HL7 v2 Artefacts

North West Genomic Medicine Service Alliance
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North West Genomic Medicine Service Alliance - Local Development build (v0.0.7) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Message Definitions
- OML_O21 Laboratory Order
- ORU_R01 Unsolicited transmission of an observation message
Segments
- MSH
- PID
- PV1
- ORC
- OBR
- NTE
- DG1
- OBX
- OBX (type = ED)
- SPM
Data Types
- CE
- CX
- EI
- PL
- NDL
- XCN
- XON
HL7 v2 to FHIR Message Conversion
Example: Example Instances
- OML_O21 Laboratory Order
- ORU_R01 Unsolicited transmission of an observation message

Message Definitions

OML_O21 Laboratory Order

HL7 over HTTP is preferred for this message, MLLP is also supported.

POST [base]/
Authorization: Basic {accessToken}
Content-Type: application/hl7-v2+er7

References

EPIC HL7 v2 See Outgoing Ancillary Orders (EPR to RIE)
MEDITECH HL7 v2

Message

Segment HL7	Optionality	Notes
MSH	1..1
PID	1..1
PV1	0..1	PV1 should be populated if PV1-19 Visit Number is known
ORDER	1..*
- ORC	1..*
- OBSERVATION REQUEST	1..*
– OBR	1..*
– NTE	0..*
– DG1	0..*
– OBSERVATION	0..*
— OBX	0..*
- SPECIMEN	0..*	Conditional - required for complete order
– SPM	0..1

ORU_R01 Unsolicited transmission of an observation message

HL7 over HTTP is preferred for this message, MLLP is also supported.

POST [base]/
Authorization: Basic {accessToken}
Content-Type: application/hl7-v2+er7

References

Digital Health and Care Wales - HL7 ORU_R01 2.5.1 Implementation Guide
- See Appendix A – Using ORU to Publish PDF Reports
HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), Release 1 from May 2017 includes Data Standards
EPIC HL7 v2 See Discrete Genomic Results (RIE to EPIC EPR)

Message

Segment HL7	Optionality	Notes
MSH	1..1
PID	1..1
PV1	0..1	PV1 should be populated if PV1-19 Visit Number is known
ORDER OBSERVATION	1..*
- ORC	1..*
- OBR	1..*
– OBSERVATION	1..*
– OBX	1..*

Segments

MSH

This is based on the definition of MSH from NHS England HL7 v2 ADT Message Specification.

Field HL7	Fieldname	Data Type	Optionality	Identifier Type or ValueSet	Example Values
MSH-1	Field Separator		R			`
MSH-2	Encoding Characters		R		^~\&
MSH-3	Sending Application		R		iGene
MSH-4	Sending Facility	HD	R	ODS Code	699X0
MSH-5	Receiving Application	HD	R		EPIC
MSH-6	Receiving Facility		R	ODS Code	R0A
MSH-7	Date/Time Of Message		R		20170126143602
MSH-9	Message Type		R		ORU^R01^ORU_R01
MSH-10	Message Control ID		R		2017012614360280000
MSH-11	Processing ID		R		P
MSH-12	Version ID		R		2.5.1
MSH-13	Accept AcknowledgmentType		R		AL

PID

This is based on the definition of PID from NHS England HL7 v2 ADT Message Specification and Digital Health and Care Wales - HL7 ORU_R01 2.5.1 Implementation Guide

Field HL7	Fieldname	Data Type	Optionality	Identifier Type or ValueSet	Example Values
PID-1	Set ID-PID		R		1
PID-3	Patient Identifier List	CX	R	NHS Number Medical Record Number.	633^^^R0A^MR~9449305552^^^NHS^NH
PID-5	Patient Name		R		CHISLETT^Octavia^^Miss
PID-7	Date/Time of Birth		R		20080920
PID-8	Administrative Sex		R		F
PID-11	Patient Address		R		1 RAVENSFIELD GARDENS^^EPSOM^SURREY^KT19 0ST
PID-13	Phone Number - Home		R		01656 123123^PRN^PH~07927655295^ORN^CP^NET^X.400^abc@home.com~01656 123123~01656123123^PRN^PH^^^abc@home.com~01656123123^PRN^PH
PID-32	Identity Reliability Code		O	Mandatory if the the NHS Number tracing status is not known.	01

v2 to FHIR Conversion: PID to FHIR Patient
FHIR Profile: Patient

Examples

PID|1||633^^^R0A^MR~9449305552^^^^NH||CHISLETT^Octavia||20080920|F|||1 RAVENSFIELD GARDENS^^EPSOM^SURREY^KT19 0ST

FHIR Resource Example: Patient - Octavia CHISLETT NHS Number: 9449305552

PV1

The PV1 segment should represent the episode/stay/visit number, not a consultant episode.

This is based on the definition of PV1 from NHS England HL7 v2 ADT Message Specification

Field HL7	Fieldname	Data Type	Optionality	Identifier Type or ValueSet	Example Values
PV1-1	Set ID - PV1	PL	R		1
PV1-3	Assigned Patient Location		R		^^^R0A09^^^^^^^R0A ^^^P1S8J^^^^^^^699X0
PV1-8	Referring Doctor	XCN	R	Practitioner Identifier	C3456789^Darwin^Samuel^^^Dr^^^GMC
PV1-10	Hospital Service		R	Service	311
PV1-19	Visit Number	CX	O - SHOULD	Hospital Provider Spell Identifier	12345^^^R0A

v2 to FHIR Conversion: PV1 to FHIR Encounter
FHIR Profile: Encounter

Examples

PV1|1|O|^^^R0A09^^^^^^^R0A||||C3456789^Darwin^Samuel^^^Dr^^^GMC|||100|||||||||1001166717|||||||||||||||||||||||||20250129103726+0000

FHIR Resource Example: Encounter ‘episode/stay’ Example

ORC

This is based on the definition of ORC from Digital Health and Care Wales - HL7 ORU_R01 2.5.1 Implementation Guide.

Field HL7	Fieldname	Data Type	Optionality	Identifier Type or ValueSet	Example Values
ORC-2	Placer Order Number	EI	R	Placer Order Number	1601737^R0A^150^L
ORC-3	Filler Order Number	EI	R	Filler Order Number	1001166717^699X0^^255^ISO
ORC-4	Placer Group Number	EI	R	Placer Group Number	1001166717^699X0^^255^ISO
ORC-5	Order Status		O
ORC-9	Date/Time of Transaction		O
ORC-12	Ordering Provider	XCN	R	Practitioner Identifier	C3456789^Darwin^Samuel^^^Dr^^^GMC
ORC-21	Ordering Facility Name	XON	R	Organisation Code

v2 to FHIR Conversion: ORC to FHIR ServiceRequest
FHIR Profile: ServiceRequest

Examples

ORC|NW|1601737^R0A|1001166717^699X0||||||20250129|||C3456789^Darwin^Samuel^^^Dr^^^GMC|||||||||^^R0A^^^ODS

FHIR Resource Example: ServiceRequest Coded Entries Example

OBR

This is based on the definition of OBR from Digital Health and Care Wales - HL7 ORU_R01 2.5.1 Implementation Guide

Field HL7	Fieldname	Data Type	Optionality	Identifier Type or ValueSet	Example Values
OBR-1	Set ID - OBR		R		1
OBR-2	Placer Order Number	EI	R	Placer Order Number	1601737^ R0A^150^L
OBR-3	Filler Order Number	EI	R	Filler Order Number	1001166717^699X0^^255^ISO
OBR-4	Universal Service Identifier		R	Genomic Test Directory	R240.1^Diagnostic testing for known variant(s)^England-GenomicTestDirectory
OBR-6	Requested Date/Time		R for OML_O21		20170126135745
OBR-7	Observation Date/Time		R for ORU_R01		20170126135745
OBR-16	Ordering Provider		R	Practitioner Identifier	C3456789^Darwin^Samuel^^^Dr^^^GMC
OBR-22	Results Rpt/Status Chng -Date/Time		R		20170126135745
OBR-25	Result Status
OBR-32	Principal Result Interpreter	NDL	O - SHOULD	DiagnosticReport.resultsInterpreter[primaryReporter]
OBR-33	Assistant Result Interpreter	NDL	O - SHOULD	DiagnosticReport.resultsInterpreter[secondaryReporter]
OBR-34	Technician	NDL	O - SHOULD	DiagnosticReport.performer[operator]

v2 to FHIR Conversion OML_O21: OBR to FHIR ServiceRequest
v2 to FHIR Conversion ORU_R01: OBR to FHIR DiagnosticReport
FHIR Profile: DiagnosticReport

Examples

OBR|1|1601737^R0A|1001166717^699X0|R240.1^^England-GenomicTestDirectory||20250129||||||||||C3456789^Darwin^Samuel^^^Dr^^^GMC

FHIR Resource Example: Diagnostic Report Example

NTE

Multiple NTE should be converted to a single FHIR Annotation using markdown

Field HL7	Fieldname	Data Type	Optionality	Identifier Type or ValueSet	Example Values
NTE-1	Set ID - NTE
NTE-2	Source of Comment
NTE-3	Comment
NTE-4	Comment Type

v2 to FHIR Conversion OML_O21: NTE to FHIR ServiceRequest
v2 to FHIR Conversion ORU_R01: NTE to FHIR Observation

Examples

NTE|1||Referral lab PLEASE do following tests:
NTE|2||
NTE|3||Test(s) required: WGS
NTE|4||Sample type: Blood
NTE|5||Transport used: Merlin Courier
NTE|6||Tracking Number: ABC123
NTE|7||Sample sent to: LWH Genetics
NTE|8||By: PDAY       on: 02/04/25
NTE|9||
NTE|10||.Speciality Requesting Clinician: PAEDS
NTE|11||Test Group: Neurology
NTE|12||Ethnic Group: White British
NTE|13||Patient is from consanguineous union? : Unknown
NTE|14||Specimen Collection Status: Collect & send with order
NTE|15||Infection Risk: No Specific Risk
NTE|16||Clinical details:
NTE|17||
NTE|18||TESTING
NTE|19||Contact/Bleep No: 123

FHIR Resource Example OML_O21: ServiceRequest Coded Entries Example

FHIR Resource Example ORU_R01: TODO

DG1

Field HL7	Fieldname	Data Type	Optionality	Identifier Type or ValueSet	Example Values
DG1-3	Diagnosis Code	CE
DG1-4	Diagnosis Description

v2 to FHIR Conversion: DG1 to FHIR Condition Note: In orders this is likely to be a coded entry in ServiceRequest.reasonCode as only a code is present.
FHIR Profile: Condition

Examples

DG1|1||363349007^Malignant tumour of stomach^SNM3||20250129103726+0000

FHIR Resource Example ORU_R01: TODO

OBX

This is based on the definition of OBX from Digital Health and Care Wales - HL7 ORU_R01 2.5.1 Implementation Guide

Field HL7	Fieldname	Data Type	Optionality	Identifier Type or ValueSet	Example Values
OBX-1	Set ID – OBX		R		1
OBX-2	Value Type		R	See next section for ED	CE
OBX-3	Observation Identifier	CE	R		842009^Consanguinity^SNM3 97209-1^Shipment tracking number^LN 161714006^Estimated date of delivery^SNM3
OBX-5	Observation Value	Varies	R		LN^Yes^LA33-6 (value type=CE) UK3096580215 (value type=ST) 20250512103726+0000 (value type=DT)
OBX-11	Observation Result Status		R		F
OBX-14	Date/Time of the Observation		O - SHOULD		20190514102417+0000

v2 to FHIR Conversion: OBX to FHIR Observation
FHIR Profile: Observation

Examples

OBX|1|CE|GENEAP^GENETICS TEST PERFORMABLE^https://nw-gmsa.github.io/CodeSystem/MFTQuestionIds|||||||||||20250129103726+0000
OBX|2|CE|230056^What Type of Referral Do You Require?^https://nw-gmsa.github.io/CodeSystem/MFTQuestionIds|||||||||||20250129103726+0000
OBX|3|CE|281269004^High infection risk sample^SNM3|||||||||||20250129103726+0000
OBX|4|ST|230016^Test Type^https://nw-gmsa.github.io/CodeSystem/MFTQuestionIds||Diagnostic Screen/Test|||||||||20250129103726+0000

FHIR Resource Example: Consanguinity (value type=CE)

FHIR Resource Example: Order Tracking Number (value type=ST)

FHIR Resource Example: Pregnancy Expected Delivery Date (value type=DT)

OBX (type = ED)

This is based on the definition of OBX from Digital Health and Care Wales - HL7 ORU_R01 2.5.1 Implementation Guide

Field HL7	Fieldname	Data Type	Optionality	Identifier Type or ValueSet	Example Values
OBX-1	Set ID – OBX		R		1
OBX-2	Value Type	ED	R		ED
OBX-3	Observation Identifier	ED	R	Document Entry Type	1054161000000101^Genetic report^SNM3
OBX-5	Observation Value		R		MOL^IM^PDF^Base64^JVBERI0X…
OBX-11	Observation Result Status		R		F
OBX-14	Date/Time of the Observation		O - SHOULD		20190514102417+0000

v2 to FHIR Conversion: OBX to FHIR DocumentReference
FHIR Profile: DocumentReference

Examples

OBX|1|ED|1054161000000101^Genetic report^SNM3||MOL^IM^PDF^Base64^JVBERi0x...||||||F

FHIR Resource Example: Document Reference Laboratory Report

SPM

This is based on the definition of SPM from Digital Health and Care Wales - HL7 ORU_R01 2.5.1 Implementation Guide

Field HL7	Fieldname	Optionality	Identifier Type or ValueSet	Example Values
SPM-2	Specimen ID	O	Placer Specimen Number^Filler Specimen Number	25GEN-029GN00001&R0A
SPM-3	Specimen Parent IDs	O		^1001166717&699X0
SPM-4	Specimen Type	O	Specimen Type	119325001^Skin specimen^SNM3
SPM-8	Specimen Source Site	O		299706009^Bone structure of wrist and/or hand^SNM3
SPM-9	Specimen Source Site Modifier	O		7771000^Left^SNM3
SPM-17	Specimen Collection Date/Time	O
SPM-18	Specimen Received Date/Time	O
SPM-20	Specimen Availability	O
SPM-30	Accession ID	O	Accession Number
SPM-32	Shipment Tracking Number	O	Shipment Tracking Number

v2 to FHIR Conversion: SPM to FHIR Specimen
FHIR Profile: Specimen

Examples

SPM|1|25GEN-029GN00001&R0A|^1001166717&699X0|258580003^Whole blood specimen^SNM3|||||||||||||20250129103726+0000|||Y

FHIR Resource Example: Specimen Example

Data Types

This applies to HL7 v2 ORU_R01 feeds to the RIE.

ORC-3, ORC-12 (XCN) and ORC-21 (XON) SHALL be populated.

CE

Coded Element. UK SNOMED CT is preferred and may be mandatory depending on use, for example for OXB Type ED, it will be required.

Example

SNOMED

1054161000000101^Genetic report^SNM3

LOINC (from HL7 International)

53577-3^Reason for study^LN 51967-8^Genetic disease(s) assessed^LN 48018-6^Gene studied^LN

CX

Extended Composite ID with Check Digit CX.1 - Id Number, CX-4 - Assigning authority and CX.5 - Identifier Type Code are mandatory

Example

NHS Number

9449305552^^^NHS^NH

Medical Record Number

633^^^R0A^MR

EI

Entity Identifier. EI.1 - Entity Identifier and EI.2 - Namespace Id are mandatory

Example

Manchester University NHS Foundation Trust

1601737^R0A

North West GLH Hub

1001166717^699X0

PL

This is based on the definition of PL from NHS England HL7 v2 ADT Message Specification SHOULD be followed and SHALL be used in ORC-12. In addition, this includes of PL.11 to hold organisation ODS code.

The ODS Site Code SHALL belong to the ODS Code. This is to help avoid data issues in this codesystem.

Field HL7	Fieldname	Data Type	Optionality	Identifier Type or ValueSet	Example Values
PL.4	Facility	HD	R	Organisation Site Code	R0A09
PL.11	Assigning Authority For Location	HD	R	Organisation Code	R0A

NDL

This is based on the definitions of NDL from Royal College of Radiologists

Field HL7	Fieldname	Data Type	Optionality	Identifier Type or ValueSet
NDL-1.CNN.1	Id Number	ST	O	Practitioner Identifier
NDL-1.CNN.2	Family Name	ST	O	Surname
NDL-1.CNN.3	Given Name	ST	O	Forename
NDL-7	Facility	HD	O	Organisation Code

XCN

Extended Composite ID Number and Name for Persons. The definition of XCN from NHS England HL7 v2 ADT Message Specification SHOULD be followed and SHALL be used in ORC-12.

Example

GMC Code

C3456789^Darwin^Samuel^^^Dr^^^GMC

XON

Extended Composite Name and Identification Number for Organizations. The definition of XON from NHS England HL7 v2 ADT Message Specification SHOULD be followed and SHALL be used in ORC-21.

Example

MANCHESTER UNIVERSITY NHS FOUNDATION TRUST^^R0A^^^ODS

HL7 v2 to FHIR Message Conversion

Example: Example Instances

OML_O21 Laboratory Order

Genomics Order with Coded Entries

For the FHIR version see Bundle ‘Message’ - Genomics Order with Coded Entries

MSH|^~\&|HIVE|R0A|LIMS|699X0|20241013103300+0000||OML^O21^OML_O21|urn:uuid:9612365d-52a4-4fab-87e7-8a09d753f095|T|2.4|||AL
PID|1||633^^^R0A^MR~9449305552^^^NHS^NH||CHISLETT^Octavia||20080920|F|||1 RAVENSFIELD GARDENS^^EPSOM^SURREY^KT19 0ST
PV1|1|O|^^^R0A09^^^^^^^R0A||||C3456789^Darwin^Samuel^^^Dr^^^GMC|||100|||||||||1001166717|||||||||||||||||||||||||20250129103726+0000
ORC|NW|1601737^R0A|1001166717^699X0||||||20250129|||C3456789^Darwin^Samuel^^^Dr^^^GMC|||||||||^^R0A^^^ODS
OBR|1|1601737^R0A|1001166717^699X0|R240.1^^England-GenomicTestDirectory||20250129||||||||||C3456789^Darwin^Samuel^^^Dr^^^GMC
NTE|1||Referral lab PLEASE do following tests:
NTE|2||
NTE|3||Test(s) required: WGS
NTE|4||Sample type: Blood
NTE|5||Transport used: Merlin Courier
NTE|6||Tracking Number: ABC123
NTE|7||Sample sent to: LWH Genetics
NTE|8||By: PDAY on: 02/04/25
NTE|9||
NTE|10||Speciality Requesting Clinician: PAEDS
NTE|11||Test Group: Neurology
NTE|12||Ethnic Group: White British
NTE|13||Patient is from consanguineous union? : Unknown
NTE|14||Specimen Collection Status: Collect & send with order
NTE|15||Infection Risk: No Specific Risk
NTE|16||Clinical details:
NTE|17||
NTE|18||TESTING
NTE|19||Contact/Bleep No: 123
DG1|1||363349007^Malignant tumour of stomach^SNM3||20250129103726+0000
DG1|2||363349007^Malignant tumour of stomach^SNM3
OBX|1|CE|GENEAP^GENETICS TEST PERFORMABLE^NWGMSA|||||||||||20250129103726+0000
OBX|2|CE|230056^What Type of Referral Do You Require?^NWGMSA||1186936003^Storage of specimen (procedure)^SNM3|||||||||20250129103726+0000
OBX|3|CE|281269004^High infection risk sample^SNM3||LA32-8^No^LN|||||||||20250129103726+0000
OBX|4|ST|230016^Test Type^NWGMSA||Diagnostic Screen/Test|||||||||20250129103726+0000
OBX|5|CE|77386006^Pregnancy^SNM3||LA33-6^Yes^LN|||||||||20250129103726+0000
OBX|6|ST|231284^Please Select R240 Test(s):^NWGMSA||R240.1: Targeted variant testing|||||||||20250129103726+0000
OBX|7|ST|231285^Please Select R242 Test(s):^NWGMSA||R242.1: Targeted variant testing|||||||||20250129103726+0000
OBX|8|ST|230027^Email Addresses of Non-MFT Clinicians for Result Reports^NWGMSA||charu|||||||||20250129103726+0000
OBX|9|CE|762911000000102^Informed consent given for treatment^SNM3||LA33-6^Yes^LN|||||||||20250129103726+0000
OBX|10|ST|230037^Please Acknowledge That a DNA Sample Will be Stored in the Laboratory on Completion of Testing^NWGMSA||Acknowledged|||||||||20250129103726+0000
OBX|11|ST|230039^Is the Person Ordering the Test the Referring Clinician^NWGMSA||No|||||||||20250129103726+0000
OBX|12|ST|unknown^Name of Supervising Clinician^NWGMSA||DESHPANDE, CHARULATA|||||||||20250129103726+0000
OBX|13|ST|97209-1^Shipment tracking number^LN||UK3096580215|||||||||20250129103726+0000
OBX|14|CE|842009^Consanguinity^SNM3||LA32-8^No^LN|||||||||20250129103726+0000
OBX|15|DT|161714006^Estimated date of delivery^SNM3||20250512103726+0000|||||||||20250129103726+0000
SPM|1|25GEN-029GN00001&R0A|^1001166717&699X0|258580003^Whole blood specimen^SNM3|||||||||||||20250129103726+0000|||Y

NonWGSTestOrderForm-CancerSolidTumor-Example

For the FHIR version see Bundle-NonWGSTestOrderForm-CancerSolidTumor-Example

MSH|^~\&|HIVE|RAX|LIMS|RJZ|20241013103300+0000||OML^O21^OML_O21|156bb6ab-15e7-42f3-a819-ecd16a5b4fbd|T|2.4|||AL
PID|1||9449307555^^^NHS^NH||Hadjkiss^Zelma||20110319||||2 Barclay Close^Fetcham^^^KT22 9SY
ORC|NW||||||||20230908|||9999999998^Smith^Hazel^^^Dr.^^^SDS|||||||||Kingston Hospital NHS Foundation Trust^^RAX01^^^ODS
OBR|1|||M119.5^Multi Target NGS Panel Small^England-GenomicTestDirectory||20230908||||||||||9999999998^Smith^Hazel^^^Dr.^^^SDS
NTE|1||Free text for diagnosis/reason for referral, transplant, life status at time of request details/ e.g. malignant tumour - molecular assessment will aid management
DG1|1||363358000^Malignant tumour of lung^SNM3
DG1|2||relapse^Relapse^England-ReasonForTesting
OBX|1|CE|128462008^Metastatic malignant neoplasm (disorder)^SNM3|||||||||||20230908
OBX|2|CE|6574001^Necrosis (morphologic abnormality)^SNM3|||||||||||20230908
SPM|1|RA257630||364611000000101^Tissue resection sample^SNM3|||||||||||||20230909110000Z|||Y

ORU_R01 Unsolicited transmission of an observation message

MSH|^~\&|iGene|699X0|EPIC|R0A|20190514102527+0200||ORU^R01^ORU_R01|5051095-201905141025|T|2.5.1|||AL
PID|1||633^^^R0A^MR~9449305552^^^NHS^NH||CHISLETT^Octavia^^Miss||20080920|F|||1 RAVENSFIELD GARDENS^^EPSOM^SURREY^KT19 0ST
PV1|1|N|^^^R0A09^^^^^^^R0A|||||C3456789^Darwin^Samuel^^^Dr^^^GMC||311|||||||||12345^^^R0A
ORC|RE|1601737^R0A|1001166717^699X0||CM||||20170126143602|||C3456789^Darwin^Samuel^^^Dr^^^GMC|||||||||MANCHESTER UNIVERSITY NHS FOUNDATION TRUST^^R0A^^^ODS
OBR|1|1601737^R0A|1001166717^699X0|R240.1^Diagnostic testing for known variant(s)^England-GenomicTestDirectory|||20190514102000+0200|||SCC|O|||20190514102000+0200||C3456789^Darwin^Samuel^^^Dr^^^GMC||||||20190514102417+0200
OBX|1|ED|1054161000000101^Genetic report^SNM||MOL^IM^PDF^Base64^JVBERi0x...||||||F

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