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Exploring FHIR
Brad edited this page Aug 27, 2020
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3 revisions
This example encodes a frame in the set of surgical data in supplementary table 1 in this paper, Heidelberg Colorectal Data Set for Surgical Data Science in the Sensor Operating Room. This FHIR example is used as a reference source.
It combines the observations made across four devices; the endoscope, the thermoflator, the OR lights, and the endoscopic light source. This could be organized in several different ways; I chose to represent this as a bundle.
{
"resourceType": "Bundle",
"id": "frame0",
"meta": {
"lastUpdated": "2020-08-01T08:00:00-04:00"
},
"type": "batch",
"entry": [
{
"resourceType": "Observation",
"id": "endoscope_frame0",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>(human readable text)</p></div>"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "procedure",
"display": "Procedure"
}
]
}
],
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(appropriate code for endoscope)",
"display": "(appropriate label for endoscope)"
}
]
},
"subject": {
"reference": "Patient/12345678",
"display": "SMITH, J (ID:12345678)"
},
"effectiveDateTime": "2020-08-01T08:00:00-04:00",
"performer": [
{
"reference": "Practitioner/87654321",
"display": "DOE, J"
}
],
"device": {
"display": "Endoscope"
},
"component": [
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for white balance)",
"display": "(MDC description for white balance)"
}
]
},
"valueInteger": 0
},
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for gains)",
"display": "(MDC description for gains)"
}
]
},
"valueInteger": -1
},
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for exposure index)",
"display": "(MDC description for exposure index)"
}
]
},
"valueInteger": -1
}
}
},
{
"resourceType": "Observation",
"id": "thermoflator_frame0",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>(human readable text)</p></div>"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "procedure",
"display": "Procedure"
}
]
}
],
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(appropriate code for thermoflator)",
"display": "(appropriate label for thermoflator)"
}
]
},
"subject": {
"reference": "Patient/12345678",
"display": "SMITH, J (ID:12345678)"
},
"effectiveDateTime": "2020-08-01T08:00:00-04:00",
"performer": [
{
"reference": "Practitioner/87654321",
"display": "DOE, J"
}
],
"device": {
"display": "Thermoflator"
},
"component": [
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for current gas flowrate)",
"display": "(MDC description for current gas flowrate)"
}
]
},
"valueInteger": 115
},
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for target gas flowrate)",
"display": "(MDC description for target gas flowrate)"
}
]
},
"valueInteger": 160
},
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for current gas pressure)",
"display": "(MDC description for current gas pressure)"
}
]
},
"valueInteger": 9
},
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for target gas pressure)",
"display": "(MDC description for target gas pressure)"
}
]
},
"valueInteger": 15
},
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for used gas volume)",
"display": "(MDC description for used gas volume)"
}
]
},
"valueInteger": 42
},
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for gas supply pressure)",
"display": "(MDC description for gas supply pressure)"
}
]
},
"valueInteger": 670
},
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for device on)",
"display": "(MDC description for device on)"
}
]
},
"valueInteger": 0
}
}
}
{
"resourceType": "Observation",
"id": "orlights_frame0",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>(human readable text)</p></div>"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "procedure",
"display": "Procedure"
}
]
}
],
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(appropriate code for or lights)",
"display": "(appropriate label for or lights)"
}
]
},
"subject": {
"reference": "Patient/12345678",
"display": "SMITH, J (ID:12345678)"
},
"effectiveDateTime": "2020-08-01T08:00:00-04:00",
"performer": [
{
"reference": "Practitioner/87654321",
"display": "DOE, J"
}
],
"device": {
"display": "OR Lights"
},
"component": [
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for all lights off)",
"display": "(MDC description for all lights off)"
}
]
},
"valueInteger": 0
},
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for intensity light 1)",
"display": "(MDC description for intensity light 1)"
}
]
},
"valueInteger": 100
},
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for intensity light 2)",
"display": "(MDC description for intensity light 2)"
}
]
},
"valueInteger": 100
}
}
}
{
"resourceType": "Observation",
"id": "endoscopiclightsource_frame0",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>(human readable text)</p></div>"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "procedure",
"display": "Procedure"
}
]
}
],
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(appropriate code for endoscopic light source)",
"display": "(appropriate label for endoscopic light source)"
}
]
},
"subject": {
"reference": "Patient/12345678",
"display": "SMITH, J (ID:12345678)"
},
"effectiveDateTime": "2020-08-01T08:00:00-04:00",
"performer": [
{
"reference": "Practitioner/87654321",
"display": "DOE, J"
}
],
"device": {
"display": "Endoscopic Light Source"
},
"component": [
{
"code": {
"coding": [
{
"system": "urn:oid:2.16.840.1.113883.6.24",
"code": "(MDC code for intensity)",
"display": "(MDC description for intensity)"
}
]
},
"valueInteger": 5
}
}
}
]
}
- SMART on FHIR Python client, SMART FHIR Parser in Python: Flexible Python client for FHIR servers supporting the SMART on FHIR protocol
- Python FHIR library: HL7 FHIR Reference in Python
- fhir-py: This package provides an API for CRUD operations over FHIR resources
- HAPI: HAPI Java FHIR library
- DotNet FHIR Client: Reference client with branches supporting each version of FHIR