seminar on standardization of laboratory data with … · relma! advanced topics and practicum –...
TRANSCRIPT
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RELMA Advanced Topics and Practicum – Part 1
Daniel J. Vreeman, PT, DPT, MSc Assistant Research Professor, Indiana University School of Medicine
Associate Director for Terminology Services, Regenstrief Institute, Inc
Seminar on Standardization of Laboratory Data with LOINC Hong Kong Hospital Authority
02.27.2012 © 2012 [email protected]
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Overview
1. General recommendations for getting started with LOINC
2. Importing Local terms 1. Import options 2. Data clean-up
3. Advanced search limits
photo via Vernio77
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Getting Started with LOINC and RELMA
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Not just an IT problem
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Don’t Assume Units of measure are critical.
Sample results can help identify the correct LOINC Scale.
Local experts, package inserts can be very informative.
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Clean water act
photo via Fishking_1
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A journey. Not a destination.
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Ongoing Journey
Plan for updating as your testing changes (less common), or your local code identifiers change (more common).
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Ongoing Journey
Replace mappings to deprecated terms with new LOINC releases.
(RELMA can help)
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Prioritization Local or national policies may help prioritize mapping subsets.
For example:
common results
+ panel elements + public health reportable tests
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Installing RELMA
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Installation Steps Need Windows (or a VM on a Mac) Got disk space? 2Gb is recommended
Start installer <drive>:\RELMA\Setup
Specify installation directory: keep default Two database files installed
RELMA.MDB – LOINC terms database
LMOF3.MDB – Local Master Observation File
Two sample files included Run it!
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File Locations Database and Ancillary Files Windows XP
Windows Vista and 7
Sample files Windows XP
Windows Vista and 7
C:\Documents and Settings\All Users\Documents\RELMA\
C:\Users\Public\Documents\RELMA\
C:\Documents and Settings\All Users\Documents\RELMA\Samples\
C:\Users\Public\Documents\RELMA\Samples\
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Running RELMA
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Main Menu/Welcome Screen
File->Set Preferred Language
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Select Linguistic Variant(s)
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LOINC Terms with Spanish Linguistic Variant
All Spanish!
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Setting User Preferences
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select User Preferences
from the File Menu
...or from Welcome Screen
Set User Preferences
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Set User Preference Dialog
startup screen preference
File locations:
(see prior slide for location)
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User Map Screen Preferences
Include/exclude battery terms
add comments on mappings
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User Map Screen Preferences
Download details pages from loinc.org
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Importing Local Terms into RELMA
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4 Ways to Build LMOF 1. Hand enter 2. Make your own table
3. Import your test catalog from text file
4. Import from real HL7 v2.x messages
bad bad
good
best
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Make a Local Dataset Extract from your test catalog
Battery code Battery description or name *Local code *Test description or name
Include method if important
Units Example values Laboratory section
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Make a Delimited Text File Need separate fields Use any delimiter Fields in any order Required fields (minimum):
Local Code Local Description Units (highly recommended)
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Importing Local Terms 1. Start it up 2. Find local term file
3. Name your working set 4. Identify field delimiter in your file 5. Match your fields to LMOF
attributes 6. Import!
C:\Documents and Settings\All Users\Documents\RELMA\Samples\
C:\Users\Public\Documents\RELMA\Samples\
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Example Tab-Delimited File
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Importing Local Files
select “Import Local Terms from Delimited File”
or just click here
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Navigate to File Location
select File and click Open
sample files stored in RELMA Directory
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Open File in RELMA
Give it a name
(RELMA allows multiple sets in one LMOF database)
select your delimiter
Import button
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Open File in RELMA
oh no!
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Match Your Fields
assign LMOF attribute
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Match Your Fields
choose field name
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Now You’re Ready!
minimum assignments
Do It!
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After import, RELMA will search for words it does not
recognize
Stay tuned for what’s next…
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Alternate Import (best) Nothing closer to the truth than real data
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Big Pile of HL7 Messages
RELMA parses into dataset OBR ID OBR description OBX ID OBX description Sample results:
actual values, units, abnormal flags, normal ranges
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Generate Local term file from HL7 messages
select Import Terms from HL7 File
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Select File to Import
select HL7 file
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Specify HL7 File Name and Sample Size name the local term file (working set)
select which codes to store
select the number of sample values
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HL7 Messages Data Statistics
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Your turn! Import Local Terms
(or sample OBX file)
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Cleaning Your Data A little time upfront saves more later
photo via Muffet
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Prep Your Data for Mapping
Improve mapping success Expand abbreviations Ignore “administrative” words Standardize idiosyncratic words Standardize time references
RELMA can help
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RELMA Cleaning Tools
use this tool to edit unknown terms
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Review Unknown Local Terms
may re-scan file for unknown terms
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Replace Local Terms
Assign LMOF Attribute replacement options
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RELMA Cleaning Tools
use this tool to make global substitutions
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Term Substitution
save this global substitution for only this working set
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Clean Up! Take some time to
clean up your sample file
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Reviewing your Local Terms
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Change Local Term File
Select the Working Set
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Manual Enter/Edit
View/Add/Edit Local Terms
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Local Term Screen
Edit\Add\Delete Terms
Export Terms
Print Preview List Text alignment option
Search Terms by Keyword
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Local Term Screen
click on “Edit Term” to see sample data
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Sample Results for Observation
Sample values from HL7 messages
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Search Local Term File
Enter Keyword from any Field
Return to full list
Calcium
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Mapping to LOINC
Photo via Jeffrey Beall
Advanced RELMA Features
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More on Searching and Grids
Photo via Jeffrey Beall
Tips and Tricks
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Wildcards “*” replaces any number of characters “?” replaces a single character
Gluc*
*cose
Glu*se
Glucos?
?lucose
Gluc?se
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Search Qualifiers
Includes Glucuronidase, Glucosidase,
Glucosylceramidase, etc.
Detailed help available
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Other Syntax Tips
Choriogonadotropin commonlabresult:true
aldolase status:deprecated
gestational age method:(reported OR estimated)
Remember, these are ADDED to the constraints indicated on the Search Limits tab
hemoglobin class:chem
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Exporting Rows from Grid
export
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Configure Export Options
Output options
Include
column headers Save configuration and/or export
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Excel Export Format
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Limiting Your Searches Sometimes 68,000+ terms is too many
Photo via Joe Shlabotnik
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Quick Access Toggles For Common Restrictions
On/Off Toggles
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Search Constraints
Specimen constraints
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Terms Consistent with Specimen
CSF
enter default specimen
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Terms Consistent with Specimen
Only CSF Terms are returned
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Setting Search Limits
Methodless Terms Restriction
Override Methodless Terms Restriction
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Limit to Methodless Terms
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Limit to Methodless Terms
only Methodless terms appear
Differ in one or more components
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Methodless Only Unchecked
All terms returned
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Conditional Methodless
More terms returned
No methodless term; all shown
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Setting Search Limits
Limit to Lab Tests Only
(No Clinical LOINC Terms)
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Setting Search Limits
include Trial, Deprecated or Discouraged LOINC codes with
returned terms
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LOINC Term Status Trial Discouraged Deprecated
Concept is experimental in nature. Use with caution as the concept and associated attributes may change.
Concept is not recommended for current use. New mappings to this concept are discouraged although existing mappings may continue to be valid in context.
Concept is retired and should not be used, but it is retained in LOINC for historical purposes.
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Include Deprecated LOINC Terms
Deprecated LOINC Terms appear as strikethrough text with a “Do Not” symbol
Discouraged LOINC Terms appear as an inverted triangle
Can’t map to a deprecated term Warning before mapping to discouraged term
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LOINC Hierarchies – Class Tree
Three top-level branches
Tree Navigation Buttons
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Before Class Restriction
Large number of candidate terms
Most terms have class of “CHAL”
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Hierarchies
Restrict eligible tests to non-challenge
chemistry tests only
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Following Class Restriction
Only Non-Challenge Chemistry tests returned
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Component Hierarchy
Show the LOINC Codes associated with these
components
“right click” for context menu with “view details” option
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Details Screen: LOINC Part
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Show Associated LOINCs
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photo via milos milosevic