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|pdfUrl=https://ceur-ws.org/Vol-1327/icbo2014_paper_60.pdf
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https://ceur-ws.org/Vol-1327/icbo2014_paper_60.pdf
ICBO 2014 Proceedings
Linking LOINC and SNOMED CT:
A cooperative approach to enhance each terminology and facilitate co-usage
Suzanne Santamaria, Farzaneh Ashrafi, Kent Spackman
International Health Terminology Standards Development Organisation (IHTSDO)
Copenhagen, Denmark
ssa@ihtsdo.org
II. PLANNED APPROACH
Abstract—A cooperative agreement between the owners of LOINC terms are named by the five main LOINC parts
SNOMED CT and LOINC was signed in 2013. Here we describe which describe the term: component, property, timing, sample
plans for and benefits of linking the two terminologies, progress type, and scale. Some LOINC terms include an optional
thus far, and challenges faced during the initial project phase. method or additional subparts. SNOMED codes are organized
into a polyhierarchical structure and description logic (DL) is
Keywords—LOINC, SNOMED CT, ontology, terminology, utilized to provide linkages between codes following defined
Meaningful Use
models with specified attributes and value types.
I. INTRODUCTION The approach to link LOINC and SNOMED follows. The
first three items are illustrated in Fig. 1.
LOINC and SNOMED CT are medical terminologies that
overlap in the area of laboratory medicine. In this domain, 1. Map LOINC parts to SNOMED codes. This map is not
LOINC laboratory tests have traditionally represented always 1:1. For example, the LOINC part Leukocytes could be
questions and SNOMED codes have been used as answers to mapped to the SNOMED code for an individual leukocyte cell
these questions. As both terminologies have a growing or to a code for a population of leukocytes depending on the
international user base and are named in Meaningful Use property type and scale used in a LOINC term.
initiatives in the United States, there is increased interest in 2. Associate LOINC terms with post-coordinated SNOMED
enhancing the use of SNOMED and LOINC together to expressions. Each LOINC term will be aligned with a
improve the delivery of healthcare. combination of SNOMED attribute and value codes
A cooperative agreement between the Regenstrief Institute (expressions) intended to represent the meaning of the term.
(owners of LOINC) and the IHTSDO (owners of SNOMED The expressions follow the SNOMED Observables model
CT) was ratified in July 2013 [1]. Tenets of this agreement which partially aligns with Basic Formal Ontology (BFO) and
include minimizing further duplication between SNOMED and Biotop. An illustrative example of a LOINC term and its
LOINC, providing linkages between LOINC and SNOMED, equivalent SNOMED expression is shown below.
enabling the two to work better together, and providing LOINC Code: 17861-6
additional value for their use. In January 2014 work LOINC Term Long Common Name: Calcium
commenced on the project with an initial scope of laboratory [Mass/volume] in Serum or Plasma
LOINC. Equivalent SNOMED Expression:
Is a: Observable entity
Specified by: Observation procedure
Direct site: Serum or plasma specimen
Observes: Quality
Inheres in: Plasma
Property type: Mass concentration
Towards: Calcium
Scale: Quantitative
3. Map existing pre-coordinated SNOMED Observable
entity and Evaluation procedures to LOINC terms. For
Fig. 1. Diagram showing where maps between SNOMED and LOINC
will be created and where SNOMED expressions for LOINC terms will example, the SNOMED code for 24 hour urine calcium output
be developed. Missing content may need to be added to either measurement (procedure) would be mapped to the LOINC
terminology. term Calcium [Mass/volume] in 24 hour Urine with a
designation that the SNOMED meaning is broader than that of
the LOINC term as it does not specify a property type. This
mapping will focus on targeted, relevant content areas.
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ICBO 2014 Proceedings
4. Develop lists of SNOMED value sets for LOINC terms. 3. Verifying cases of possible duplication in LOINC or in
Lists of SNOMED codes that are potential answers to LOINC SNOMED.
test questions will be prepared. For example, the LOINC term
Mycobacterium sp identified in Body fluid by Organism 4. Cases where SNOMED lacks the type of information
specific culture could have a value set including the SNOMED needed to complete a map. For example, SNOMED lacked pre-
identifier and name for all the Mycobacterium species codes existing codes to represent a population of cells so it was
(Mycobacterium abscessus, Mycobacterium bovis, etc.) necessary to create a new sub-hierarchy for them.
5. Document and provide guidance for implementing 5. Lack of clear differentiation between general categories
SNOMED and LOINC together. This includes surveys of of classes and specific types, present in both SNOMED and
existing and potential use cases for utilizing SNOMED and LOINC. Examples include Amphetamines (the category of
LOINC together. Descriptions of how to use them together will substances) and Amphetamine (the specific substance).
be provided in extensive implementation documentation. Reorganizing the existing SNOMED substance hierarchy,
revising some terms and creating new codes and terms was
necessary to reduce the ambiguity in the area of amphetamines.
III. ACCOMPLISHMENTS THUS FAR
Projects groups with a distinct focus and membership have V. SIGNIFICANCE
formed and meet regularly. Initial efforts have focused on the
LOINC parts used to define the top 2000 LOINC lab tests (US Improvements in both terminologies are expected and have
and SI versions). An existing map of more than 2200 LOINC already been realized on a small scale. Mapping between the
parts to SNOMED codes was evaluated and corrected, and two has identified errors, inconsistencies, ambiguities, missing
around 200 codes were added to SNOMED to complete this content and duplication within terminologies. Use of
partial map. Using this map as a base, an ontology was created description logic in LOINC to identify areas for improvement
in OWL-2-EL including almost 10,000 LOINC terms defined has previously been reported by Adamusiak and Bodenreider
[2]. They found using DL in LOINC can lead to enhanced error
with the SNOMED Observables model. This allowed us to
utilize a classifier to identify mismappings and duplication, detection, navigation, subsumption and maintenance. Quality
which led to corrections in our mappings and expressions. The improvements in SNOMED and LOINC as a result of this
classifier also created hierarchical arrangements of LOINC project will benefit numerous hierarchies in SNOMED as well
terms which enabled further evaluation of mappings. 117 as a multitude of users and implementations of SNOMED and
LOINC terms mapped to SNOMED codes were released in an LOINC across the globe.
alpha prototype OWL file to solicit feedback in May 2014. An It has been shown that development of a hierarchy of
additional 9600 LOINC terms will be included in an upcoming LOINC terms facilitates management of lab reporting for
Technology Preview release. This release will include post- public health reportable diseases [3-4]. Linking LOINC and
coordinated SNOMED expressions for each LOINC term. Two SNOMED on a larger scale should enhance these efforts as
drafts of implementation guidance have been released for well as create new opportunities for managing and analyzing
community feedback. the secondary use of healthcare data.
IV. CHALLENGES ACKNOWLEDGMENT
The US Department of Veterans Affairs and the US
Establishing meaning and semantic equivalence between National Library of Medicine provide funding support for this
terms in LOINC and SNOMED can be challenging. Specific work. We acknowledge Kaiser Permanente for their
areas of difficulty encountered thus far include: contributions in the initial mapping and ongoing problem
investigation.
1. Cases where mapping of LOINC parts to SNOMED
codes cannot be 1:1. We will describe two examples. For
LOINC terms that describe a property of the specimen (e.g. REFERENCES
Appearance of Urine), the LOINC component was considered [1] Cooperation Agreement dated July 2013 Between The International
redundant (duplicate of property type) and was not mapped to Health Terminology Standards Development Organisation (IHTSDO)
SNOMED. For LOINC codes containing Crystals.unidentified and The Regenstrief Institute, Incorporated (RII). Available at:
http://ihtsdo.org/fileadmin/user_upload/Docs_01/About_IHTSDO/Harm
(e.g. Unidentified crystals [Presence] in Urine sediment by onization/Cooperation_Agreement_between_IHTSDO_and_RII_201308
Light microscopy) the LOINC parts Crystal.unidentified 17.pdf.
(component) and Light microscopy (method) were mapped to [2] T Adamusiak and O Bodenreider, “Quality Assurance in LOINC Using
SNOMED codes: Crystal – body material (substance) and Description Logic,” AMIA Annu Symp Proc 2012: 1099-1108.
Detecting by light microscopy without classifying (qualifier [3] K Eilbeck, J Jacobs, S McGarvey, C Vinion and C Staes, “Exploring the
value). use of ontologies and automated reasoning to manage selection of
reportable condition lab tests from LOINC,” ICBO 2013.
2. Cases where LOINC parts such as Leukocytes other do [4] S Steindel, J Loonsk, A Sim, T Doyle, R Chapman and S Groseclose,
not appear to have a clear, reproducible meaning. Clarification “Introduction of a hierarchy to LOINC to facilitate public health
on the intended definition is needed to be able to create an reporting,” Proc AMIA Symp 2002: 737-41.
appropriate map.
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ICBO 2014 Proceedings
Linking LOINC and SNOMED CT: A Cooperative Approach to
Enhance Each Terminology and Facilitate Co-usage
Suzanne Santamaria, Farzaneh Ashrafi, Kent Spackman
IHTSDO
INTRODUCTION CURRENT APPROACH PRELIMINARY RESULTS
• LOINC and SNOMED CT • LOINC – SNOMED CT • Focus on laboratory LOINC initially • Groups meeting regularly
• Terminologies that cover Cooperation Project began • Collaborate with each other and with community • Mapping of Parts and Terms underway
laboratory medicine in 2014 • Content development • Errors, inconsistencies, ambiguities identified and fixed in
• Different strengths and • Map LOINC Parts and Terms to SNOMED in spreadsheet and database terminologies
usage • Create ontology by exporting from database and running script
• Traditionally used together • Classify ontology and review in Protégé (internal and external collaborators) Description Logic revealed errors in
in microbiology results mapping
reporting
• Regenstrief Institute and LOINC terms defined by SNOMED post-coordinated expressions are The highlighted term should not subsume
IHTSDO classified with a reasoner, producing additional relationships useful in the shown terms. SNOMED and the mapping
evaluating maps and for future querying were both corrected and the subsumption
• Signed long-term did not recur.
cooperative agreement in
2013 to work together
OBJECTIVE
• Report on survey of scoping and current use of LOINC and
• Collaborate to: SNOMED released April 2014
• Make it easier to use LOINC and SNOMED together • Alpha prototype of 117 LOINC Terms mapped to SNOMED
• Provide links in multiple aspects between terminologies • Perform quality assurance checks in database
• Use OWL API to create SNOMED post-coordinated expressions
Expressions released for community feedback May 2014
• Deliver guidance on new ways to use them together such as for
• Query database to create SNOMED reference sets of maps • Draft implementation guidance released July 2014
clinical decision making, in public health surveillance, and
secondary analysis of healthcare data • Implementation guidance development • Technology preview to be released soon
• Minimize future duplication between them • Survey and report on current and future use cases • 9700 LOINC Terms mapped to SNOMED Expressions
• Improve each terminology • 2100 LOINC Parts mapped to SNOMED codes
Survey reveals areas of current use and areas where combined use
LOINC Term SNOMED Pre-Coordinated Code valuable in future: laboratory observations and test results Mapping performed (September 2014)
is a
Mycobacterium Mycobacteria culture
sp:ACnc:Pt:Bld:Ord:Organism
specific culture SNOMED Post-Coordinated
equals
Expression
LOINC Part 363787002:70434600=(38605300
0:704327008=119297000,246501
Mycobacterium sp LOINC LOINC LOINC LOINC
002=703752003,370132008=1173
Parts to Terms to Terms to Answers to
63000,704347000=(414237002:7
equals SNOMED SNOMED SNOMED SNOMED
LOINC Answer 04319004=87612001,704320005=
Codes Expressions Codes Codes
243368001,704318007=11856900
Mycobacterium 0))
abscessus • Develop documentation for guidance on using SNOMED and LOINC together,
SNOMED Attribute Value
equals including innovative activities:
Mycobacterium • A practitioner queries using SNOMED to find all LOINC lab tests related to
SNOMED Attribute Value
Mycobacterium tuberculosis when she needs to confirm a case of ACKNOWLEDGEMENTS
pulmonary tuberculosis
Mycobacterium abscessus • Using the SNOMED hierarchy to dynamically maintain a set of LOINC lab The US Department of Veterans Affairs and the US National Library of Medicine provide funding
tests needed for public health disease reporting support for this work. We acknowledge Kaiser Permanente for their contributions in the initial
mapping and ongoing problem investigation.
REFERENCES
• COOPERATION AGREEMENT dated July 2013 Between The International Health Terminology Standards Development Organisation (IHTSDO) and The Regenstrief Institute, Incorporated (RII): http://www.ihtsdo.org/about-ihtsdo/governance-and-advisory/harmonization/loinc
• Alpha prototype release file of LOINC SNOMED Cooperation Project: https://csfe.aceworkspace.net/sf/frs/do/viewRelease/projects.snomed_ct_international_releases/frs.3_other_releases.loinc_snomed_alpha_prototype
• SNOMED CT Parser (OWL API): https://github.com/danka74/SnomedCTParser
• Draft LOINC – SNOMED Implementation Guidance: https://csfe.aceworkspace.net/sf/go/projects.implementation_and_innovation_co/docman.root.community.loinc_and_snomed_ct_implementati
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