Essential SNOMED. Simplifying S-CT. Supporting integration with health Essential SNOMED Simplifying S-CT Supporting integration with health information models Don Walker Peter MacIsaac Rachel Richesson Heather Grain Peter Elkin Jon Patrick On behalf of the authors I would like to thank the conference organisers for the opportunity to present this paper and have the opportunity to discuss an idea which grew from empirical research on SNOMED-CT applicability for general or family practice usage in 2002. SNOMED CT is becoming the international standard for clinical terminology both in application and design, with other terminologies drawing on S_CT as an example of excellent terminology design. What we are presenting today is a proposal which has been aired informally in health terminology circles. Over the past years a number of senior colleagues in applied health informatics have raised the fate of Essential SNOMED with us, spurring an effort to flesh out some of the ideas. Maybe it is an idea that’s time has come? This is a conceptual paper looking at the way S-CT and terminologies in general handle pre-coordination. We have not proceeded to the step of empirically testing our proposal, however do consider how this might be achieved as follow-up work. We have deliberately chosen to use simple examples to illustrate our proposal and acknowledge the need for further technical work to determine the best way forward.. KR-Med 2008 Phoenix

Don Walker – University Adelaide Peter MacIsaac – Terminology Central Rachel Richesson – Uni. South Florida Heather Grain - La Trobe University Peter Elkin – Mayo Clinic John Patrick – University of Sydney

Overview Historical development S-CT Functional requirements of S-CT “in use” Role of Pre & Post Coordination Features of Essential SNOMED Relation to existing SNOMED Implementation issues Relationship to current SCT development Return to first principles – desiderata

language of use language of meaning. SNOMED-CT has sourced content from many terminologies and classifications, each reflecting their own user requirements and usage in applications SNOP SNOMED INT NIC SNOMED-RT NOC Read 2 Read 3 ICD-9 language of use We all stand on the shoulders of giants. S-CT is itself a compilation of pre-existing terminologies and classifications, as well as much original development work. SNOMED-CT has included content which describes both the language of use and the language of meaning. Meaning in that a key function of a terminology is to enumerate and define concepts, via the use of description logic and sometimes formal text definitions. Language of Use refers to the requirement that the terminology must support clinical applications which need terminology to capture both the human readable and machine processable content. Many of the early and current health information systems were based on very simple information models which placed a great deal of responsibility on the use of terminology to represent meaning and this in turn has led terminologies to favour the use of pre-coordination to represent a complex concept by a single code. language of meaning. SNOMED-CT

S-CT contains a mix of pre-coordinated and atomic or essential concepts; clinical terminology and classification concepts Atomic concepts Precoordination Recurrent capsul Ulcer left femur Chronic Amoxycillin Left Hepatitis Primary Acute Pregestational diabetes mellitus AND/OR impaired glucose tolerance Amoxycillin 250mg capsule Bleeding chronic gastric ulcer Left paramedian incision SCT contains many pre-coordinated concepts that have varying levels of semantic complexity alongside the component or essential concepts which are themselves the building blocks of these complex clinical expressions. The use of pre-coordinated concepts contributes to the large size of the terminology and complexity of the hierarchical structures. While SCT provides a theoretical mechanism for testing equivalence between a pre-coordinated concept and the same concept represented in a post coordination expression or data model, the requirements for achieving this in all cases are currently incomplete as many concepts are not adequately defined. Terminology is designed to support semantic interoperability. Interoperability between pre and post coordinated expressions is hindered by the current model, implementation in a consistent fashion is impacted. Acute gastric ulcer with hemorrhage Posttransfusion hepatitis Dendritic cell sarcoma, not otherwise specified Recurrent hernia Fractured left femur Atomic = Semantic Unit of thought

Amoxycillin 250mg capsul No allergy to latex Pre-coordinated- complex concepts supports the language of use and are very valuable Amoxycillin 250mg capsul Simple Health Record Problem Allergy Medicines This pharmacist is handing over a medicine bottle containing capsules which are recognisably well described by this precoordinated expression, defined by concepts of active drug, strength and dose form. Many of the early and current health information systems were based on very simple information models which placed a great deal of responsibility on the use of terminology to represent meaning and this in turn has led terminologies to favour the use of pre-coordination to represent a complex concept by a single code or identifier. While there are sound historical and ongoing pragmatic reasons for this evolutionary development, the resulting mix of concept structures makes implementation within various information models complex and prone to variation. No allergy to latex

Communication EHR Data retrieval Terminology concepts support the language of meaning when used within an appropriate information model to support: Communication EHR The role of the information model married with terminology is well accepted for : messaging (HL7 V3 model), -EHR (Open EHR archetype) - data retrieval (showing the information model inherent within the hierarchies of SNOMED-CT). The next three examples demonstrate the close relationship between the information model and terminologies that populate it. Data retrieval

160274005: no family history diabetes Harmonisation and transformation between the terminology model and the data model is better supported by atomic terminology HL7- version 3 example: negation In HL7 version 3 negation can be managed within the information model as an attribute of the coded value for the observation or in the terminology as shown in this SNOMED code. 160274005: no family history diabetes

Bleeding chronic gastric ulcer Terminology model vs. Data Model (Archetype) In this archtetype for Diagnosis the precoordinated concept is actually represented as a diagnosis, clinical description and a body site. Bleeding chronic gastric ulcer OpenEHR archetype - diagnosis http://svn.openehr.org/knowledge/archetypes/dev/html/en/openEHR-EHR-EVALUATION.problem-diagnosis.v1.html

Uni. Sydney example - ICU Concepts identified build compositional expressions. Codes for concepts and relationships stored in database. Used for indexing and searching the records. Uni. Sydney example - ICU This parsed note from a Sydney Intensive Care Unit is made up of compositional expressions which are used for indexing and retrieval.

Free Text Record – Mayo Clinic This example of a free text note from the MAYO clinic can be analysed using natural language processing

Anterior curciate ligament injury Positive assertions Negative assertions Uncertain assertions Right Anterior curciate ligament injury This record is parsed into Injury Has finding site - anterior cruciate ligament Has laterality – right NLP programs and text parsing to support users to enter text where appropriate into EHRs rely on the use of essential or atomic concepts which can be post coordinated.

Atomic Terminology Complex Complex Concept 2 Concept 1 Data Retrieval: Searching across multiple sources using different codesets eg US National Cancer Institute (NCI) Data Collection (acknowledgement Harold Solbrig – NCI/Apelon) Atomic Terminology Lastly a usecase for a more atomic approach to terminology was highlighted in a review of this paper by Harold Solbrig in relation to data analysis where different terminologies were used and have to be related to a standard reference terminology.. When attempting to gather data from multiple different sources and harmonise and map terminologies, having an atomic core terminology with a robust post-coordination syntax facilitates the matching of terminologies from different sources. This approach is also recognised in SNOMED in the idea of the normal form for each concept. Terminology B Terminology A Complex Concept 2 Complex Concept 1

Terminology must support pre and post coordination – more gracefully Complex hierarchies, combinatorial explosion, incomplete modelling. Terminology – information model mismatch interoperability Terminology must support pre and post coordination – more gracefully Terminology must support pre and post coordination – more gracefully The chickens come home to roost:

Separate pre-coordinated concepts from the core hierarchical representation LINKING back via a formal pre-coordinated concept definition. Eureka + Use the existing S-CT structures that manage compositional grammar (expressions), normal forms, description logic & computation of equivalence We contend that a natural extension of the development direction of S-CT is a representational form of SNOMED that uses existing structures for linking pre and post coordination. While flagging or removing to a separate structure within SNOMED concepts which are clearly pre-coordinated. Don Walker, the originator of this approach would not consent to being photographed in the bath…

We would create “pre-defined post-coordinated concepts”. 370221004 severe asthma = 195967001|asthma|:246112005|severity|=24484000|severe| Each pre-coordinated concept has a post-coordination expression and is related to hierarchy by this link. Essential SNOMED Or running naked through the streets of Adelaide either.. Existing pre-coordinated concepts remain and are matched to their atomic or essential concepts by the post – coordination grammar. Severe asthma is asthma - severity description - severe Existing and newly developed pre-coordinated concepts become “Pre-defined Post –Coordinated concepts.” The pre-coordinated concepts exist within a separate logical or physical data structure and are linked to the core or essential SNOMED by the compositional form..

Linkage of Pre-coordinated Concepts to S-CT hierarchies Now pre-coordinated concepts are related to their components and the hierarchies of SCT by this syntatical link This is analogous to how SCT or terminologies related to classifications – not within the core but by a defined relationship. 195967001|asthma|:246112005|severity|=24484000|severe| Is defined by

SNOMED-CT current model Post-coordination Grammar S-CT current model Atomic & Pre-coordinated concepts Term 1 2,* 1,* Description logic Normal form 1 This simplified model describes the core features of SCT as it now stands. Concepts Terms Relationships Post coordination grammer Description logic Mapping to classfiications 1,* Relationship type Classification map 18 18

Proposed Structure of SNOMED-ET Pre-coordinated concepts to “move” to a new home PCC PCC PCC PCC PCC PCC PCC PCC PCC PCC PCC Pre-coordinated concepts and their terms move to their new homes Post coordination grammar links the concept to the atomic content. Existing Pre-coordinated concepts remain, and new ones can be added. All pre-coordinated concepts would be defined

Pre-conditions A complete and expressive syntax for post-coordination Core requirements: Complete and expressive post-coordination syntax Ability to identify the pre-coordinated concepts and to do so cost effectively the Piper must be paid ( I think we all know the story here) Ability to identify pre-coordinated concepts/expressions Research & Resources

Strategies for identifying atomic concepts Ontological Unit (Solbrig) Concepts likely to be found in a medical dictionary – commonly used Analyse existing S-CT relationships Cannot be adequately defined by post-coordinated expression Commence with known subsets/domains Strategies for identifying atomic concepts – Is this an ontological unit - with real world representation (thanks to NCI for sharing their work on proposals for cleaning up the NCI) Concepts found in the dictionary – tend to reflect this principle Using existing SCT relationships

Essential SNOMED: Why bother? EHR and messaging information models Natural language processing & Multi-site data retrieval Tackle the morbid obesity and complexity of SCT core To recap: It will be a major effort to research and pilot and then to implement the model of structured pre-coordination. Terminology has to be aligned with the objectives of health information systemes and embodied and tested in usecases.

Pre-coordination management SNOMED-International Read 2 ICD-8 ICD-9 Read 3 SNOMED-RT SNOMED-CT ICD-10 Pre-coordination management Translation to Classifications ICD-11 Essential Core Earlier we used the meat mincer analogy to describe S-CT. While we can look back and see evolution of the product the improvements have not been random and do reflect a great deal of intelligent design. We are indebted to Jim Cimino for summarising the requirements of a clinical terminology in “the desiderata” and for his encouragement of our efforts. Essential SNOMED can contributes to several desiderata – the relation between atoms and molecules (under "Content") and the notion of "Formal Definitions". It also supports the concept of graceful evolution to meet changing user needs ?? SNOMED-ET Desiderata

“that’s the international symbol for don’t rock the boat” Peer feedback IT industry-user views IHTSDO development directions? Research Parallel efforts – NCI Thesaurus What comes after? Next Steps The purpose of a conceptual paper is to propose and explore a concept – we see this as the start. Maybe it wont turn out like this, but we hope the discussion will happen You know an ideas that’s time has come when you see others actually implementing it - I would like to acknowledge the input of Harold Solbrig and sharing the work Apelon is doing for the NCI to support the national cancer grid. NCI is going even further in terms of creating an essential terminology by focusing on differentiating between ontological and navigational nodes within the hierarchies. “that’s the international symbol for don’t rock the boat”

Change is the essence of life Change is the essence of life. Be willing to surrender what you are for what you could become “those charged with maintaining the vocabulary must accommodate graceful evolution of their content and structure. Jim Cimino

Essential SNOMED OR