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Difference between revisions of "SequenceConsensusSequenceBlock FHIR Profile Proposal"

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Current version: https://confluence.hl7.org/display/FHIR/SequenceConsensusSequenceBlock+FHIR+Profile+Proposal<div style="float: left;">[[Image:OpenHotTopic.GIF|35px| ]]</div>
 
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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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=PutProposedProfileNameHere=
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=SequenceConsensusSequenceBlock=
  
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<!-- Profile names should meet the following characteristics:
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Describes consensus sequence block used in HLA typing report.
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* Lower camel case
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* U.S. English
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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
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* Domain-friendly
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Hum Immunol. 2015 Dec;76(12):954-62. doi: 10.1016/j.humimm.2015.09.011. Epub 2015 Sep 25.
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* Short
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A technical implementation of MIRING was developed in the Histomimmungenetics Markup Language (HML) and published in
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* Clear
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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/
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* Unique
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* Avoid non-universal abbreviations (e.g. URL would be ok)
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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.
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* Be expressed as a noun
 
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* Be consistent with other similar Profiles
 
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* Incorporate the name of the Resource being profiled
 
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-->
 
  
 
==Profile balloting plans==
 
==Profile balloting plans==
  
 +
STU3
  
 
==Profile Details==
 
==Profile Details==
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===Profiled Resource(s)===
 
===Profiled Resource(s)===
  
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<!--Put a link to the resource/datatype (or group of resources) that will be profiled here.-->
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*[http://hl7-fhir.github.io/sequence.html Sequence]
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* [[ParentResourceAddress|ResourceName]]
 
  
 
====Constraints to be Applied====
 
====Constraints to be Applied====
  
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<!--Describe how the current resource will be constrained.-->
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The following constraints are applied to the Sequence resource as necessary:
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* Constraint 1
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* Constraint 2
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*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====
 
====Extensions to be Applied====
  
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<!--Describe how the current resource will be extended.-->
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The following extensions are applied to the Sequence resource as appropriate:
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* Extension 1
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* Extension 2
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*Clinical genomics specific extensions.
  
 
===Example Scenarios===
 
===Example Scenarios===
  
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<!-- Provide a listing of the types of scenarios to be represented in the examples produced for this Profile. They should demonstrate the full scope of the Profile and allow exercising of the Profiles capabilities (full element coverage, inclusion & omission of optional elements, repeating and singleton repeating elements, etc.) -->
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*Query Examples for each resource.
 +
*Query Result Examples for each resource.
  
 
===Scope of coverage===
 
===Scope of coverage===
  
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<!-- Define the full scope of coverage for the Profile.  The scope must be clearly delineated such that it does not overlap with any other existing or expected Profile.  The scope will be used to govern "what is the set of potential applications to consider when evaluating what elements are 'core' – i.e. in the 80%"
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*Subject: patient
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*Disciplines: Patient Care, Clinical Research, Public Health
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Scope should consider numerous aspects of breadth of scope, including:
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*Delivery Environment: Inpatient, Ambulatory, Community, Emergency, etc.
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* Subject: Human vs. non-human vs. non-patient (e.g. lab bench medicine)
 
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* Disciplines: Environmental Health, Palliative, Respiratory, Psychology, Maternity, Clinical Research
 
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* Delivery environment (Community, Geriatric, Home care, Emergency, Inpatient, Intensive, Neonatal, Pediatric, Primary)
 
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* Locale: Country, region
 
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As a rule, Profiles should encompass all of these aspects.
 
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-->
 
  
 
===Realm===
 
===Realm===
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Please describe the realm to which this profile applies, or indicate that it is realm neutral.
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Clinical genomics.
  
 
==Ownership==
 
==Ownership==
 
===Owning committee name===
 
===Owning committee name===
  
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<!-- The name of the committee that is proposed to have responsibility for developing and maintaining the Profiles. -->
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[[Clinical Genomics]]
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[[YourCommitteeName]]
 
  
 
===Contributing or Reviewing Work Groups===
 
===Contributing or Reviewing Work Groups===
  
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<!-- Additional work groups that may have an interest in contributing to, or reviewing  the content of the Profile (optional) -->
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*None
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* Work Group Name
 
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* or link
 
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* or "None"
 
  
 
===Expected implementations===
 
===Expected implementations===
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===gForge Users===
 
===gForge Users===
  
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<!-- Identify the userids who will require commit access to gForge to maintain the Profile.  (Ensure all users have registered for gForge.) -->
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*Gil Alterovitz
−
 
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*Gaston Fiore
  
 
===FHIR Profile Development Project Insight ID===
 
===FHIR Profile Development Project Insight ID===
  
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<!-- 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 -->
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1110
  
 
==Plans==
 
==Plans==
 
===Timelines===
 
===Timelines===
  
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<!-- Indicate the target date for having the Profile complete from a committee perspective and ready for vetting and voting -->
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*July 2016
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*TargetDateForInternalReview
 
  
 
===Balloting Requirements===
 
===Balloting Requirements===
  
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<!-- Indicate the intended method of balloting by choosing one of the options below, or propose alternative.  If Realm Specific or No Ballot indicate the amount of informal review required by the FHIR community.-->
 
−
 
−
Choose one:
 
 
*Ballot with next FHIR DSTU or Normative Edition
 
*Ballot with next FHIR DSTU or Normative Edition
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*or Ballot independently as DSTU
 
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*or Realm specific ballot
 
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*or No Ballot
 
  
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<!-- Indicate the desired ballot date.-->
 
 
Desired Ballot Date
 
Desired Ballot Date
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*PutDesiredBallotDateHere
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 +
*End 2016

Latest revision as of 16:22, 31 October 2019

Current version: https://confluence.hl7.org/display/FHIR/SequenceConsensusSequenceBlock+FHIR+Profile+Proposal
OpenHotTopic.GIF

This page documents a Pending FHIR Resource Proposal



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

Clinical Genomics

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
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