1 Introduction

This four-hour workshop for the advanced participant will promote interoperability and analytics in healthcare datamarts being developed and implemented for decision support, research and public health. It will guide the participant in implementing the guidelines of the ONC Interoperability Standards Advisory(ISA). The workshop team will employ their research and experience with HL7 and SNOMED CT to demonstrate the integration of SNOMED CT, LOINC and RxNORM as domain ontologies integrated with FHIR resources. Using a series of use cases taken from implementation of research network datamarts, they will present and discuss the relevant ISA specifications, and the associated ontology standards, some being developed at Nebraska. For each use case they will highlight any ambiguities in the ONC specifications and discuss the decisions to be made relative to deploying the semantics of the reference domain standards. They will present resources for managing and implementing relevant ONC sanctioned ontologies within the ISA model, including an integrated ontology of SNOMED-LOINC-RXNORM developed and published as terminology resources by Nebraska. Special attention will be focused on addressing problem areas of translational research that require integration of reference domain standards to bridge laboratory medicine, pathology, microbiology, genomics and patient phenomics. Each use case will be accompanied by demonstration of the data analytic utility of ontologies for extraction of meaningful knowledge from the EHR. Participants will conclude the workshop with an understanding of and access to a set of open source resources and tools for binding, integrating and maintaining the ontologies at their own institutions.

1.1 Learning Objectives

After participating in this session the learner should be better able to:

  • Describe and discuss features of an interoperable data model compliant with the 2021 ONC Interoperability Standards Advisory for EHR core data domains

  • Understand the semantic scope, strengths and weaknesses and tooling for terminology standards: SNOMED CT, LOINC, RxNorm, NDC, (CPT-4, ICD-10-CM/PCS, CVX)

  • Identify and manage knowledge gaps present in domain ontologies in support logical integration of ontologies

  • List resources and tools of use in deploying, maintaining and updating ONC interoperability standards

1.2 How to Use this Pamphlet

This accompanying pamphlet contains references and resources that accompany the sections of this workshop. We have compiled a list of important resources on the management and maintenance of medical terminology and other measures that are available for use during and following the workshop in the handouts folders.

1.2.1 Handouts Inventory

  • RUCA2010ZIPCODE.csv
  • RXNORM_NDC_RELATIONSHIPS_20220501.zip
    • Comprehensive and historically complete file of useful relationships which have been published by NLM and the FDA. This includes relationships for RXCUIs, NDCs and VA Drug Classes that might now be listed as inactive in current UMLS releases. The Relationship types included are:
      1. VA Class to Ingredient,
      2. Active Ingredient to Clinical Drug,
      3. Active Ingredient to Manufactured Product Package code, and
      4. Clinical Drug to Manufactured Product package Code.
    • Active ingredients are RXCUIs from TTY classes PIN, MIN and IN. Clinical Drugs are RXCUIs from TTYs of SCDC,SCD,GPCK, SBD and BPCK. Manufactured Product Package codes are exclusively NDC.

  • SDH_COLUMNS.csv
    • Data dictionary including for the current release of community-level Social Determinants of Health Observation concepts in Nebraska Lexicon©

  • SDH_Stats.csv
    • Data inventory and Nebraska Lexicon© SNOMED CT extension codes for 63 Community-level data items computed from American Community Survey 2019 Census data including Bird Index, Wisconsin Area Deprivation Index, American Community Survey detail and the Social Vulnerability Index.

  • SNOMEDCT_USExtension_NebLexicon_LOINC_RXNORM.zip
    • OWL file with integrated ontology of SNOMED CT© International Edition 20220130 + US Extension© 20220330 from NLM + Nebraska Lexicon© SNOMED Extension + 23K Laboratory LOINC© concepts imported as axioms + RxNorm© generic clinical drugs imported as axioms

  • SVI2018DocumentatioN-h.pdf
  • Doc_ExpressionConstraintLanguage_v2.0-en-US_INT_20220404.pdf
    • SNOMED CT Expression Constraint Language Specification and Guide Version 2.0 This includes the technical specifications and ABNF syntax for current version of Expression Constraint Language.

  • SNOMED CT Editorial Guide-2022-01-31.pdf
    • Current version of the authoritative technical reference guide for the structure and function of SNOMED CT© and the specifications of its concept model (ontology conceptualization)

  • Logical Observation Identifiers Names and Codes (LOINC®) Users’ Guide

1.3 About the Presenters

James R. Campbell, MD

Jim Campbell MD, FACP, FACMI mustered out of the Air Force in 1972 and earned his MD from the University of Nebraska in 1976. He is boarded in Internal Medicine and has served as a primary care physician for 45 years. He became interested in informatics through involvement in the newly formed Society for Computer Applications in Medical Care(SCAMC) and developed his first electronic health record(EHR) for installation in the outpatient medicine clinic in 1982. He was convinced at then that standardization of healthcare terminologies were core requirements for an EHR that could support reliable and consistent outcomes for his patients and joined the SNOMED Editorial Board in 1990, He has worked actively with Standards Development Organizations including HL7 Decision Support and Guidelines projects, LOINC and SNOMED International and ICD-11 technical advisory team through the intervening years.He is a certified Consultant Terminologist with SNOMED International and has certified as an Epic® Ambulatory Analyst. His ongoing research interest is the standardization and interoperation of healthcare terminologies in service of research analytics and clinical decision support.

James C. McClay, MD, MS

James McClay, MD, MS, has over thirty years of clinical, informatics, and research experience as an Emergency Physician. He recently became the Chief Research Informatics Officer at the University of Missouri. Prior to this role, he was principal investigator for the University of Nebraska Clinical Research Analytics Environment (CRANE), director of the Great Plains IDeA Clinical and Translational Research Center Biomedical Informatics Core, and chaired the University of Nebraska Medical Center (UNMC) Biomedical Informatics Graduate Degree Program. His work focused on developing and operationalizing evidence generation pipelines for learning health systems. Dr. McClay is a long-standing Health Level Seven (HL7) participant as a workgroup chair and a clinical leader in the development of FHIR specifications.

Carol R. Geary, PhD, RN, MBA

Carol Geary, PhD, RN, MBA, is a nurse researcher who began her focus on use of structured electronic health record research during postdoctoral study with Dr. McClay. She spends much of her time focused on developing and instituting infrastructure necessary to support such usage. She has recently become the UNMC PCORnet Principal Investigator, building upon previous experience as Patient Engagement Officer. In this context, she aims to enhance availability and usability of structured electronic health data in nursing research.

W. Scott Campbell, PhD

Scott Campbell, PhD, MBA is a tenured, associate professor in the Department of Pathology and Microbiology at the University of Nebraska Medical Center (UNMC) in Omaha, Nebraska, USA. He is also the Director of Informatics for the Nebraska Public Health Laboratory and the Sr. Director of Research Information Technologies for UNMC. Dr. Campbell specializes in clinical informatics with special emphasis in cancer pathology and microbiology.

The development of SNOMED CT concept expressions for use in cancer synoptic reporting which includes biomarker and next generation sequencing data comprises significant aspects of Dr. Campbell’s research efforts. He currently serves as the Chair of the Cancer Synoptic Reporting Working Group for SNOMED International which is creating the necessary knowledge representation and concepts for the SNOMED CT international release for use in structured cancer reporting.

A. Jerrod Anzalone, MS Jerrod Anzalone, MS, is a PhD candidate in biomedical informatics and works as a clinical research informatics specialist for the University of Nebraska Medical Center (UNMC). His research interests are in applied clinical informatics, the secondary analysis of healthcare data for research, and the maintenance of medical terminology.. Over the past two years, he has worked heavily in the National COVID Cohort Collaborative (N3C), focusing on rural populations, immunosuppresed/compromised persons, and data quality issues in multi-center studies.

1.4 Learn More

To learn more about the work done by this research team on terminology development, please visit: