Difference between revisions of "SequenceConsensusSequenceBlock FHIR Profile Proposal"
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Describes consensus sequence block used in HLA typing report. | Describes consensus sequence block used in HLA typing report. | ||
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| + | This profile was created to attempt to satisfy the requirements for a specific use case: HLA genotyping by NGS methods. It is based on the principles of the Minimum Information for ReportIng Next generation sequence Genotyping (MIRING) as described in | ||
| + | Hum Immunol. 2015 Dec;76(12):954-62. doi: 10.1016/j.humimm.2015.09.011. Epub 2015 Sep 25. | ||
| + | A technical implementation of MIRING was developed in the Histomimmungenetics Markup Language (HML) and published in | ||
| + | Hum Immunol. 2015 Dec;76(12):963-74. doi: 10.1016/j.humimm.2015.08.001. Epub 2015 Aug 28. The schema for HML may be found in http://schemas.nmdp.org/ | ||
| + | |||
| + | We are using MIRING and HML to inform how FHIR profile(s) may be developed. In this case, a Consensus Sequence is composed of one or more Consensus Sequence Blocks. Metadata about each block is important, but not yet captured in the Sequence Resource, or other profiles. These include: phase set, expected copy number, block continuity, and strand. This profile extends the Sequence Resource to add these elements. | ||
==Profile balloting plans== | ==Profile balloting plans== | ||
Revision as of 14:11, 26 May 2016
This page documents a Pending FHIR Resource Proposal
Contents
SequenceConsensusSequenceBlock
Describes consensus sequence block used in HLA typing report.
This profile was created to attempt to satisfy the requirements for a specific use case: HLA genotyping by NGS methods. It is based on the principles of the Minimum Information for ReportIng Next generation sequence Genotyping (MIRING) as described in Hum Immunol. 2015 Dec;76(12):954-62. doi: 10.1016/j.humimm.2015.09.011. Epub 2015 Sep 25. A technical implementation of MIRING was developed in the Histomimmungenetics Markup Language (HML) and published in Hum Immunol. 2015 Dec;76(12):963-74. doi: 10.1016/j.humimm.2015.08.001. Epub 2015 Aug 28. The schema for HML may be found in http://schemas.nmdp.org/
We are using MIRING and HML to inform how FHIR profile(s) may be developed. In this case, a Consensus Sequence is composed of one or more Consensus Sequence Blocks. Metadata about each block is important, but not yet captured in the Sequence Resource, or other profiles. These include: phase set, expected copy number, block continuity, and strand. This profile extends the Sequence Resource to add these elements.
Profile balloting plans
STU3
Profile Details
Profiled Resource(s)
Constraints to be Applied
The following constraints are applied to the Sequence resource 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 Sequence resource as appropriate:
- Clinical genomics specific extensions.
Example Scenarios
- Query Examples for each resource.
- Query Result Examples for each 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
