© 2024 IQVIA - All Rights Reserved

ClinSpark / ClinAxys Lab Integration

Owned by Riggi Luckiesh
Last updated: 19-Dec-2024 by Ravishankar Prakash
10 min read

Introduction

ClinAxys is a third-party LIMS supplied by Clinical Systems Ltd., UK Office: PO Box 1346, Wilburton, Ely, Cambridgeshire CB6 3QY, United Kingdom.

The trademark ClinAxys® is a registered trademark of Clinical Systems Holdings Ltd.

ClinSpark has been successfully interfaced with ClinAxys LIMS instances using the approach defined below.

Overview

The lab integration is a bi-directional interface where messages in the form of HL7 files pass back and forth via a set of shared SFTP directories.

ClinSpark will host the SFTP server, these credentials will be provided securely to the lab via email.

HL7 files are used for orders sent by ClinSpark to the lab, with results and optionally confirmation messages sent from the lab to ClinSpark.

The format of these messages is governed by HL7 specifications Caristix HL7-Definition V2 and the requirements of the safety lab.

Order Message Segments

Each specimen tube will have a unique barcode and HL7 file.

Barcodes are typically 12 digits in length. The first character is a fixed prefix, which is configurable. It can be any alpha or numeric character. The next digits are a digit sequence unique to the specimen tube. The last 2 digits represent the specimen container suffix when a container is assigned to a panel and/or test.

A best practice is for ClinSpark to pass study context information about each sample, such as study name, study event name, cohort and subject numbers. These should be visible to the lab techs, to facilitate conversations with the clinical site when there are issues. We can accommodate many ways to do this, it is up to the lab.

Example Order Message

MSH|^~\&|ClinSpark|FH|Lab|ST|202403131824||ORM|1710372276819cf57c38|P|2.3 PID|1|5920||P1001^|Garcia^Dennis^||19980823|F||C|1ST STREET^^SOMEWHERE^WI^53090||^^^|C||||^^^C^^^|||| CSS|b Data Stu|| CTI|REPEAT|| ORC|NW|B00104277-C99^|B00104277-C99^LAB|Urine aliquot 10 ml||||||||123^Fredrickson^Francine^^^^^N||||^^ OBR|1|B00104277-C99^LAB|^LAB|12206^CALCIUM URINE^L|||202403131816||^||N||^|||123^Fredrickson^Francine^^^^^N||||^^||||||^||| ORC|NW|B00104277-C99^|B00104277-C99^LAB|Urine aliquot 10 ml||||||||123^Fredrickson^Francine^^^^^N||||^^ OBR|2|B00104277-C99^LAB|^LAB|12207^PHOSPHATE URINE^L|||202403131816||^||N||^|||123^Fredrickson^Francine^^^^^N||||^^||||||^||| ORC|NW|B00104277-C99^|B00104277-C99^LAB|Urine aliquot 10 ml||||||||123^Fredrickson^Francine^^^^^N||||^^ OBR|3|B00104277-C99^LAB|^LAB|12201^POTASSIUM URINE^L|||202403131816||^||N||^|||123^Fredrickson^Francine^^^^^N||||^^||||||^||| ORC|NW|B00104277-C99^|B00104277-C99^LAB|Urine aliquot 10 ml||||||||123^Fredrickson^Francine^^^^^N||||^^ OBR|4|B00104277-C99^LAB|^LAB|12200^SODIUM URINE^L|||202403131816||^||N||^|||123^Fredrickson^Francine^^^^^N||||^^||||||^|||

MSH Segment

Sequence

Name

Value

Comment

1

Field Separator

|

Hard Coded

2

Encoding Characters

^~\&

Hard Coded

3

Sending Application

[Sending Application]

Obtained from Lab Interface Config

4

Sending Facility

[Sending Facility]

Obtained from Lab Interface Config

5

Receiving Application

[Receiving Application]

Obtained from Lab Interface Config

6

Receiving Facility

ST

Hard Coded

7

Date/Time of Message

Time of order file creation

 

Format: yyyyMMddHHmm

8

Security

NULL

Not Required

9

Message Type

ORM

Hard Coded

 

10

Message Control ID

System current time and ID

 

ClinSpark generates for each file

11

Processing ID

Environment ID

If production = P

12

Version ID

2.3

Hard Coded

PID Segment

Sequence

Name

Value

Comment

1

Set ID

1

Hard Coded

2

Patient ID

[Subject Volunteer ID]

Obtained from Volunteer Profile

3

Patient Identifier List

NULL

Not Required

4

Alternate Patient ID - PID

4.1 [Subject Screening Number]

4.2 [Subject Randomization Number]

Each sub-field will be separated with “^”

*Randomization number only present if subject is randomized

5

Patient Name

5.1 [Subject Last Name Initial]

5.2 [Subject First Name Initial]

5.3 [Subject Middle Name Initial]

Initials will be the first character (alpha, numeric or character) of the Subject First, Last and Middle name within the Volunteer Database in ClinSpark

If no middle initial = empty

Each sub-field will be separated with “^”

Example 1:

 

|J^2^|

Example 2:

|J^J^J|

6

Mother's Maiden Name

NULL

Not Required

7

Date/Time of Birth

[Subject Birth Date]

 

Format:

yyyyMMdd

8

Administrative Sex

[Subject Gender]

Male and Female which will be stored as ‘M' and 'F’

9

Patient Alias

NULL

Not Required

10

Race

[Subject Race Code]

Race Codes:

American Indian or Alaskan Native = I

Asian = A

Black or African American = B

Native Hawaiian or Other Pacific Islander = O

White = C

Other Race = O

Unknown = X

11

Patient Address

11.1 [Site Address]

11.2 NULL

11.3 [Site City]

11.4 [Site State]

11.5 [Site Postal Code]

Each sub-field will be separated with “^”

Obtained from Site Details

12

County Code

NULL

Not Required

13

Phone Number - Home

NULL

Not Required

14

Phone Number - Business

NULL

Not Required

15

Primary Language

NULL

Not Required

16

Marital Status

NULL

Not Required

17

Religion

NULL

Not Required

18

Patient Account Number

^^^C^^^

 

Hard Coded

Not Required

CSS Segment

Sequence

Name

Value

Comment

1

Sponsor Study Identifier

[Study Name]

Trim the first two characters from the study name to allow no more than 10 characters

*Study must be set up on ClinAxys

2

Study Phase Identifier

[Cohort Name]

 

 

CTI Segment

Sequence

Name

Value

Comment

1

Study Scheduled Time Point

[Visit Number]

Study Event Visit Number for non-repeat lab test

2

REPEAT

REPEAT

In case of repeat lab test, visit number will be replaced by “REPEAT”

3

Study Scheduled Patient Time Point

[Timepoint]

 

Format:

hh:mm:ss (segment # )

4

Fasting Status

[Fasting Alias]

Answer to Fasting Question

ORC Segment

Sequence

Name

Value

Comment

1

Order Control

NW

Hard Coded

2

Placer Order Number

[Barcode]

Must be returned to ClinSpark

This field must contain the same value as OBR-2

3

Filler Order Number

[Barcode]^LAB

‘LAB’ is Hard Coded

4

Placer Group Number

NULL

Not Required

5

Order Status

NULL

Not Required

6

Response Flag

NULL

Not Required

7

Quantity/Timing

NULL

Not Required

8

Parent Order

NULL

Not Required

9

Date/Time of Transaction

NULL

Not Required

10

Entered By

NULL

Not Required

11

Verified By

NULL

Not Required

12

Ordering Provider

12.1 [ Site Investigator ID] (Required for billing)

12.2 [Site Investigator Last Name]

12.3 [Site Investigator First Name]

12.4 NULL

12.5 NULL

12.6 NULL

12.7 NULL

12.8 [Site NPI Number] (N)

Each sub-field will be separated with “^”

13

Enterer’s Location

NULL

Not Required

14

Call Back Phone Number

NULL

Not Required

15

Order Effective Date/Time

NULL

Not Required

16

Order Control Code Reason

^^

Not Required

OBR Segment

Sequence

Name

Value

Comment

1

Set ID - OBR

[OBR Sequence]

For the first repeat of the OBR segment, the sequence number shall be one (1), for the second repeat, the sequence number shall be two (2), etc.

2

Placer Order Number

[Barcode]^LAB

‘LAB’ is hardcoded

3

Filler Order Number

^LAB

Hard Coded

4

Universal Service Identifier

4.1 [Lab Test ID]

4.2 [Lab Test Name]

4.3 [L]

Identifier for the orderable tests

Each sub-field will be separated with “^”

'L' is Hard Coded

5

Priority - OBR

NULL

Not Required

6

Request Date/Time

NULL

Not Required

7

Observation Date/Time

[Sample Collection Date/Time]

Format: yyyyMMddHHmm

8

Observation End Date/Time

NULL

Not Required

9

Collection Volume

NULL

Not Required

10

Collector Identifier

NULL

Not Required

11

Specimen Action Code

N (New Order)

Hard Coded

12

Danger Code

NULL

Not Required

13

Relevant Clinical Information

NULL

Not Required

14

Specimen Received Date/Time

NULL

Not Required

15

Specimen Source

NULL

Not Required

16

Ordering Provider

16.1 [Investigator ID] (Required for billing)

16.2 [Investigator Last Name]

16.3 [Investigator First Name]

16.4 NULL

16.5 NULL

16.6 NULL

16.7 NULL

16.8 [NPI Number] (N)

This field will contain the same value as ORC.12 and each sub-field will be separated with “^”

Result Message Segments

ClinSpark does not accept any embedded binary content, such as PDFs or images. We can consume textual results only.

ClinSpark looks only for result information, and ignores any information in the MSH or PID segments. This is because ClinSpark is already the source of truth for this information, and we do not update any of this core subject data based on results of the lab.

ClinSpark expects to find the original specimen barcode in ORC-2 and OBR-2, the same value which was passed for that same sample in the HL7 order file from us. This value is used on our end to look up that specimen so that the contained results can be applied properly.

Example Result Message

MSH|^~\&|CLINSPARKMOCK||||20240313181712||ORU^R01||T|2.4||||||||| PID|1|5920|5920||G^D||19980823|F||||||||||||||||||||| ORC|RE|B00104277-C99^CLINSPARK|1710371832440||CM||||20240313181712|||123^CPU^^^^Doctor||||^| OBR|1|B00104277-C99|1710371832440|112^24-Hour Urine Panel|||20240313181712|||||||20240313181712||123^CPU^^^^Doctor||||||||112|F||^^^^^R|||||||||| OBX|1|NM|12201^Potassium Urine||27.7|mmol/L|17.0 - 99.0||||F|||20240313181712||||| OBX|2|NM|12206^Calcium Urine||0.78|mmol/L|0.13 - 8.90||||F|||20240313181712||||| OBX|3|NM|12207^Phosphate Urine||37.23|mmol/L|1.60 - 61.00||||F|||20240313181712||||| OBX|4|NM|12200^Sodium Urine||171.3|mmol/L|30.0 - 90.0|H|||F|||20240313181712|||||

MSH Segment

Sequence

Name

Value

Comment

1

Field Separator

|

Received from ClinAxys

2

Encoding Characters

^~\&

Received from ClinAxys

3

Sending Application

[Sending Application]

Received from ClinAxys

4

Sending Facility

[Sending Facility]

Received from ClinAxys

5

Receiving Application

[Receiving Application]

Received from ClinAxys

6

Receiving Facility

[Receiving Facility]

Received from ClinAxys

7

Date/Time of Message

Time of result file creation

Received from ClinAxys

Format: yyyyMMddHHmmss

8

Security

NULL

Not Required

9

Message Type

ORU^R01

Received from ClinAxys

10

Message Control ID

System generated

Received from ClinAxys

11

Processing ID

System generated

Received from ClinAxys

12

Version ID

HL7 Version ID

Received from ClinAxys

PID Segment

Sequence

Name

Value

Comment

1

Set ID

1

Received from ClinAxys

2

Patient ID

[Subject Volunteer ID]

Received from ClinAxys

ClinSpark is Source

3

Patient Identifier List

NULL

Not Required

4

Alternate Patient ID - PID

4.1 [Subject Screening Number]

4.2 [Subject Randomization Number]

Each sub-field will be separated with “^”

Received from ClinAxys

ClinSpark is Source

5

Patient Name

5.1 [Subject Last Name]

5.2 [Subject First Name]

5.3 [Subject Middle Name]

Each sub-field will be separated with “^”

Received from ClinAxys

ClinSpark is Source

6

Mother’s Maiden Name

NULL

Not Required

7

Date/Time of Birth

[Subject Birth Date]

Received from ClinAxys

Source is ClinSpark

8

Administrative Sex

[Subject Gender]

Received from ClinAxys

Source is ClinSpark

9

Patient Alias

NULL

Not Required

10

Race

[Subject Race]

Received from ClinAxys

Source is ClinSpark

ORC Segment

Sequence

Name

Value

Comment

1

Order Control

[NW]

New: NW

Update: XO

Cancel: CA

Schedule: SC

2

Placer Order Number

[Barcode]

Must be returned to ClinSpark

This field must contain the same value as OBR-2

3

Filler Order Number

3.1 [Barcode]

3.2 [Lab ID]

Each sub-field will be separated with “^”

Remaining Segments

NULL

Not Required

OBR Segment

Sequence

Name

Value

Comment

1

Set ID - OBR

[OBR Sequence]

For the first repeat of the OBR segment, the sequence number shall be one (1), for the second repeat, the sequence number shall be two (2), etc.

2

Placer Order Number

[Barcode]

Must be returned to ClinSpark

3

Filler Order Number

3.1 [Barcode]

3.2 [Lab ID]

Each sub-field will be separated with “^”

4

Universal Service Identifier

4.1 [Test ID]

4.2 [Test Name]

Each sub-field will be separated with “^”

Identifier for the ordered tests

5

Priority - OBR

NULL

Not Required

6

Requested Date/Tim

NULL

Not Required

7

Observation Date/Time

[Sample Collection Date/Time]

Format: yyyyMMddHHmm

8

Observation End Date/Time

NULL

Not Required

9

Collection Volume

NULL

Not Required

10

Collector Identifier

NULL

Not Required

11

Specimen Action Code

[Code]

'N' - New orders accompanying new specimen (original order)

12

Danger Code

NULL

Not Required

13

Relevant Clinical Information

NULL

Not Required

14

Specimen Received Date/Time

NULL

Not Required

15

Specimen Source

NULL

Not Required

16

Ordering Provider

NULL

Not Required

OBX Segment

Sequence

Name

Default Value

Comment

1

Set ID – OBX

[OBX Sequence]

For the first repeat of the OBX segment, the sequence number shall be one (1), for the second repeat, the sequence number shall be two (2), etc.

2

Value Type

[Result Type]

Result messages will contain one of the following values:

CE - Coded Entry

CWE - Coded with Exceptions

CX - Extended Composite ID With Check Digit

DT - Date

ED - Encapsulated Data

FT - Formatted Text (Display)

NM - Numeric

RP - L Pointer

SN - Structured Numeric

ST - String Data

TM - Time

TS - Time Stamp (Date & Time)

TX - Text  Data (Display)

3

Observation Identifier

3.1 [Test ID]

3.2 [Test Name]

Each sub-field will be separated with “^”

Dept, test code will be sent in compatible ClinAxys format.

4

Observation Sub-ID

[LOINC Code]

Not Required

5

Observation Value

[Result]

Always defined by ClinAxys

6

Units

[Units]

Always defined by ClinAxys

7

References Range

[Reference Range]

Always defined by ClinAyxs

8

Abnormal Flags

[Abnormal Flags]

Abnormal flags are user-defined on ClinAxys for each Study/Test/Gender – these can be included if required or it can be left blank

9

Probability

NULL

Not Required

10

Nature of Abnormal Test

NULL

Not Required

11

Observation Result Status

[Status]

F - Final results; Can only be changed with a corrected result

12

Effective Date of Reference Range

NULL

Not Required

13

User-Defined Access Checks

NULL

Not Required

14

Date/Time of the Observation

[Sample Collection Date/Time]

 

Format: yyyyMMddHHmm

15

Producer’s Reference

NULL

Not Required

16

Responsible Observer

NULL

Not Required

17

Observation Method

NULL

Not Required

18

Equipment Instance Identifier

NULL

Not Required

19

Date/Time of the Analysis

[Result Date/Time]

Format: yyyyMMddHHmm

20

Reserved for harmonization with Version 2.6

NULL

Not supported

21

Reserved for harmonization with Version 2.6

NULL

Not supported

22

Reserved for harmonization with Version 2.6

NULL

Not supported

23

Performing Organization Name

NULL

Not Required

24

Performing Organization Address

NULL

Not Required

25

Performing Organization Medical Director

NULL

Not Required

NTE Segment

Sequence

Name

Default Value

Clinical Systems Comment

1

Set ID – NTE

[NTE Sequence]

For the first repeat of the NTE segment, the sequence number shall be one (1), for the second repeat, the sequence number shall be two (2), etc.

2

Source of Comment

NULL

Not Required

3

Comment

[Comment]

Provided from Lab Tech

PDF Requisition

Upon creating an order within ClinSpark a PDF requisition will download to accompany the samples to the laboratory for chain of custody purposes. This requisition is configurable upon request.

Example PDF Requisition

 

Name

Value

Comment

Receiving Facility

[Receiving Facility]

Obtained from Lab Interface Config

Account Number

[Sending Facility]

Obtained from Lab Interface Config

Name

[Lab Interface Site Name]

Obtained from Lab Interface Config

Creation Time

Time of order file creation

Format: ddMMMyyyy HH:mm:ss

Bill Code

Client

Hard Coded

Address

[Lab Interface Site Address]

Obtained from Lab Interface Config

Total

Total samples in order

Each unique barcode increments this total

Physician Name

[Lab Interface Site Investigator Name]

Obtained from Lab Interface Config

City, State, Zip

[Lab Interface City, State, Zip]

Obtained from Lab Interface Config

Initials

[Subject FirstMiddleLast Name Initial]

Obtained from Volunteer Profile

Sex

[Subject Gender]

Male and Female which will be stored as ‘M' and 'F’

ID

[Subject Volunteer ID](Subject #; Study Name)

Obtained from Volunteer Profile and study details

DOB

[Subject Birth Date]

 

Format:

dd-MMM-yyyy

Barcode

[Barcode]

Unique Identifier for Each Sample

Container

[Specimen Container]

*If containers are assigned to a test/panel then present

Lab Test Code

[Order ID]

Obtained from Test Compendium

Test Name

[Test Name]

Obtained from Test Compendium

Collection Date

[Sample Collection Date/Time]

Format: ddMMMyyyy hh:mm:ss

Quantity / Units

NULL

Not Needed

AOE

[Ask on Order Entry]

*If questions / answers are included in data collection those questions / answers are then present

Exported and Printed Copies Are Uncontrolled