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This document is part of the BioCompute Object User Guide

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2.3.1 Extension to External References: SMART on FHIR Genomics

The external references example extension to FHIR resource demonstrates how specific data elements can be extracted from EHR systems or other secure FHIR endpoints via technologies such as SMART on FHIR Genomics (https://www.ncbi.nlm.nih.gov/pubmed/26198304) without compromising patient and providers’ information. This is because the portions being transferred contain no identifiable information about the patient. Instead there is a reference to the actual resource instance (via FHIR URL) through which all data is accessed.

The fhir_extension is defined as an array of endpoints from which to fetch resources.

fhir_endpoint is a string containing the URL of the endpoint of the FHIR server containing the resource. fhir_version must be present showing the FHIR version used.

fhir_resources is an array of resources to fetch from the endpoint, where fhir_resource is a string containing the type of resource used according to the specified version. (a full list of permitted FHIR 3 resources is available at http://hl7.org/fhir/STU3/resourcelist.html) fhir_id is a string containing the server-specific identifier for the resource instance.

The link to FHIR can also be added to the usability domain. More on FHIR Genomics in release 3 of FHIR can be found here: https://www.hl7.org/fhir/genomics.html

SMART on FHIR Genomics provides a framework for EHR-based apps built on FHIR that integrate clinical and genomic information. For more information on how to use the SMART on FHIR Genomics apps, please visit http://projects.iq.harvard.edu/smartgenomics/.

    "extension_domain":{
        "fhir_extension": [
            {
                "fhir_endpoint": "http://fhirtest.uhn.ca/baseDstu3",
                "fhir_version": "3",
                "fhir_resources": [
                    {
                        "fhir_resource": "Sequence",
                        "fhir_id": "21376"
                    },
                    {
                        "fhir_resource": "DiagnosticReport",
                        "fhir_id": "6288583"
                    },
                    {
                        "fhir_resource": "ProcedureRequest",
                        "fhir_id": "25544"
                    },
                    {
                        "fhir_resource": "Observation",
                        "fhir_id": "92440"
                    },
                    {
                        "fhir_resource": "FamilyMemberHistory",
                        "fhir_id": "4588936"
                    }
                ]
            }