Specimen

: Public Class

Created:	8/8/2006 2:22:28 PM
Modified:	3/25/2015 9:58:43 PM

Project:
Author:	BRIDG SCC
Version:	1.0
Phase:	1.0
Status:
Complexity:	Easy
Difficulty:
Priority:
Multiplicity:
Advanced:
UUID:	{2D175F44-7249-4f42-B967-BDD5FBE0CDE6}
Appears In:	UML-Based Comprehensive BRIDG Model Diagram, View BSP: Biospecimen, View PR: Protocol Representation, View SC: Study Conduct

DEFINITION: A substance or portion of material originally obtained from an entity for use in testing, examination, or study. EXAMPLE(S): Blood obtained by a specimen collection activity performed on a study subject. A few grains of cattle feed obtained from a feed sack. A randomly selected pill from a blister pack. A serum specimen that resulted from Centrifugation procedure performed on a blood specimen. A DNA specimen extraction from a saliva specimen. A Formalin-Fixed, Paraffin-Embedded (FFPE) block that resulted from a paraffin embedding procedure performed on a formalin fixed tissue specimen. A pooled blood sample that resulted from a mixing procedure performed on several blood samples taken from individual animals. OTHER NAME(S): Biologic specimen Product specimen NOTE(S):

Attributes
Associations To
Associations From
Tagged Values
Other Links

Attribute

Public DSET<CD>
conditionCode

Details:

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

Map:CDASHv1.1=LB.LBSPCCND
Map:CTRv1.0=Specimen.conditionCode
Map:Lab=Specimen.condition
Map:LabViewer2.2=Specimen.condition
Map:NCI CRF Standard=CDE 2829883v1.0: Laboratory Specimen Condition Gross Type
Map:PGx v1.0=BS.BSSPCCND
Map:SDTM IGv3.1.1=LB.LBSPCCND
Map:SDTM IGv3.1.2=PC.PCSPCCND
Map:SDTM IGv3.1.2=MB.MBSPCCND
Map:SDTM IGv3.1.2=LB.LBSPCCND

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;A coded value specifying one of a discreet list of values describing the condition of the specimen at time of receipt at the lab.#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;Hemolyzed, Icteric, Lipemic#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;Derived from PerformedObservationResult.value(ANY=#gt;CD).code WHERE PerformedObservationResult #gt; PerformedObservation #gt; DefinedObservation.nameCode = "assess specimen condition"#lt;br /#gt;#lt;/p#gt;

Public ST.SIMPLE
accessionNumberText

Details:

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

Map:CDASHv1.1=LB.LBREFID
Map:CTRv1.0=Specimen.accessionNumberText
Map:Lab=Specimen.accessionNumber
Map:LabViewer2.2=Specimen.accessionNumber
Map:NCI CRF Standard=CDE 2230047v4.0: Specimen Accession Number
Map:SDTM IGv3.1.2=LB.LBREFID

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;An alphanumeric identifier assigned by a receiving lab to specimens that are received together as a set.#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;Derived from SpecimenCollectionGroup.accessionNumberText if the specimen is part of a SpecimenCollectionGroup#lt;br /#gt;#lt;/p#gt;

Public CD
typeCode

Details:

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

Map:CTRv1.0=Specimen.typeCode
Map:ICSRr2=Specimen.code (in R_Specimen universal)

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;A coded value specifying the kind of the specimen derived from other specimens.#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;EXAMPLE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;specimen, aliquot, isolate#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;OTHER NAME(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;#lt;br /#gt;#lt;/p#gt;#lt;p#gt;NOTE(S):#lt;br /#gt;#lt;/p#gt;#lt;p#gt;The semantic represented by the Specimen.typeCode attribute has been clarified by the LSDAM team during harmonization of the LS DAM v2.2.3Plus model. The semantic actually is an identification of the kind of activity that produced the Specimen, which means it maps to PerformedMaterialProcessStep #gt; DefineMaterialProcessStep.nameCode. Therefore, the Specimen.typeCode attribute is DEPRECATED. #lt;br /#gt;#lt;/p#gt;

Element	Source Role	Target Role
PerformedSpecimenCollection Class	Name: producedSpecimen	Name: producingPerformedSpecimenCollection
Details: DESCRIPTION:<br /></p><p>Each Specimen might be a result of one PerformedSpecimenCollection. Each PerformedSpecimenCollection might result in one or more Specimen.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
SpecimenCollectionGroup Class	Name: containedSpecimen	Name: containingSpecimenCollectionGroup
Details: DESCRIPTION:<br /></p><p>Each Specimen might be a part of one SpecimenCollectionGroup. Each SpecimenCollectionGroup might contain one or more Specimen.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
Material Class	Name: performedSpecimen	Name: performingMaterial
Details: DESCRIPTION:<br /></p><p>Each Specimen always is a function performed by one Material. Each Material might function as one Specimen.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>

Element	Source Role	Target Role
DefinedSpecimenCollection Class	Name: producingDefinedSpecimenCollection	Name: producedSpecimen
Details: DESCRIPTION:<br /></p><p>Each DefinedSpecimenCollection always results in one or more Specimen. Each Specimen might be a result of one or more DefinedSpecimenCollection.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
ExperimentalUnit Class	Name: performedExperimentalUnit	Name: performingSpecimen
Details: DESCRIPTION:<br /></p><p>Each ExperimentalUnit might be a function performed by one Specimen. Each Specimen might function as one or more ExperimentalUnit. <br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
Subject Class	Name: performedSubject	Name: performingSpecimen
Details: DESCRIPTION:<br /></p><p>Each Subject might be a function performed by one Specimen. Each Specimen might function as one or more Subject.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>
DefinedMaterialStorage Class «DEPRECATED»	Name: storingDefinedSpecimenStorage	Name: storedSpecimen
Details: DESCRIPTION:<br /></p><p>Each DefinedMaterialStorage always stores one Specimen. Each Specimen might be stored during one or more DefinedMaterialStorage.<br /></p><p><br /></p><p>DEFINITION:<br /></p><p><br /></p><p>EXAMPLE(S):<br /></p><p><br /></p><p>OTHER NAME(S):<br /></p><p><br /></p><p>NOTE(S):<br /></p>

Tag	Value
Map:CTRPv1.0	Material
Details:
Map:CTRRr3	BiologicSpecimen
Details:
Map:CTRv1.0	Specimen
Details:
Map:ICSRr2	Specimen (in R_Specimen universal)
Details:
Map:ICSRr2	Product (in R_Specimen universal)
Details:
Map:LabViewer2.2	Specimen
Details:

Object	Type	Connection	Direction	Notes
BiologicSpecimen	Class	Generalization	From	DESCRIPTION: Each BiologicSpecimen always specializes one Specimen. Each Specimen might be specialized by one BiologicSpecimen. DEFINITION: EXAMPLE(S): OTHER NAME(S): NOTE(S):