: Public Class
Created: 3/3/2015 11:49:23 PM
Modified: 12/8/2017 2:05:24 PM
Project:
Advanced:
DEFINITION:<br/>The completed action of assessing a genetic characteristic of a biologic specimen or assessing a contextual characteristic of the genetic test itself.<br/><br/>EXAMPLE(S):<br/>For CDISC's PG domain, Exon Sequenced, Sequence Start, Sequence Length<br/>For CDISC's PF domain, Amino Acid, Nucleotide, Allele, Observed Level, Raw Ct Value, Copy Number, Normalized Intensity 1 Value, Fold Change, New Assessment<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>Because of their similar attributes, observations about genetic tests themselves as well as genetic observations about specimens are both represented by this single class.<br/>
Attribute
Public II
  runIdentifier
Details:
Map:PGx v1.0=PF.PFRUNID
Map:PGx v1.0=PG.PGRUNID
Notes: DEFINITION:<br/>A unique symbol that establishes identity of a particular execution of a test on a biospecimen.<br/><br/>EXAMPLE(S):<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>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.<br/>
Public SC
  geneticRegionOfInterest
Details:
Map:PGx v1.0=PF.PFGENRI
Map:PGx v1.0=SB.SBGENRI
Notes: DEFINITION:<br/>The portion of the genome serving as a locus for the test, often a gene.  <br/><br/>EXAMPLE(S):<br/>EGFR, KRAS, CYP2D6, MYC, MFNG<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>These are typically obtained from the gene symbol list maintained by the Human Genome Variation Society (HGVS)  =#gt;  HUGO Genome Nomenclature Consortium (HGNC), a committee of the Human Genome Organization (HUGO). This can be a gene, a protein, or a sector as described by geneticRegionTypeCode.<br/>
Public CD
  geneticRegionTypeCode
Details:
Map:PGx v1.0=PF.PFGENTYP
Map:PGx v1.0=SB.SBGENTYP
Notes: DEFINITION:<br/>A coded value specifying the kind of portion of the genome serving as a locus for the test.  <br/><br/>EXAMPLE(S):<br/>GENE, SECTOR, DOMAIN, PROTEIN  <br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
Public IVL<INT>
  geneticLocationOfInterest
Details:
Map:PGx v1.0=PF.PFGENLI
Notes: DEFINITION:<br/>The portion of the sequence that is the focus of this test or observation.  <br/><br/>EXAMPLE(S):<br/>In CDISC's PGx domains, a PFGENLI of "34" would be 34, or "2235_2249" would be 2235-2249.<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>
Public CD
  analysisMethodCode
Details:
Map:PGx v1.0=PF.PFANMETH
Notes: DEFINITION:<br/>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.<br/><br/>EXAMPLE(S):<br/>Lowess, Paired-end mapping, Probe Signal Intensity, SNP Genotyping<br/><br/>OTHER NAME(S):<br/><br/>NOTE(S):<br/>There are often a range of analysis method codes that are appropriate for a given method code.<br/>
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):