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| − | This page documents a [[:category: | + | This page documents a [[:category:Approved FHIR Resource Proposal|Approved]] [[:category:FHIR Resource Proposal|FHIR Resource Proposal]] |
</div> | </div> | ||
</div> | </div> | ||
[[Category:FHIR Resource Proposal]] | [[Category:FHIR Resource Proposal]] | ||
| − | [[Category: | + | [[Category:Approved FHIR Resource Proposal]] |
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| − | = | + | =Sequence= |
<!-- Resource names should meet the following characteristics: | <!-- Resource names should meet the following characteristics: | ||
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<!-- The name of the committee that is proposed to have responsibility for developing and maintaining the resources. --> | <!-- The name of the committee that is proposed to have responsibility for developing and maintaining the resources. --> | ||
| − | [[ | + | [[CG]] |
| + | |||
| + | ==Committee Approval Date:== | ||
| + | |||
| + | <i>May 5, 2015</i> | ||
| + | <p>[http://wiki.hl7.org/index.php?title=CG_WG_Call_Notes_leading_to_2015_May_WGM CG WG Call Notes leading to 2015 May WGM]</p> | ||
==Contributing or Reviewing Work Groups== | ==Contributing or Reviewing Work Groups== | ||
| − | <!-- Additional work groups that may have an interest in contributing to, or reviewing the content of the resource (optional) | + | <!-- Additional work groups that may have an interest in contributing to, or reviewing the content of the resource (optional) |
* Work Group Name | * Work Group Name | ||
* or link | * or link | ||
* or "None" | * or "None" | ||
| − | + | --> | |
==FHIR Resource Development Project Insight ID== | ==FHIR Resource Development Project Insight ID== | ||
<!-- Please specify the id of your work group’s PSS for doing FHIR work. (If submitted but not yet approved, just write “pending”.) The link to the PSS template can be found here: http://gforge.hl7.org/gf/download/docmanfileversion/6832/9398/HL7FHIR_DSTUballotPSS-20120529.doc --> | <!-- Please specify the id of your work group’s PSS for doing FHIR work. (If submitted but not yet approved, just write “pending”.) The link to the PSS template can be found here: http://gforge.hl7.org/gf/download/docmanfileversion/6832/9398/HL7FHIR_DSTUballotPSS-20120529.doc --> | ||
| + | 1110 | ||
==Scope of coverage== | ==Scope of coverage== | ||
| − | + | This resource is designed to describe a sequence variation from a patient with information such as: | |
| + | |||
| + | *Name of the variation represented | ||
| + | *Type of the variation | ||
| + | *Coordinate of the variant | ||
| + | *Gene region occupied by the variation | ||
| + | *Name of the gene | ||
| + | *Tissue source used to determine genotype of the variation | ||
| + | *Reads | ||
| − | + | Users are encouraged to provide all available information in this resource 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. | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | Implementers should be aware that semantic equivalency of results of genetic variants cannot be guaranteed unless there is an agreed upon standard between sending and receiving systems. | |
| − | |||
==RIM scope== | ==RIM scope== | ||
<!-- Identify the formal RIM mapping for the root concept of the resource. The expectation is that the RIM mapping will be sufficiently precise so as to not overlap with any other resource definition. --> | <!-- Identify the formal RIM mapping for the root concept of the resource. The expectation is that the RIM mapping will be sufficiently precise so as to not overlap with any other resource definition. --> | ||
| + | A new entity which is not covered by the RIM directly. | ||
==Resource appropriateness== | ==Resource appropriateness== | ||
| + | The Sequence resource is designed to describe the basic information about sequence variations of direct relevance to clinical decision-making. Complete genetic sequence information, of which specific genetic variations are a part, is reported by reference to the GA4GH repository. This resource 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). | ||
| + | |||
| + | This resource will be referenced as part of the Observation resource, which can be used to report a sequence variant observation. By introducing this resource, we are also able to simplify of the Standard genetics profile particularly as it applies to the DiagnosticReport resource, while extending it to capture family history and diagnosed conditions. The DiagnosticReport can refer to a bundle of sequence variant observations to accomplish a genetics report. Making the Observation resource and the DiagnosticReport more useful as well as more versatile, our design – taken together – simplifies the implementation, production, and consumption of genomic payloads for the clinical purposes for which FHIR is suited. | ||
<!-- Does the resource meet the following characteristics? | <!-- Does the resource meet the following characteristics? | ||
| Line 76: | Line 89: | ||
==Expected implementations== | ==Expected implementations== | ||
| − | + | Referenced as part of Observation. We add an extension - valueReference in value element in the Observation resource. This element will refer to the Sequence resource to contain the sequence variant representation for genomic payloads. | |
<!--Key resources are justified by CCDA, for resources not deemed "key", what interest is there by implementers in using this particular resource. Provide named implementations if possible - ideally provide multiple independent implementations. --> | <!--Key resources are justified by CCDA, for resources not deemed "key", what interest is there by implementers in using this particular resource. Provide named implementations if possible - ideally provide multiple independent implementations. --> | ||
==Content sources== | ==Content sources== | ||
| − | + | *HL7 Version 3 Domain Analysis Model | |
| + | *GA4GH Data Model | ||
<!-- List all of the specifications (beyond those in the "standard" (FHIR_Design_Requirements_Sources) list of source specifications) that you’re planning to consult | <!-- List all of the specifications (beyond those in the "standard" (FHIR_Design_Requirements_Sources) list of source specifications) that you’re planning to consult | ||
| Line 86: | Line 100: | ||
==Example Scenarios== | ==Example Scenarios== | ||
| − | + | *Specimen Identification | |
| + | *Clinical Sequencing (Germline) | ||
| + | *Cancer Profiling (Somatic) | ||
| + | *CDS (Family History and Drug Dosage Calculator) | ||
| + | *Public Health Reporting | ||
| + | *Clinical and Research Data Warehouses | ||
<!-- Provide a listing of the types of scenarios to be represented in the examples produced for this resource. They should demonstrate the full scope of the resource and allow exercising of the resources capabilities (full element coverage, inclusion & omission of optional elements, repeating and singleton repeating elements, etc.) --> | <!-- Provide a listing of the types of scenarios to be represented in the examples produced for this resource. They should demonstrate the full scope of the resource and allow exercising of the resources capabilities (full element coverage, inclusion & omission of optional elements, repeating and singleton repeating elements, etc.) --> | ||
==Resource Relationships== | ==Resource Relationships== | ||
| + | *Observation | ||
<!-- What are the resources do you expect will reference this resource and in what context? | <!-- What are the resources do you expect will reference this resource and in what context? | ||
| Line 101: | Line 121: | ||
==Timelines== | ==Timelines== | ||
| − | + | <i>Nov 15, 2015</i> | |
<!-- Indicate the target date for having the resource complete from a committee perspective and ready for vetting and voting --> | <!-- Indicate the target date for having the resource complete from a committee perspective and ready for vetting and voting --> | ||
==gForge Users== | ==gForge Users== | ||
| − | + | DSrcl | |
| + | gil | ||
<!-- Identify the userids who will require commit access to gForge to maintain the resource. (Ensure all users have registered for gForge.) --> | <!-- Identify the userids who will require commit access to gForge to maintain the resource. (Ensure all users have registered for gForge.) --> | ||
Latest revision as of 20:05, 9 March 2016
This page documents a Approved FHIR Resource Proposal
Contents
- 1 Sequence
- 1.1 Owning committee name
- 1.2 Committee Approval Date:
- 1.3 Contributing or Reviewing Work Groups
- 1.4 FHIR Resource Development Project Insight ID
- 1.5 Scope of coverage
- 1.6 RIM scope
- 1.7 Resource appropriateness
- 1.8 Expected implementations
- 1.9 Content sources
- 1.10 Example Scenarios
- 1.11 Resource Relationships
- 1.12 Timelines
- 1.13 gForge Users
Sequence
Owning committee name
Committee Approval Date:
May 5, 2015
CG WG Call Notes leading to 2015 May WGM
Contributing or Reviewing Work Groups
FHIR Resource Development Project Insight ID
1110
Scope of coverage
This resource is designed to describe a sequence variation from a patient with information such as:
- Name of the variation represented
- Type of the variation
- Coordinate of the variant
- Gene region occupied by the variation
- Name of the gene
- Tissue source used to determine genotype of the variation
- Reads
Users are encouraged to provide all available information in this resource 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.
Implementers should be aware that semantic equivalency of results of genetic variants cannot be guaranteed unless there is an agreed upon standard between sending and receiving systems.
RIM scope
A new entity which is not covered by the RIM directly.
Resource appropriateness
The Sequence resource is designed to describe the basic information about sequence variations of direct relevance to clinical decision-making. Complete genetic sequence information, of which specific genetic variations are a part, is reported by reference to the GA4GH repository. This resource 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).
This resource will be referenced as part of the Observation resource, which can be used to report a sequence variant observation. By introducing this resource, we are also able to simplify of the Standard genetics profile particularly as it applies to the DiagnosticReport resource, while extending it to capture family history and diagnosed conditions. The DiagnosticReport can refer to a bundle of sequence variant observations to accomplish a genetics report. Making the Observation resource and the DiagnosticReport more useful as well as more versatile, our design – taken together – simplifies the implementation, production, and consumption of genomic payloads for the clinical purposes for which FHIR is suited.
Expected implementations
Referenced as part of Observation. We add an extension - valueReference in value element in the Observation resource. This element will refer to the Sequence resource to contain the sequence variant representation for genomic payloads.
Content sources
- HL7 Version 3 Domain Analysis Model
- GA4GH Data Model
Example Scenarios
- Specimen Identification
- Clinical Sequencing (Germline)
- Cancer Profiling (Somatic)
- CDS (Family History and Drug Dosage Calculator)
- Public Health Reporting
- Clinical and Research Data Warehouses
Resource Relationships
- Observation
Timelines
Nov 15, 2015
gForge Users
DSrcl gil
