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How to Map Tests to LOINC Presented by Riki Merrick, MPH Contractor to APHL May 28, 2014.

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Presentation on theme: "How to Map Tests to LOINC Presented by Riki Merrick, MPH Contractor to APHL May 28, 2014."— Presentation transcript:

1 How to Map Tests to LOINC Presented by Riki Merrick, MPH Contractor to APHL May 28, 2014

2 Contractor to Association of Public Health Laboratories (APHL) Lead Terminologist for the APHL Informatics Program Author of ELR Release 2 Member of HL7 PHER Workgroup and Orders and Observation Workgroup IHE Lab Committee Planning Chair Author of NIST 2014 Test Tools for Certification Background: licensed physician in Germany About Me…

3 Examples of “Tests” and “Orders” in context of ELR

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6 In the HL7 message Structure, Tests and Results are analogous to Question and Answer pairs This field (OBR.4) is for order This field (OBX.3) is for observable test. This field (OBX.5) is for the result.

7 Example Pilot message for Long Beach Public Health Lab(coded vocabulary in red) MSH|^~\&|ApolloLIMS^ApolloOID^ISO|Long Beach Public Health Laboratory^05D ^CLIA|CalREDIE^ ^ISO|CDPH^ ^ISO| ||ORU^R01^ORU_R01|53|T|2.5.1|||NE|NE|||||USELR1.0^^ ^ISO| SFT|Common Cents Systems^L^^^^ApolloLIMS&ApolloOID&ISO^XX^^^| |ApolloLIMS|binary ID unknown|| PID|1||318521^^^Long Beach Public Health Laboratory^ &ISO^AN||TEST^APOLLO^^^^^|| |M|| ^White^CDCREC^W^WHITE^L|2456 DAISY AVENUE^^LONG BEACH^CA^90806^^|||||||||||2186-5^Not Hispanic or Latino^CDCREC^N^Non-Hispanic^L^2.5.1||||||||||||| ORC|RE|^Long Beach PHL Test Account^^ISO|Z000672^Long Beach Public Health Laboratory^ ^ISO|||||| |RAW||^Test^Maurice^^^Dr.^MD^^NPI& &ISO^L^^^NPI^^^^^^^^MD||^WPN^PH^^^615^ |||||||Long Beach PHL Test Account^^^^^^^^^|2525 Grand Avenue^^Long Beach^CA^90815|^WPN^PH^^^615^ |4701 Trousdale Lane^^Nashville^TN^37167^^^^||||||| OBR|1|35^^^ISO|Z000672^Long Beach Public Health Laboratory^ ^ISO| ^Chlamydia trachomatis rRNA [Presence] in Unspecified specimen by Probe and target amplification method^LN^1020^CHLAMYDIA TRACHOMATIS rRNA^L||| |||||||||^Test^Maurice^^^Dr.^MD^^NPI& &ISO^L^^^NPI^^^^^^^^MD|^WPN^P H^^^615^ ||||| |||C|||||||||| OBX|1|CWE| ^Chlamydia trachomatis rRNA [Presence] in Unspecified specimen by Probe and target amplification method^LN^1020^CHLAMYDIA TRACHOMATIS rRNA^L|1| ^Positive^SCT^POS^POSITIVE^L|^^^^^L|||||C|||||^^^^^^^^&&ISO||| SPM|1|^Z000672&ApolloLIMS&ApolloOID&ISO|| ^First void urine specimen^SCT^UV^Urine, voided^L^^^Urine, voided|||^^^UV^STERILE CONTAINER^L^^^STERILE CONTAINER||||||||||||||||||

8 Generic vs Specific tests Sometimes the Question is very specific and the answer is generic… Example Question: Hepatitis B virus core Ab [Presence] in Serum Answer: Reactive or vice versa … Example Question: Bacteria identified in Stool by Culture Answer: Salmonella enterica ss enterica

9 Resources: Vocabulary PHINVADS/RCMT: https://phinvads.cdc.gov/vads/SearchVocab.action https://phinvads.cdc.gov/vads/SearchVocab.action LOINC o Online Search: o Download “Relma”:

10 LOINC & SNOMED So how do you do it?

11 What is LOINC ? Logical Observation Identifier Names and Codes (LOINC): o Standard names & codes set that identifies laboratory and clinical observations o Established in 1994 by Clement McDonald at the Regenstrief Institute o More information is available at:

12 What is LOINC used for? Logical Observation Identifier Names LOINC is the Question: What test would you like us to perform? What test was performed? Ask at order Entry Question In HL7 speak: OBR-4 and OBX-3

13 Anatomy of a LOINC code Shortname: Salmonella Stl Cult Long Common Name:Salmonella sp identified in Stool by Organism specific culture LOINC parts: 1.COMPONENT:Salmonella Sp Identified 2.SCALE:Nom 3.PROPERTY: Prid 4.TIMING: Pt 5.SAMPLE: Stl 6.METHOD:Organism Specific Culture

14 COMPONENT What am I looking for? o Bacteria, Virus, Fungus o Genus specific, i.e. Influenza Virus o Species specific, i.e. Salmonella enteriditis o Part of the organism like AG, or RNA / DNA o Ab against an organism (species or genus level) IgG, IgM, Total

15 Property What exactly is being measured? Knowing the results (including units) is paramount here! o QN scale – Mass, concentration, catalytic activity, ratio, count, volume, length, Titer, rate o ORD scale – is often assigned an arbitrary property (most often, Threshold, ACNC) o NOM scale – for micro is PRID = Presence or Identity otherwise can be finding, appearance etc

16 Scale What format are my results in? Knowing the results is paramount here! o Quantitative QN – numeric values (mass, distance, concentration, volume, titers, ranges) o Ordinal ORD – list of terms with some order, but without scale (pos/neg, 1+,2+,3+) o Nominal NOM – list of names without order (organism names, categories) Narrative – descriptive text o Narrative NAR – descriptions (pathology result) o MULTI – textglob with different result types together as one observation

17 Timing What timeframe will my information cover? o PT – Point in time – most common in micro o Measured over a time period where different abbreviations are used depending on the time elapsed – most common would be 24 hours or 12 hours – this affects the property designation of a rate

18 System What type of specimen was examined? o This refers to the actual tested form of the specimen - If more than one specimen type is tested, use XXX – transmitted elsewhere in the message (Note XXX = “Unspecified Specimen” in the long common name description.) o If test is only performed on Isolates, then use ISLT o For serology, if it is always either serum or plasma use Ser or Ser/Plas

19 Method What method was used? o This is defined to a certain level, for example PCR is only expressed as target amplified probe (includes TMA, PCR, LCR, SDA) o More detail of the method can be sent in another part of the HL7 message o Can use “methodless” codes in LOINC too o Some Common ones include, EIA, PCR,IF,IB, Culture, Organism Specific Culture,

20 100 labs working separately could all correctly code their local tests using LOINC and SNOMED, and yet the process could generate 100 different electronic messages for the same tests.

21 Harmonization of Vocabulary and Messaging Guides. Implementation of Production Level Messages. Building Collaboration and Cross Project Fertilization. The Three Pieces To PHLIP

22 APHL approach to mapping Step 1 - Collect information about test o Local code and description o First and foremost: really helpful to know what the possible results will be. o Know as many of the following 6 properties of the test in order of importance ( can usually map with only the first two) 1. component - analyte/What is being observed? 2. Scale – Qualitative results is “Ord” – Numeric is “Qn” or “TItr” – Name of Organism is “Nom”

23 APHL approach to mapping LOINC properties( contin) 3. “Property” – think units for numeric results -For qualitative results is either “ACNC” or“Threshold” -For nominal results is usually “PRID” or “ID” 4. For Specimen can look for the XXX codes – Or common specimen types Ser, Stool 5. Method can look for the methodless codes – Some common ones include: » “EIA” » “IF” for DFA and IFA » “Probe.amp.tar” for NAATs » “Culture” 6. Time is essentially always “PT”

24 APHL approach to mapping - Simplifications “XXX” or “unspecified specimen” LOINCs Why? – Specimen is identified in another field in the HL7 message

25 Cultures are mapped to a generic culture LOINCs unless they are “Organism Specific” APHL approach to mapping - Simplifications Why? The result is specific

26 APHL approach to mapping - Simplifications “methodless” LOINCs Why? – When method is unknown from input

27 Test Metadata Collection Sheet

28 Influenza Encoding Guidelines

29 Process For Consistent Reporting Any PH Lab SME who develops new test Contact PHLIP Vocab Team Engage other programs: LIMSi, CSTE/ELR, etc Resolve language issues (e.g. CAP guidelines) Assign proper LOINC and SNOMED codes Include codes in package insert submission to FDA Quality control submits package insert to FDA Publish codes via APHL Sharepoint and PHINVADS

30 Resources for Finding the Right LOINC for ELR o Use Online LOINC for getting codes :

31 Resources for Finding the Right LOINC for ELR Can download Relma too to use locally:

32 Resources for Finding the Right LOINC for ELR Can download the LOINC Database and query directly from that too to use locally:

33 Reportable Condition Mapping Tables (RCMT) Resources for Finding the Right LOINC for ELR

34 Drafted Common Condition-based LOINC and SNOMED Encoding Guidance for Public Health and “coding tree diagrams ” for common reportable tests. Resources for Finding the Right LOINC for ELR

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36 GC/CT Combination LOINC: ^Chlamydia trachomatis and Neisseria gonorrhoeae rRNA panel in Unspecified specimen by Probe and target amplification method Component: GC LIONC: ^Neisseria gonorrhoeae rRNA [Presence] in Unspecified specimen by Probe and target amplification method Positive SNOMED Code ^Positive(qualifier value) Negative SNOMED Code ^Negative(qualifier value) Other(Inconclusive, etc) Component: CT LOINC: ^Chlamydia trachomatis rRNA [Presence] in Unspecified specimen by Probe and target amplification method Positive SNOMED Code ^Positive(qualifier value) Negative SNOMED Code ^Negative(qualifier value) Other(Inconclusive, etc)

37 LOINC Copyright Notice "This product includes all or a portion of the LOINC® database, or is derived from the LOINC® database, subject to a license from Regenstrief Institute, Inc. Your use of the LOINC database and LOINC codes also is subject to this license, a copy of which is available at The current complete LOINC database and Users' Guide are available for download at The LOINC database and LOINC codes are copyright (c) , Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee. All rights reserved. THE LOINC DATABASE IS PROVIDED "AS IS." ANY EXPRESS OR IMPLIED WARRANTIES ARE DISCLAIMED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. LOINC® is a registered United States trademark of Regenstrief Institute, Inc. A small portion of the LOINC table may include content (e.g., survey instruments) that is subject to copyrights owned by third parties. Such content has been mapped to LOINC terms under applicable copyright and terms of use. Notice of such third party copyright and license terms would need to be included if such content is included."

38 Helpful links from loinc.org For newbies: More slide shows: Recommended readings: d-readings.html FAQs:

39 Questions? Contact me at:


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