Difference between revisions of "ObservationGenetics FHIR Profile Proposal"
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This page documents a [[:category:Pending FHIR Resource Proposal|Pending]] [[:category:FHIR Resource Proposal|FHIR Resource Proposal]] | This page documents a [[:category:Pending FHIR Resource Proposal|Pending]] [[:category:FHIR Resource Proposal|FHIR Resource Proposal]] | ||
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Genetic Standards and Resources include: | Genetic Standards and Resources include: | ||
| − | * Variant Databases: dbSNP , ClinVar , and COSMIC | + | |
| − | * Reference Sequences: RefSeq and ENSEMBL | + | *Variant Databases: dbSNP , ClinVar , and COSMIC |
| − | * Gene Symbols and Identifiers: HGNC - Human Genee Nomenclature Committee | + | *Reference Sequences: RefSeq and ENSEMBL |
| − | * Variant Nomenclature: HGVS nomenclature from the Human Genome Variantion Society | + | *Gene Symbols and Identifiers: HGNC - Human Genee Nomenclature Committee |
| − | * Locus: Gene | + | *Variant Nomenclature: HGVS nomenclature from the Human Genome Variantion Society |
| + | *Locus: Gene | ||
==Profile balloting plans== | ==Profile balloting plans== | ||
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The following FHIR resource is profiled: | The following FHIR resource is profiled: | ||
| − | * [http://hl7-fhir.github.io/observation.html Observation] | + | |
| + | *[http://hl7-fhir.github.io/observation.html Observation] | ||
====Constraints to be Applied==== | ====Constraints to be Applied==== | ||
The following constraints are applied to the FHIR resources as necessary: | The following constraints are applied to the FHIR resources as necessary: | ||
| − | * Constrain the cardinality of the data elements within the resource. | + | |
| − | * Constrain the mustSupport attribute of the data elements within the resource. | + | *Constrain the cardinality of the data elements within the resource. |
| − | * Define searchParameters as necessary for the resource. | + | *Constrain the mustSupport attribute of the data elements within the resource. |
| − | * Constrain vocabularies for the resources as applicable. | + | *Define searchParameters as necessary for the resource. |
| + | *Constrain vocabularies for the resources as applicable. | ||
====Extensions to be Applied==== | ====Extensions to be Applied==== | ||
The following extensions are applied to the Observation resource as appropriate: | The following extensions are applied to the Observation resource as appropriate: | ||
| − | * Clinical genomics specific extensions. | + | |
| + | *Clinical genomics specific extensions. | ||
===Example Scenarios=== | ===Example Scenarios=== | ||
| − | * Query Examples for the Observation resource. | + | *Query Examples for the Observation resource. |
| − | * Query Result Examples for the Observation resource. | + | *Query Result Examples for the Observation resource. |
===Scope of coverage=== | ===Scope of coverage=== | ||
| − | * Subject: patient | + | *Subject: patient |
| − | * Disciplines: Patient Care, Clinical Research, Public Health | + | *Disciplines: Patient Care, Clinical Research, Public Health |
| − | * Delivery Environment: Inpatient, Ambulatory, Community, Emergency, etc. | + | *Delivery Environment: Inpatient, Ambulatory, Community, Emergency, etc. |
===Realm=== | ===Realm=== | ||
| Line 73: | Line 77: | ||
===Contributing or Reviewing Work Groups=== | ===Contributing or Reviewing Work Groups=== | ||
| − | * None | + | *None |
===Expected implementations=== | ===Expected implementations=== | ||
| Line 81: | Line 85: | ||
===gForge Users=== | ===gForge Users=== | ||
| − | * Gil Alterovitz | + | *Gil Alterovitz |
| − | * Gaston Fiore | + | *Gaston Fiore |
===FHIR Profile Development Project Insight ID=== | ===FHIR Profile Development Project Insight ID=== | ||
| − | * 1110 | + | *1110 |
==Plans== | ==Plans== | ||
| Line 98: | Line 102: | ||
Desired Ballot Date | Desired Ballot Date | ||
| + | |||
*End 2016 | *End 2016 | ||
Latest revision as of 16:21, 31 October 2019
This page documents a Pending FHIR Resource Proposal
Contents
ObservationGenetics
The ObservationGenetics profile extends the Observation resource to enable reporting of structured genetic test results. In addition, the genetics profile contextualizes well established standards from the field of clinical genetics into the standards of healthcare (e.g. HGNC - HUGO Gene Nomenclature Committee's international standard for gene names, symbols, and identifiers).
Genetic Standards and Resources include:
- Variant Databases: dbSNP , ClinVar , and COSMIC
- Reference Sequences: RefSeq and ENSEMBL
- Gene Symbols and Identifiers: HGNC - Human Genee Nomenclature Committee
- Variant Nomenclature: HGVS nomenclature from the Human Genome Variantion Society
- Locus: Gene
Profile balloting plans
STU3
Profile Details
The ObservationGenetics profile supports reporting of a DNA variant at the genomic, cDNA, and protein change level. In addition, a condition context may be provided, as AssessedCondition. For large genomic tests, a condition may be used as an input into the analytic pipeline to aid in the identification of clinically relevant variants related to the test order. It is strongly encouraged to provide all available information in this profile for any reported variants, because receiving systems (e.g. discovery research, outcomes analysis, and public health reporting) may use this information to normalize variants over time or across sources. However, these data should not be used to dynamically correct/change variant representations for clinical use outside of the laboratory, due to insufficient information.
Profiled Resource(s)
The following FHIR resource is profiled:
Constraints to be Applied
The following constraints are applied to the FHIR resources as necessary:
- Constrain the cardinality of the data elements within the resource.
- Constrain the mustSupport attribute of the data elements within the resource.
- Define searchParameters as necessary for the resource.
- Constrain vocabularies for the resources as applicable.
Extensions to be Applied
The following extensions are applied to the Observation resource as appropriate:
- Clinical genomics specific extensions.
Example Scenarios
- Query Examples for the Observation resource.
- Query Result Examples for the Observation resource.
Scope of coverage
- Subject: patient
- Disciplines: Patient Care, Clinical Research, Public Health
- Delivery Environment: Inpatient, Ambulatory, Community, Emergency, etc.
Realm
Clinical genomics.
Ownership
Owning committee name
Contributing or Reviewing Work Groups
- None
Expected implementations
gForge Users
- Gil Alterovitz
- Gaston Fiore
FHIR Profile Development Project Insight ID
- 1110
Plans
Timelines
- July 2016
Balloting Requirements
- Ballot with next FHIR DSTU or Normative Edition
Desired Ballot Date
- End 2016
