Concatenating a Lab Report

One common transformation is to take a lab result message where all the lines are displayed in separate OBX segments, and then concatenate them together into an easy-to-read report. The following message provides you with an example of this problem:

MSH|^~\&|||||200207251030||ORU|0000000072|P|2.0|34|
PID|||0000006||DOE^JOHN^A^^^||19090909|M|||199 MAIN^^BOSTON^MA^02114||(617)555-5555||||||000-00-0000
PV1||O|^P^||||51637^SNEEZY^D.^K^^^MD||||||||||||||||||||||||||||||||||||||200008091827
ORC|RE|1157542|0000001||||||200207251030|||00001^GRUMPY^D^S^^^MD
OBR||1157542|0000001|CTCH+^CT CHEST+|||200205071425|||||||||00001^GRUMPY^D^S^^^MD|||||||||F
NTE|1|L|I+ vmc~|
NTE|2|L|BLADDER CANCER COMPARE TO PREVIOUS~~|
ZRP||
ZTT|^SMITH^TEST^^^^|^Interface^Talkstation^^^^|^P^|^P^|00007^IGNORE^J.^K^^^MD|MED
ZTM|CTCH+^CT CHEST+||CTCH+^CT CHEST W CON
ZAU|
ZRI|00004^DOE^JANE^L^^^MD|||00004^DOE^JANE^L^^^MD|20020508|1120|00004^DOE^JANE^L^^^MD
ZAS|0000001||
OBX|1|FT|CTCH+&GDT|1|Comparison with CT scan on December 14, 2001||||||F
OBX|2|FT|CTCH+&GDT|1|||||||F
OBX|3|FT|CTCH+&GDT|1|History: Bladder cancer||||||F
OBX|4|FT|CTCH+&GDT|1|||||||F
OBX|5|FT|CTCH+&GDT|1|Technique: Serial helical CT scan images of the thorax were||||||F
OBX|6|FT|CTCH+&GDT|1|performed from the thoracic inlet through the lung bases with||||||F
OBX|7|FT|CTCH+&GDT|1|intravenous contrast. Slice thickness was at 5 mm. Additional||||||F
OBX|8|FT|CTCH+&GDT|1|high resolution CT scan images were obtained at 1 mm slice||||||F
OBX|9|FT|CTCH+&GDT|1|thickness. Images were reviewed in lung, soft tissue and bone||||||F
OBX|10|FT|CTCH+&GDT|1|windows.||||||F
OBX|11|FT|CTCH+&GDT|1|||||||F
OBX|12|FT|CTCH+&GDT|1|Findings:||||||F
OBX|13|FT|CTCH+&GDT|1|||||||F
OBX|14|FT|CTCH+&GDT|1| The heart is within normal limits. No evidence for mediastinal or||||||F
OBX|15|FT|CTCH+&GDT|1|hilar lymphadenopathy.The pleura is normal. Chest wall shows no||||||F
OBX|16|FT|CTCH+&GDT|1|evidence for lymphadenopathy.||||||F
OBX|17|FT|CTCH+&GDT|1|||||||F
OBX|18|FT|CTCH+&GDT|1|Please see separate dictated report of abdominal CT scan findings.||||||F
OBX|19|FT|CTCH+&GDT|1|||||||F
OBX|20|FT|CTCH+&GDT|1|The lungs are clear. No evidence for interstitial, airspace or||||||F
OBX|21|FT|CTCH+&GDT|1|airways disease. No nodules identified.||||||F
OBX|22|FT|CTCH+&GDT|1|||||||F
OBX|23|FT|CTCH+&GDT|1|Skeleton shows degenerative changes in the spine. No evidence for||||||F
OBX|24|FT|CTCH+&GDT|1|any lytic or blastic lesions.||||||F
OBX|25|FT|CTCH+&GDT|1|||||||F
OBX|26|FT|CTCH+&GDT|1|Impression:||||||F
OBX|27|FT|CTCH+&GDT|1|||||||F
OBX|28|FT|CTCH+&GDT|1|No evidence for new metastatic disease.||||||F
OBX|29|FT|CTCH+&GDT|1|||||||F
OBX|30|FT|CTCH+&GDT|1|||||||F

Each OBX segment has one line of the report that you would like to treat as a single report. By using Python, you can concatenate them all together and map the result into a single column.

To hold the report data you must define a Python variable called LabText in the Global Inbound Script window:

# We need to reset this variable to empty for each message.
LabText = ''

In Procedure

Then for field 5 of the OBX segment, you use the following piece of Python code:

#Concatenate lines of the lab report
LabText = LabText + value + '\r\n'

OBX - Field 5 Observation Value Inbound Script

Finally we have a LabResult table which has one field called LabResult. In the incoming script for this field, you assign the value of the column to the LabText variable:

# The LabText variable should contain
# the concatenated body of the report which
# we wish to map out.
value = LabText

Inbound Table Column Script

You can test out this functionality yourself by:

Loading Chameleon with this sample lab VMD file;
Copying the above sample HL7 message into the top pane of the Message Browser; and
Clicking Parse.


	Notice this example VMD file uses a very flat segment grammar for mapping out the Lab Result message. Generally using flatter grammars makes it easy to manipulate HL7 messages. Avoid highly nested HL7 message grammars if possible.

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Concatenating a Lab Report