PF.PFNSPCES
Map:PGx v1.0=PB.PBNSPCES
Map:PGx v1.0=PG.PGNSPCES

Notes:

DEFINITION: A coded value specifying the scientific term for the taxon, generally, the genus and species of the organism. EXAMPLE(S): Homo Sapiens or Mus. OTHER NAME(S): NOTE(S):

Public CD
taxonomyIdentifierCode

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:DICOM=Patient Module - Patient Species Code Sequence > Code Value (0008,0100)
Map:DICOM=Patient Module - Patient Species Code Sequence (0010,2202)
Map:DICOM=Patient Module - Patient Species Code Sequence > Coding Scheme Designator (0008,0102)
Map:DICOM=Patient Module - Patient Species Code Sequence > Coding Scheme Version (0008,0103)
Map:DICOM=Patient Module - Patient Species Code Sequence > Code Meaning (0008,0104)
Map:DICOM=Patient Module - Patient Species Code Sequence > URN Code Value (0008,0120)
Map:DICOM=Patient Module - Patient Species Code Sequence > Long Code Value (0008,0119)
Map:LSDAMv2.2.3Plus=Organism.taxonomyIdentifier

Notes:

DEFINITION: A coded value specifying the stable unique identifier for the taxon from a taxonomy database. EXAMPLE(S): A taxon identifier from the National Center for Biotechnology Information (NCBI)'s Taxonomy database OTHER NAME(S): NOTE(S):

Public CD
taxonomyRankCode

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:LSDAMv2.2.3Plus=Organism.taxonomyRange

Notes:

DEFINITION: A coded value specifying the name of the node in a taxonomic tree. EXAMPLE(S): genus, species OTHER NAME(S): NOTE(S):

Public DSET<CD>
synonymCode

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to *
Transient:	False
Derived:	False
IsID:	False

Map:LSDAMv2.2.3Plus=AdditionalOrganismName.source
Map:LSDAMv2.2.3Plus=Organism.(AdditionalOrganismName)
Map:LSDAMv2.2.3Plus=AdditionalOrganismName.value
Map:LSDAMv2.2.3Plus=AdditionalOrganism.value

Notes:

DEFINITION: A coded value specifying an alternate common or scientific name by which the biologic entity classification is known. EXAMPLE(S): Mus muscaris (as a misnomer for "Mus musculus") as a coded value coming from NCBI Taxonomy Database OTHER NAME(S): NOTE(S):

Public CD
breedCode

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:AE=Animal.breed
Map:CTRv1.0=Animal.breedCode
Map:DICOM=Patient Module - Patient Breed Description (0010,2292)
Map:DICOM=Patient Module - Patient Breed Code Sequence (0010,2293)
Map:DICOM=TID 1007 SubjectContext,Patient > Subject Breed
Map:LSDAMv2.2.3Plus=Animal.breedCode

Notes:

DEFINITION: A coded value specifying a group of animals presumably related by descent from common ancestors and visibly similar in most characteristics. EXAMPLE(S): Holstein, Angora, Himalayan cat, Labrador Retriever OTHER NAME(S): NOTE(S):

Public SC
strain

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:CTRv1.0=Animal.strain
Map:DICOM=Patient Module - Strain Nomenclature (0010,0213)
Map:DICOM=Patient Module - Strain Description (0010,0212)
Map:DICOM=Patient Module - Strain Code Sequence (0010,0219)
Map:HL7SP=Animal.strainText
Map:LSDAMv2.2.3Plus=BiologicEntity.subSpeciesRank
Map:PGx v1.0=SB.SBNSTRN
Map:PGx v1.0=PB.PBNSTRN
Map:PGx v1.0=PG.PGNSTRN
Map:PGx v1.0=PF.PFNSTRN

Notes:

DEFINITION: The text (and optional code) specifying a group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions. EXAMPLE(S): Minnesota5 (swine strain), DXL (poultry strain) For DICOM’s Strain Code Sequence (0010,0219): string = “C57BL/6J”, code = “3028467”. For DICOM's Strain Nomenclature (0010,0213): codeSystem(OID).extension = "MGI_2013", codeSystem(OID).root = #lt;OID for DICOM assigned terms for strain nomenclature#gt; OTHER NAME(S): NOTE(S): The specific genotypic or phenotypic variant of an animal, microorganism, fungus, or pathogen. DICOM defines this to be a group of animals that are genetically uniform.

Public ST
strainComment

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:
Transient:	False
Derived:	False
IsID:	False

Map:DICOM=Patient Module - Strain Additional Information (0010,0216)

Notes:

DEFINITION: Additional information about the strain. EXAMPLE(S): "Athymic nude" mouse which is not described by the nomenclature of "NCr-nu/nu“ OTHER NAME(S): Strain Additional Information NOTE(S):

Public II
strainStockIdentifier

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:
Transient:	False
Derived:	False
IsID:	False

Map:DICOM=Patient Module - Strain Stock Sequence > Strain Stock Number (0010,0214)
Map:DICOM=Patient Module - Strain Stock Sequence > Strain Source (0010,0217)

Notes:

DEFINITION: A unique symbol that establishes the identity of the sub-population of the strain as obtained from a particular source. EXAMPLE(S): II.extension = 000664 II.root = #lt;OID for Jrep#gt; OTHER NAME(S): Strain Stock Sequence NOTE(S):

Public BL
nonHostIndicator

Details:

Alias:
Initial:
Stereotype:
Ordered:
Range:	Range:0 to 1
Transient:	False
Derived:	False
IsID:	False

Map:PGx v1.0=PF.PFNSPCES
Map:PGx v1.0=PG.PGNSPCES

Notes:

DEFINITION: Specifies whether the biologic entity is an organism that is harbored or nourished by another organism (i.e. whether it is a parasite). EXAMPLE(S): OTHER NAME(S): NOTE(S): This concept does not include offspring.

Element	Source Role	Target Role
Genome Class	Name: containedGenome	Name: containingBiologicEntityClassification
Details: DESCRIPTION:<br/>Each Genome always is part of one BiologicEntityClassification. Each BiologicEntityClassification might contain one or more Genome. <br/><br/>DEFINITION:<br/><br/>EXAMPLE(S):<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
Biologic Class	Name: classifiedBiologic	Name: classifyingBiologicEntityClassification
Details: DESCRIPTION:<br/>Each Biologic might be classified as one BiologicEntityClassification. Each BiologicEntityClassification might classify one or more Biologic.<br/><br/>DEFINITION:<br/><br/>EXAMPLE(S):<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
Pathway Class	Name: includedPathway	Name: includingBiologicEntityClassification
Details: DESCRIPTION:<br/>Each Pathway might be included by one or more BiologicEntityClassification. Each BiologicEntityClassification might include one or more Pathway.<br/><br/>DEFINITION:<br/><br/>EXAMPLE(S):<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
MolecularSequence Class	Name: includedMolecularSequence	Name: includingBiologicEntityClassification
Details: DESCRIPTION:<br/>Each MolecularSequence always is included in one BiologicEntityClassification. Each BiologicEntityClassification might include one or more MolecularSequence.<br/><br/>DEFINITION:<br/><br/>EXAMPLE(S):<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
BiologicEntity Class	Name: classifiedBiologicEntity	Name: classifyingBiologicEntityClassification
Details: DESCRIPTION:<br/>Each BiologicEntity always is classified as one BiologicEntityClassification. Each BiologicEntityClassification might classify one or more BiologicEntity.<br/><br/>DEFINITION:<br/><br/>EXAMPLE(S):<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
Chromosome Class	Name: containedChromosome	Name: containingBiologicEntityClassification
Details: DESCRIPTION:<br/>Each Chromosome always is part of one BiologicEntityClassification. Each BiologicEntityClassification might contain one or more Chromosome.<br/><br/>DEFINITION:<br/><br/>EXAMPLE(S):<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>

Tag	Value
Map:LSDAMv2.2.3Plus	Organism
Details: