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==Orientation== | ==Orientation== | ||
| + | |||
| + | [https://docs.google.com/presentation/d/1slLQpinBVum2l0Yx4XWlC2enMyaq-GxMNKiDv8tWB1Q/edit?usp=sharing FHIR Connectathon 19 Track Orientation Slides] | ||
[http://hl7.org/fhir/uv/genomics-reporting/index.html Clinical Genomics Reporting IG] | [http://hl7.org/fhir/uv/genomics-reporting/index.html Clinical Genomics Reporting IG] | ||
| + | |||
| + | [https://youtu.be/ACb6sDqrYJ0 Clinical Genomics Track Orientation Recording] | ||
| + | |||
| + | Focus of the Connectathon: | ||
| + | ===DiagnosticReport:=== | ||
| + | [http://hl7.org/fhir/uv/genomics-reporting/diagnosticreport.html Genetics Diagnostic Report] | ||
| + | ===Findings=== | ||
| + | [http://hl7.org/fhir/uv/genomics-reporting/general.html#findings Genetic Findings] | ||
| + | ===Interpretations=== | ||
| + | [http://hl7.org/fhir/uv/genomics-reporting/general.html#interpretations Genetic Interpretations] | ||
| + | ===Impacts=== | ||
| + | [http://hl7.org/fhir/uv/genomics-reporting/general.html#impacts Genetic Impacts] | ||
| + | ===Sequenced Variants=== | ||
| + | [http://hl7.org/fhir/uv/genomics-reporting/sequencing.html#1.3 Sequenced Variants] | ||
==Zulip Chat== | ==Zulip Chat== | ||
| Line 22: | Line 38: | ||
==Justification== | ==Justification== | ||
| − | After getting Feedback from the first ballot of the Clinical Genomics Implementation Guide in the May 2018 ballot cycle the balloted IG and profiles should be tested in the Connectathon to get feedback from implementers using it. | + | After getting Feedback from the first ballot of the Clinical Genomics Implementation Guide in the May 2018 ballot cycle, the balloted IG and profiles should be tested in the Connectathon to get feedback from implementers using it. |
<!--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. --> | ||
==Proposed Track Lead== | ==Proposed Track Lead== | ||
| − | + | Patrick Werner ([mailto:patrick.werner@molit.eu patrick.werner@molit.eu]) | |
See [[Connectathon_Track_Lead_Responsibilities]] | See [[Connectathon_Track_Lead_Responsibilities]] | ||
| Line 33: | Line 49: | ||
==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 --> | ||
| − | + | :Kevin P | |
| + | :Bob M | ||
| + | :Alex M | ||
| + | :Joseph K (?) | ||
| + | :Paul Lynch (NLM) | ||
| + | :Ye Wang (NLM) | ||
| + | :Amnon Shabo (Shvo) | ||
| + | :Dora Finkeisen (?) | ||
| + | :Patrick Werner (Molit Institut) | ||
| + | :Joel Schneider | ||
==Roles== | ==Roles== | ||
| − | + | * Genomic Diagnostic Report producer (Lab)<br> | |
| − | Genomic Diagnostic Report producer (Lab)<br> | + | * Genomic Diagnostic Report consumer(Hospital) |
| − | Genomic Diagnostic Report consumer(Hospital) | ||
==Scenarios== | ==Scenarios== | ||
| + | ====Genetic Diagnostic Report (GDR) as single resources==== | ||
| + | 1. Create a GDR | ||
| + | :'''Examples of paper based Genetic Diagnostic Reports can be found [https://drive.google.com/drive/folders/18T4RS0VnrJdLS3k79skbrZ0cYyL1U53t?usp=sharing here].''' | ||
| + | :Action: GDR Producer creates a new Genomic Diagnostic Report instance, including all needed referenced Observation Resource Instances like Interpretation, Impact, Described Variant, etc., that is conformant with the Genetics Diagnostic Report profile. | ||
| + | :Precondition: none | ||
| + | :Success Criteria: GDR passes validation against the Diagnostic Report schema and is identified as valid against the GDR profile by the FHIR profile validation tool or through validation in a FHIR server. | ||
| + | |||
| + | 2. Submit GDR | ||
| + | :Action: GDR Producer submits Diagnostic Report and referenced Resources to a FHIR Test Server. | ||
| + | :Precondition: GDR has been created, GDR Producer knows base URL of the used FHIR Server. | ||
| + | :Success Criteria: GDR and referenced Resources are stored on FHIR Server | ||
| + | 3. Query GDR | ||
| + | :Action: GDR Consumer searches a FHIR Server for a specific GDR using one or more search criteria. | ||
| + | :Precondition: GDR and referenced Resources are available on the test server. | ||
| + | :Success Criteria: GDR and referenced Resources are returned | ||
| + | :Bonus point: Visual Representation of the GDR | ||
| − | :Precondition: | + | ====Exchange of Genetic Diagnostic Report (GDR) as a document==== |
| + | 1. Create a GDR document | ||
| + | :Action: GDR Producer creates a new Genomic Diagnostic Report document instance. | ||
| + | :Precondition: A validated GDR. | ||
| + | :Success Criteria: The GDR document passes validation on a FHIR server. | ||
| − | :Success Criteria: - | + | 2. Submit GDR |
| + | Action: GDR Producer submits a Diagnostic Report document bundles to a FHIR Test Server. | ||
| + | Precondition: GDR document has been created, GDR Producer knows base URL of the used FHIR Server. | ||
| + | Success Criteria: GDR document is stored on FHIR Server. | ||
| + | :Bonus point: '''POST'''ing single resources and creating the document bundle on-the-fly using the $document operation. | ||
| − | :Bonus point: | + | 3. Query GDR |
| + | :Action: GDR Consumer searches a FHIR Server for a specific GDR document using one or more search criteria. | ||
| + | :Precondition: GDR document is available on the test server. | ||
| + | :Success Criteria: GDR document is returned. | ||
| + | :Bonus point: Visual Representation of the GDR | ||
Latest revision as of 20:02, 27 September 2018
Return to September 2018 Proposals
Contents
Clinical Genomics Track
This track will focus on exchanging Genetic Diagnostic Reports in FHIR R4 as described in the Clinical Genomics Reporting IG
For this track, we will be using the balloted STU4 version of FHIR.
Orientation
FHIR Connectathon 19 Track Orientation Slides
Clinical Genomics Reporting IG
Clinical Genomics Track Orientation Recording
Focus of the Connectathon:
DiagnosticReport:
Findings
Interpretations
Impacts
Sequenced Variants
Zulip Chat
The Zulip Chat will be used to coordinate among participants during the connectathon:
Submitting WG/Project/Implementer Group
Justification
After getting Feedback from the first ballot of the Clinical Genomics Implementation Guide in the May 2018 ballot cycle, the balloted IG and profiles should be tested in the Connectathon to get feedback from implementers using it.
Proposed Track Lead
Patrick Werner (patrick.werner@molit.eu)
See Connectathon_Track_Lead_Responsibilities
Expected participants
- Kevin P
- Bob M
- Alex M
- Joseph K (?)
- Paul Lynch (NLM)
- Ye Wang (NLM)
- Amnon Shabo (Shvo)
- Dora Finkeisen (?)
- Patrick Werner (Molit Institut)
- Joel Schneider
Roles
- Genomic Diagnostic Report producer (Lab)
- Genomic Diagnostic Report consumer(Hospital)
Scenarios
Genetic Diagnostic Report (GDR) as single resources
1. Create a GDR
- Examples of paper based Genetic Diagnostic Reports can be found here.
- Action: GDR Producer creates a new Genomic Diagnostic Report instance, including all needed referenced Observation Resource Instances like Interpretation, Impact, Described Variant, etc., that is conformant with the Genetics Diagnostic Report profile.
- Precondition: none
- Success Criteria: GDR passes validation against the Diagnostic Report schema and is identified as valid against the GDR profile by the FHIR profile validation tool or through validation in a FHIR server.
2. Submit GDR
- Action: GDR Producer submits Diagnostic Report and referenced Resources to a FHIR Test Server.
- Precondition: GDR has been created, GDR Producer knows base URL of the used FHIR Server.
- Success Criteria: GDR and referenced Resources are stored on FHIR Server
3. Query GDR
- Action: GDR Consumer searches a FHIR Server for a specific GDR using one or more search criteria.
- Precondition: GDR and referenced Resources are available on the test server.
- Success Criteria: GDR and referenced Resources are returned
- Bonus point: Visual Representation of the GDR
Exchange of Genetic Diagnostic Report (GDR) as a document
1. Create a GDR document
- Action: GDR Producer creates a new Genomic Diagnostic Report document instance.
- Precondition: A validated GDR.
- Success Criteria: The GDR document passes validation on a FHIR server.
2. Submit GDR Action: GDR Producer submits a Diagnostic Report document bundles to a FHIR Test Server. Precondition: GDR document has been created, GDR Producer knows base URL of the used FHIR Server. Success Criteria: GDR document is stored on FHIR Server.
- Bonus point: POSTing single resources and creating the document bundle on-the-fly using the $document operation.
3. Query GDR
- Action: GDR Consumer searches a FHIR Server for a specific GDR document using one or more search criteria.
- Precondition: GDR document is available on the test server.
- Success Criteria: GDR document is returned.
- Bonus point: Visual Representation of the GDR
