Roche Cobas 4800 1.02

cobas 4800 system
Host Interface Manual

Software Version 1.02
r
DRAFT
March 2010 Roche Diagnostics

Host Interface manual Page i
cobas 4800 system Host interface Manual
DRAFT
Table of Contents
General 1
.................................................................................... 1
Target audience
.................................................................................... 1
References
.................................................................................... 1
Document Revision History
.................................................................................... 2
Contacts, Trademarks
.................................................................................... 3
Glossary
Overview 4
.................................................................................... 4
Communication Overview
.................................................................................... 5
Communication layers
Workflow 6
.................................................................................... 6
Communication Scenarios
.................................................................................... 6
Work Order Inquiry
.................................................................................... 8
Result export
Message types 8
.................................................................................... 8
General Information
.................................................................................... 8
Full Run Inquiry
.................................................................................... 8
Full Order Response
.................................................................................... 10
Test Result Export
.................................................................................... 13
FLAGS
Test Result Export workflow 16
Page ii Host Interface manual
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ASTM Protocol 17
.................................................................................... 19
COBAS 4800 ASTM Record Definitions
.................................................................................... 20
Inquiry records Mappings (ASTM)
.................................................................................... 20 H Segment
.................................................................................... 21 P Segment
.................................................................................... 21 Q Segment
.................................................................................... 21 L Segment
.................................................................................... 22
Inquiry Response Mapping
.................................................................................... 22 H Segment
.................................................................................... 23 P Segment
.................................................................................... 23 O Segment
.................................................................................... 24 L Segment
.................................................................................... 25 Inquiry/response examples
.................................................................................... 26
Results Mapping (ASTM)
.................................................................................... 26 H Segment
.................................................................................... 27 P Segment
.................................................................................... 27 O Segment
.................................................................................... 28 R Segment
.................................................................................... 28 L Segment
.................................................................................... 29
Results Example ASTM
HL7 Protocol 31
.................................................................................... 32
COBAS 4800 HL7 Record Definitions
.................................................................................... 33
Inquiry Records mapping (HL7)
.................................................................................... 33 Inquiry Mapping
.................................................................................... 35 Inquiry Response Mapping
.................................................................................... 37
Results Mapping (HL7)
.................................................................................... 40 Result Example HL7
Host Interface manual Page iii
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Communication setup 42
.................................................................................... 42
Network connection
.................................................................................... 42
Instrument Setup
Simulator 43
.................................................................................... 43
Installing simulators
.................................................................................... 43
HL7 Simulator
.................................................................................... 46 Setting up the simulator connection
.................................................................................... 49 Connection test
.................................................................................... 50 Sending an order to the system
.................................................................................... 54 Receiving results from the system.
.................................................................................... 57
ASTM Simulator
Troubleshooting / logfiles 58
Known restrictions 58
Roche Diagnostics March 2010
Page 1 Host Interface manual
Host interface Manual cobas 4800 system
DRAFT
General
General 1

Target audience
The intended audience for this manual is Host Interface programmers and the Roche Field engineers supporting the
system.
References
[1] HL 7 Documentation Version 2.4, Health Level Seven, Ann Arbor MI, USA, www.HL7.org
[2] ASTM Documentation 1394 LIS2
Note: Although ASTM and HL7 are the base of the data exchange, the result transmission
is not a strict ASTM or HL7 format.
The system presents CT/NG or HPV as global blocks of results and transmits them as such.

See the Result topics for the respective ASTM and HL7 formats for details.
Document Revision History
Document Version Revision Date
1.0 January 2009
1.02 Manual rev 02 March 2010
Copyright 2009, 2010, Roche Diagnostics Ltd. All rights reserved.
Rev 02: Corrected some errors and omissions.
Clarified the target audience of manual and simulators.
Added definition Client / server.
Added complete results fields tables
Added examples multiple flags
Added information regarding media types
Added information regarding order handling (Tubes without orders) at various places.
Timeout for order response from LIS increased to 180 seconds.
This manual applies to Software Version 1.02
Information in this document is subject to change without notice. No part of this document may be reproduced or
transmitted in any form or by any means, electronic or mechanical, for any purpose, without the express written
permission of Roche Diagnostics GmbH.
Every effort has been made to ensure that all the information contained in this manual is correct at the time of publishing.
However, Roche Diagnostics Ltd. reserves the right to make any changes necessary without notice as part of ongoing
product development.
Document references
These are internal Roche references
DVS Number: 05702950001
Material Number: 10330010
DRAFT
General
Contacts, Trademarks
Contact Addresses
Manufacturer Roche Diagnostics Ltd.
Forrenstrasse
CH-6343 Rotkreuz
Switzerland
Distribution Roche Diagnostics GmbH
Sandhofer Strae 116
D-68305 Mannheim
Germany
Distribution in the US Roche Diagnostics
9115 Hague Road
PO Box 50457
Indianapolis, IN 46250
USA
Questions or comments regarding the contents of this manual can be directed to the address below or to your Roche
representative.
Roche Diagnostics Ltd.
Global Service Support
Forrenstrasse
6343 Rotkreuz, Switzerland
email: rotkreuz.gssmdi@roche.com
Trademarks
cobas is a trademark of Roche.
Other brands or product names are trademarks of their respective holders.
DRAFT
General
Glossary
MTS Medium Throughput System This name is sometimes used inside the protocol.
Where the Acronym MTS is used, it means the cobas 4800 system..
A&D Amplification and detection. The system will only perform Amplification and detection on already
prepared MWP, using the z 480 instrument.
The A&D runs are not supported by the LIS workflow.
AnD Same meaning as A&D - Often used inside records as the "&" character would be interpreted as
separator and therefore cannot be used.
Full run Samples will be prepared into a MWP by the cobas x 480, then the plate will be transferred manually
to the cobas z 480 for the A&D run.
GUID Stands for Global Unique Identifier.
A unique identifier created by the system. It is a 128 bits number written in a pattern of hexadecimal
numbers similar to : 3F2504E0-4F89-11D3-9A0C-0305E82C3301
It is used to identify a unique run in the transmission records.
MWP Microwell plates.
Transformer A software module that conforms XML communication files to the communication server.
cobas x 480
instrument
The cobas x 480 prepares the samples.
The cobas x 480 is loaded with samples, consumables and reagents. After sample preparation, the
multiwell plate with the PCR-ready samples is unloaded, sealed, and transferred to the cobas z 480 for
amplification and detection.
cobas z 480
analyzer
The cobas z 480 utilizes fluorescence to detect nucleic acids amplified by using realtime
PCR methodology. the loading and unloading of the multiwell plate is done manually.
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General
Overview 2
The structure of the document is as follow
The topic General describes general functions of the subsystem or the unit having influence on the implementation.
This chapter contains no specifications but provides background information and context information for the
specifications stated in the next chapter. The goal is to increase the legibility of the document.
Topic HL7 contains all the specifications for the HL7 protocol.
Topic ASTM contains all the specifications for the ASTM protocol.
Communication Overview
The physical connection used by the cobas 4800 host interface is the standard network card (N.I.C) with Ethernet protocol.
The connection is TPC/IP over ethernet.
The RS-232 connection is not supported by the system.
The cobas 4800 system offers two transmission protocols: -ASTM
-HL 7
The communication is realized by xml files which are exchanged and evaluated between cobas 4800 sw <-> Transformer
and Transformer <-> cobas 5000 IT Communications Server.
Client /Server structure
The communication is always established by the cobas 4800 control unit; the cobas 4800 system is always the TCP/IP client
and the LIS is always the TCP/IP server.
DRAFT
Overview
Communication layers
As all the communication is based on network connections, this manual addresses mostly the upper layer (application)
related topics.
This layer corresponds to the upper layer in the well known OSI model:
DRAFT
Overview
Workflow 3
Communication Scenarios
The following table shows the communication scenarios existing for the cobas 4800.
Table 1 Communications Scenarios
Name Description Input Output
Work Order
Inquiry Full
The cobas 4800 ask the LIS
to get order details for one
or more Samples
Run Type, Test Type, Sample
Ids
For each sample: Sub
Test Type, Media Type
Work Order
Inquiry A&D
Only
This mode is not supported
by the LIS workflow
Run Type, Test Type, Id of the
MWP
For each sample: Sub
Test Type, Media Type,
MWP Position
Test Result
Upload
The cobas 4800 System
sends the test result of a Run
to the LIS
Run Id, Run Type, Test Type
Sub Test Type, Media Type,
Test Result, Flags, Sample Id,
Test Time Stamp, Order Time
Stamp, Accepted Flag
-
Once the LIS has been enable by Roche support, the LIS must always respond to order requests.
There is no possibility to work with "results sending only" and manually ordering.
If the LIS cannot respond to order requests, the system cannot run tests unless the LIS is disabled again to work completely
offline.
Work Order Inquiry
Figure 1 Work Order Inquiry
The Work Order Inquiry Scenario is described In Figure 1.
If a cobas 4800 user starts a run to test samples it loads the samples or the MWP plate. After the plate loading, the cobas
4800 system starts the above inquiry sequence to the LIS server.
DRAFT
Workflow
Missing orders:
When sample numbers are received that do not have a corresponding test request in the Host system, the whole sample
record must be skipped.
No "empty" orders shall be sent to the cobas 4800, otherwise it will result into a complete order upload failure.
See in Each protocol for details.
When order numbers are skipped, the mismatch will be signaled on the screen as shown below (1):
(Mismatch occurred between loaded and expected samples
Please press "Unload Sample" )
The sample positions are indicated in (2)
Possible correcting actions :
1. Unload the sample rack(s), remove the indicated sample tubes (2), reload the sample rack. or
2. Unload the sample rack, add orders to the indicated samples into the LIS system, reload the sample rack(s)
Work order inquiry timeout:
The timeout after a work order inquiry from the instrument is currently set at 180 seconds and cannot be changed.
The complete work order list has to be completely transmitted within these 180 seconds, otherwise a timeout message will
result.
DRAFT
Workflow
Result export
The results can be manually exported to the LIS using the selected protocol (ASTM or HL7).
The LIS has to be enabled to be able to export the results.
If the system works in offline mode and tests are ordered manually , results cannot be exported via LIS.
The total transmission time should not exceed 120 seconds otherwise the last results may not be transmitted.
Message types 4
General Information
The Full run, the A&D Only run and the result export have different data to transfer.
The following tables show the detail of this data.
Full Run Inquiry
Table 2 Full Run Inquiry
cobas 4800 Query Example HL7-Mapping ASTM-Mapping
Run Type Full QPD-3-2 Q-5-6
Test Type CT/NG QPD-3-1 Q-5-4
Software MTS MSH-3 H-5-3
Version 0.9.1.0843 MSH-4 H-5-4
Sample Ids (1-94) 100101001 QPD-4 Q-3
Full Order Response
Table 3 Full Order Response
cobas 4800 Query Example HL7-Mapping ASTM-Mapping
Run Type Full OBR-4-3 O-5-6
Test Type CT/NG OBR-4-1 O-5-4
Software LIS MSH-3-1 H-5-3
Version 6.3 MSH-4-1 H-5-4
Sample Id 0010212 OBR-3-1 O-3-1
SubTestType NG OBR-4-2 O-5-5
Media Type UT OBR-15 O-16

DRAFT
Message types

Table 4 Possible values SubTestType (order response)
Type Possible values for subtype field (order response)
CT/NG CT/NG
CT
NG
HPV HPV High Risk Panel + Genotyping
HPV High Risk Panel
Table 5 * Possible values media
Type Test subtype Possible value
field Media Type
Media names
CT/NG CT UT
UUT
= UniTrans
= Urine UniTrans
NG
CT/NG
HPV HPV High Risk
Panel
PC
SP
= PreserveCyt
= SurePath original tube is not validated on cobas 4800
PC and SP are used, whether the samples are in original
containers or in secondary tube round base 13mL
HPV16
HPV18
DRAFT
Message types
Test Result Export
Table 6 Test Result Export
Test Result
Export
Example HL7
Mapping
ASTM
Mapping
Start Time 2008-10-14T13:49:39 OBR-7 R-12
End Time 2008-10-14T13:50:45 OBR-8 R-13
Test Type CT/NG OBR-4 R-3
Run Type Full OBR-4 O-4
Run Id 83b6f32c-d31b-49a8-8239-13be65486ea3 MSH-10 O-4;H-5-1
User Id Laboperator OBX-16 R-11
Software MTS MSH-3 H-5-3
Version 0.9.3.0847 MSH-4 H-5-4
Created Admin ORC-10 O-17
Creation Date 2008-06-11T15:56:58 ORC-7-4 O-8
Plate Id (A&D
Only)
AD000012 OBX-3;OBR-3 O-3;H-5
For each
Sample
Test Result Examples:
Invalid ;
CT POS, NG POS ;
See Test results combination tables
for all possibilities.
OBX-5-1 R-4-1
Flag Pattern M1,M3 OBX-5-2 R-4-2
Sub Test Type CT OBR-4 R-3
Sample Id 100101001 OBX-3;OBR-3 O-3;H-5
Media Type UUT OBR-15 O-16
Order Date 2008-10-14T13:50:38 OBR-27 O-15
Accepted Flag False OBX-11 O-26
MWP Position A5 OBX-3;OBR-3 O-3;H-5
Test result Possible values (Samples)
invalid positive (POS) negative (NEG)

Test result Possible values (Controls)
invalid Valid
11
DRAFT
Message types
Test results combination tables :
Table 7
cobas 4800 CT/NG Test Result Report and Interpretation
CT POS, NG POS CT Positive, NG Positive. Specimen is positive for the presence of both
CT and NG DNA.
CT NEG, NG NEG CT Negative*, NG Negative*. Neither CT nor NG DNA, if present,
could be detected.
CT POS, NG NEG CT Positive, NG Negative*. Specimen is positive for the presence of CT
DNA.
NG DNA, if present, could not be detected.
CT POS, NG Invalid CT Positive, NG Invalid.
Specimen is positive for the presence of CT DNA.
NG result is Invalid. Original specimen should be re-tested to obtain
valid NG result.
CT NEG, NG POS CT Negative*, NG Positive. CT DNA, if present, could not be detected.
Specimen is positive for the presence of NG DNA.
CT Invalid, NG Positive.
CT Invalid, NG POS CT result is Invalid. Original specimen should be re-tested to obtain
valid CT result.
Specimen is positive for the presence of NG DNA.
CT Invalid, NG NEG CT Invalid, NG Negative*. CT result is Invalid. Original specimen
should be re-tested to obtain valid CT results.
NG DNA, if present, could not be detected.
CT NEG, NG Invalid CT Negative*, NG Invalid. CT DNA, if present, could not be detected.
NG result is Invalid. Original specimen should be re-tested to obtain
valid NG result.
Invalid CT Invalid, NG Invalid. Both CT and NG results are Invalid. Original
specimen should be re-tested to obtain valid CT and NG results.
Failed No Result for Specimen Consult the cobas 4800 system Operators
Manual for instructions to review run flags and recommended actions.
Original specimen should be re-tested to obtain valid CT and NG
results.
DRAFT
Message types
Table 8
cobas 4800 HPV Test Result Report and Interpretation
SubTest HPV High Risk Panel:
HR HPV POS High Risk HPV Positive Specimen is positive for the DNA of any one
of, or combination of, the following high risk HPV types: 16, 18, 31,
33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68.
HR HPV NEG High Risk HPV Negative* HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52,
56, 58, 59, 66 and 68 DNA were undetectable or below the pre-set
threshold.
Invalid
High Risk HPV Invalid Results are invalid. Original specimen should be
re-tested to obtain valid result.
Failed No Result for Specimen Consult the cobas 4800 system Operators
Original specimen should be re-tested to obtain valid result.
SubTest HPV High Risk Panel Plus Genotyping:
Other HR HPV POS, HPV16 POS, HPV18
POS
Other High Risk HPV Positive, HPV16 Positive, HPV18 Positive.
Specimen is positive for HPV types 16 and 18 DNA and the DNA of
any one of, or combination of, the following high risk HPV types: 31,
33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68.
Other HR HPV POS, HPV16 POS, HPV18
NEG
Other High Risk HPV Positive, HPV16 Positive, HPV18 Negative*.
Specimen is positive for HPV type 16 DNA and the DNA of any one
39, 45, 51, 52, 56, 58, 59, 66, 68. HPV type 18 DNA was undetectable
or below the pre-set threshold.
Other HR HPV POS, HPV16 NEG, HPV18
POS
Other High Risk HPV Positive, HPV16 Negative*, HPV18 Positive.
Specimen is positive for HPV type 18 DNA and the DNA of any one
39, 45, 51, 52, 56, 58, 59, 66, 68. HPV type 16 DNA was undetectable
or below the pre-set threshold.
Other HR HPV POS, HPV16 NEG, HPV18
NEG
Other High Risk HPV Positive, HPV16 Negative*, HPV18 Negative*.
Specimen is positive for the DNA of any one of, or combination of, the
following high risk HPV types: 31, 33, 35, 39, 45, 51, 52, 56, 58, 59,
66, 68. HPV types 16 and 18 DNA were undetectable or below the pre-
set threshold.
Other HR HPV NEG, HPV16 POS, HPV18
POS
Other High Risk HPV Negative*, HPV16 Positive, HPV18 Positive.
HPV types 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 DNA were
undetectable or below the pre-set threshold. Specimen is positive for
HPV types 16 and 18 DNA.
Other HR HPV NEG, HPV16 NEG, HPV18
POS
Other High Risk HPV Negative*, HPV16 Negative*, HPV18 Positive.
HPV types 16, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 DNA
were undetectable or below the pre-set threshold. Specimen is positive
for HPV type 18 DNA.
Other HR HPV NEG, HPV16 POS, HPV18
NEG
Other High Risk HPV Negative*, HPV16 Positive, HPV18 Negative*.
HPV types 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 DNA
were undetectable or below the pre-set threshold. Specimen is positive
for HPV type 16 DNA.
Other HR HPV NEG, HPV16 NEG, HPV18
NEG
Other High Risk HPV Negative*, HPV16 Negative*, HPV18 Negative*.
HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68
DNA were undetectable or below the pre-set threshold.
Invalid
Invalid. The results are Invalid. Original specimen should be re-tested to
obtain valid results.
Failed
No Result for Specimen Consult the cobas 4800 system Operators
Original specimen should be re-tested to obtain valid results.
DRAFT
Message types
FLAGS
Result Interpretation Table 9
Flag
Code
Source Severity Description
R1 RI Error General exception raised.
R2 RI Error The Well Result List is null or empty.
R3 RI Error The Well Result Node is invalid.
R4 RI Error The Result Interpretation Parameters Node is null.
R5 RI Error The Result Interpretation Parameters Node is invalid.
R6 RI Error Input Xml Nodes mapping failed.
R7 RI Error The Result Interpretation provides 4-dyes result interpretation.
R8 RI Error The test ingredients have not been specified.
R9 RI Error The test should have at least one target and at least one internal control.
R10 RI Error The probes have not been specified.
R11 RI Error The Well Result Node attributes are invalid.
R12 RI Error The Algorithm Results Node is incomplete.
R13 RI Error The Qualitative Interpretation Tables Node is invalid.
R14 RI Error The Result Table Node is invalid.
R15 RI Error The SubTest type or the ResultTable is invalid.
R16 RI Error The Intermediate-Result Interpretation failed.
R17 RI Error The Well-Result Interpretation failed.
R18 RI Error The Multi-Well Result Interpretation failed.
R19 RI Error The Ct ranges for the intermediate interpretation are invalid.
R20 RI Warning The positive external control is invalid.
R21 RI Warning The negative external control is invalid.
Multiple or other reason Table 10
Flag
Code
Source

Severity Description
M1 SW Error Software error. Additional information can be found in messages and the trace
log files.
M2 Other Error Aborted by the user
M5 SW Warning PCR run only with a user defined sample preparation
M6 SW Warning The connection to the instrument was temporarily lost
Note: One Result can have several flags.
DRAFT
Message types
Calculation Table 11
Flag
Code
Source

C1 CP Error General exception raised.
C2 CP Error The RawData node is null.
C3 CP Error The CalculationParameters node is null.
C4 CP Error The RawData node is invalid.
C5 CP Error The CalculationParameters node is invalid.
C6 CP Error Input XmlNodes mapping failed.
C7 CP Error The HpvCtng-CalculationPackage provides 4-dyes result interpretation.
C8 CP Error The test ingredients have not been specified.
C9 CP Error The test should have at least one target and at least one internal control.
C10 CP Error The probes have not been specified.
C11 CP Error The computation algorithm has not been specified.
C12 CP Error The specified algorithm is not supported by this calculation package.
C13 CP Error The specified algorithm version is not supported by this calculation package.
C14 CP Error The calculation parameters for the numeric algorithm are incomplete.
C15 CP Error The fluorescence measurements data is incomplete.
C101 XT Error The CrossTalk compensation has failed.
C102 XT Error The CrossTalkMatrix is null.
C103 XT Error The Background vector is null.
C104 XT Error CrossTalk Matrix has invalid entries.
C105 XT Error The length of the background vector is not equal with CrossTalkMatrix
filter combinations count.
C106 XT Error Matrix coefficients calculation has failed.
C107 XT Error Matrix inversion has failed.
C108 XT Error Resolution matrix size and channel count do not match.
C121 XT Error The RawData node is null.
C122 XT Error The CalculationParameters node is null.
C123 XT Error The RawData node is invalid.
C124 XT Error The CalculationParameters node is invalid.
C125 XT Error General exception raised.
C221 KA2 Error The RawData node is null.
C222 KA2 Error The AlgorithmParameters node is null.
C223 KA2 Error The RawData node is invalid.
DRAFT
Message types
C224 KA2 Error The AlgorithmParameters node is invalid.
C225 KA/KA2 Error General exception raised.
C301 ELCA Warning CurvatureFailure
C302 ELCA Error InterceptOutOfRange
C303 ELCA Error SlopeOutOfRange
C304 ELCA Warning CurveFitFailure
C305 ELCA Warning AFIMinFailure
C306 ELCA Error DataRangeFailure
C307 ELCA Info InsufficientCurvature
C308 ELCA Info DeclineCorrected
C309 ELCA Error CTOutOfRange
C321 ELCA Error The RawData node is null.
C322 ELCA Error The CalculationParameters node is null.
A&D errors Table 12
Flag
Code
Source

Z1 AnDI Error Hardware or software error from the instrument.
The run was aborted.
SPI errors Table 13
Flag
Code
Source

X1 SPI Error Hardware or software error from the instrument. The run was aborted.
X2 SPI Info Barcode was entered manually.
X3 SPI Error Clot detected for a sample. This sample will have an invalid result.
X4 SPI Error Not enough liquid while processing a sample. This sample will have an invalid
result.
X5 SPI Error Reagent onboard time exceeded when the user tried to start the sample
preparation process. The run was aborted.
X6 SPI Error Working Master Mix with extract timed out after sample preparation has finished.
The run was aborted.
X7 SPI Error Error during processing of external control. Run results will be invalid.
X8 SPI Error Hardware or software error from the instrument. Processing of the sample was
aborted.
DRAFT
Message types
Test Result Export workflow 5
Figure 2 Test Result Export
After a test run the results are shown to the user and become available to be exported. Figure 2 shows this scenario.
DRAFT
Test Result Export workflow
ASTM Protocol 6
The cobas 4800 ASTM protocol also implements the ASTM E1381-91 Low Level Protocol, although this is not the focus of
this manual. No changes can be made at this level and because the system is implemented over a network communication,
it just acts as an intermediate level inside the application layer, transmitting the data to the upper ASTM layer.
The short description of the ASTM lower layer is here for information.
Message example with intermediate frame:
c4800 00:08:17,763 [ENQ]
HOST 00:08:17,763 [ACK]
c4800 00:08:17,883 [STX]1H|\^&|||MTS^c9507f52-37bc-43d4-bba6-360fb
74bd898ÔrderFileValidator^1.0.0.0918^1394.LIS2
|||||LIS|TSREQ^REAL|P|1|20091001085217|[CR][ETX
]80[CR][LF]
HOST 00:08:17,883 [ACK]
c4800 00:08:17,983 [STX]2P|1|[CR][ETX]BB[CR][LF]
HOST 00:08:17,983 [ACK]
c4800 00:08:18,103 [STX]3Q|1|^RDR0003406\RDR0003408\RDR0003407\RDR
0003405\RDR0003404\RDR0003403\RDR0003424\RDR000
3423\RDR0003422\RDR0003421\RDR0003420\RDR000341
9\RDR0003418\RDR0003417\RDR0003416\RDR0003415\R
DR0003414\RDR0003413\RDR0003412\RDR0003411\RDR0
003410\RDR0[ETB]5D[CR][LF]
HOST 00:08:18,113 [ACK]
c4800 00:08:18,203 [STX]4003409\RDR0000829\RDR0003494||^^^CT/NG^^F
ull|[CR][ETX]FB[CR][LF]
HOST 00:08:18,203 [ACK]
c4800 00:08:18,314 [STX]5L|1|[CR][ETX]BA[CR][LF]
HOST 00:08:18,314 [ACK]
c4800 00:08:18,414 [EOT]

Frame Configurations
For Middle Frame
<STX> FN text <ETB>
C1 C2 <CR><LF>
For Last Frame
<STX> FN text <ETX>
C1 C2 <CR><LF>
C1C2 represent the checksum characters.
Control character (characters enclosed in < >
<ENQ> is control character (HEX 05)
<STX> is control character (HEX 02)
<ETB> is control character (HEX 17)
<CR> is control character (HEX 0D)
<LF> is control character (HEX 0A)
<ETX> is control character (HEX 03)
<ACK> is control character (HEX 06)
DRAFT
ASTM Protocol
Maximum Length of the Frame
For one frame, maximum of 240 characters for text, 7 characters for frame control characters (not included in the 240).
Messages equal to or less than 240 characters are transmitted as one final frame.
Messages greater than 240 characters are split into frames that have character lengths that fall within the 240-character
limit.
The only or final remaining frame becomes the last frame and is indicated by <ETX>. All others are intermediate (middle)
frames and are indicated by <ETB>.
Results timeout:
Timeout for messages sent by the cobas 4800 system: From the ENQ, the transmission including multiple frames should
not exceed 120 seconds. Intermediate frames sent past this time will not be sent, the system will close the transmission with
an EOT,
DRAFT
ASTM Protocol
COBAS 4800 ASTM Record Definitions
Message Structure
The Message structures are defined in the syntax also used in [2 ]
Work order inquiry
H Record MESSAGE HEADER SEGMENT
P Record Patient Record (empty, needed by protocol)
Q Record Query information
L Record ASTM message closing record
Work order response
O Record Order information
:
:
Following O records until end of message
Test result export
R Record Result information
R Record Result information
:
:
Following O / R records until end of message
1
DRAFT
ASTM Protocol
cobas 4800 Field mappings
The tables in topic Inquiry records Mappings (ASTM) are showing the mappings between the cobas 4800 xml file and
the xml file which the host interface needs to work with.
Inquiry records Mappings (ASTM)
H Segment
Table 14 ASTM Inquiry Message Header
Segment
Name and
Number
Type Comment Values Required
H-1 String The character H identifies the record as a message
header record
H Yes
H-2 String Component, Repetition, Escape and Subcomponent
delimiter exactly in this order
|^ \ & Yes
H-5-1 String Name of the application which sent this message MTS Yes
H-5-2 GUID GUID representing the unique identifier of this
message given from MTS by its xml-filename
128-Bit-Integer
Min. Value = 0
Max. Value =
FFFFFFFF-FFFF-
FFFF-FFFF-
FFFFFFFFFFFF
Yes
H-5-3 String The name or shortcut of the user which create the
message
Any string Yes
H-5-4 String The version of the sending software 0.9.4.0847 Yes
H-5-5 Number Protocol version used as a version check to make
sure that this message is interpreted correctly
1394.LIS2 Yes
H-10 String Name of the application which has to receive this
message
LIS Yes
H-11-1 String Message type
used to delegate the tasks to the analyzer
TSREQ (e.g
TSREQ^REAL)
Yes
H-11-2 String Event trigger
REAL (e.g
TSREQ^REAL)
Yes
H-12 String Processing mode (processing priority)
P = Production
P Yes
H-13 Number Version number currently a constant number set
to 1
1 Yes
H-14 DateTime DateTime of the message put by the creating system
on creation of this message
YYYYMMDDhhmm
ss
e.g.
20081122121212
Yes
20
DRAFT
ASTM Protocol
P Segment
The MTS software doesnt have any patient informations but the ASTM protocol does need a P record.
Table 15 ASTM Inquiry Patient Information
Segment
Name and
Number
P-1 String The character P identifies the record as a patient
record
P Yes
P-2 Number For the first patient transmitted, 1 shall be entered,
for the second, 2, ... until the last as defined
1 Yes
Q Segment
Table 16 ASTM Inquiry Request Information
Segment
Name and
Number
Q-1 String This field is coded as Q. Q Yes
Q-2 Number For the first patient transmitted, 1 shall be entered,
1 Yes
Q-3-2 String List of specimens separated by \ or
The Plate Id for AnD Only runs (AnD workflow not
supported)
020404~789043
2~098398 or
AD0000034
Yes
Q-5-4 String Test type. Example CT/NG or HPV ^^^CT/NG
^^Full
Yes
Q-5-6 Run type - Can only be Full
(Not supported SpiOnly, AnDiOnly)
^^^CT/NG^^
Full
Yes
L Segment
ASTM Inquiry L Segment (Message Terminator)
Segment
Name and
Number
L-1 String This field is coded as L. L Yes
L-2 int The Terminator field 1 Yes
DRAFT
ASTM Protocol
H Segment
This table is showing the field mappings between the MTS xml file / Transformer and the ASTM message header segment.
Table 17 ASTM Response Message Header
Segment
Name and
Number
H-1 String The character H identifies the record as a
message header record
H Yes
H-2 String Component, Repetition, Escape and
Subcomponent delimiter exactly in this order
|^ \ & Yes
H-5-1 String Name of the application which sent this message LIS Yes
128-Bit-Integer
Min. Value = 0
Max. Value = FFFFFFFF-
FFFF-FFFF-FFFF-
FFFFFFFFFFFF
Yes
H-5-3 String The name or shortcut of the user which create
the message
Any string Yes
H-5-4 String The version of the sending software 6.2 Yes
H-5-5 Number Protocol version used as a version check to
make sure that this message is interpreted
correctly
1394.LIS2 Yes
message
MTS Yes
TSREQ (e.g
TSREQ^REAL)
Yes
REAL (e.g
TSREQ^REAL)
Yes
H-12 String Processing mode (processing priority)
P = Production
P Yes
H-13 Number Version number currently a constant number
set to 1
1 Yes
H-14 DateTime DateTime of the message put by the creating
system on creation of this message
YYYYMMDDhhmmss
e.g. 20081122121212
Yes
DRAFT
ASTM Protocol
P Segment

The cobas 4800 software does not have any patient information but the ASTM protocol does need a P record.
Table 18 ASTM Response Patient Information
Segment
Name and
Number
P-1 String The character P identifies the record as a patient
record
P Yes
P-2 Number For the first patient transmitted, 1 shall be entered,
1 Yes
O Segment
This table is showing the field mappings between the MTS xml file / Transformer and the ASTM test order segment.
The test order segment is holding all information related to a sample.
Note: Missing orders. For samples that do not have a corresponding test request in the Host system, the whole O segment
record must be skipped.
Table 19 ASTM Response Test Order
Segment
Name and
Number
O-1 String The character assigned to the order record shall
be O
O Yes
O-2 Number Set ID for each order which is transmitted a
own number is set starting from 1 to n
Continuous ID starting by 1
1, 2, n
Yes
O-3-1 String Unique identifier of the sample usually a
barcode assigned to the sample (Specimen ID)
0001301ÂD0000013Â6 Yes
O-3-2 String
Plate ID only for "AnD Only" runs (see
Note 1)
0001301ÂD0000013Â6 NO
O-3-3 String MWP Position only for "AnD Only" runs 0001301ÂD0000013Â6 NO
O-5-4 String Identifies the testtype of the sample
Known values are:
- CT/NG
- HPV
^^^CT/NG^NG^Full Yes
O-5-5 String Identifies the sub test type of a sample. Can be
different for each sample but must be a sub type
of the TestType.
Values, see Table
^^^CT/NG^NG^Full YES
O-5-6 String Identifies the runtype of the sample
Allowed values are:
- Full = Full run of all system components
- AnDiOnly = AmpDetect only. See Note 1
O-8 DateTime Contents the Time when the order was created YYYYMMDDHHMMSS
e.g. 20081203143400
Yes
(Note see
restriction
)
O-16 String Media Type. Allowed values, see Table String ex: UT Yes
O-17 String Contents the user who has created the order admin Yes
Note 1: A&D mode not supported by LIMS workflow
9
58
9
DRAFT
ASTM Protocol
L Segment
ASTM response L Segment (Message Terminator)
Segment
Name and
Number
DRAFT
ASTM Protocol
Inquiry/response examples
outgoing - ASTM:
H|\^&|||MTS^65745d86-7a00-49ae-98b3-8a67d18f8e31^none^0.9.8.0912^1394.
LIS2|||||LIS|TSREQ^REAL|P|1|20090403081313|
P|1|
Q|1|^15200049\15200059\15200043\15200073\15200013\15200071\15200041
\15200011\15200069\15200039\15200009\15200067\15200037\15200007\15200065
\15200035\15200005\15200093\15200063\15200033\15200003\15200091\15200061
\15200031\15200027||^^^CT/NG^^Full|
L|1|
incoming - ASTM:
H|\^&|||LIS^65745d86-7a00-49ae-98b3-8a67d18f8e31^none^0.9.8.0912^1394.
LIS2|||||MTS|TSREQ^REAL|P|1|20090403083315|
P|1
O|1|15200049^^||^^^CT/NG^CT^Full|||20090403083315||||||||UUT|none
O|9|15200069^^||^^^CT/NG^CT^Full|||20090403083315||||||||UT|none
O|10|15200039^^||^^^CT/NG^NG^Full|||20090403083315||||||||UT|none
O|11|15200009^^||^^^CT/NG^CT/NG^Full|||20090403083315||||||||UT|none
O|12|15200067^^||^^^CT/NG^CT/NG^Full|||20090403083315||||||||UUT|none
O|13|15200037^^||^^^CT/NG^NG^Full|||20090403083315||||||||UUT|none
L|1
Note: When sample numbers are received that do not have a corresponding test request in the Host system, the whole
sample record must be skipped.
No "empty" orders shall be sent to the cobas 4800, otherwise it will result into a complete order upload failure.
Example: If the sample numbers 15200065 and 15200027 do not have a test for cobas 4800, the lines marked in bold in the
ASTM response from the Host would not exist.
DRAFT
ASTM Protocol
Results Mapping (ASTM)
H Segment
This table is showing the field mappings between the MTS xml file / Transformer and the ASTM message header segment.
Table 20 ASTM Response Message Header
Segment
Name and
Number
H-1 String The character H identifies the record as a
message header record
H Yes
H-2 String Component, Repetition, Escape and
Subcomponent delimiter exactly in this order
|^ \ & Yes
H-5-1 String Name of the application which sent this message LIS Yes
128-Bit-Integer
Min. Value = 0
Max. Value = FFFFFFFF-
FFFF-FFFF-FFFF-
FFFFFFFFFFFF
Yes
H-5-3 String The name or shortcut of the user which create
the message
Any string Yes
H-5-4 String The version of the sending software 6.2 Yes
H-5-5 Number Protocol version used as a version check to
make sure that this message is interpreted
correctly
1394.LIS2 Yes
message
MTS Yes
TSREQ (e.g
TSREQ^REAL)
Yes
REAL (e.g
TSREQ^REAL)
Yes
H-12 String Processing mode (processing priority) P = Production Yes
H-13 Number Version number currently a constant number
set to 1
1 Yes
H-14 DateTime DateTime of the message put by the creating
system on creation of this message
YYYYMMDDhhmmss
e.g. 20081122121212
Yes
DRAFT
ASTM Protocol
P Segment

The cobas 4800 software does not have any patient information but the ASTM protocol does need a P record.
Table 21 ASTM Response Patient Information
Segment
Name and
Number
P-1 String The character P identifies the record as a patient record P Yes
P-2 Number For the first patient transmitted, 1 shall be entered, for
the second, 2, ... until the last as defined
1 Yes
O Segment
This table is showing the field mappings between the MTS xml file / Transformer and the ASTM test order segment.
The test order segment is holding all information related to a sample.
Table 22 ASTM Test Order
Segment
Name and
Number
O-1 String The character assigned to the order record shall be O O Yes
O-2 Number Set ID for each order which is transmitted a own
number is set starting from 1 to n
Continuous ID starting by
1
1, 2, n
Yes
O-3-1 String Unique identifier of the sample usually a barcode
assigned to the sample (Specimen ID)
0001301ÂD0000013Â6 Yes
O-3-2 String Plate ID only for AnD Only runs 0001301ÂD0000013Â6 NO
O-3-3 String MWP Position only for AnD Only runs 0001301ÂD0000013Â6 NO
O-4 String Run type of the test Full or AnD Only Yes
O-5-4 String Identifies the testtype of the sample
allowed values are:
- CTNG
- HPV
O-5-5 String Identifies the sub test type of a sample. Can be
diffrent for each sampl but must be a sub type of the
TestType. See Table
O-5-6 String Identifies the runtype of the sample
Allowed values are:
- AnDiOnly = AmpDetect only
O-8 DateTime Contents the Time when the order was created YYYYMMDDHHMMSS
e.g. 20081203143400
Yes
O-16 String Media Type
Allowed values see Table
String ex: UT Yes
O-17 String Contents the user who has created the order admin Yes
O-26 String Type of Results: F=Final Results; P=preliminary
results depends of the result export flag
ccepted.
F Means result was accepted
P Means result was not accepted (yet)
F or P Yes
9
9
DRAFT
ASTM Protocol
.
R Segment
Note:
The Host system may have to further parse the result block if a further separation of individual subcomponents is required
. See the tables for details and possible combinations inside result blocks.
Table 23 ASTM Result Record
Segment
Name and
Number
Type Comment Values Require
d
R-1 String The record type ID is coded as R. R Yes
R-2 Number Set ID for each order which is transmitted a own
Continuous ID starting
by 1
1, 2, n
Yes
R-3-4 String Identifies the testtype of the sample
Known values are:
- CT/NG
- HPV
R-3-5 String Identifies the sub test type of a sample. Can be diffrent
for each sampl but must be a sub type of the TestType Ex:
CT see table
R-3-6 String Identifies the runtype of the sample
Allowed values are:
R-4-1 String Application package defined test result e.g. Positive, see
table .
Positive^M1\M2 Yes
R-4-2 String Flags for the test result See example Positive^M1\M2 Yes
R-4-3 String CT-Values of the controls CT_DYE1^NaN^
CT_DYE5^NaN^
CT_DYE3^NaN^
CT_DYE0^NaN
NO
R-11 String User who has run the test laboperator Yes
R-12 DateTime Time when the test was started on the instrument YYYYMMDDHHMMS
S
e.g. 20081203143400
Yes
R-13 DateTime Time when the test was finished on the instrument YYYYMMDDHHMMS
S
e.g. 20081203143400
Yes
L Segment
Segment
Name and
Number
11
9
10
30
DRAFT
ASTM Protocol
Results Example ASTM
(Simulator log)
outgoing - ASTM:

c4800 00:11:52,652 [ENQ]
HOST 00:11:52,652 [ACK]
c4800 00:11:52,762 [STX]1H|\^&|||MTSê5052475-cdb3-4c13-97d4-2bb43
467e75f^^1.0.0.0918^1394.LIS2|||||LIS|TSREQ^REA
L|P|1|20091001085550|[CR][ETX]FA[CR][LF]
HOST 00:11:52,782 [ACK]
c4800 00:11:52,872 [STX]2P|1|[CR][ETX]BB[CR][LF]
HOST 00:11:52,872 [ACK]
c4800 00:11:52,982 [STX]3O|1|0NCL010145A03DCÂD6002095^B1||CT/NG^F
ull|||20090825020548|||||||20090825143017|NegCt
rl||||||||||F|[CR][ETX]B0[CR][LF]
HOST 00:11:52,992 [ACK]
c4800 00:11:53,092 [STX]4R|1|^^^CT/NG^N/A^Full|Valid^^CT_DYE0\NaN\
CT_DYE5\34.949874877929688\CT_DYE1\NaN|||||||La
bmanager|20090825140628|20090825170656|[CR][ETX
]7F[CR][LF]
HOST 00:11:53,102 [ACK]
c4800 00:11:53,203 [STX]5O|2|1C1M014196A012RÂD6002095Â1||CT/NG^F
ull|||20090825020548|||||||20090825143017|PosCt
rl||||||||||F|[CR][ETX]B4[CR][LF]
HOST 00:11:53,213 [ACK]
c4800 00:11:53,313 [STX]6R|1|^^^CT/NG^N/A^Full|Valid^^CT_DYE0\36.5
50521850585938\CT_DYE5\35.303115844726562\CT_DY
E1\35.388565063476562|||||||Labmanager|20090825
140628|20090825170656|[CR][ETX]B4[CR][LF]
HOST 00:11:53,323 [ACK]
c4800 00:11:53,423 [STX]7O|3|RDR0003428ÂD6002095^H1||CT/NG^Full||
|20090825020548|||||||20090825141222|UT||||||||
||F|[CR][ETX]98[CR][LF]
HOST 00:11:53,433 [ACK]
c4800 00:11:53,533 [STX]0R|1|^^^CT/NG^CT/NG^Full|CTPOS,NGPOS^||
|||||Labmanager|20090825140628|20090825170656|[
CR][ETX]B4[CR][LF]
HOST 00:11:53,543 [ACK]
c4800 00:11:53,643 [STX]1O|4|RDR0003430ÂD6002095^G1||CT/NG^Full||
|20090825020548|||||||20090825141222|UT||||||||
||F|[CR][ETX]8B[CR][LF]
HOST 00:11:53,653 [ACK]
c4800 00:11:53,753 [STX]2R|1|^^^CT/NG^CT/NG^Full|CTPOS,NGPOS^||
|||||Labmanager|20090825140628|20090825170656|[
CR][ETX]B6[CR][LF]
HOST 00:11:53,753 [ACK]
c4800 00:11:53,854 [STX]3O|5|RDR0003432ÂD6002095^F1||CT/NG^Full||
|20090825020548|||||||20090825141222|UT||||||||
||F|[CR][ETX]8F[CR][LF]
HOST 00:11:53,864 [ACK]
c4800 00:11:53,964 [STX]4R|1|^^^CT/NG^CT/NG^Full|CTNEG,NGPOS^|
||||||Labmanager|20090825140628|20090825170656|
[CR][ETX]C0[CR][LF]
HOST 00:11:53,974 [ACK]
c4800 00:11:54,074 [STX]5O|6|RDR0003433ÂD6002095Ê1||CT/NG^Full||
|20090825020548|||||||20090825141222|UT||||||||
HOST 00:11:54,084 [ACK]
c4800 00:11:54,184 [STX]6R|1|^^^CT/NG^CT/NG^Full|CTPOS,NGNEG^|
DRAFT
ASTM Protocol
||||||Labmanager|20090825140628|20090825170656|
[CR][ETX]C2[CR][LF]
HOST 00:11:54,194 [ACK]
c4800 00:11:54,294 [STX]7O|7|RDR0003435ÂD6002095^C1||CT/NG^Full||
|20090825020548|||||||20090825141222|UT||||||||
HOST 00:11:54,304 [ACK]
c4800 00:11:54,404 [STX]0R|1|^^^CT/NG^CT/NG^Full|CTNEG,NGNEG^
X2|||||||Labmanager|20090825140628|200908251706
56|[CR][ETX]4E[CR][LF]
HOST 00:11:54,414 [ACK]
c4800 00:11:54,515 [STX]1O|8|RDR0003436ÂD6002095^D1||CT/NG^Full||
|20090825020548|||||||20090825141222|UT||||||||
HOST 00:11:54,525 [ACK]
c4800 00:11:54,625 [STX]2R|1|^^^CT/NG^CT/NG^Full|CTNEG,NGNEG^
|||||||Labmanager|20090825140628|20090825170656
|[CR][ETX]C6[CR][LF]
HOST 00:11:54,635 [ACK]
c4800 00:11:54,725 [STX]3L|1|[CR][ETX]B8[CR][LF]
HOST 00:11:54,735 [ACK]
c4800 00:11:54,835 [EOT]
Note: The bullet character inside results is just a placeholder to visualize the spaces inside strings.
example |CTPOS,NGNEG^| should look in reality: |CT POS, NG NEG^|
The character used in the transmission is a regular space (Hex 20).
Example multiple flags (R segment only, simulator log)
outgoing - ASTM:
c4800 06:53:16,137 [STX]6R|1|^^^HPV^HPVHighRiskPanel+Genotypi
ng^Full|Failed^X3\X4\X1|||||||GT|20091211133042
|20091211153236|[CR][ETX]69[CR][LF]
DRAFT
ASTM Protocol
HL7 Protocol 7
Minimal Layer Protocol
The data framing uses the MLLP, Minimal Lower Layer Protocol defined in the HL7
standard.
HL7 messages are embedded in block delimited by special (non printable) characters.
<start_block>data<end_block><CR>
The values of the special characters are <VT> for the start block and <FS> for the end block. See table below.
<start_block> Start Block character (1 byte) ASCII <VT>
Data (variable number of bytes) The HL7 data is comprised of any displayable ASCII characters
and the carriage return character, <CR>.
<end_block> End Block character (1 byte) ASCII <FS>.
.
<CR> Carriage Return (1 byte)
Char (ASCII) Dcimal Octal Hex Name
VT 011 013 0B Vertical Tab
FS 028 034 1C File Separator
CR 013 015 0D Carriage Return
Graphical representation of data framing:
<VT> HL7 data <FS><CR>
DRAFT
HL7 Protocol
COBAS 4800 HL7 Record Definitions
The tables in the topic Inquiry Records mapping (HL7) show the mappings between the cobas 4800 xml file and the
HL7 segment / records file which the host interface needs to work with.
Message Structure
The Message structures are defined in the syntax also used in [1]
Work order inquiry
MSH MESSAGE HEADER SEGMENT
QPD QUERY PARAMETER DEFINITION
RCP RESPONSE CONTROL PARAMETER SEGMENT
Work order response
{
ORC COMMON ORDER SEGMENT - Multiple times ORC + OBR
{
OBR OBSERVATION REQUEST SEGMENT
}
}
Test result export
{
ORC COMMON ORDER SEGMENT - Multiple times ORC + OBR + OBX
{
OBR OBSERVATION REQUEST SEGMENT
OBX OBSERVATION/RESULT SEGMENT
}
}
33
1
DRAFT
HL7 Protocol
Inquiry Records mapping (HL7)
Inquiry Mapping
MSH Segment (Message Header)
Table 24 HL7 Inquiry Message Header
Segment
Name and
Number
MSH-1 String Field delimiter | Yes
MSH-2 String Component, Repetition, Escape and Subcomponent
^ ~ \ & Yes
MSH-3 String Name of the application which sent this message MTS Yes
MSH-4 String The version of the sending software e.g. 1.3.5 Yes
MSH-5 String Name of the application which has to receive this message LIS Yes
MSH-7 DateTime DateTime of the message YYYYMMDDhh
mmss
e.g.
20081122121212
Yes
MSH-9-1 String Message type code see HL7 Doc.:
[1] Table 0076 - Message type
QBP (QBP^Q11) Yes
MSH-9-2 String Trigger event code see HL 7 Doc.:
[1] Table 0003 - Event type
Q21 (QBP^Q11) Yes
MSH-10 GUID Message Id Generated by the Transformer Software 128-Bit-Integer
Min. Value = 0
Max. Value =
FFFFFFFF-FFFF-
FFFF-FFFF-
FFFFFFFFFFFF
Yes
MSH-11 String Processing mode (processing priority)
see HL7 Doc.:
[1] Table 0103 - Processing ID
P = Production Yes
MSH-12 Number HL7 Version ID used as a version check to make sure that
this message is interpreted correctly
see HL7 Doc.:
[1] Table 0104 Version ID
2.4 Yes
MSH-17 String Country ISO code used for currency-, datetime- and other
specifications.
[1] Table 0399 Country code
[A-Z]{3}
e.g. CHE =
Switzerland, USA
= United States
Yes
MSH-18 String Character char set used for the whole message - see HL7
Doc.:
[1] Table 0211 Alternate character sets
The COBAS 4800 project has decided to use the not
documented character set UTF-8
UTF-8 Yes
DRAFT
HL7 Protocol
QPD - Query Parameter Definition
Table 25 HL7 Inquiry Query Parameter Definition
Segment
Name and
Number
QPD-1 String This field contains the name of the query FullRunQuery or
AnDOnlyQuery
YES
QPD-3 String Test Specification contains the Test Type and the Run
Type (only "Full" supported)
CT/NG^FULL YES
QPD-4 String All Samples or the Plate ID of the MWP Plate AD0000012 or
0001~0002~000
3~0004
YES
RCP - Response Control Parameter Segment
Table 9 HL7 Inquiry Response Control Parameter Segment
Segment
Name and
Number
RCP-1 String Query priority For cobas 4800 always I=Immediate I YES
RCP-3 String Response modality For cobas 4800 always R=Real Time R YES
DRAFT
HL7 Protocol
Table 26 HL7 Response Message Header
Segment
Name and
Number
MSH-2 String Component, Repetition, Escape and Subcomponent
^ ~ \ & Yes
MSH-3-1 String Name of the application which sent this message LIS Yes
MSH-4-1 String The version of the sending software 6.2 Yes
MSH-5-1 String Name of the application which has to receive this message MTS Yes
MSH-7 DateTime DateTime of the message YYYYMMDDhhm
mss
e.g.
20081122121212
Yes
OML (OMLÔ21) Yes
O21 (OMLÔ21) Yes
MSH-10 GUID Message Id Generated by the Transformer Software 128-Bit-Integer
Min. Value = 0
Max. Value =
FFFFFFFF-FFFF-
FFFF-FFFF-
FFFFFFFFFFFF
Yes
see HL7 Doc.:
P = Production Yes
MSH-12 Number Version ID used as a version check to make sure that
this message is interpreted correctly
see HL7 Doc.:
2.4 Yes
specifications.
The value is mapped from the current thread of the
Transformer application
[A-Z]{3}
e.g. CHE =
Switzerland, USA =
United States
Yes
MSH-18 String Character char set used for the whole message - see HL7
Doc.:
The cobas 4800 project has decided to use the not
documented character set UTF-8
UTF-8 Yes
DRAFT
HL7 Protocol
ORC Segment (Common Order)
Table 11 HL7 Response Common Order
Segment
Name and
Number
ORC-1 Number Set ID for each order which is transmitted a own
Continuous ID
starting by 1
1, 2, n
Yes
ORC-7-4 DateTime This field contains the creation time of the order out of
the cobas 4800 order file
20081202154500 YES
ORC-10 String This field contains the identity of the user who actually
created the order out of the cobas 4800 order file.
e.g ADMIN YES
OBR Segment (Observation Request)
This table is showing the field mappings between the cobas 4800 xml file / Transformer and the HL7 message version 2.4
observation request segment.
The observation request segment is holding all information related to a sample.
Table 12 HL7 Response Observation Request
Segment
Name
d
OBR-1 Number Set ID for each order which is transmitted a
own number is set starting from 1 to n
Continuous ID starting by
1
1, 2, n
Yes
OBR-3-1 String Unique identifier of the sample usually a
barcode assigned to the sample
0001301
ÂD0000013Â6
YES
OBR-3-2 String Plate ID only for A&D Only runs.
See Note 1
0001301ÂD0000013
Â6
NO
OBR-3-3 String MWP Position only for A&D Only runs 0001301ÂD0000013^
A6
NO
OBR-4-1 String Identifies the testtype of the sample
Known values are:
CTNG - HPV
CT/NG^NG^Full Yes
OBR-4-2 String The sub test type of a sample. Values, see
Table
CT/NG^NG^Full YES
OBR-4-3 String Identifies the runtype of the sample
Allowed values are: See Note 1
- SpiOnly = Sample Extraction only
CT/NG^NG^Full Yes
OBR-15 String Media Type
Allowed values : see Table
String ex: UT Yes
OBR-27 XML
DateTime
Xml DateTime of the message put by the
creating system on creation of this message
YYYYMMDDhhmmss
e.g. 20081122121212
Yes
Note 1 : Only "Full" is supported by the HIF workflow.
Note 2 : Missing orders For samples that do not have a corresponding test request in the Host system, the whole ORC +
OBR segment records pair must be skipped.
9
9
DRAFT
HL7 Protocol
Results Mapping (HL7)
Table 13 HL7 Result Message Header
Segment
Name and
Number
Type Comment Values Requir
ed
MSH-2 String Component, Repetition, Escape and Subcomponent delimiter
exactly in this order
^ ~ \ & Yes
MSH-3-1 String Name of the application which sent this message MTS Yes
MSH-4-1 String The version of the sending software 0.9.4.847 Yes
MSH-5-1 String Name of the application which has to receive this message LIS Yes
MSH-7 DateTime DateTime of the message YYYYMMDDhh
mmss
e.g.
20081122121212
Yes
ORU
(ORUÔ21)
Yes
O21 (ORUÔ21) Yes
MSH-10 GUID Message Id Generated by the Transformer Software TBD Yes
see HL7 Doc.:
P = Production Yes
MSH-12 Number Version ID used as a version check to make sure that this
message is interpreted correctly
see HL7 Doc.:
2.4 Yes
specifications.
[A-Z]{3}
e.g. CHE =
Switzerland, USA
= United States
Yes
MSH-18 String Character char set used for the whole message - see HL7 Doc.:
The cobas 4800 project has decided to use the not documented
character set UTF-8
UTF-8 Yes
ORC Segment (Common Order)
Table 14 HL7 Result Common Order
Segment
Name and
Number
Type Comment Values Requir
ed
ORC-1 Number Set ID for each order which is transmitted a own number is
set starting from 1 to n
Continuous ID
starting by 1
1, 2, n
Yes
ORC-7-4 DateTime This field contains the creation time of the order out of the
cobas 4800 order file
20081202154500 YES
ORC-10 String This field contains the identity of the user who actually created
the order out of the cobas 4800 order file.
e.g ADMIN YES
DRAFT
HL7 Protocol
OBR - Segment (Observation Request)
This table is showing the field mappings between the cobas 4800 xml file / Transformer and the HL7 message observation
request segment.
The observation request segment is holding all information related to a sample.
Table 15 HL7 Result Observation Request
Segment
Name and
Number
d
OBR-1 Number Set ID for each order which is transmitted a own
Continuous ID
starting by 1
1, 2, n
Yes
OBR-3-1 String Unique identifier of the sample usually a barcode
assigned to the sample
0001301ÂD000001
3Â6
YES
OBR-3-2 String Plate ID only for AnD Only runs 0001301ÂD000001
3Â6
NO
OBR-3-3 String MWP Position only for AnD Only runs 0001301ÂD000001
3Â6
NO
OBR-4-1 String Identifies the testtype of the sample
Known values are:
CT/NG - HPV
CT/NG^NG^FULL YES
OBR-4-2 String The sub test type of a sample
See possible value table :
CT/NG^NG^FULL YES
OBR-4-3 String The run type of the test CT/NG^NG^FULL YES
OBR-7 DateTime Time the test was started on the instrument YYYYMMDDhhmms
s
e.g. 20081122121212
YES
OBR-8 DateTime Time the test was finished on the instrument YYYYMMDDhhmms
s
e.g. 20081122121212
YES
OBR-15 String Allowed values are:
See table
UUT YES
OBR-27 DateTime Time when the order was created YYYYMMDDhhmms
s
e.g. 20081122121212
YES
9
9
DRAFT
HL7 Protocol
OBX - Segment (Observation / Result Segment)
Note:
The Host system may have to further parse the result block if a further separation of individual subcomponents is required
. See the tables for details and possible combinations inside result blocks.
Table 16 HL7 Result Observation / Result Segment
Segment
Name and
Number
d
OBX-1 String Set ID for each order which is transmitted a own
Continuous ID
starting by 1
1, 2, n
Yes
OBX-2 String This field contains the format of the observation
value in OBX For the cobas 4800 the format is ST
= String Data
ST YES
OBX-3-1 String Unique identifier of the sample usually a barcode
assigned to the sample
0001301ÂD000001
3Â6
YES
OBX-3-2 String Plate ID only for AnD Only runs 0001301ÂD000001
3Â6
NO
OBX-3-3 String MWP Position only for AnD Only runs 0001301ÂD000001
3Â6
NO
OBX-5-1 String Application package defined test result e.g. Postive,
Failed, See table
Positive^M1~M2 YES
OBX-5-2 String Flags for the test result Positive^M1~M2 YES
OBX-5-3 String CT-Values of the controls CT_DYE1^NaN^
CT_DYE5^NaN^
CT_DYE3^NaN^
CT_DYE0^NaN
NO
OBX-11 String Accepted Flag possible values are: Final results = F
or Final results = P it depends on the accepted
flags from the cobas 4800 result export file
F Means result was accepted
P Means result was not accepted (yet)
F or P YES
OBX-16 String User of the instrument who run the test laboperator YES
11
10
DRAFT
HL7 Protocol
Result Example HL7
HL7 Result Export (Simulator log)
c4800 10:14:27,257 [VT]
c4800 10:14:27,257 MSH|^~\&|MTS|1.0.0.0918|LIS||20090918101319||OR
UÔ21|9a7b5dab-8049-4ba8-83b7-6e8aefcbbed1|P|2.
5.1|||||CHE|UTF-8|[CR]
c4800 10:14:27,257 ORC|1||||||^^^20090826114803||||[CR]
c4800 10:14:27,257 OBR|1||0NCL010145A037YÂD6002084^B1|HPV^N/A^Ful
l|||20090826120921|20090826154328|||||||NegCtrl
||||||||||||20090826114803|[CR]
c4800 10:14:27,257 OBX|1|ST|0NCL010145A037YÂD6002084^B1||Valid^^C
T_DYE3~NaN~CT_DYE5~NaN~CT_DYE1~NaN~CT_DYE0~NaN|
|||||P|||||Labmanager|[CR]
c4800 10:14:27,273 ORC|2||||||^^^20090826114803||||[CR]
c4800 10:14:27,273 OBR|2||R0000814ÂD6002084^G1|HPV^HPVHighRisk
Panel+Genotyping^Full|||20090826120921|200908
26154328|||||||PC||||||||||||20090826114803|[CR
]
c4800 10:14:27,273 OBX|2|ST|R0000814ÂD6002084^G1||OtherHRHPVNE
G,HPV16POS,HPV18NEG^||||||P|||||Labmanager|
[CR]
c4800 10:14:27,288 ORC|3||||||^^^20090826114803||||[CR]
c4800 10:14:27,288 OBR|3||R0000815ÂD6002084^F1|HPV^HPVHighRisk
26154328|||||||PC||||||||||||20090826114803|[CR
]
c4800 10:14:27,288 OBX|3|ST|R0000815ÂD6002084^F1||OtherHRHPVNE
G,HPV16NEG,HPV18POS^||||||P|||||Labmanager|
[CR]
c4800 10:14:27,288 ORC|4||||||^^^20090826114803||||[CR]
c4800 10:14:27,304 OBR|4||R0000816ÂD6002084^D1|HPV^HPVHighRisk
26154328|||||||PC||||||||||||20090826114803|[CR
]
c4800 10:14:27,304 OBX|4|ST|R0000816ÂD6002084^D1||OtherHRHPVPO
S,HPV16NEG,HPV18NEG^||||||P|||||Labmanager|
[CR]
c4800 10:14:27,304 ORC|5||||||^^^20090826114803||||[CR]
c4800 10:14:27,304 OBR|5||R0000817ÂD6002084Ê1|HPV^HPVHighRisk
26154328|||||||PC||||||||||||20090826114803|[CR
]
c4800 10:14:27,320 OBX|5|ST|R0000817ÂD6002084Ê1||OtherHRHPVPO
S,HPV16POS,HPV18NEG^||||||P|||||Labmanager|
[CR]
c4800 10:14:27,320 ORC|6||||||^^^20090826114803||||[CR]
c4800 10:14:27,320 OBR|6||R0000819ÂD6002084^C1|HPV^HPVHighRisk
26154328|||||||PC||||||||||||20090826114803|[CR
]
c4800 10:14:27,335 OBX|6|ST|R0000819ÂD6002084^C1||OtherHRHPVPO
S,HPV16POS,HPV18POS^||||||P|||||Labmanager|
[CR]
c4800 10:14:27,335 ORC|7||||||^^^20090826114803||||[CR]
c4800 10:14:27,335 OBR|7||R0000818ÂD6002084^H1|HPV^HPVHighRisk
DRAFT
HL7 Protocol
26154328|||||||PC||||||||||||20090826114803|[CR
]
c4800 10:14:27,335 OBX|7|ST|R0000818ÂD6002084^H1||OtherHRHPVIn
valid,HPV16Invalid,HPV18POS^||||||P|||||Lab
manager|[CR]
c4800 10:14:27,351 ORC|8||||||^^^20090826114803||||[CR]
c4800 10:14:27,351 OBR|8||2H1M015776A02IGÂD6002084Â1|HPV^N/A^Ful
l|||20090826120921|20090826154328|||||||PosCtrl
||||||||||||20090826114803|[CR]
c4800 10:14:27,351 OBX|8|ST|2H1M015776A02IGÂD6002084Â1||Valid^^C
T_DYE3~37.381362915039062~CT_DYE5~35.7265472412
10938~CT_DYE1~36.203384399414062~CT_DYE0~35.940
170288085938||||||
Note: The bullet character inside results is just a placeholder to visualize the spaces inside strings.
example OtherHRHPVPOS should look in reality: Other HR HPV POS
The character used in the transmission is a regular space (Hex 20).
Example multiple flags (OBX segment only, simulator log)
outgoing - HL7:
c4800 08:05:32,833 OBX|79|ST|A2482185ÂD6201793^D3||Failed^X3~X4~X1||
||||F|||||GT|[CR]
DRAFT
HL7 Protocol
Communication setup 8
Network connection
The physical connection used by the cobas 4800 host interface is the standard network card (N.I.C) with Ethernet protocol.
The network address of the instrument is normally determined by the installation of a cobas IT firewall.
To change the network address, you must log into the operating system as local Administrator.
Please ask the Roche service representative.
Instrument Setup
By default the HIF modules are not installed, for the instrument setup, please refer to the Network Configuration Guide
cobas 4800 system.
This installation has to be performed by qualified Roche service personnel.
Once the software for host interface has been installed, some parameters can be changed to match the requirements of the
LIS system.
The default protocol after installation is HL7. To change to ASTM, or back to HL7, change the target IP (LIS system) or the
port, see the the Network Configuration Guide cobas 4800 system.
DRAFT
Communication setup
Simulator 9
Installing simulators
Roche has developed specific host simulators to make simple testing of the ASTM or HL7 protocol, for the cobas 4800
Instrument.
This software can be installed on Windows computers and are intended to be used only by Roche trained personnel.
When used as an instrument simulator, the goal is to provide only a quick test tool for testing the transmission formats.
Please keep in mind that the simulator does not react like a real instruments in all situations.
The simulator is intended to be used for several Roche instruments, periodically new ones will
be added.
From version 2.0 on, all the host interface tools come together in a common installation package.
They will be installed by default under Host Interface tools.
Requirements
The Roche ASTM/HL7 simulators can be installed on Windows XP computers.
The user needs administrator rights to be able to install the host tools package properly.
After the basic installation of the "Host tools" package, some patches may be required depending on the simulator you
intend to use.
Please ask the Roche service representative for further information.
Software requirement:
Windows XP professional SP2, with current patches.
Access to network settings
Recommended hardware:
Any computer able to run Windows XP professional.
Network card
HL7 Simulator
Roche has developed a specific host simulator to make simple testing of the HL7 protocol, for
the cobas 4800 Instrument.
To start the simulator, simply select from the stat menu as shown.
DRAFT
Simulator
You must accept the disclaimer to be able to start the program.
DRAFT
Simulator
DRAFT
Simulator
Setting up the simulator connection
Some parameters must be setup before the cobas 4800 system is able to communicate with the simulator.
The simulator must be set up as a server. That is, it will listen on a defined port. Port 5555 is often used as a default.
The server IP address is the address of the network card and cannot be changed for a server.
It comes from the network settings of the computer hosting the simulator.
This is the same as the LIS address that must be set on the cobas 4800 when installing or setting up the Host. See
Instrument setup 42
DRAFT
Simulator
Select the Instrument "cobas 4800" from the drop down list and "Host" as shown. This has the effect of enabling the
correct responses from the simulator to the selected type of instrument.
Note: The simulator can also simulate a cobas 4800 system, but this mode goes beyond the scope of this manual
DRAFT
Simulator
Once parameters are setup correctly the simulator will start listening on the defined port. Once every minute, the cobas
4800 communication server will attempt a connection on the defined IP address and port.
If the simulator is reached, the connection indicator will turn from yellow to green as shown.
Additionally, the IP address of the connected system will appear in the lower part of the blue box (Remote).
At this point the simulator can be used and will display the HL7 records received and sent.
DRAFT
Simulator
Connection test
When the simulator is connected, the connection test gives a possibility to check the responsiveness of the client.
In some circumstances, the simulator may erroneously indicate an active connection.
This can be the case if there are elements in the network that where temporarily disconnected.
If the LIS seems unresponsive although the connection is displayed as active, make the connection check.
In case of test failure, close the simulator and restart it. If the connection is not re-established within two minutes,
shutdown the cobas 4800 system and restart it.
DRAFT
Simulator
Sending an order to the system
Actually, you cannot "send" an order, as the instrument is always master.
The simulator is able to reply to an order request. For this it must have certain information in its
database. You can edit this database manually to prepare a correct answer to instrument queries.
Simulator Database:
The simulator has a small database where basic records can be stored. The simulator will use its
database records to respond to the instrument requests.
If the instrument sends a request related to a certain Sample ID, the simulator will search its
database for a matching record.
If one is found, the simulator will attempt to generate an order upload, using the information
stored in the simulator database record.
To open the database on the simulator:
Then in the DB, select the table as shown.
DRAFT
Simulator
You can generate new records, either blank ones:
Or duplicate existing ones and editing them:
DRAFT
Simulator
Editing the duplicate record:
DRAFT
Simulator
There are further fields on the right that can be edited: (Use lower slide bar to view them).
Note: Be aware that the simulator does not perform any check on the type of data. Verify with the
protocol definitions that you enter valid data. For example, if you type a number where another
type is required, an error will probably be generated at the instrument level and the order rejected.
(see also restrictions )
58
DRAFT
Simulator
Receiving results from the system.
Once the LIS systems have been installed by a Roche engineer, the system must be configured to work with LIS:
To configure cobas 4800 software for LIS communication, the user must first open cobas 4800 software and log in with
username FSE. Only a user with administrator rights to the application can switch the LIS on.
Go to 1)utilities tab, select 2) configuration tab, select 3) System Settings and 4) enable the checkbox LIS present.
Exit cobas 4800 software.
TO be able to transmit results, once the LIS has been activated, it is necessary to log in as
1. Open the cobas 4800 Software
2. Login with user name FSE
Go to 1) result tab, select 2) performed run, select 3) sample, click 4) Export
All results present in the page will be transmitted, even if only one is selected.
DRAFT
Simulator
Results received by the simulator will be stored in the database as shown below.
DRAFT
Simulator
DRAFT
Simulator
ASTM Simulator
Roche has developed a specific host simulator to make simple testing of the ASTM protocol, for
the cobas 4800 Instrument.
This software can be used on Windows XP computers and can be delivered upon request.
Contact your Roche Diagnostics representative.
The simulator is intended to be used for several Roche instruments, periodically new ones will
be added.
Requirements
The Roche ASTM simulator can be installed on Windows XP computers and is part of the complete host tools package.
refer to the previous topic HL7 simulator, the ASTM simulator works in a very similar way and shares the loacl simulator
database with the HL7 simulator.
The user needs administrator rights to be able to install the host tools package properly.
Software requirement:
Windows XP professional SP2, with current patches.
Access to network settings
Recommended hardware:
Any computer able to run Windows XP professional.
Network card
Setting up and operating the ASTM simulator
To setup and operate the ASTM simulator as a host, read the HL7 simulator sections .
The ASTM simulator operates in a very similar way and shares the simulator datatabase for cobas 4800.
43
DRAFT
Simulator
Troubleshooting / logfiles 10
Troubleshoting:
Most errors in the incoming communications i.e. a missing parameter in a filed, will result in a timeout message on the
instrument.
Errors generated by the conversion from incoming HTML or ASTM are not passed to the application, the Transformer
program will only pass XML files if the parsing or the different fields succeeds. If any error occur it will just stop parsing
the information and do nothing, therefore if the application is awaiting an answer, it will just timeout. To find the source
of the problem, see the logfiles section.
If the cobas 4800 system has an active connection to the host system but fails to request order information after loading
sample racks, one possible cause is the "operator" is not logged into the operating system of the cobas 4800 control unit.
If an administrator is logged into the windows operating system, the LIS service will connect to the ASTM or HL7 server
but the system will not be able to communicate.
Corrective action: log off the administrator user in Windows, the system will automatically re-log as "operator"
Logfiles:
In the directory c:\data\log, the trafic for the selected protocol is logged:
Hl7_trace.log for the Hl7 data exchange.
astm_trace.log for the astm data exchange.
The transformation activity of the transformer program .xml <=> active protocol is logged in the file cserver.log
cserver logfiles are collections of incremental files like cserver.log.1, cserver.log.2 .......
As soon as the cserver.log reaches a size of 1025 kB, a number is appended to the extension and a new cserver.log is
created.
In the directory C:programm files\Roche diagnosticsAG\cobas_4800_v1.0.0.0918\bin\log\
the file MTS-Transformer-session-trace-file.log contains the parsing activity for the active protocol.
To find the captured errors, open the file with the windows notepad program and make a search fro "ERROR".
You may find some limited indications about protocol errors. (e.g an incorrect type or missing mandatory parameter).
Known restrictions 11
Workflow:
Only the Full run is supported by LIS. The "A&D" and "Sample extraction only" modes are not supported by the LIS
system.
The timeout after an order request from the instrument is currently set at 30 seconds and cannot be changed.
Because of this relatively short time out, it is recommended to use only direct network connections between the LIS and
the cobas 4800 system. Avoid any bottlenecks, i.e. converters to RS232 serial line. Order processing on the LIS should be
optimized to avois a timeout when loading the maximum samples.
Troubleshooting errors:
In case of protocol errors (i.e. the LIS sending an incorrect data type or unexpected values), the instrument will report
LIS system does not answer (timeout) in most cases.
This can be misleading, however some information might be available in the logfiles. See Troubleshooting
ASTM:
58
DRAFT
Known restrictions
O segment in order response:
Field O-8 if left blank will not create a failure, although this is documented as required field.
HL7:
No Known problem
Keywords index
- A -
A&D 3, 8, 13
A&D Only 6
active connection 49
AnD 3
ASCII 31
ASTM simulator 57
- C -
Calculation 13
checksum 17
Client /Server structure 4
cobas x 480 3
cobas z 480 3
Control character 17
- D -
data framing 31
- E -
empty orders 6
error 13, 50
errors 58
- F -
FLAGS 13
Frame
final frame 17
intermediate frame 17
Length of the Frame 17
Middle Frame 17
Full 6
Full run 3, 8
- G -
GUID 3, 20, 22, 26, 33, 35
- H -
host simulator 43
- I -
inquiry timeout 6
installation Manual 42
- L -
layer 5
Logfiles 58
- M -
Media Type 8
Message Terminator 24
Micro Well Plate 3
Minimal Layer
Minimal Layer Protocol 31
Missing orders 6, 23, 35
MLLP 31
MTS 3
MWP 3
MWP plate 6
- N -
Network Configuration Guide 42
- O -
order request 50
OSI model 5
- P -
patient information 23, 27
physical connection 4
- R -
requirement 43
Requirements 43
reserveCyt 8
Results timeout 17
run 8
Run Type 6, 8
- S -
server 6, 46
server IP address 46
simulator 43, 57
Database 50
Simulator database 50
Simulator Database 50
special characters
FS 31
VT 31
SPI 13
SubTestType 8
SurePath 8
- T -
TCP/IP client 4
TCP/IP server 4
Test Type 6, 8
timeout 6, 58
Timeout (Results) 17
Transformer 4
transmit results 54
- U -
UniTrans 8
Urine UniTrans 8
- W -
Warning 13
Work Order 6
Work order inquiry timeout 6
Workflow 58
Personal notes:
Roche Diagnostics Ltd.
Forrenstrasse
CH-6343 Rotkreuz
Switzerland 2009 Roche Diagnostics Ltd.
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Host Interface Manual

March 2010 Roche Diagnostics

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