Stream: genomics
Topic: Jan 2019 Connectathon
Bob Dolin (Nov 27 2018 at 23:15):
Greetings,
Is anyone planning on being a supplier of genomics data, or a genomics data server, for the upcoming connectathon? If so, is there interest in participating in the PGx CDS use case [http://wiki.hl7.org/index.php?title=201901_Clinical_Genomics#Scenario_9_PGx_CDS]?
Thanks
Kevin Power (Jan 12 2019 at 14:46):
Hi all - For anyone participating at the Connectathon in San Antonio, we can use this thread to share information, answer questions. Welcome to San Antonio!
Jamie Jones (Jan 12 2019 at 14:58):
Intro slides >>> https://tinyurl.com/cgconnectathon
Bret H (Jan 12 2019 at 15:22):
5 to 6 pm today in FRIO we have the space for a CG discussion on validating against our IG
will be trying to get Bob Dolin on the line as he has had some (rough) recent experience
Jamie Jones (Jan 12 2019 at 15:24):
And 3-4pm tomorrow we have the PECAN room for everyone to get together and share results before the final wrap ups back here in the main room
Patrick Werner (Jan 12 2019 at 15:28):
5 to 6 pm today in FRIO we have the space for a CG discussion on validating against our IG
will be trying to get Bob Dolin on the line as he has had some (rough) recent experience
great! I'll join.
Bob Milius (Jan 12 2019 at 15:48):
fyi, some info about FHIR Validation
-
overview of how the FHIR specification supports validation of resources.
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standalone FHIR Validator
-
download
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documentation
-
-
youtube videos for Validation in .NET and Java
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javascript FHIR validator
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and see thread here about validating against the IG
Bob Milius (Jan 12 2019 at 17:50):
Here's a simple transaction bundle that contains a Patient and a Specimen that references that Patient.
<Bundle xmlns="http://hl7.org/fhir"> <type value="transaction"/> <entry> <fullUrl value="urn:uuid:13f34265-335c-4853-bc38-0815315edafa"/> <resource> <Patient> <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"> <p>name: John Storm</p> <p>gender: male</p> <p>born: 1986-12-31</p> </div> </text> <name> <use value="official"/> <text value="John Storm"/> <family value="Storm"/> <given value="John"/> </name> <gender value="male"/> <birthDate value="1986-12-31"/> </Patient> </resource> <request> <method value="POST"/> <url value="Patient"/> </request> </entry> <entry> <fullUrl value="urn:uuid:e44fbe33-6084-4ae2-a95e-8bc451c63340"/> <resource> <Specimen xmlns="http://hl7.org/fhir"> <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><pre>a buccal swab</pre></div> </text> <subject> <reference value="urn:uuid:13f34265-335c-4853-bc38-0815315edafa"/> <display value="John Storm"/> </subject> <collection> <collectedDateTime value="2016-11-10"/> <method> <coding> <system value="http://hl7.org/fhir/v2/0488"/> <code value="SWA"/> </coding> </method> <bodySite> <coding> <system value="http://snomed.info/sct"/> <code value="261063000"/> <display value="Buccal space"/> </coding> <text value="Buccal space"/> </bodySite> </collection> </Specimen> </resource> <request> <method value="POST"/> <url value="Specimen"/> </request> </entry> </Bundle>
This validates with the standalone FHIR validator, e.g.,
$ java -jar org.hl7.fhir.validator.jar PatientSpecimenTransactionBundle_R3.xml -version 3.0
FHIR Validator Build ??
Arguments: PatientSpecimenTransactionBundle_R3.xml -version 3.0
.. connect to tx server @ http://tx.fhir.org
.. definitions from hl7.fhir.core#3.0.1
(v3.0.1-null)
.. validate [PatientSpecimenTransactionBundle_R3.xml]
Success...validating PatientSpecimenTransactionBundle_R3.xml: error:0 warn:0 info:0
and can be uploaded to fhirtest.b1x.org using this curl command:
$ curl -X POST -d @PatientSpecimenTransactionBundle_R3.xml -H "Content-Type: text/xml" http://fhirtest.b12x.org/r3
<Bundle xmlns="http://hl7.org/fhir">
<id value="4da86f0c-4207-4b97-83c3-0e3415e6a980"/>
<type value="transaction-response"/>
<link>
<relation value="self"/>
<url value="http://fhirtest.b12x.org/r3"/>
</link>
<entry>
<response>
<status value="201 Created"/>
<location value="Patient/2892/_history/1"/>
<etag value="1"/>
<lastModified value="2019-01-12T17:41:59.875+00:00"/>
</response>
</entry>
<entry>
<response>
<status value="201 Created"/>
<location value="Specimen/2893/_history/1"/>
<etag value="1"/>
<lastModified value="2019-01-12T17:41:59.876+00:00"/>
</response>
</entry>
</Bundle>
Jamie Jones (Jan 12 2019 at 21:03):
CG in the HL7 blog: http://blog.hl7.org/hl7-publishes-valuable-clinical-genomics-domain-analysis-model
Jamie Jones (Jan 12 2019 at 22:31):
If everyone could ensure recap slides (feel free to group up per project/group) get added to the presentation (https://tinyurl.com/cgconnectathon) it would be a great help to make use of our breakout time tomorrow at 3
Bret H (Jan 12 2019 at 22:58):
From the PGx track. Minimal FHIR genetic described variant cloud-based server. Example transactions:
Use Patient MRN to learn patient resource id (watch out there is a spurious line return in this link): https://d5fkhad4o4.execute-api.us-east-1.amazonaws.com/dev/Patient?identifier=http://example.com/fhir/identifier/mrn|10002970
Use the patient ID to retrieve described genetic variants: https://d5fkhad4o4.execute-api.us-east-1.amazonaws.com/dev/Observation?subject=Patient/HG03239&code='TBD-Described'
Best,
Bret
Bret H (Jan 12 2019 at 23:12):
FYI: Aziz and Kevin completed the circuit - EMR trigger to App, App to FHIR genetic variant repo, App back to EMR. Very cool stuff!
Bret H (Jan 12 2019 at 23:57):
from 5 to 6 pm. some rough notes:
Grahame's opinion O and O gets to be given a tracker to remove the examples in CORE.
project manager is happy to receive technical correction requests to modify genetic examples to indicate the more recent IG which is available
request to technical correction once IG is published to point relevant genomics work to our new IG
Bob Dolin - validated against our IG?
validation of example instances?
put in a brief instruction for validating?
- Graham ask on chat and we can improve documentation and tool
Kevin
Patrick and he were fighting with examples where it turns out that the profile is to blame
profiles not completely correct and there might be some validator
Bob M
left awesome notes in zulip chat
Graham - JAVA validator is the authoritative one at the moment
-- Please add or correct ---
Jamie Jones (Jan 13 2019 at 15:30):
Hey all-- it looks like FMG wants our report by 2:00 so we'll need to recap outcomes/progress before the 3pm breakout. Please add info to the slides (https://tinyurl.com/cgconnectathon) as you can. Thanks!
Bret H (Jan 13 2019 at 17:21):
Potential example for Region Studied to deliver all the observations that relate to a specific patient and specific gene:
{
"resourceType": "Observation",
"id": "studReg",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-region-studied"
]
},
"status": "final",
"category": {
"coding": [
{"coding":[{"system":"http://loinc.org","code":"TBD-RegionsStudied"}]}
]
},
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "TBD-Described",
"display": "Genetic variant assessment"
}
]
},
"subject": {
"reference": "Patient/HG03239"
},
"issued": "2019-01-07T17:48:34+05:30",
"valueCodeableConcept": {
"coding": [
{
"system": "willBeRemoved",
"code": "None",
"display": "NotNeeded"
}
]
},
"specimen": {
"reference": "Specimen/specimen1"
},
"component": [
{
"code": {
"coding": [
{"coding":[{"system":"http://loinc.org","code":"48018-6"}]}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:2625",
"display": "CYP2D6"
}
]
}
},
{
"code": {
"coding": [
{"coding":[{"system":"http://loinc.org","code":"TBD-RegionScope"}]}
]
},
"valueCodeableConcept": {
"coding": [
{
"system:"CG"
"code": "SpecificVariants"
}
]
}
},
"hasMember":[
{
"reference":"Observation/descrete1"
},
{
"reference":"Observation/descrete2"
}
]
}
Jamie Jones (Jan 13 2019 at 17:26):
corresponding query draft: Observation?code=TBD-RegionsStudied&combo-code=http://loinc.org|48018-6&combo-value-concept=http://www.genenames.org|HGNC:2625
Kevin Power (Jan 13 2019 at 23:44):
Here is the progress on resolving QA errors from the last two days (good progress): ig-start.png ig-end.png
Bret H (Jan 15 2019 at 18:35):
Anyone have a full spec-compliant R4 server that we can 1) put a profile into, 2) test query syntax on?
Last updated: Apr 12 2022 at 19:14 UTC
