HL7 FHIR

HL7 FHIR

NMDP hosted FHIR Server

• 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
    • http://fhirtest.b12x.org/
  • Base URL for REST (POST, GET, etc)
    • http://fhirtest.b12x.org/baseDstu3

Example data

• This is a set of xml files representing resource instances that the following scenario.

  • 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.

  • 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.

Background material

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.

• 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)

• 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.

  • recorded presentation
  • PDF files
    • May 2016 HL7_WGM_& FHIR_Connectathon - Bob Milius

• The most recent version of the FHIR specification (currently being balloted) can be found here:

  • http://hl7.org/fhir/2016Sep/

• 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.
    • http://hl7.org/fhir/2016Sep/genomics.html#hla
  • An overview of the FHIR activities of the HL7 Clinical Genomics workgroup can be found here:
    • fhirgenomics.org

• 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

• You can also look at the wiki found at

  • http://wiki.hl7.org/index.php?title=FHIR
    There's a "Help/Getting Started" section there that may be useful.

• Finally, there are a number of blogs out there talking about FHIR. One that I've found useful is this:

  • https://fhirblog.com/getting-started/