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Difference between revisions of "201601 FHIR Genomics"

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==Justification==
 
==Justification==
 
<!--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. -->
FHIR Genomics focuses on reporting clinical genomics data
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The Sequence resource is a core resource in FHIR Genomics. It is used to represent complex genetics data.
  
 
==Proposed Track Lead==
 
==Proposed Track Lead==
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==Expected participants==
 
==Expected participants==
 
<!-- List of the individuals and/or organizations that have indicated a desire to attend the connectathon and implement this track -->
 
<!-- List of the individuals and/or organizations that have indicated a desire to attend the connectathon and implement this track -->
The expected participants are those attending a Connectathon for the first time and returning participants who wish to support this track for themselves and others.
 
 
The number of the participants may be 20-50.
 
The number of the participants may be 20-50.
  
 
==Roles==
 
==Roles==
 
<!-- Roles are sets of functionality (generally defined by a Conformance resource) that a single system can take on -->
 
<!-- Roles are sets of functionality (generally defined by a Conformance resource) that a single system can take on -->
===Role 1 Name===
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===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 -->
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Support the sending of the Sequence resource operations: create, history, read, search and update.
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===FHIR Server===
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<!-- Provide a description of the capabilities this role will have within the connectathon -->
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Support the receiving and processing of the Patient resource 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 Name===
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===Scenario Step 1 Register a new sequence===
:Action: <!--Who does what?  (Use the role names listed above when referring to the participants -->
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:Precondition: <!-- What setup is required prior to executing this step? -->
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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 -->
:Success Criteria: <!-- How will the participants know if the test was successful? -->
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:Precondition: This sequence instance does not exist in service prior to action. <!-- What setup is required prior to executing this step? -->
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: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 -->
 
:Bonus point: <!-- Any additional complexity to make the scenario more challenging -->
 
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Example for genetics data representation:
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* [http://genomics-advisor.smartplatforms.org:4000/sequence-example.html somatic variant in lung cancer]
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* [http://genomics-advisor.smartplatforms.org:4000/sequence-genetics-example3.html RNA variant]
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* [http://genomics-advisor.smartplatforms.org:4000/sequence-genetics-example4.html structural variant]
 
<!-- Provide a description of each task -->
 
<!-- Provide a description of each task -->
  
 
==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 17:32, 11 November 2015

Sequence resource

Submitting WG/Project/Implementer Group

CG

Justification

The Sequence resource is a core resource in FHIR Genomics. It is used to represent complex genetics data.

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 operations: create, history, read, search and update.

FHIR Server

Support the receiving and processing of the Patient resource operations: create, history, read, search and update.

Steps

Scenario Step 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:

Example for genetics data representation:

TestScript(s)