Survey of Medical Informatics

CS 493 – Fall 2004

September 27, 2004

Health Care Data Standards

Chapter 4: Patient Safety - Achieving a New Standard of Care.

IOM Report

Terminology Standards

Why terminology standards?

Standardized terminologies facilitate: Electronic data collection Retrieval of relevant data or knowledge Allows data to be reused for multiple purposes

such as syndromatic surveillance, clinical decision support and quality and cost monitoring

Criteria for terminologies

Technical Criteria used by NCVHS for evaluating and selecting terminologies Page 145 – Table 4-2

CHI focus areas Page 146 – Table 4-3

Terminology Standards

November 13, 2003 – NCVHS recommends: the adoption of SNOMED CT as the terminology of choice

for representing clinical terms LOINC is endorsed as the standard to use for Laboratory

concepts coding RxNORM National Drug File Clinical Drug Reference Terminology

(NDF RT) Also have recommended the adoption of ICD-10

January 29, 2004 – CHI endorses SNOMED CT for anatomy, nursing, diagnosis and problems, and non-lab interventions and procedures

Overview of Core and Supplemental Terminologies Box 4-1

Pages 150-151

Figure 4-4 Page 157

Unified Medical Language System

UMLS

Presentation Source Material: Oliver Bodenreider: “The Unified MedicalLanguage System (UMLS) integrating biomedical terminologies,” Nucleic AcidsResearch, 2004, Vol. 32, Database issue D267-D270

UMLS

Repository of Biomedical Vocabularies It integrates

2 million names 900,000 concepts 60 families of biomedical vocabularies 12 million relations among concepts

UMLS Metathesaurus

Sample vocabularies integrated here: NCBI taxonomy Gene Ontology The Medical Subject Headings (MeSH) OMIM Digital Anatomist Symbolic Knowledge Base ICD-9 CPT

UMLS Metathesaurus

Repository of biomedical concepts drawn from all the different terminologies integrated

Figure Source Material: Oliver Bodenreider: “The Unified MedicalLanguage System (UMLS) integrating biomedical terminologies,” Nucleic AcidsResearch, 2004, Vol. 32, Database issue D267-D270

National CenterFor BiotechnologyInformation

Online MendelianInheritance in Man

University of WashingtonDigitalAnatomist

Gene Ontology

Terminology Integration Principles Knowledge organized by concept/meaning Synonymous terms associated with concepts Concepts can be linked to other concepts Hierarchical, part-of, inheritance, associative

links and statistical relations between concepts are represented in the Metathesauraus.

Each Metathesauraus concept is categorized currently into one of 135 high-level categories

Structure of Metathesaurus

Allows Collecting terms associated with a particular

concept Exploring relationship between concepts Browsing the concepts associated with a

particular category

Section of the UMLS Semantic Network

Source: http://www.nlm.nih.gov/research/umls/META3_Figure_1.html

Section of the UMLS Semantic Network

UMLS Tools

MetamorphoSys – helps users customize Metathesaurus

lvg : a program to generate lexical variants MetaMap : extracts Metathesaurus concepts

from text

LOINCSource: “LOINC, a Universal Standard for Identifying Laboratory Observations: A 5-Year Update” Clement J. McDonald, Stanley M. Huff, et. al. Clinical Chemistry 49:4, 624-633 (2003) http://www.clinchem.org/cgi/reprint/49/4/624

Logical Observation Identifiers Names and Codes Started by a group of researchers who met in

1994 in Regenstrief Institute 1995 first release of 6000 laboratory test

results 17 releases since then Regenstrief LOINC Mapping Assistant

(RELMA)

Examples

LOINC codes for partial pressure of arterial blood oxygen (Po2) and percentage lymphocytes

EKG measurements Vital signs LOINC only codes for observation types not

the values that are associated with a particular test

Knowledge Representation

Clinical Guideline Representation Model

Clinical Guidelines

National Guideline Clearinghouse contains 1,000 publicly accessible guidelines

Box 4-2 pg. 159