Stream: genomics
Topic: Connectathon 30 - Genomic operations
Bret H (Feb 26 2022 at 01:27):
This stream will be for the May 2022 Connectathon track on Genomic Operations.
Kevin Power (Feb 26 2022 at 15:00):
Thanks @Bret H - Once you have a draft track document here, can you post it here?
Bret H (Feb 28 2022 at 19:44):
The HL7 connectathon page (https://confluence.hl7.org/display/FHIR/2022+-+05+Connectathon+30) has details on all tracks and important information, such as a general tutorial on FHIR. Our track specific page can be reached from there or at: https://confluence.hl7.org/pages/viewpage.action?pageId=90360164
This chat is meant for participant QA or QA on the track. Please read the track document first, it has all the details but:
Short Description
Operations expand the capabilities of a FHIR server to deliver genomics functionality to answer key clinical queries in a streamlined fashion, that is agnostic to the format used to report genetic data (i.e. the input parameters use a single format modality rather than an application needing to know a priori how the data is stored in the server). New operations are proposed that return associated Diagnostic or Therapeutic implications – answering such a request as ‘return the diagnostic implications associated with a specific genetic variation’ without needing to know the variant formatting on the server.
Long Description
Operations expand the capabilities of a FHIR server to deliver genomics functionality. Key clinical queries such as ‘find all patients with genetic variants like my patient,’ ‘does my patient have a specific variant?’, ‘does my patient have a variation in a specific gene of interest?’, and ‘does the patient’s tumor qualify for a specific trial’ are all examples of queries that are simplified using operations. New operations are operations proposed that can answer the question ‘do any of my patient’s genetic variations have diagnostic or therapeutic implications?’ We invite you to try these operations out using a reference implementation of the operations with data from oncology, pharmacogenomic and general genomic knowledge resources. Use cases such as pharmacogenomics reanalysis, therapeutic treatment recommendations, ACMG screening for common conditions and population – cohort – based retrieval are now supported.
Our goal is to try out as many of the proposed operations as possible. We are seeking feedback, including utility of responses, additional parameters, speed of development (with/out operations), coverage of use cases, gaps, additional operations needed. While scenarios are presented here, we are eager to work with/support you on your use cases.
We invite application developers, EHR vendors, Business and Data analysts/scientists, especially, to make use of the reference server. See the scenario section for example scenarios, additional scenarios are welcome during the connectathon. If one would like to develop their own server that is in-scope and we will be happy to try out your server. Additionally, if a knowledge-base, e.g. PharmGKB, would like to test out delivering their content using the Implication operations that would be encouraged.
LINKS BELOW ARE LIABLE TO CHANGE goto the track specific page https://confluence.hl7.org/pages/viewpage.action?pageId=90360164 for most updated links. But if you want a jump on the track check out the following:
Artifacts of focus
https://build.fhir.org/ig/HL7/genomics-reporting/branches/operations/operations.html
will be moving to https://build.fhir.org/ig/HL7/genomics-reporting/operations.html
Reference Implementation: https://fhir-genomics-apis.herokuapp.com/
Description of Reference Implementation (patient lists, capabilities, etc... of reference server): https://docs.google.com/document/d/1b6u-AfjPKfyGZ3orUC7jJUMIJfFUhu3Sk5KOFhjuV0g/edit#
Last updated: Apr 12 2022 at 19:14 UTC
