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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 | + | The Sequence resource is a core resource in FHIR Genomics. It is used to represent complex genetics data. |
==Proposed Track Lead== | ==Proposed Track Lead== | ||
| Line 14: | Line 14: | ||
==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 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 --> | ||
| − | === | + | ===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. | ||
| + | |||
| + | ===FHIR Server=== | ||
| + | <!-- 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. | ||
==Steps== | ==Steps== | ||
<!-- What will be the actions performed by participants? --> | <!-- What will be the actions performed by participants? --> | ||
| − | ===Scenario Step 1 | + | ===Scenario Step 1 Register a new sequence=== |
| − | :Action: <!--Who does what? (Use the role names listed above when referring to the participants --> | + | |
| − | :Precondition: <!-- What setup is required prior to executing this step? --> | + | :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? --> | + | :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? --> | ||
:Bonus point: <!-- Any additional complexity to make the scenario more challenging --> | :Bonus point: <!-- Any additional complexity to make the scenario more challenging --> | ||
| − | + | 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-genetics-example3.html RNA variant] | ||
| + | * [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
Contents
Sequence resource
Submitting WG/Project/Implementer Group
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:
