Bioinformatics

Bioinformatics combines biology, computer science, and mathematics to gather, analyze and interpret biological data, making it a relatively new and powerful interdisciplinary science. Bioinformatics capitalizes on the growing body of knowledge regarding the use of patient data.

Our department regards the establishment of bioinformatics research within the university health system as an opportune environment for scientists to understand the genetic makeup of patients and disease progression through basic biomedical research; for bioinformaticists to generate and analyze data and to predict outcomes; and for clinicians to develop novel diagnostic and identify treatment strategies. The results can create an impactful network “in which scientific evidence informs clinical practice while data gathered from clinical practice and administrative sources inform scientific investigation,” according to the NIH.

Within our department, we have several bioinformatics projects that focus on basic science, translation and clinical outcomes. Dr. Weiwei Zhang is using next-generation sequencing to detect large-scale genetic abnormalities in lymphoid malignancies and establish pipelines for translational research and clinical care. 

Big Data to Knowledge

A critical component of the federal architecture for the Nationwide Health Information Network is the Electronic Health Record employing 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 include SNOMED CT and RXNORM.
 

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:

Cancer Synoptic Report Terminology Binding

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 contained in the Nebraska Lexicon© may be freely downloaded with a valid UMLS login.

Clinical Terminology for OneChart© (an installation of EPIC®)

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 and published for use by collaborating health centers. This terminology work has been published in the U.S. in cooperation with the U.S. extension to SNOMED CT and supplements the International Release.

Nebraska Lexicon release notes

Full Nebraska Lexicon 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.