2.16.840.1.113883.10.20.20.2/static-2013-02-01T000000

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Id2.16.840.1.113883.10.20.20.2
ref
gtr-
Gültigkeit2013‑02‑01
StatusKyellow.png EntwurfVersions-Label
NameClinicalGenomicStatementAnzeigenameClinical Genomic Statement
Beschreibung
EN-US.png The ClinicalGenomicStatement (CGS) template is the main vehicle of representing structured data in the GTR Implementation Guide. At its core, there is a genetic observation finding (result), e.g., a genetic variation, which can be associated with the following: more observations that describe the core observation in more detail (GenomicAssociatedObservation), e.g., amino acid change type; indications for performing this genetic observation (IndicationObservation), e.g., the genetic disease being assessed; and interpretations of the observation finding (InterpretivePhenotype), e.g., the mutation is pathogenic. In addition, it is important to associate a specimen and genomic source class with the core genetic finding, and optionally other performers of the genetic observation or the interpretation than those listed in the GTR header could be specified as part the CGS template.
The overall structure of CGS is depicted in chart 5 of the slide deck enclosed in the GTR package.


Due to the complexity of the interpretation of genetic observations, this template disallows the use of the interpretationCode attribute, rather uses an association to InterpretivePhenotype. The latter is constrained by several of its sub-templates in order to suggest binding to LOINC value sets describing interpretations of genetic testing. For example, ClinicalGenomicStatementGeneticVariation is a sub-template of ClinicalGenomicStatement and is associated with InterpretivePhenotypeGeneticVariation which is a sub-template of InterpretivePhenotype and its code and value attributes may be bound to LOINC codes representing interpretations of genetic findings.

All GTR structured data entries shall be part of CGS instances so that parsing applications can find the full semantics explicitly represented in this single and coherent structure. Sub-sections such as Indications, Interpretations and Specimen are mainly for presenting the data for human viewing (narrative), but they may also contain structured data that shall reference or be referenced from CGS. By using the referencing mechanism (explained in the GenomicObservationReference template), it is possible to have less redundant documents, e.g., in the case where all tests reported in a GTR document have the same indication, an Indications section in the Summary section consists of a full-blown indication observation which all CGS indication observations reference.


Note that CGS structured entries may point to the respective narrative in sub-sections by means of XML ID (see examples in the GTR samples enclosed in the GTR package). This mechanism can be useful in cases where the structured data has been generated by automated processes rather than by human coders.
KontextElternknoten des Template-Element mit Id 2.16.840.1.113883.10.20.20.2
KlassifikationCDA Entry Level Template
Offen/GeschlossenOffen (auch andere als die definierten Elemente sind erlaubt)
Benutzt
Benutzt 4 Templates
Benutzt als NameVersion
2.16.840.1.113883.10.20.20.3.3ContainmentKyellow.png Indication ObservationDYNAMIC
2.16.840.1.113883.10.20.20.2.5ContainmentKyellow.png Interpretive PhenotypeDYNAMIC
2.16.840.1.113883.10.20.20.3.2ContainmentKyellow.png Genomic Source ClassDYNAMIC
2.16.840.1.113883.10.20.20.4ContainmentKyellow.png Genomic Associated ObservationDYNAMIC
Beispiel
Beispiel
<observation classCode="OBS" moodCode="EVN">
  <templateId root="2.16.840.1.113883.10.20.20.2.1"/>  <id root="2.16.840.1.113883.18.12.7.30.9.8.1"/>  <code code="55208-3" codeSystemName="LOINC" displayName="DNA Analysis Discrete Sequence Variant Panel"/>  <statusCode code="completed"/>  <effectiveTime value="200512011500"/>  <entryRelationship typeCode="SUBJ">
    <observation classCode="OBS" moodCode="EVN">
      <id root="2.16.840.1.113883.18.12.7.30.9.3.7"/>      <code/>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="SUBJ">
    <observation classCode="OBS" moodCode="EVN">
      <templateId root="2.16.840.1.113883.10.20.20.2.1.5"/>      <code code="48018-6" codeSystemName="LOINC" displayName="Gene Identifier"/>      <value xsi:type="CD" code="GJB2" codeSystemName="HGNC"/>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="SUBJ">
    <observation classCode="OBS" moodCode="EVN">
      <templateId root="2.16.840.1.113883.10.20.20.2.1.8"/>      <code code="48013-7" codeSystemName="LOINC" displayName="Genomic Reference Sequence Identifier"/>      <value xsi:type="CD" code="NC_000013.10" codeSystem="REFSEQ" codeSystemName="NCBI Reference Sequence"/>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="SUBJ">
    <observation classCode="OBS" moodCode="EVN">
      <templateId root="2.16.840.1.113883.10.20.20.2.1.6"/>      <code code="51958-7" codeSystemName="LOINC" displayName="Transcript Reference Sequence Identifier"/>      <value xsi:type="CD" code="NM_004004.5" codeSystem="REFSEQ" codeSystemName="NCBI Reference Sequence"/>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="SUBJ">
    <observation classCode="OBS" moodCode="EVN">
      <templateId root="2.16.840.1.113883.10.20.20.2.1.7"/>      <code code="48003-8" codeSystemName="LOINC" displayName="DNA Sequence Variation Identifier"/>      <value xsi:type="CD" code="rs72474224" codeSystemName="dbSNP"/>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="SUBJ">
    <observation classCode="OBS" moodCode="EVN">
      <templateId root="2.16.840.1.113883.10.20.20.2.1.2"/>      <code code="48004-6" codeSystemName="LOINC" displayName="DNA Sequence Variation"/>      <value xsi:type="CD" code="109G>A" codeSystemName="HGVS nomenclature for the description of sequence variations"/>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="SUBJ">
    <observation classCode="OBS" moodCode="EVN">
      <templateId root="2.16.840.1.113883.10.20.20.2.1.2.1"/>      <code code="48019-4" codeSystemName="LOINC" displayName="DNA Sequence Variation Type"/>      <value xsi:type="CD" code="LA6690-7" codeSystemName="LOINC" displayName="Substitution"/>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="SUBJ">
    <observation classCode="OBS" moodCode="EVN">
      <templateId root="2.16.840.1.113883.10.20.20.2.1.1"/>      <code code="48005-3" codeSystemName="LOINC" displayName="Amino Acid Change"/>      <value xsi:type="CD" code="Val37Ile"/>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="SUBJ">
    <observation classCode="OBS" moodCode="EVN">
      <templateId root="2.16.840.1.113883.10.20.20.2.1.1.1"/>      <code code="48006-1" codeSystemName="LOINC" displayName="Amino acid change type"/>      <value xsi:type="CD" code="LA6698-0" displayName="Missense"/>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="SUBJ">
    <observation classCode="OBS" moodCode="EVN">
      <templateId root="2.16.840.1.113883.10.20.20.2.1.3"/>      <code code="47999-8" codeSystemName="LOINC" displayName="DNA Region Name"/>      <value xsi:type="ST">Exon 2</value>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="SUBJ">
    <observation classCode="OBS" moodCode="EVN">
      <templateId root="2.16.840.1.113883.10.20.20.2.1.4"/>      <code code="53034-5" codeSystemName="LOINC" displayName=" Allelic State"/>      <value xsi:type="CD" code="LA6705-3" codeSystemName="LOINC" displayName="Homozygous"/>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="RSON">
    <observation classCode="OBS" moodCode="EVN">
      <id root="2.16.840.1.113883.18.12.7.30.9.2.1"/>      <code/>    </observation>
  </entryRelationship>
  <entryRelationship typeCode="SPRT">
    <observation classCode="OBS" moodCode="DEF">
      <templateId root="2.16.840.1.113883.10.20.20.2.5.3"/>      <code code="53037-8" codeSystemName="LOINC" displayName="Genetic disease sequence variation interpretation"/>      <value xsi:type="CD" code="LA6668-3" codeSystemName="LOINC" displayName="Pathogenic"/>    </observation>
  </entryRelationship>
</observation>
ItemDTKardKonfBeschreibungLabel
hl7:observation
(Cli...ent)
Treetree.pnghl7:templateId
II1 … 1M(Cli...ent)
Treeblank.pngTreetree.png@root
uid1 … 1F2.16.840.1.113883.10.20.20.2
Treetree.pnghl7:code
1 … 1REN-US.png
The code attribute of a clinical genomic statement characterizes the type of data it represents (e.g., genetic
variation) and specifically it indicates the type of information assigned to the value attribute of that clinical
genomic statement.
(Cli...ent)
Treetree.pnghl7:value
0 … 1(Cli...ent)
Treetree.pnghl7:entryRelationship
1 … 1REN-US.png Indication Observation
Beinhaltet 2.16.840.1.113883.10.20.20.3.3 Indication Observation (DYNAMIC)
(Cli...ent)
Treeblank.png wo [hl7:observation]
Treeblank.pngTreetree.png@typeCode
cs1 … 1FRSON
Treetree.pnghl7:entryRelationship
0 … 1REN-US.png Interpretive Phenotype
Beinhaltet 2.16.840.1.113883.10.20.20.2.5 Interpretive Phenotype (DYNAMIC)
(Cli...ent)
Treeblank.png wo [hl7:observation]
Treeblank.pngTreetree.png@typeCode
cs1 … 1FSPRT
Treetree.pnghl7:entryRelationship
0 … 1REN-US.png Genomic Source Class
Beinhaltet 2.16.840.1.113883.10.20.20.3.2 Genomic Source Class (DYNAMIC)
(Cli...ent)
Treeblank.png wo [hl7:observation [hl7:code [(@code = '48002-0' and @codeSystem = '2.16.840.1.113883.6.1') or @nullFlavor]]]
Treeblank.pngTreetree.png@typeCode
cs1 … 1FSUBJ
Treetree.pnghl7:performer
0 … *EN-US.png
Use this performer association if the performer(s) of the genomic observation (i.e., the source of this performer association) are different than the performer(s) indicated at a higher level (e.g., the GTR header).
(Cli...ent)
 ConstraintEN-US.png Contains exactly one [1..1] CDA Performer2
Treetree.pnghl7:entryRelationship
1 … 1REN-US.png Genomic Associated Observation
Beinhaltet 2.16.840.1.113883.10.20.20.4 Genomic Associated Observation (DYNAMIC)
(Cli...ent)
Treeblank.png wo [hl7:observation]
Treeblank.pngTreetree.png@typeCode
cs1 … 1FSUBJ