HL7 FHIR
- A FHIR test server operated by NMDP®/Be The Match® Bioinformatics Research. This server is entirely built using HAPI-FHIR, a 100% open-source Java implementation of the FHIR specification.
- Web interface
- Base URL for REST (POST, GET, etc)
- This is a set of xml files and snippets of python3 code to POST resource instances to a FHIR server.
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00_Patient
contains a simple example of an instance of a Patient resource. Also included are short examples of python3 code that sends the resource instance to http://fhirtest.b12x.org/baseDstu3/Patient. POSTing this to a FHIR server will return the URI endpoint of the resource instance. For example, the URI that is returned might look like<br > http://fhirtest.b12x.org/baseDstu3/Patient/27/_history/1<br> Keep track of the URI if you want to reuse the same Patient with another resource instance. -
01_Specimen
example of an instance of Specimen resource, that represents a buccal swab from the Patient described above. -
02_SimpleTransactionBundle
A single transaction bundle that creates a Patient, a Specimen from that patient, a Sequence from that Specimen, and an Observation about a single HLA-A allele -
todo: A buccal smear collected on a swab (Specimen) is collected from a potential donor (Patient) and is sent to a HLA typing lab (Organization) and requests that HLA typing for HLA-A, HLA-B, and HLA-DBR1 (DiagnosticRequest). The lab does DNA sequencing for each locus (Sequence) and assigns allele names (Observation) and generates genotypes for each locus (Observation). These are aggregated into a single report (DiagnosticReport) and sent back to the requestor.
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- a DiagnosticReport contains a collection of Observations, each referring to a separate locus
- One locus expanded to show how genotypes, alleles, and sequence are related for a particular locus
There's a lot of information around FHIR, and if you aren't already familiar with HL7, it can be a bit intimidating to find your way around.
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First, here are links to powerpoint presentations that were given in recent HL7 FHIR webinars/tutorials, aimed at three different audiences. These may be shared through the Creative Commons license.
- FHIR for Executives Part 1
- FHIR for Executives Part 2
- FHIR for Architects
- [FHIR for Developers](FHIR for Developers-baltimore.pptx)
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Here is a meeting report by Bob Milius after attending a FHIR Connectathon in May 2016. A brief description of FHIR is presented, and what Bob learned from attending the Connectathon, including a strategy for developing HLA genotyping report.
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The most recent version of the FHIR specification (currently being balloted) can be found here:
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HL7 Clinical Genomics Workgroup
- The HL7 Clinical Genomics Work Group is developing a Genomics Implementation Guidance document, which describes how to use FHIR resources and profiles for reporting genetics results. In that, there's a section on HLA genotyping with a few examples. It's just a draft, but it should give you an idea of an approach we have been exploring.
- An overview of the FHIR activities of the HL7 Clinical Genomics workgroup can be found here:
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ClinFHIR - a wonderful web tool with a GUI to create resource instances and profiles
- http://clinfhir.com/
- brief description on how to use ClinFHIR
- blog about ClinFHIR by the developer, David Hay
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You can also look at the wiki found at
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http://wiki.hl7.org/index.php?title=FHIR
There's a "Help/Getting Started" section there that may be useful.
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http://wiki.hl7.org/index.php?title=FHIR
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Finally, there are a number of blogs out there talking about FHIR. One that I've found useful is this: