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=Sequence resource=
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=�FHIR Genomics=
  
 
==Submitting WG/Project/Implementer Group==
 
==Submitting WG/Project/Implementer Group==
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==Justification==
 
==Justification==
  The Sequence resource is a core resource in FHIR Genomics. It is used to represent complex genetics data.
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  FHIR Genomics consists of the Sequence resource and several profiles built on top of existing FHIR resources (DiagnosticReport-genetics profile, DiagnosticOrder-genetics profile, Observation-geneitcs profile). The Sequence resource is a core resource in FHIR Genomics. It is used to represent complex genetics data. FHIR Genomics focuses on clinical genetics data reporting.
 
<!--Why is this an important track to include in the connectathon - include implementer need, impact on ballot, FMM readiness of the resources, etc. -->
 
<!--Why is this an important track to include in the connectathon - include implementer need, impact on ballot, FMM readiness of the resources, etc. -->
  
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===FHIR Client===
 
===FHIR Client===
 
<!-- Provide a description of the capabilities this role will have within the connectathon -->
 
<!-- Provide a description of the capabilities this role will have within the connectathon -->
Support the sending of the Sequence resource operations: create, history, read, search and update.
+
Support the sending of the Sequence resource/genetics profiles operations: create, history, read, search and update.
  
 
===FHIR Server===
 
===FHIR Server===
 
<!-- Provide a description of the capabilities this role will have within the connectathon -->
 
<!-- Provide a description of the capabilities this role will have within the connectathon -->
Support the receiving and processing of the Patient resource operations: create, history, read, search and update.
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Support the receiving and processing of the Sequence resource/genetics profiles operations: create, history, read, search and update.
  
 
==Steps==
 
==Steps==
 
<!-- What will be the actions performed by participants? -->
 
<!-- What will be the actions performed by participants? -->
  
===Scenario Step 1 Register a new sequence===
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===Scenario 1 Register a new sequence===
  
:Action: FHIR Client. Create a sequence instance to represent genetics data (DNA variant, RNA sequence, structural variant, etc). <!--Who does what?  (Use the role names listed above when referring to the participants -->
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:Action: (FHIR Client) Create a sequence instance to represent genetics data (DNA variant, RNA sequence, structural variant, etc). <!--Who does what?  (Use the role names listed above when referring to the participants -->
 
:Precondition: This sequence instance does not exist in service prior to action. <!-- What setup is required prior to executing this step? -->
 
:Precondition: This sequence instance does not exist in service prior to action. <!-- What setup is required prior to executing this step? -->
 
:Success Criteria: Sequence created correctly on server and in the desired format. <!-- How will the participants know if the test was successful? -->
 
:Success Criteria: Sequence created correctly on server and in the desired format. <!-- How will the participants know if the test was successful? -->
:Bonus point: <!-- Any additional complexity to make the scenario more challenging -->
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:Bonus point: New profiles can be built on top of the Sequence resource for complex representation<!-- Any additional complexity to make the scenario more challenging -->
 
Example for genetics data representation:
 
Example for genetics data representation:
 
* [http://genomics-advisor.smartplatforms.org:4000/sequence-example.html somatic variant in lung cancer]
 
* [http://genomics-advisor.smartplatforms.org:4000/sequence-example.html somatic variant in lung cancer]
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<!-- Provide a description of each task -->
 
<!-- Provide a description of each task -->
  
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===Scenario 2 Search genetics observations from germline analysis===
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:Action: (FHIR Client) Search target observation with patient ID and value for source ("germline")
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:Precondition: Relevant patient and observations have been created
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:Success Criteria: A bundle of genetics observations from germline analysis of that patient are returned.  <!-- How will the participants know if the test was successful? -->
 +
:Bonus point: More parameters can be added for searching<!-- Any additional complexity to make the scenario more challenging -->
 +
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.tuuqdmgk56k3 Example for corresponding API call and search results]
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===Scenario 3 Clinical and Research Data Warehouses===
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:Action: (FHIR Client) Get all genetic-profile-based observations of patients with the variant c.181T>G
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:Precondition: Relevant observations have been created
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:Success Criteria: A bundle of genetics observations, whose extesion 'sequence' referring to sequence instance of variant c.181T>G, are returned.  <!-- How will the participants know if the test was successful? -->
 +
:Bonus point: More parameters can be added for searching<!-- Any additional complexity to make the scenario more challenging -->
 +
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.tsazjrove5a1 Example for corresponding API call and search results]
 +
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===Scenario 4 Family Member History===
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:Action: (FHIR Client) Get the genetics diagnostic reports of patient's family members.
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:Precondition: Relevant diagnostic reports have been created
 +
:Success Criteria: The genetics diagnostic reports of patient's family members are returned<!-- How will the participants know if the test was successful? -->
 +
:Bonus point: More parameters can be added for searching<!-- Any additional complexity to make the scenario more challenging -->
 +
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.djh8kninnwp4 Example for corresponding API call and search results]
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===Scenario 5 Comprehensive Genetics Report===
 +
 +
:Action: (FHIR Client) Create a comprehensive genetics report for a patient.
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:Precondition: Relevant diagnostic reports have been created
 +
:Success Criteria: The genetics diagnostic reports of patient's family members are returned<!-- How will the participants know if the test was successful? -->
 +
:Bonus point: More parameters can be added for searching<!-- Any additional complexity to make the scenario more challenging -->
 +
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.djh8kninnwp4 Example for corresponding API call and search results]
 
==TestScript(s)==
 
==TestScript(s)==
 
<!-- Optional (for initial proposal): Provide links to the TestScript instance(s) that define the behavior to be tested-->
 
<!-- Optional (for initial proposal): Provide links to the TestScript instance(s) that define the behavior to be tested-->

Revision as of 22:53, 11 November 2015

�FHIR Genomics

Submitting WG/Project/Implementer Group

CG

Justification

FHIR Genomics consists of the Sequence resource and several profiles built on top of existing FHIR resources (DiagnosticReport-genetics profile, DiagnosticOrder-genetics profile, Observation-geneitcs profile). The Sequence resource is a core resource in FHIR Genomics. It is used to represent complex genetics data. FHIR Genomics focuses on clinical genetics data reporting.

Proposed Track Lead

Gil Alterovitz

Expected participants

The number of the participants may be 20-50.

Roles

FHIR Client

Support the sending of the Sequence resource/genetics profiles operations: create, history, read, search and update.

FHIR Server

Support the receiving and processing of the Sequence resource/genetics profiles operations: create, history, read, search and update.

Steps

Scenario 1 Register a new sequence

Action: (FHIR Client) Create a sequence instance to represent genetics data (DNA variant, RNA sequence, structural variant, etc).
Precondition: This sequence instance does not exist in service prior to action.
Success Criteria: Sequence created correctly on server and in the desired format.
Bonus point: New profiles can be built on top of the Sequence resource for complex representation

Example for genetics data representation:

Scenario 2 Search genetics observations from germline analysis

Action: (FHIR Client) Search target observation with patient ID and value for source ("germline")
Precondition: Relevant patient and observations have been created
Success Criteria: A bundle of genetics observations from germline analysis of that patient are returned.
Bonus point: More parameters can be added for searching

Example for corresponding API call and search results

Scenario 3 Clinical and Research Data Warehouses

Action: (FHIR Client) Get all genetic-profile-based observations of patients with the variant c.181T>G
Precondition: Relevant observations have been created
Success Criteria: A bundle of genetics observations, whose extesion 'sequence' referring to sequence instance of variant c.181T>G, are returned.
Bonus point: More parameters can be added for searching

Example for corresponding API call and search results

Scenario 4 Family Member History

Action: (FHIR Client) Get the genetics diagnostic reports of patient's family members.
Precondition: Relevant diagnostic reports have been created
Success Criteria: The genetics diagnostic reports of patient's family members are returned
Bonus point: More parameters can be added for searching

Example for corresponding API call and search results

Scenario 5 Comprehensive Genetics Report

Action: (FHIR Client) Create a comprehensive genetics report for a patient.
Precondition: Relevant diagnostic reports have been created
Success Criteria: The genetics diagnostic reports of patient's family members are returned
Bonus point: More parameters can be added for searching

Example for corresponding API call and search results

TestScript(s)