Campbell Lab

Our laboratory is using data standards and terminologies to represent the words represented in the pathology report so that the data is readily accessible to both humans and computers.

Data standards are designed to render clinical information into machine readable, computable formats. In so doing, the rich information recorded during every day clinical encounters between patient and health care providers can be analyzed using computational techniques to support clinical care, population health and analytics.

Encoding data at the time of the diagnostic reporting process prepares the data for multiple uses without manual chart reviews. The information can be electronically exchanged between clinical information systems, and it can be used for population health management or research through the simple act of pairing computable terminology with common humanly readable documents. We employ SNOMED CT and LOINC for this work as both terminologies are broadly deployed and in use worldwide.

Dr. Campbell is a certified SNOMED CT Implementation expert. Working in the context of SNOMED International provides a venue to collaborate with the international community interested in this work and allows a platform to extend this work to the various professional societies operating in other nations. We collaborate with investigators associated with the College of American Pathologists (CAP) within the US to coordinate and extend this work throughout the US. Internationally, we are working with the National Colleges of Pathology in the United Kingdom and Australia, as well as, Sweden. This effort began with UNMC's involvement with SNOMED International.

In conjunction with data standards, our laboratory works with various database technologies to expose clinical data encoded with terminology standards to clinicians and clinical researchers to support their needs. NoSQL and SQL technologies are employed to manage tissue repositories (biobanks) and support a variety of research and clinical quality objectives.

Big Data to Knowledge

A critical component of the Federal architecture for the Nationwide Health Information Network is the Electronic Health Recordemploying structured clinical data encoded with Office of the National Coordinator standard reference terminologies that support interoperable repurposing of the data for research and public health. These reference terminologies, including SNOMED CT and RXNORM, are large and complex, thereby complicating and historically limiting terminology implementation in support of big data research objectives.

This research and development proposal seeks to: a) expand the scope and clinical applicability of these terminologies, b) create metadata tooling in support of  reference terminology deployment in clinical data repositories and c) assess the utility of that deployment for organizing tissue biobanks and supporting networked research queries. Metadata and software tooling will be developed and made available to the biomedical research community through the National Center for Biomedical Ontologies. The harmonization of SNOMED CT and LOINC in the domain of observable entities is an important unification of clinical ontologies.

This project will expedite this harmonization to include the domains of anatomic pathology, molecular genetics, and microbiology and create an observables ontology for distribution through the NCBO. Distribution and implementation of an observables ontology will facilitate research that binds patient phenomic data with disease-specific genomic observations in support of research into the genetic basis of disease. The observables ontology will be tested within an i2b2-based CDR in the areas of breast cancer and antimicrobial stewardship. The Patient Centered Outcome Research Initiative (PCORI) seeks to provide timely answers to the research questions of our day by standardizing datasets across research institutions. While employing a common clinical data model, efficient and interoperable query of data employing ONC reference terminologies requires expanded information models, coordination between EHR vendors and shared network protocols. This proposal will deploy the ONC reference terminology metadata including the observables ontology to members of the Greater Plains Consortium (GPC) PCORnet CDRN. Breast cancer and antimicrobial stewardship queries will be deployed between collaborating GPC members for testing of interoperability and demonstration of network functionality.

UNMC Terminology Development Center

The Nebraska Lexicon© is a SNOMED CT extension namespace authored, developed and deployed at the University of Nebraska Medical Center and Nebraska Medicine.  Conceptual content includes multiple features:

Investigators at UNMC with collaboration from the College of American Pathologists, the International Health Terminology Standards Development Organization and the Regenstreif Institute, Inc. have authored an ontology of Observable entities for the purpose of encoding cancer diagnostic data as reported by pathologists.  The terminology is based on the harmonized concept model arising from the LOINC/SNOMED International Collaborative agreement and addresses histopathology, biomarkers and molecular pathology.  All content is contained in the Nebraska Lexicon© may be freely downloaded with a valid UMLS login.

SNOMED CT® was first used in electronic health records at UNMC in 1992 in the EHR PHAMIS®.  Since that time, clinicians requiring more expressive or precise  terminology for the record could request SNOMED CT extension concepts and terms to be developed.  Those concepts were modeled in compliance with the SNOMED CT concept model (URL for SNOMED CT Editorial Guide) and published for use by collaborating health centers.  This terminology work has been published in the US in cooperation with the US extension to SNOMED CT and supplements the International Release.

Nebraska Lexicon release notes.

Full Nebraska Lexicon contents. 

Contents include:

• Release notes
• RF2 formatted SNOMED CT files including LOINC codes
• Annotated CAP cancer worksheets
  • Colorectal Cancer and biomarkers
  • Invasive breast cancer and biomarkers

By downloading the links above you acknowledge the following:

A brief registration with contact information is requested.  Contact information will be used to solicit feedback on the terminology.

This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO). All rights reserved. SNOMED CT®, was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.

Annotated Cancer Protocols from the College of American Pathologists© CAP 2017 are provided with permission of the College of American Pathologists (CAP).

If you do not have a UMLS number you will need one to download the information, please go here for your UMLS Authentication.