This wiki has undergone a migration to Confluence found Here

Difference between revisions of "201601 FHIR Genomics"

From HL7Wiki
Jump to navigation Jump to search
Line 30: Line 30:
 
<!-- What will be the actions performed by participants? -->
 
<!-- What will be the actions performed by participants? -->
 
Scenario 2/3/4 are taken from use case in the [https://www.hl7.org/documentcenter/public_temp_E815EAB1-1C23-BA17-0C77D5BDAF63744A/wg/clingenomics/docs/V3DAM_CG_CLINSEQ_R1_O1_2013JAN.pdf HL7 Domain Analysis Model (DAM): Clinical Genomics, Release 1, September 2014 Informative Ballot]
 
Scenario 2/3/4 are taken from use case in the [https://www.hl7.org/documentcenter/public_temp_E815EAB1-1C23-BA17-0C77D5BDAF63744A/wg/clingenomics/docs/V3DAM_CG_CLINSEQ_R1_O1_2013JAN.pdf HL7 Domain Analysis Model (DAM): Clinical Genomics, Release 1, September 2014 Informative Ballot]
 +
- Scenario 2: Page 5
 +
- Scenario 3: Page 11
 +
- Scenario 4: Page 13
 
===Scenario 1 Register a new sequence===
 
===Scenario 1 Register a new sequence===
  
Line 50: Line 53:
 
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.tuuqdmgk56k3 Example for corresponding API call and search results]
 
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.tuuqdmgk56k3 Example for corresponding API call and search results]
  
===Scenario 3 Clinical and Research Data Warehouses===
+
===Scenario 3 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<!-- 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]
 +
 
 +
===Scenario 4 Clinical and research data warehouses===
  
 
:Action: (FHIR Client) Get all genetic-profile-based observations of patients with the variant c.181T>G
 
:Action: (FHIR Client) Get all genetic-profile-based observations of patients with the variant c.181T>G
Line 58: Line 68:
 
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.tsazjrove5a1 Example for corresponding API call and search results]
 
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.tsazjrove5a1 Example for corresponding API call and search results]
  
===Scenario 4 Family Member History===
+
===Scenario 5 Comprehensive genetics report===
: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<!-- 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]
 
 
 
===Scenario 5 Comprehensive Genetics Report===
 
 
:Action: (FHIR Client) Create a comprehensive genetics report for a patient.
 
:Action: (FHIR Client) Create a comprehensive genetics report for a patient.
 
:Precondition: This diagnostic report has never been created
 
:Precondition: This diagnostic report has never been created
Line 73: Line 76:
 
[http://genomics-advisor.smartplatforms.org:4000/diagnosticreport-genetics-comprehensive-bone-marrow-report.xml.html xml codes for comprehensive report]
 
[http://genomics-advisor.smartplatforms.org:4000/diagnosticreport-genetics-comprehensive-bone-marrow-report.xml.html xml codes for comprehensive report]
  
===Scenario 6 Sequence Quality===
+
===Scenario 6 Sequence quality===
 
:Action: (FHIR Client) Get the quality of the sequence under consideration.
 
:Action: (FHIR Client) Get the quality of the sequence under consideration.
 
:Precondition: This sequence instance has been created
 
:Precondition: This sequence instance has been created

Revision as of 21:04, 17 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 2/3/4 are taken from use case in the HL7 Domain Analysis Model (DAM): Clinical Genomics, Release 1, September 2014 Informative Ballot - Scenario 2: Page 5 - Scenario 3: Page 11 - Scenario 4: Page 13

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 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 4 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 5 Comprehensive genetics report

Action: (FHIR Client) Create a comprehensive genetics report for a patient.
Precondition: This diagnostic report has never been created
Success Criteria: Sequence created correctly on server and in the desired format.
Bonus point: Extensions can be added.

Example for comprehensive report and xml codes for comprehensive report

Scenario 6 Sequence quality

Action: (FHIR Client) Get the quality of the sequence under consideration.
Precondition: This sequence instance has been created
Success Criteria: Target sequence instance is returned.
Bonus point: More parameters can be added for searching

Example for corresponding API call and search results

TestScript(s)

The staging page can be found at: http://genomics-advisor.smartplatforms.org:4000/resourcelist.html