| DESCRIPTION OF ENHANCEMENTS |
VISTA Laboratory Package patch LR*5.2*279 contains no changes to
LOINC mapping of CH subscripted verified results. The software will use
is terminated by the user. If the process runs successfully to
completion, there will be an END alert for each START alert for each
batch sequence number.
It has been seen at some test sites that the LRDFN may not be in the
proper form. Test sites have seen the LRDFN set to an inverse date/time
(LRIDT) value, and in some cases the LRDFN contained a decimal
(ex.123.5). If such a situation is discovered during the LOINC mapping
process, a properly formatted LRDFN will be created in the ^LR(0) global
as the next available LRDFN.
the existing LOINC mapping configuration defined in WKLD CODE (#64) file.
There is a special sequence number (9999999) assigned to those LRDFNs
having LRIDT like format. This sequence will only be established if
required.
Most sites will not have a 9999999 batch sequence number.
NEW OPTIONS:
============
The following options are provided to manage the LOINC mapping processes.
This file's definition will be used to determine the LOINC code to be
They are contained on the LOINC Historical Mapping Menu [LR LOINC
HISTORICAL MAP MENU]. This menu is locked with the XUPROGMODE security
key and located under the LOINC Mapping Utility Menu [LR LOINC UTILITY].
It is highly recommend that options provided by this patch be run during
a 24 hour period of low system usage. Normally this would be during the
week end.
A. LAB DATA LOINC Mapping [LR LOINC HISTORICAL MAPPER 63] option
assigned to a given result. The historical mapping process extends to the
This is the primary historical LOINC mapping option that must be run at
least once to update ^LR with appropriate LOINC mapping codes. This
option can be run multiple times if required. This option will initiate
the required number of background tasks to inspect the entire LAB DATA
file and map verified CH subscripted tests with LOINC codes. This option
should only be run during a 24-hour period when the system has low user
activity. Note: This option is used also to restart the mapping process
from the point of interruption. The mapping process will continue until
all LRDFNs have been inspected.
past 5-6 years of verified 'CH' subscripted data.
The option is Locked by the XUPROGMODE security key.
Example of the option: User's responce inclosed in < >
Select LOINC Mapping Utility Menu Option:
LOINC Historical Mapping Menu
Select LOINC Historical Mapping Menu Option: ?
1 LAB DATA LOINC Mapping
2 Restart LOINC Historical Mapping
3 STOP LOINC Mapping
4 Modify LOINC Historical Mapping
Select LOINC Historical Mapping Menu Option: <1>
D STOP^LRLNC63 to stop all background historical mapping.
This option should be run during 24 hour off peak time frame!!
Information on the historical LOINC mapping process:
This option will queue multiple tasks to LOINC map
historical data in the LAB DATA (#63).
Are you certain you wish to proceed? <YES>
LRDFN Conversion Sequence 1-20001 Task number is 8718
LRDFN Conversion Sequence 20001-40001 Task number is 8719
End of Option example:
==========
After successful completion of LOINC mapping for all tasks, the members
of the G.LMI mail group will receive two types of notifications:
1. MailMan message containing all tests that were not LOINC mapped
2. Mailman message containing all tests that were mapped. This message is
designed to be imported into a non VistA spread sheet program.
Using these two reports, the LIM will be able to determine mapping
completeness and identify systematic mapping errors.
The historical mapping is an option that cannot be queued. Installation
Here is an example of each.
Subj: LOINC Historical Mapping Exception Report [#89761] 15 Feb 02 10:29
From: POSTMASTER (Sender: ) In 'IN' basket. Page 1 *New*
--------------------------------------------------------------------------
List of tests missing RNLT codes in LABORTORY TEST (#60) file,
found during LOINC Historical Mapping process.
These test(s) will have no historical LOINC mapping performed.
of this patch provides options to perform historical mapping of verified
[Test IEN] Test Name Type
[37] BLEEDING TIME -- Type: BOTH
[353] SPHEROCYTES -- Type: OUTPUT (CAN BE DISPLAYED)
[356] HYPERSEGMENTED NEUTROPHILS -- Type: BOTH
[357] SMUDGE CELLS -- Type: BOTH
[137] RPR -- Type: BOTH
Subj: LOINC Historical Mapped LOINC tests [#89762] 15 Feb 02 10:29
software controlled by VHA DIRECTIVE 99-053, titled VISTA BLOOD BANK
'CH' subscripted tests.
From: POSTMASTER (Sender:) In 'IN' basket. Page 1 *New*
--------------------------------------------------------------------------
List of test mapped to LOINC codes formatted with '^' as field delimiter.
DataName#^Test Name^Specimen^Specimen IEN^RNLT^NLT suffix^LOINC Code
2^GLUCOSE^PHARYNX^60^84330.0000^0^2339-0
2^GLUCOSE^BLOOD^70^84330.0000^0^2339-0
2^GLUCOSE^BLOOD^70^84330.0000^8638^2339-0
2^GLUCOSE^SERUM^72^84330.0000^0^2342-4
2^GLUCOSE^SERUM^72^84330.0000^3035^2342-4
2^GLUCOSE^SERUM^72^84330.0000^3103^2342-4
2^GLUCOSE^SERUM^72^84330.0000^8638^2342-4
3^UREA NITROGEN^RIGHT KIDNEY^11^84520.0000^0^3097-3
3^UREA NITROGEN^SERUM^72^84520.0000^0^6299-2
3^UREA NITROGEN^SERUM^72^84520.0000^3035^6299-2
3^UREA NITROGEN^SERUM^72^84520.0000^3103^6299-2
4^CREATININE^Missing^.8^82565.0000^0^2160-0
4^CREATININE^Missing^.9^82565.0000^0^2160-0
4^CREATININE^SERUM^72^82565.0000^0^2160-0
4^CREATININE^SERUM^72^82565.0000^3103^2160-0
Historical LOINC mapping is a disk and system intensive process.
B. STOP LOINC Mapping [LR LOINC HISTORICAL STOP 63] option
This option will stop all background LOINC historical mapping tasks. If
for some reason the user wishes to stop/suspend LOINC mapping, this
option will stop all background tasks. To continue the mapping process
from the last LRDFN, use the primary option, LAB DATA LOINC mapping
Option.
Example of the option:
Select LOINC Historical Mapping Menu Option: STOP LOINC Mapping
Stopping all background LOINC historical mapping jobs
Are you certain you want to continue? <YES>
End of example
===========
C. Restart LOINC Historical Mapping [LR LOINC HISTORICAL RESTART 63]
Journaling has not been a problem at test sites, but with any conversion
This option will restart the mapping process from the very beginning.
This option will reset all counters and reinitiate the ^XTMP("LRLNC63")
global. After the temporary mapping globals have been reset, a call is
made to the LAB DATA LOINC Mapping entry point. Rerunning this option is
not harmful but the same 24 hours of low system usage considerations
should be honored.
Option is locked with the XUPROGMODE security key.
process, journal files should be monitored. Temporary data is stored in
Example of the option:
Restart LOINC Historical Mapping
This will re-run LOINC Historical Mapping from the beginning
resetting all globals to zero.
To restart from a stopping point use the
LAB DATA LOINC Mapping Option.
Are you certain you want to proceed? <YES>
the ^XTMP Global. A significant amount of LOINC code related data will be
D STOP^LRLNC63 to stop all background historical mapping tasks.
This option should be run during 24 hour off peak time frame!!
This option will queue multiple tasks to LOINC map
historical data in the LAB DATA (#63).
Are you certain you wish to proceed? <YES>
set into the ^LR( global.
End of option example.
=================
D. Modify LOINC Historical Mapping [LR LOINC HISTORICAL MODIFY]
This is a very powerful utility option to be used to reconcile previous
LOINC historical mapping. A knowledgeable LOINC mapper (Laboratory
Information Manager) is required to properly implement this functionality.
After the initial historical mapping has been completed, adjustments
maybe required to modify the LOINC code lookup parameters to properly map
past results. Careful review of current LOINC mapping should be done to
establish IF there is a systematic error in LOINC code assignments. File
definition corrections should be done to prevent future LOINC mapping
errors. Re-running LAB DATA LOINC Mapping [LR LOINC HISTORICAL MAPPER 63]
option will correct incorrectly assigned LOINC code problems.
In those situations when editing LOINC mapping definition is not
desirable, this option provides a method for the user to intervene in the
The Historical Mapper functions should be run during a 24 hour period of
mapping lookup logic for specific tests.
The user is able to select a lab test(s) [Atomic or Panel], then assign a
specific suffix code to be used during LOINC mapping logic. In addition
the user is able to force the Result NLT CODE (#64.1) of LABORATORY TEST
(#60) for the test and the designated suffix code pair to override
previous LOINC mapping.
This is a very powerful feature, great care and study of systematic
errors should be used before attempting correct past LOINC mapping
SOFTWARE.
low system demand. Typically this would be during a week end.
systematic errors.
After the user has completed the modify LOINC mapping procedures, the LAB
DATA LOINC Mapping option is called. All considerations of this option
still apply. Most notably, only performing this mapping exercise during
week ends or in a 24 period of lowest system activity. Even with the
increased logic iterations, the process should complete within the 24 hr
window of time.
This option will allow the user to manage how a specific data name (test)
will be mapped to LOINC Codes for historical data. The user is able to
override file definitions to correct past LOINC mappings.
1. Select the CH subscripted test
2. Indicate the suffix to be used.
3. The user can indicate if this suffix should override previous LOINC
Mapping.
Example of the option:
2. Installs 'LRRESOURCE' Resource Device
This option will REMAP your entire database using the parameters defined
by this option.
This option should only be run on week ends or after hours.
Do you wish to continue ? <YES>
Selection can be a 'CH' Atomic or Panel test .
Select test you want to modify mapping: <CBC>
Select Suffix Code: <.4322> COULTER ELECTRONICS
Override previous LOINC mapping? <YES>
Selection can be a 'CH' Atomic or Panel test.
Select test you want to modify mapping: <CALCIUM>
Select Suffix Code: <AA DIRECT> .3901 NOT SPECIFIED
Override previous LOINC mapping? <ret>
This patch will install a new resource device called 'LRRESOURCE'. This
Selection can be a 'CH' Atomic or Panel test
Select test you want to modify mapping: <ret>
Here is a list of what you have selected.
[O] indicates override current mapping
. DEVICE: HOME// Right Margin:80//
1 [0] WBC COULTER A /.4322
2 [0] MCV COULTER A /.4322
device is installed with eight slots. The number of slots determines the
3 [0] MCH COULTER A /.4322
4 [0] MCHC COULTER A /.4322
5 [0] RDW COULTER A /.4322
6 CALCIUM AA DIRECT /. 3901
You wish to add more? <ret>
Do you want to delete an entry? <ret>
[NOTE: Those tests in the panel or atomic test that do not have a RESULT
number of active LOINC mapping background tasks. The maximum number of
NLT CODE (RNLT) assigned will be omitted. If this is the case, abort and
attend to the missing tests RNLT codes.]
3. Resolving the $SELECT statements for normal ranges
This functionality provided by this patch is to resolve the normal
range data stored in a $SELECT format in the LAB DATA file (63). This
patch will determine the appropriate normal range for the result by
resolving the $S( statement using the age of the patient at the time the
specimen was collected. The $SELECT statement will be replaced with the
concurrently running background tasks is eight, the number of slots
appropriate numerical value.
The routines LRVER4 and LRVR4 are installed with this patch to prevent
the storage of the $S statement in ^LR(LRDFN,"CH",LRIDT,LRSB) for future
results.
The routine LRDAGE provides the patient's age at the time when the
specimen was collected. The resulting age is used to determine normal
range values for historical data.
defined in LRRESOURCE. If the user adjusts the number slots of the
NEW FILES OR FIELDS:
===================
Two new fields are added during installation of this patch.
In the LABORATORY SITE (#69.9) file the following fields have been added.
LOINC HISTORICAL MAPPING DATE (#95.3) field.
This is the date that the LOINC Historical mapping was completed. The
resource device, it must have at least one slot to initiate the mapping
LAB DATA LOINC Mapping [LR LOINC HISTORICAL MAPPER 63] option populates
this field after it has successfully completed all mapping.
LOINC HISTORICAL LAST LRDFN (#95.31) field.
This field is populated by the primary LOINC mapping option if all batch
(sequences) successfully run to completion.
This field contains the last LRDFN that was mapped by the LAB DATA LOINC
Mapping [LR LOINC HISTORICAL MAPPER 63] option.
ASSOCIATED NOIS
process. Reducing the number of slots will increase the total mapping
===============
NONE
TEST SITES
==========
Minneapolis, MN
North Chicago, Il
Milwaukee, WI
Salem, NC
processing time. Increasing the number of resource slots may NOT reduce
Martinez, CA
Palo Alto, CA
Durham, NC
Long Beach, CA
Muskogee, OK
Fargo, ND
Cincinnati, OH
ROUTINE SUMMARY
===============
the total mapping processing time.
The following routines are included in this patch. The second line of
these routines now looks like:
<tab> ;;5.2;LAB SERVICE;<patch list>;Sep 27, 1994
Routine Checksum Checksum
Name Before Patch After Patch Patch List
LR279 N/A 6316492 279 (Deleted
by KIDS)
LRDAGE N/A 1480375 279
LRLNC63 N/A 14818231 279
LRLNC63A N/A 9008516 279
LRLNC63B N/A 7526980 279
LRVER4 19181995 18527473 14,42,112,121,140
171,153,188,279
LRVR4 8661306 8664360 14,42,121,153,221
263,279
List of preceding required patches:
LR*5.2*188, LR*5.2*232, LR*5.2*263, LR*5.2*278
The Mapping Process in Detail
Sites should use CHECK^XTSUMBLD to verify checksums.
INSTALLATION INSTRUCTIONS
=========================
The install time for this patch is less than 5 minutes. Laboratory users
should be off the system during installation. All other user may remain
on the system.
Patch installation should be coordinated with the Laboratory Information
Manager (LIM).
1. If any of the above routines are mapped, disable mapping for those
routines.
2. Use the 'INSTALL/CHECK MESSAGE' option of the PackMan Menu. This
option will load the KIDS patch onto your system.
3. The patch has now been loaded into a Transport global on your system.
The LOINC mapping processes are divided in to batches of 20,000 LRDFN
You now need to use KIDS to install the transport global.
4. On the 'Kernel Installation & Distribution System's Menu (KIDS)
select the 'Installation' menu.
5. Use the 'Verify Checksum in transport Global' option and verify that
all routines have the correct checksums.
6. On the KIDS menu, under the 'Installation' menu, use the following
options:
records each. The number of batches are determined by the number of
Print Transport Global
Compare Transport Global to Current System
Backup a Transport Global
If you wish to preserve a copy of the routines exported in this patch
prior to installation, you should use the 'Backup a Transport Global'
option. You may also compare the routines on your system to the routines
in the patch by using the 'Compare a Transport Global to your Current
System' option.
records found in the LAB DATA (#63) file. One could estimate the number
7. Use the 'Install Package(s)' option under the 'Installation' menu and
select the package 'LR*5.2*279'.
When prompted 'Want KIDS to INHIBIT LOGONs during install? YES// choose
'NO'.
When prompted 'Want to DISABLE Scheduled Options, Menu Options, and
Protocols? YES//', choose 'NO'
8. On mapped system, rebuild map set
of batches by dividing the number of LRDFN records by 20,000. If more
9. Routine LR279 will be deleted after successful patch installation.
POST-INSTALLTION INSTRUCTIONS:
=============================
Perform LOINC historical mapping functions.
******************************************
The patch provides the following:
than eight mapping tasks are required, the remainder tasks will
Installation Example:
Select INSTALL NAME: LR*5.2*279 Loaded from Distribution
2/26/02@17:15:29
=> LR*5.2*279
This Distribution was loaded on Feb 26, 2002@17:15:29 with header of
LR*5.2*279
It consisted of the following Install(s):
automatically start when a resource slot becomes available. Resource
LR*5.2*279
Checking Install for Package LR*5.2*279
Will first run the Environment Check Routine, LR279
Sending install started alert to mail group G.LMI
--- Environment Check is Ok ---
Install Questions for LR*5.2*279
slots become available when a mapping sequence batch runs to completion.
Incoming Files:
69.9 LABORATORY SITE (Partial Definition)
Note: You already have the 'LABORATORY SITE' File.
Want KIDS to Rebuild Menu Trees Upon Completion of Install? YES// NO
Want KIDS to INHIBIT LOGONs during the install? YES// NO
Want to DISABLE Scheduled Options, Menu Options, and Protocols? YES// NO
Enter the Device you want to print the Install messages.
You can queue the install by enter a 'Q' at the device prompt.
Enter a '^' to abort the install.
DEVICE: HOME// TELNET
Install Started for LR*5.2*279 :
Feb 26, 2002@17:18:32
The objective of the mapping batch size and number is to ensure mapping
Build Distribution Date: Feb 25, 2002
Installing Routines:
Feb 26, 2002@17:18:32
Running Pre-Install Routine: PRE^LR279
*** Pre install started ***
*** No action required ***
is completed within twenty-four (24) hours. After benchmarking timing
*** Pre install completed ***
Installing Data Dictionaries:
Feb 26, 2002@17:18:33
Installing PACKAGE COMPONENTS:
Installing OPTION
Feb 26, 2002@17:18:33
exercises, it has been determined that eight batch jobs of 20,000 records
Running Post-Install Routine: POST^LR279
*** Post install started ***
Adding 'LRRESOURCE' to the Device (#3.5) file
*** Post install completed ***
Sending install completion alert to mail group G.LMI
each would achieve the mapping time goal.
Updating Routine file
Updating KIDS files
LR*5.2*279 Installed.
Feb 26, 2002@17:18:34
Install Message sent #XXXXX
Install Completed
End of example
Each LRDFN in a batch that is not from LAB CONTROL NAME (#62.3) file, is
checked to determine if NEW PERSON CONVERSION (.12) field of sub-multiple
CHEM, HEM, TOX, RIA, SER, etc. (#4) of the LAB DATA (#63) file has a
designation of 2. If the check is satisfied the process continues for
that LRDFN's inverse date time sub-file.
Each data name (test) of the CH subscript is subjected to a lookup
process to determine the RESULT NLT CODE (#64.1) field of the LABORATORY
TEST (#60) file.
This value is stored in the
^XTMP("LRLNC63",1,DATANAME IEN)=Result NLT Code.
1. Historical LOINC mapping
^XTMP("LRLNC63",1,2) = 84330.0000
^XTMP("LRLNC63",1,3) = 84520.0000
^XTMP("LRLNC63",1,4) = 82565.0000
^XTMP("LRLNC63",1,5) = 84295.0000
The software then performs a LOINC lookup using the data from the
DATANAME subscripted node [^XTMP("LRLNC63", 1,DATANAME)] global and the
file definitions of WKLD CODE file to determine the LOINC code for the
result. If a LOINC code is found the value is stored in the third '^'
piece in the third piece of '!' delimited field.
^LR(713,"CH",6979880.8746,357)=75^^84009.0000!84009.0000!
[27057]!3103!1^104^72!50!220!!!!UG/ML!!!75^^^^170^1
Where [27057] is the LOINC code.
The last LRDFN processed record for each batch (sequence) is stored in
the ^XTMP("LRLNC63","SEQ",#). Where '#' is the batch sequence number in
increments of 20,000.
This patch contains options and software required to perform historical
Other information stored in the ^XTMP global are:
^XTMP("LRLNC63","SEQ",#,"START")=FileMan date/time
^XTMP("LRLNC63","SEQ",#,"END")=FileMan date/time
The time difference between the START and END nodes represent the lapse
time for that batch's LOINC mapping.
Status activity of the mapping process is reported to the LMI mail group
via VistA Alerts. An alert is generated when each batch process is
started. An alert is also generated when each batch reaches completion or
|
