PerformedGeneticObservation

: Public Class

Created:	3/3/2015 11:49:23 PM
Modified:	3/25/2015 4:09:53 PM

Project:
Author:	wverhoef
Version:	1.0
Phase:	1.0
Status:
Complexity:	Easy
Difficulty:
Priority:
Multiplicity:
Advanced:
UUID:	{982B6C8C-A4F5-48a7-B6D2-500FDBF8DA83}
Appears In:	UML-Based Comprehensive BRIDG Model Diagram, View MB: Molecular Biology

DEFINITION: The completed action of assessing a genetic characteristic of a biologic specimen or assessing a contextual characteristic of the genetic test itself. EXAMPLE(S): For CDISC's PG domain, Exon Sequenced, Sequence Start, Sequence Length For CDISC's PF domain, Amino Acid, Nucleotide, Allele, Observed Level, Raw Ct Value, Copy Number, Normalized Intensity 1 Value, Fold Change, New Assessment OTHER NAME(S): NOTE(S): Because of their similar attributes, observations about genetic tests themselves as well as genetic observations about specimens are both represented by this single class.

Attributes
Tagged Values
Other Links

Attribute

Public II
runIdentifier

Details:

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

Map:PGx v1.0=PF.PFRUNID
Map:PGx v1.0=PG.PGRUNID

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;A unique symbol that establishes identity of a particular execution of a test on a biospecimen.#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;The clinical genomics community is encouraged to comment on whether this is the correct data type for this concept. It is assumed that even if a RUNID is not unique across multiple labs, if that lab can be uniquely identified, then the RUNID has a namespace in which it is unique and an OID or UUID or LSID could be constructed.#lt;br /#gt;#lt;/p#gt;

Public SC
geneticRegionOfInterest

Details:

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

Map:PGx v1.0=PF.PFGENRI
Map:PGx v1.0=SB.SBGENRI

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;The portion of the genome serving as a locus for the test, often a gene. #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;EGFR, KRAS, CYP2D6, MYC, MFNG#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;These are typically obtained from the gene symbol list maintained by the Human Genome Variation Society (HGVS). This can be a gene, a protein, or a sector as described by geneticRegionTypeCode.#lt;br /#gt;#lt;/p#gt;

Public CD
geneticRegionTypeCode

Details:

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

Map:PGx v1.0=PF.PFGENTYP
Map:PGx v1.0=SB.SBGENTYP

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;A coded value specifying the kind of portion of the genome serving as a locus for the test. #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;GENE, SECTOR, DOMAIN, PROTEIN #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;

Public IVL<INT>
geneticLocationOfInterest

Details:

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

Map:PGx v1.0=PF.PFGENLI

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;The portion of the sequence that is the focus of this test or observation. #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;In CDISC's PGx domains, a PFGENLI of "34" would be 34, or "2235_2249" would be 2235-2249.#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;

Public CD
analysisMethodCode

Details:

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

Map:PGx v1.0=PF.PFANMETH

Notes:

DEFINITION:#lt;br /#gt;#lt;/p#gt;#lt;p#gt;A coded value specifying the technique used for secondary processing applied to a complex observation result (e.g. an image or a genetic sequence) to obtain a summarized result.#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;Lowess, Paired-end mapping, Probe Signal Intensity, SNP Genotyping#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;There are often a range of analysis method codes that are appropriate for a given method code.#lt;br /#gt;#lt;/p#gt;

Tag	Value
Map:PGx v1.0	PF
Details:
Map:PGx v1.0	SB
Details:
Map:PGx v1.0	PG
Details:

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