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2011 12 08 - LOINC and RELMA Workshop and Tutorial
- 1. Using RELMA
Or…In Search of the Missing LOINC
Laboratory LOINC Meeting – December 2011
James T. Case MS, DVM, PhD
Health Program Specialist, SNOMED CT
National Library of Medicine
©2011 Regenstrief Institute and James Case
- 2. Acknowledgements
• LOINC Development Team
Clem Mcdonald, Dan Vreemen, Kathy Mercer, Jaci
Phillips, Ian Pyle, David Baorto, Fran Brahmi
• RELMA Development Team
John Hook, Mark Fisher, Karen Ahmed, Anandhi
Sowmyan, James Dennis
• LOINC Committee
• Supporters:
NLM, Regenstrief (including the Indiana Center of
Excellence in Public Health Informatics), Regenstrief
Foundation
©2011 Regenstrief Institute and James Case
- 3. What will we cover today?
• Overview of LOINC
• Reviewing new RELMA features!
• Installing RELMA
• Setting personal preferences
• Loading a Local Observation File (LMOF)
• Searching for a LOINC Term
• Preparing LMOF for Mapping
• Review of Map Screen Functions
• Setting Search Limits
• Mapping Local Terms to LOINC
• Viewing LOINC Term Details
• Proposing/Submitting New LOINC Terms
• Exporting/Printing Mapped Terms
• Mapping your own LMOF data
©2011 Regenstrief Institute and James Case
- 5. Why are we doing this?
Goals of Health Information Standards
• Interoperability – the ability to exchange
information between organizations
• Comparability – the ability to ascertain the
equivalence of data from different sources
• Data Quality – the measurement of
accessibility, completeness, accuracy and
precision (and more)
©2011 Regenstrief Institute and James Case
- 6. Levels of Interoperability
• Basic – allows data to be exchanged between
computer systems
• Word processing documents, text messages
• Functional – describes the standard syntax
(format) of the data
• Document templates, forms, data structures
• Message standards
• Semantic – requires use of standardized
content (vocabularies) within the data
structure
©2011 Regenstrief Institute and James Case
- 7. Comparability
• Meaning of the data is consistent when shared
among different parties
• Erysipelas – Human skin disease; Streptococcus Grp A
• Erysipelas – Animal Septicemia/dermatitis; Erysipelothrix
rhusiopathiae
• Common terminology required
• Should work in the background
• Words are not enough
• Codes – uniquely identify terms
• Vocabulary – specialized, precise terms that remove
ambiguity
• Ontology – describes nature of entities and their relations
• Classification – groups related terms
©2011 Regenstrief Institute and James Case
- 8. Potential Uses of Health Data are
Constrained by Data Quality Factors
• Data quality issues
• Different for client/patient communications vs.
clinical decision support vs. epidemiological
analysis
• Often constrained by external forces
• e.g. criteria for diagnosis often differs from the criteria
for reporting
• Unidirectional effect of data consolidation
• Detailed → General
• General → Detailed
©2011 Regenstrief Institute and James Case
- 9. The Problem
“In attempting to arrive at the truth, I have applied
everywhere for information, but in scarcely an
instance have I been able to obtain hospital
records fit for any purpose of comparison. If they
could be obtained, they would enable us to
decide many other questions… They would show
[subscribers] how their money was being spent
[and] what amount of good was really being done
with it…”
Florence Nightingale - Notes on a Hospital, 1873
©2011 Regenstrief Institute and James Case
- 10. Test comparisons
What you see in the order list
Lab A Lab B
Test Name: Lyme Disease Serology Test Name: Lyme Disease Antibody
Measures: B. burgdorferi Ab IgG Measures: B. burgdorferi Ab IgM
Method: ELISA Method: Immune blot
Scale: quantitative Scale: qualitative
e.g.: Titer 1:40 e.g.: Positive
LOINC Code = 5062-5 LOINC Code = 6321-4
©2011 Regenstrief Institute and James Case
- 11. Why LOINC?
“Within one laboratory, local jargon terms
may be used which are usually well
understood between colleagues, but
would not be sufficiently widely known for
communication with the outside world.”
U. Forsum et al., Pure Appl. Chem 72:555-745, 2000 Properties and Units in the Clinical
Laboratory Sciences Part VII. Properties and Units in Clinical Microbiology
©2011 Regenstrief Institute and James Case
- 12. LOINC ® 101
Emphasis on Laboratory
LOINC
©2011 Regenstrief Institute and James Case
- 13. Anatomy of a LOINC Term
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
5193-8 LOINC Code
Hepatitis B virus surface Ab Component
ACnc Property Measured
Pt Timing
Ser System
Qn Scale
EIA Method
There are six major LOINC axes
©2011 Regenstrief Institute and James Case
- 14. What is NOT part of a LOINC Name?
• The instrument used in testing
• Specific details about the specimen
• Priority (e.g. STAT)
• Where testing was done
• Who did the test
• Test interpretation
• Anything that is not an intrinsic part of the name of
the result
• Other things that are carried in;
• The OBR or OBX segment
• An HL7 Version 3 Observation Object
©2011 Regenstrief Institute and James Case
- 15. Component/Analyte
The substance or entity that is measured,
evaluated, or observed
- Sodium
- Glucose
- Brucella sp. organism
- Influenza A Virus antigen
- Cytomegalovirus Virus antibody
- Lipids.Total
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
©2011 Regenstrief Institute and James Case
- 16. Component/Analyte Structure
Analyte Name^Challenge^Adjustments
• Formal name of Analyte (e.g. Calcium)
• Must specify any “subanalyte”
• e.g. Coronavirus Ag
• May have a subclass – separated by “.”
• e.g. Calcium.Free
• Challenge - e.g, 1H post 100 gm Glucose PO
• Two subparts separated by “post”
• <time delay> post <challenge type>
• Adjustments/corrections
• E.g. Adjusted to pH 7.4
©2011 Regenstrief Institute and James Case
- 17. Property
the most difficult LOINC axis
The characteristic or attribute of the analyte that is
measured, evaluated, or observed
Major Categories
• Mass: Observations reported with mass (milligrams, grams, etc.)
in the numerator of their units of measure
• Substance: Observations reported with moles or milliequivalents
in the numerator of their units of measure
• Catalytic activity: Observations that report enzymatic activity
• Arbitrary: Results that report arbitrary units in the numerator of
their units of measure
• Number: Counts
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
©2011 Regenstrief Institute and James Case
- 18. Property
the most difficult LOINC axis
Combine Major Categories with Subtypes for Full Property
• MCnc – mass concentration (mass/unit vol)
• MCnt – mass content (mass/unit mass)
• NCnc – number concentration (number/unit vol)
• TmStp – time
• CCnc – catalytic concentration (activity)
• Prid – presence or identity
• Imp – impression/interpretation
• Find – subjective or objective observation
• Type – “Kind-of”
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
©2011 Regenstrief Institute and James Case
- 19. Common Issues with LOINC Properties
Fraction (proportion) vs. Ratio
a/a+b vs. a/b
• Fraction = Part/whole
• Number fraction (NFr): % Eosinophils
• Substance fraction (SFr): % HGB which is A2
• Ratio = Measures multiple analytes from the same
system (specimen)
• Mass concentration ratio - MCrto
• e.g., BUN/Creat in urine specimen
• Substance ratio-SCrto
• Urea/Creatinine expressed as mmol/L (SI units)
• Relative Ratio = Measures from different systems
• RelRto
• RlTm – time from actual Institute and James Case control
©2011 Regenstrief
and normal
- 20. Timing*
The interval of time over which the observation or
measurement was made
• Pt - at a point in time
• 12H - a twelve hour collection
• 24H - a twenty four hour collection
*non-Pt timings are usually associated with Rate Property
©2011 Regenstrief Institute and James Case
- 21. System
The system (context) or specimen type upon which
the observation was made.
• Ser - Serum • Gast – Gastric
• Bld - Whole blood fluid/contents
(RBC) • Food – Food or
• Ur- Urine feedstuff
• BldA - Arterial blood • Tiss – Tissue
• Liver - Liver • XXX – To be specified
• Flu – Body Fluid, in another part of the
unspecified message
©2011 Regenstrief Institute and James Case
- 22. System Structure
System^Super System
• Super System
• Patient is the default
• Used to indicate
• blood product unit
• bone marrow donor
• fetus
photo via Xurble
818-5:A Ag:ACnc:Pt:RBC^BPU:Ord:
54417-1:ABO+Rh group:Type:Pt:Bld^fetus:Nom:
©2011 Regenstrief Institute and James Case
- 23. Scale
• Qn - Quantitative
• Continuous numeric (real, integer, ratio)
• Optional operator (>, , , <)
• When assay detection limits are exceeded
• Ord - Ordinal
• a ranked set of possible values (1+, 2+, 3+)
• Nom - Nominal
• an unranked collection of possible values
• a taxonomy (e.g list of bacteria)
• Nar - Narrative
• free text narrative (e.g., visit note)
©2011 Regenstrief Institute and James Case
- 24. Scale (Special)
• OrdQn – Ordinal or Quantitative
• Primarily used for antimicrobial observations e.g.
MIC reported as resistant, intermediate, susceptible
or as the mm diameter of the inhibition zone
• Use is discouraged in other contexts
• Multi – structured text “globs”
• e.g. chromatography output
• Use is discouraged
• Doc – Clinical documents
• Set – Clinical attachments (headers)
©2011 Regenstrief Institute and James Case
- 25. Method
• Methods only needed if interpretation affected
• Different normal ranges
• Test Sensitivity/Specificity
• Generally listed only at the generic level
• Agglutination (limited subtypes)
• Immunoassay
• Probe with target amplification
©2011 Regenstrief Institute and James Case
- 26. Hierarchies
• LOINC ‘class’
• Each LOINC axis
• Multi-axial
• Component | System
• Separate download
©2011 Regenstrief Institute and James Case
- 27. Mapping Terms to LOINC
Things to Remember
• The thing ordered is not always the thing measured:
• Blood Culture – live organism(s) identified
• VDRL – Treponema pallidum Ab
• Urinalysis – lots of different things
• The question (what am I measuring? e.g. Glucose) is
not the answer (e.g. 90 mg/dl)
• You are mapping the question, not the answer!
• You must know the specifics of the component being
tested for (what is this test actually measuring?)
©2011 Regenstrief Institute and James Case
- 28. What is in LOINC?
Content
• Term structures
• Submitted units, Example UCUM units
• aiming toward preferred units sorting
• Synonyms
• Answer lists (increasing number)
• Text descriptions – links to info sources
about individual tests
• Panel structures
• Foreign language translations
©2011 Regenstrief Institute and James Case
- 30. Purpose of Tutorial
• “Eliminate” need to read the User’s Manual
• Become familiar with RELMA features
• Provide some insight into mapping tips/pitfalls
• Help begin the mapping process for your
institution
©2011 Regenstrief Institute and James Case
- 31. RELMA Functions
• LOINC files and indexes
• Manual and automated mapping functions
• Same free use as LOINC (see license)
• RELMA tools transform local words in local file
• User creates file of local term/name and codes
• Assigns LOINC term to local test/battery code
• “Common tests” subset to speed mapping
• Context sensitive hierarchies for local use.
• Flexible “Google-like” search functions
©2011 Regenstrief Institute and James Case
- 32. New in This Version (Rel. 5.4)
• Default - latest copy of LOINC details retrieved from
the loinc.org website.
• Configurable from File -> User Preferences -> Details Pages ->
Get from Internet.
• Build locally File -> User Preferences -> Details Pages -> Build
Locally.
• Common order rank displayed as "Common Order
Rank" in the LOINC Details displays.
• New search restriction - "Exclude LOINCs containing
'left' or 'right'“. Bilateral LOINCs and LOINCs without
laterality remain in the search results.
©2011 Regenstrief Institute and James Case
- 33. New in This Version (Rel. 5.4)
• "Terms consistent with local units" search
restriction status is saved between editing
sessions.
• Answer string descriptions displayed with
answer string (configurable).
• Images are now displayed on Part details
pages, if available.
• Obsolete LOINC fields deleted from the
Details displays -- ANSWERLIST and
DEFINITION_DESCRIPTION_HELP.
©2011 Regenstrief Institute and James Case
- 35. What’s available to download?
• RELMA - mapping and browsing tool
• HL7 message converter- Makes a database
suitable for mapping
• HL7 lint (finds bad messages)
• LOINC database and spreadsheets
• LOINC User guide; RELMA User Guide
• Tools to assist language translations by part
• Tools for building databases to map from
HL7 messages
• New guidance documents for mappers
©2011 Regenstrief Institute and James Case
35
- 36. RELMA Highlights
• Browse-able hierarchies of LOINC parts
• Display search results in tree view
• Enhanced “details” view of terms/parts
• References
• Descriptions
• Sample units
• Empirically-derived common test list
• Empirically-derived common order list
• Special features for panels/forms
• Enhanced export/copy-paste options
©2011 Regenstrief Institute and James Case
- 38. Installation Steps
• Make sure you have enough free disk space!
• 2Gb is recommended
• From CD - Start – Run – <drive>:RELMASetup
• Specify installation directory
• Life will be easier if you accept the default
• Two database files installed
• RELMA.MDB – LOINC Terms Database
• LMOF3.MDB – Local Master Observation File
• Two sample files included
• Run from Start – (All) Programs – Regenstrief – RELMA
©2011 Regenstrief Institute and James Case
- 39. File Locations
• Database and Ancillary Files
• Windows XP = C:Documents and SettingsAll
UsersDocumentsRELMA
• Windows Vista = C:UsersPublicDocumentsRELMA
• Windows 7 = C:UsersPublicDocumentsRELMA
• Sample files
• Windows XP = C:Documents and SettingsAll
UsersDocumentsRELMASamples
• Windows Vista =
C:UsersPublicDocumentsRELMASamples
• Windows 7 =
C:UsersPublicDocumentsRELMASamples
©2011 Regenstrief Institute and James Case
- 40. Running RELMA®
Version 5.4
©2011 Regenstrief Institute and James Case
- 45. LOINC Terms with Spanish Linguistic Variant
All Spanish!
©2011 Regenstrief Institute and James Case
- 47. Set User Preferences
Select User Preferences
From the File Menu
...or from Welcome Screen
©2011 Regenstrief Institute and James Case
- 48. Set User Preference Dialog
New File Locations:
(See prior slide for location)
Startup Screen Preference
©2011 Regenstrief Institute and James Case
- 49. User Map Screen Preferences
Click Map Screen Tab
Auto create search terms
Include/Exclude Battery Terms
Add comments on Mappings
©2011 Regenstrief Institute and James Case
- 51. 4 Ways to Load LMOF Files
• Direct entry into LMOF from within RELMA (painful)
• Handy for individual entries/edits
• Create an Access table that mimics the LMOF structure
(less painful but tedious)
• Appendix A: RELMA Manual
• Create a delimited ASCII file from your local test
catalog (good choice)
• Load directly from HL7 v2.x messages
• Pulls data from OBR and OBX segments
• Stores NTE segment data
©2011 Regenstrief Institute and James Case
- 52. Constructing a Local Dataset
Create extract of your test catalog with:
• Battery/Panel Code
• Battery/Panel Description or Name
• *Local Code
• *Test Description or Name
• Include Method if Important
• Units
• Example Values
• Laboratory Section
©2011 Regenstrief Institute and James Case
- 53. Creating Delimited ASCII File
• RELMA can’t parse free text
• Need to create separate fields
• Can use any of these delimiters
• Tab, Semicolon, Comma, Space
• Can define your own
• Fields can be in any order
• Minimum required fields
• Local Code
• Local Description
• Units (highly recommended)
©2011 Regenstrief Institute and James Case
- 55. Manual Enter/Edit
View/Add/Edit Local Terms
©2011 Regenstrief Institute and James Case
- 56. Edit Term Dialog
EditAddDelete Terms
Export Terms
Text alignment option
Print Preview List
©2011 Regenstrief Institute and James Case
- 57. Export Local Term File
Delimiters supported:
Tab, comma, bar (|)
©2011 Regenstrief Institute and James Case
- 59. Search Local Term File
Calcium
Enter Keyword from any
Return to Full List
Field
©2011 Regenstrief Institute and James Case
- 61. Steps to Import Local Terms
1. Click Import Local Terms Button from Main Menu
a) File>Import Local Terms from Delimited File
2. Locate your local terms text file
a) E.g. WinXP Sample files loaded into C:Documents and
SettingsAll UsersShared DocumentsRELMA
3. Name your Working Set
a) LMOF database can contain multiple work sets
4. Define default section (Optional)
5. Identify file delimiter
6. Assign fields to LMOF attributes
a) Ignore fields you don’t need
b) Combine fields if needed
7. Check “Case-sensitive” if needed
8. Click Import.
©2011 Regenstrief Institute and James Case
- 63. Importing Local Files
Select Import Local Terms
from Delimited File…
©2011 Regenstrief Institute and James Case
- 64. Navigate to File Location
Select Filefiles stored in
Sample and Click Open
RELMA Directory
©2011 Regenstrief Institute and James Case
- 65. Open File in RELMA
Name your working set.
RELMA allows multiple sets in
LMOF database
Select your delimiter
Import Button
©2011 Regenstrief Institute and James Case
- 66. Fields Segregated
Assign LMOF Attribute
Choose field name
©2011 Regenstrief Institute and James Case
- 67. Ready to Import
Minimum assignments
Now you can click the
Import button!
©2011 Regenstrief Institute and James Case
- 68. Post-Processing of Local File
• After import, RELMA Searches for terms
(words) that it does not recognize
• Stored in a file for future reconciliation
©2011 Regenstrief Institute and James Case
- 70. Change Local Term File
Select the Working Set
Current mapping status
©2011 Regenstrief Institute and James Case
- 71. Alternative Pragmatic Way
• Use large set of HL7 messages
• Automatically make dataset of:
• OBR ID
• OBR description
• OBX ID
• OBX description
• Sample of results with
• Real values
• Units
• Abnormal flags
• Normal ranges
©2011 Regenstrief Institute and James Case
- 72. Generate Local term file from HL7 messages
Select Import Terms from
HL7 File
©2011 Regenstrief Institute and James Case
- 73. Select File to Import
Select HL7 File
©2011 Regenstrief Institute and James Case
- 74. Specify HL7 File Name and Sample Size
Skip import of
sample values
Name the Local Term Select the number of
File (working set) sample values
Select which codes to store
©2011 Regenstrief Institute and James Case
- 76. New Terms added to LMOF
Click on “Edit Term” to see
Sample Data
New Battery Code
©2011 Regenstrief Institute and James Case
- 77. Sample Results for Observation
New Test Code
Sample Values from
Messages
©2011 Regenstrief Institute and James Case
- 78. Lenny L’OINC says:
“Load the Sample Files
Into RELMA now!”
• Import the two sample files
provided
• Import_Sample_OBR.txt
• Contains battery code and
description
• Import_Sample_OBX.txt
• Contains test code and
description
• Create 2 working sets
• Load your personal data set
©2011 Regenstrief Institute and James Case
- 80. Preparing your Data for Mapping
• Improve mapping success by:
• Expanding abbreviations
• Standardizing colloquial terms
• Ignoring “administrative” terms
• Standardizing time references
• Can be done prior to importing
• Better to use tools built into RELMA
©2011 Regenstrief Institute and James Case
- 81. RELMA Cleaning Tools
Use this tool to edit
unknown terms
©2011 Regenstrief Institute and James Case
- 82. Review Unknown Local Terms
May Re-Scan File for
Unknown Terms
©2011 Regenstrief Institute and James Case
- 83. Replace Local Terms
Replacement Options
Assign LMOF Attribute
©2011 Regenstrief Institute and James Case
- 84. RELMA Cleaning Tools
Use this tool to make
global substitutions
©2011 Regenstrief Institute and James Case
- 86. Lenny L’OINC says:
“Begin to clean your
data now!”
• Using the OBR or OBX sample
files, take 15-20 minutes to
clean up these unrecognized
terms
• You may use your own data if
you wish.
©2011 Regenstrief Institute and James Case
- 89. Search Window
Help File
Enter Search Terms
Limit to Restrict to “Common
Results”
Specific Units
Restrict to “Common
Use Automapper
Orders”
logic
©2011 Regenstrief Institute and James Case
- 94. Mapping Local Terms
• Select your Working Set to Map
• File>Select Local Term File to Process
• Select “Map Local Terms to LOINC” from
Welcome Screen
• Select the subset of terms to work with:
• All
• Mapped
• Unmapped
• Set your Search Limits
• Set Search Limits Button
©2011 Regenstrief Institute and James Case
- 95. Standard Mapping Window Features
• Customizable grid
• View details of LOINC term
• Sort by column
• Click column
• Custom Sort
• Print or export results grid
• Spell check squiggly line to signify words
not known to RELMA
©2011 Regenstrief Institute and James Case
- 96. Mapping Screen
View or edit local term
Enter local term number
Quick select button list
Custom Grid Configuration
©2011 Regenstrief Institute and James Case
- 97. Configure Grid
Select elements to display
Reorder grid elements
Visually resize elements
Reset Default Configuration
©2011 Regenstrief Institute and James Case
- 99. View Local Term Details
Select level of detail to
display
©2011 Regenstrief Institute and James Case
- 100. View Local Term Details
Select text size
©2011 Regenstrief Institute and James Case
- 101. Select detail display level
Select level of detail to
display
©2011 Regenstrief Institute and James Case
- 102. Standard Mapping Screen
EEK! What’ll
Begin a search I do?!
(or hit “enter”)
©2011 Regenstrief Institute and James Case
- 104. Initial Mapping Results
Number of LOINC
terms containing
Use term Battery terms
keyword
checkbox included in
search
©2011 Regenstrief Institute and James Case
- 105. Revised Mapping Results
Match units Number of
selected by matching
default records found
©2011 Regenstrief Institute and James Case
- 106. Re-revised Mapping Results
Number of
matching
Match units
records found
unselected
©2011 Regenstrief Institute and James Case
- 107. Standard Mapping Screen
CANINE DISTEMPER VIRUS IF
Enter keywords here
Clear all
input fields
©2011 Regenstrief Institute and James Case
- 108. Ad hoc term search
©2011 Regenstrief Institute and James Case
- 110. Tabbed Access to Functions
Navigate to Functions
from Mapping Page
Switch between Grid and
Tree Views
©2011 Regenstrief Institute and James Case
- 112. Tree View
• Results displayed hierarchically
• Defined by the multi-axial hierarchy in search
restrictions (covered later)
• Map to a term in tree by clicking Map button
or double clicking term
• Only rows that have LOINC Codes
©2011 Regenstrief Institute and James Case
- 113. Tree View
Can map to terms Cannot map to
with LOINC Codes terms
representing
LOINC parts
Tree Navigation
Buttons
©2011 Regenstrief Institute and James Case
- 114. Assigning a LOINC Map
Click “Map” Button
(or doubleclick)
Highlight correct
term
©2011 Regenstrief Institute and James Case
- 115. Adding Mapping Comments
Check with Frank in Chemistry
If comments
option is selected,
prompt appears
©2011 Regenstrief Institute and James Case
- 116. Assigning a LOINC Map
LOINC Term
Assigned
©2011 Regenstrief Institute and James Case
- 117. View LOINC Term Details
View details for a
specific LOINC Term
Right clicking on a LOINC
term brings up a Task Menu
©2011 Regenstrief Institute and James Case
- 118. LOINC Term Details
Can scroll down a single
formatted page
Can scroll through
Change to expanded returned subset of
details view terms
Change text size
©2011 Regenstrief Institute and James Case
- 121. Configure Export Options
Output Options
Include
Save Configuration column headers
and/or Export
©2011 Regenstrief Institute and James Case
- 124. Basic Search Syntax
Special Example Definition
Character(s)
“ “ Influenza “virus A” Linked terms must appear together
AND Morphine AND Both terms must appear in the search result
Opiates term
OR Influenza OR Either or both terms must appear in the
Parainfluenza search result term
NOT Influenza NOT equine Excludes terms with the word following the
NOT. Cannot be used alone.
? Gluc?se Substitutes a single character in the string.
(glucose,glucase) Cannot be used as the first character; cannot
be used in “phrases”
* Gluc*se Substitute multiple characters in the string.
(glucose, Cannot be used as the first character; cannot
glucuronidase, etc.) be used in “phrases”
©2011 Regenstrief Institute and James Case
- 125. Search Qualifiers
Detailed help available
Includes Glucuronidase,
Glucosidase,
Glucosylceramidase, etc.
©2011 Regenstrief Institute and James Case
- 126. Combining Search Terms
Exclude Glucosidase
Reduced number of terms
©2011 Regenstrief Institute and James Case
- 127. Advanced Search Syntax
based on Google-like search syntax
Parameter Description
+ Term must be included in search
- Term must be excluded from the search
() Group terms for subquery (i.e. A OR B; A AND B)
Fieldname: Limit term search to the associated field (e.g. Component: glucose)
Fieldname:() Group multiple terms in a single field
~ Fuzzy search (e.g. Hemofhilus~)
“ “~ Proximity search for multiple terms (e.g. “function panel”~1)
{}, [] Upper and lower bounds; {} exclusive, [] inclusive
Special character escape
©2011 Regenstrief Institute and James Case
- 130. Setting Search Limits
• Narrows search to specific subset of LOINC terms
• Reduces number of candidate terms
• Limits can be applied to all components
• Component attribute can be further restricted by
number of words
• Tree structure allows for hierarchical constraints
©2011 Regenstrief Institute and James Case
- 131. General Search Constraints
• Controls features including:
• Limit to LOINC terms compatible with submitted units
• Forced match with any specimen contained in name
• Method-less terms only
• Limit to components/analytes with N or fewer words in their
name
• Pop up search timing statistics after each search
• Use carefully or search may not be successful
(Note parallel control switches at bottom of screen)
©2011 Regenstrief Institute and James Case
- 133. Setting search limits
Can also set most of them by toggling
buttons at the bottom of the screen
Toggle Buttons
©2011 Regenstrief Institute and James Case
- 134. Search Constraints
Attribute trees
Local Unit Constraint:
Default is “ON”
Type toggle boxes
Predefined, general search
constraints
©2011 Regenstrief Institute and James Case
- 135. Terms Consistent with Units
New! - Status
saved between
editing sessions
Only terms consistent
with mmol/L appear
©2011 Regenstrief Institute and James Case
- 137. Terms Consistent with Specimen
CSF
Enter default
Specimen
©2011 Regenstrief Institute and James Case
- 138. Terms Consistent with Specimen
Only CSF Terms are
returned
©2011 Regenstrief Institute and James Case
- 142. Restriction to common orders
Large number of
New! Common candidates
orders rank
©2011 Regenstrief Institute and James Case
- 144. Limit to Methodless Terms
Both method and
method-less terms
©2011 Regenstrief Institute and James Case
- 145. Limit to Methodless Terms
Only Methodless
Terms Appear
©2011 Regenstrief Institute and James Case
- 146. More on Methodless Terms
• Some LOINC categories do not have
methodless terms
• Checking methodless only will remove these
from view on results grid
• Checking additional box allows these to be
seen
©2011 Regenstrief Institute and James Case
- 148. Methodless Only Checked
Only Methodless
terms returned
Differ in one or
more components
©2011 Regenstrief Institute and James Case
- 149. Conditional Methodless
More terms
returned
No method-less
term; all shown
©2011 Regenstrief Institute and James Case
- 150. Setting Search Limits
Limit to Lab Tests Only
(No Clinical LOINC Terms)
©2011 Regenstrief Institute and James Case
- 153. Limit Number of Component Words
Without Limit Applied:
850 terms returned
©2011 Regenstrief Institute and James Case
- 154. Limit Number of Component Words
Restriction appears on
Toggle Bar
(cannot toggle off)
Component limited to
1 word With Limit Applied:
68 terms returned
©2011 Regenstrief Institute and James Case
- 155. Setting Search Limits
Include Trial, Deprecated or
Discouraged LOINC Codes with
Returned Terms
©2011 Regenstrief Institute and James Case
- 156. Include Deprecated LOINC Terms
-You cannot map to
deprecated LOINC terms
- You are warned before
mapping to discouraged
LOINC terms
Discouraged LOINC Terms appear as an
inverted triangle
Deprecated LOINC Terms appear as
Strikethrough Text with a “Do Not”
Symbol
©2011 Regenstrief Institute and James Case
- 157. Favor Property Restriction
Favor one type of
property over others
All other components
being equal MCnc
only will be displayed
©2011 Regenstrief Institute and James Case
- 159. LOINC Hierarchies – Class Tree
Three top-level
branches
Tree Navigation
Buttons
©2011 Regenstrief Institute and James Case
- 160. Before Class Restriction
Many terms have class
of “CHAL”
Large number of
candidate terms
©2011 Regenstrief Institute and James Case
- 161. Search Trees
+Chem* +non
Restrict eligible tests
to non-challenge
chemistry tests only
©2011 Regenstrief Institute and James Case
- 164. Component Hierarchy
Click on details for more
information about the
selection
Show the LOINC Codes
associated with these
components
©2011 Regenstrief Institute and James Case
- 167. LOINC Term Details Screen
Detailed Information on
LOINC Parts
©2011 Regenstrief Institute and James Case
- 168. Tree Export Tools
Export according to
Configuration
Configure Export Format
©2011 Regenstrief Institute and James Case
- 170. RELMA - Tree Features
• All trees operate the same way
• Shows terms spelled out
• Can expand and collapse parts or all of tree.
• Tree is string searchable
• Search can be based on one or more
branches of a tree with or without other
criteria
• Use “Clear Most Limits” button on Mapping
Screen to remove all tree selections
©2011 Regenstrief Institute and James Case
- 171. LOINC Part Search
• Same look as term search
• Uses “Google-like” query language
• Extremely fast
• Include and exclude criteria
• Partial string matching (using wildcards)
• Demo
• Campylobacter fetus, not Ab
©2011 Regenstrief Institute and James Case
- 173. LOINC Mapping Tactics
• Limit effort to one lab section at a time and
focus expertise
• Chemistry and hematology will be easiest
• For manufactured assays, use package insert as
source information
• Sample results give clue to property and scale
• Consider prioritizing by frequency of use
©2011 Regenstrief Institute and James Case
- 174. Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term
Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775.
©2011 Regenstrief Institute and James Case
- 175. More LOINC Mapping Tactics
• Try using method-less terms first
• Specific methods can be transmitted in:
• OBX–17 (v2.x), Observation.methodCode (v3.0)
• Examine local units or real results to verify
correct property and scale
• Properties are rarely distinguishable in test names
• You don’t have to do it all at one sitting
• Use the “Unmapped” function to return where you
left off
• With every release - Update previous mappings
to identify deprecated terms
©2011 Regenstrief Institute and James Case
- 176. Common Mapping Issues
• Locally Defined Test Name Ambiguity
• Reuse of local test code
• “Analyte-free” Local Test Names
• (Miscellaneous serology)
• Incongruent Value sets (Scale ambiguity)
• Result vs. Interpretation
• Available LOINC Terms too Specific/General
• Panel vs. Discrete Test
• Common in Microbiology
©2011 Regenstrief Institute and James Case
- 177. Using your Mapped Terms
• Print results of LOINC Mapping
• Export to File
©2011 Regenstrief Institute and James Case
- 180. Print Mapped Terms from View/Add/Edit Menu
Click Print button to Preview
May highlight terms to be
output
printed
©2011 Regenstrief Institute and James Case
- 182. Custom Export Configuration
Select the Format you wish
to Export
Select the Fields you wish to
Export
©2011 Regenstrief Institute and James Case
- 184. Lab Auto Mapper
• Run in batch mode to find N- closest terms
• Can then use this output to do final mapping
• Again units are VERY important
• Can pick all limits available to regular mapping
©2011 Regenstrief Institute and James Case
- 185. Picking the Lab Auto Mapper
©2011 Regenstrief Institute and James Case
- 186. Lab Auto Mapper Start Screen
Can restrict search to Maximum number of terms
common tests to return
©2011 Regenstrief Institute and James Case
- 187. Lab Auto Mapper Start Screen
Local test code Local terms used for
mapping
©2011 Regenstrief Institute and James Case
- 188. Lab Auto Mapper - Mapping Screen
©2011 Regenstrief Institute and James Case
- 190. Export Terms Dialog
Select Term Set
Select Delimiter
Check Fields you
wish to export
©2011 Regenstrief Institute and James Case
- 191. Other RELMA®
Features
©2011 Regenstrief Institute and James Case
- 192. Panels, Forms and Survey Review
Review Panels, Forms and
Surveys
Review Panels, Forms and
Surveys
©2011 Regenstrief Institute and James Case
- 193. Government Forms
Component LOINC
terms
Form Name
©2011 Regenstrief Institute and James Case
- 194. Laboratory Panels
Expand category to
see panels
Double-click
panel name to see
components
©2011 Regenstrief Institute and James Case
- 200. HIPAA Attachments
View Various HIPAA
Attachments
©2011 Regenstrief Institute and James Case
- 203. Can’t find the
term you
want?
©2011 Regenstrief Institute and James Case
- 204. Search Hints and Tips
• Keywords with zero frequency are ignored
• May need to rephrase – use synonym
• Some causes for no returned terms
• Too many keywords in search – uncheck some
• Limits applied that don’t make sense
• E.g. Method-less tests plus Method tree set to EIA
• Did not find and revise words not in RELMA
• Local units not in RELMA
• Units are GREAT discriminators
• You may have tests that need to be added to
LOINC
©2011 Regenstrief Institute and James Case
- 206. Proposing New Terms
• Make sure the term is really needed
• Think of other names for the same concept
• Avoid detailed methods or localizations
• Is the distinction really important?
• Supply sufficient annotation to justify the new term
• Package inserts, sample reports (email to Regenstrief)
• The more the better!
• Construct new terms within RELMA
• File>Propose a new LOINC
• Linked to the “trees” to allow browsing
• Can review and submit them to LOINC from within
RELMA
©2011 Regenstrief Institute and James Case
- 207. Propose new LOINC terms
Select Propose a
new LOINC
©2011 Regenstrief Institute and James Case
- 208. Advanced/Simple
toggle
Required fields in Navigate through Create new term,
red proposed terms save current term
or Exit form
©2011 Regenstrief Institute and James Case
- 210. Review Proposed Terms
James T. Case DVM, PhD 301-555-1314
NIH/NLM 301-555-1315
James.case@mail.nih.gov
X
X
X
Choose whether to
send or postpone
All proposed terms
fully editable
©2011 Regenstrief Institute and James Case
- 211. Submitting New Terms
• Must supply name, organization, phone
and email of submitter
• Must select at least one proposed term to
send
• “Configure export” does not affect
submission output
• Email resulting file to Regenstrief
©2011 Regenstrief Institute and James Case
- 212. Use Existing Terms as Template
Click the Propose
Term button
Select your closest
match
©2011 Regenstrief Institute and James Case
- 213. Use Existing Terms as Template
All required
components filled in
©2011 Regenstrief Institute and James Case
- 214. Using LOINC and SNOMED
Together
©2011 Regenstrief Institute and James Case
- 215. Where do LOINC and SNOMED Fit?
Remember:
• LOINC represents the question:
• Is there any Botulism toxin in my specimen?
(33708-9)
• Organisms identified in specimen? (634-6)
• SNOMED represents the answer:
• Negative (SCTID 260385009)
• E. coli O157:H7 (SCTID 103429008)
©2011 Regenstrief Institute and James Case
- 216. Where do LOINC and SNOMED Fit?
• In an HL7 message, LOINC may be used:
• In OBR-4 (Universal Service Identifier)
• In OBX-3 (Observation Identifier
• SNOMED may be used:
• In OBX-5 (where nominal values are needed)
• Almost anyplace else in an HL7 message where
coded values are needed
©2011 Regenstrief Institute and James Case
- 217. OBX: With a Coded Value
A code that
identifies the
data type in
The code is The code is
OBX-5 as a
from LOINC from SNOMED
coded element
OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT
OBX-3:A code that
identifies the data in OBX-5: Data
OBX-5 A code for L.
(Listeria culture) monocytogenes
©2011 Regenstrief Institute and James Case
- 218. HL7 2.5 Example (ER-7 format)
MSH|^~&| LABGL1|| DMCRES|| 199812300100|| ORU^ R01|
LABGL1199510221838581| P| 2.3||| NE| NE
First Order OBR
PID||| 6910828^ Y^ C8|| Newman^ Alfred^ E|| 19720812| M|| W| 25 Centscheap Ave^^
(Culture and ID)
Whatmeworry^ UT^ 85201^^ P||( 555) 777- 6666|( 444) 677- 7777|| M|| 773789090
First Result Value
(SNOMED)
OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult
Second Order OBR
^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^
UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN (Susceptibility)
OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium
^SCT|||||| F||| 199812292128|| CA20837
OBR|| 110801^ LABGL| 387209373^ DMCRES| 29567-9^Bacterial Susceptibility
Second Result(s)
First Result First Result Description
Panel^ LN||| 199812300934||||||||Bacterial isolate| IN2973^ Schadow^
OBXs
Gunther^^^^ OBX (LOINC)
(Culture and ID)MD^ UPIN||||||||| Salmonella typhimurium ||||||| CA20837^ Spinosa^
John^^^^ MD^ UPIN
OBX|| CE|23631-5^Trimethoprim/Sulfasoxazole^ LN||264841006^Intermediate
^SCT|||||| F||| 199812300934|| CA20837
OBX|| CE|18967-7^Penicillin^LN||30714006^Resistant^SCT|||||| F||| 199812300934||
CA20837
OBX|| CE|18928-2^Gentamicin^ LN||131196009^Susceptible^SCT|||||| F|||
199812300934|| CA20837
©2011 Regenstrief Institute and James Case
- 219. Q and A Session
©2011 Regenstrief Institute and James Case