The Medical Entities Dictionary - © 2005 - James J. Cimino

The Columbia University/ NewYork Presbyterian Hospital

Medical Entities Dictionary(The MED)

Ontology and Cancer BioinformaticsOctober 14, 2005

The Medical Entities Dictionary - © 2005 - James J. Cimino

MED History

• 1997 – Paul Clayton charged with developing clinical information system

• 1988 – Recruitment of Hripcsak, Johnson, Sideli, Sengupta and Cimino

• Overall design – repository of data from ancillary systems

• Dictionary – to keep track of all the ancillary terminologies (a local UMLS)

• Cimino – UMLS researcher

The Medical Entities Dictionary - © 2005 - James J. Cimino

New York Presbyterian HospitalClinical Information Systems Architecture

Clinical Database

Medical Entities Dictionary

Database Monitor

Medical Logic Modules

DatabaseInterface

Research

Administrative

Alerts & Reminders

Results Review

. . .. . .Radiology LaboratoryDischarge

Summaries

Reformatter Reformatter Reformatter

The Medical Entities Dictionary - © 2005 - James J. Cimino

Medical Entities Dictionary: A Central Terminology Repository

The Medical Entities Dictionary - © 2005 - James J. Cimino

K#1 = 4.2K#1 = 3.3

K#2 = 3.2

K#1 = 3.0

Communicating Terminology Changes

K#1

K#2

K#3 = 2.6

K#3

The Medical Entities Dictionary - © 2005 - James J. Cimino

K#1 = 4.2K#1 = 3.3

K#2 = 3.2

K#1 = 3.0

Solution: Hierarchical Integration

K#1

K#2

K

K#3

K#3 = 2.6

The Medical Entities Dictionary - © 2005 - James J. Cimino

MED Structure

MedicalEntity

LaboratoryProcedure

CHEM-7PlasmaGlucose

LaboratorySpecimen

PlasmaSpecimen

Substance

Sampled

Part of

Has S

pecimen

Event

LaboratoryTest

DiagnosticProcedure

Substance MeasuredGlucose

Plasma

AnatomicSubstance

Substance

BioactiveSubstance

Chemical

Carbo-hydrate

The Medical Entities Dictionary - © 2005 - James J. Cimino

What is in the MED?

• Sunquest lab terms

• Cerner lab terms

• Digimedix drugs

• Cerner Drugs

• Sunquest Radiology

• ICD9-based problem list terms

• Other applications

• Knowledge terms

The Medical Entities Dictionary - © 2005 - James J. Cimino

The MED Today

• “Concept”-based (98,028)

• Multiple hierarchy (145,553)

• Synonyms (244,072)

• Translations (141,972)

• Semantic links (233,454)

• Attributes (227,820)

The Medical Entities Dictionary - © 2005 - James J. Cimino

Single Result Laboratory Test

Serum Digoxin Test

Serum Antiarrhythmic

Drug Level Tests

Laboratory Diagnostic Procedure

Laboratory Diagnostic

Battery

Intravascular Chemistry Specimen

Body Substance Specimen

Medical Entity

Body Substance

Sampleable Entity

Anatomic Substance

Physical Anatomic Substance

Specimen

Carbohydrate

Pharmacologic Substance

Steroid

Biologically Active Substance

Organic Chemical

Chemical Viewed Structurally

Chemical Viewed Functionally

Chemical

Substance

Physical Object

Measurable Entity

Display Information

Display Types

Laboratory Results Spreadsheet

Rogosin

Profile 2NYH Lab

Procedure: Digoxin

NYH Single Result Laboratory Test

NYH Laboratory Diagnostic

Battery

Therapeutic Drug Level

Display

Pharmacy Item

Cardiovascular Drugs

Cardiac Drugs

Digoxin Preparations

Digoxin Tablets

Digoxin 0.25mg Tablet

Digimedex CPMC

Formulary Drug Items

CPMC Drug:

Digoxin 0.25mg Tab

Serum Chemistry Specimen

Intravascular Fluid

Intravascular Fluid Specimen

Serum

Serum Specimen

NYH Serum Specimen

Sample Entity

Digoxin

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

Using the MED• Translation

– What is the ICD9 Code for …?– What is the display name for …?– What is the aggregation class for …?

• Translation Tables

• Class-based questions– Is Altace an antihypertensive?– What are all the antibiotics?

• Knowledge queries– What are the pharmaceutic ingredients of…?

The Medical Entities Dictionary - © 2005 - James J. Cimino

Using the MED

MED QueryMEDTranslation

TableInterfaceEngine

WebCIS

DecisionSupport

The Medical Entities Dictionary - © 2005 - James J. Cimino

The MED and Messaging

AncillarySystem

LocalCodes

MEDCodes

ClinicalData

Repository

OtherSubscribers

Interface EngineTranslation

Table

The Medical Entities Dictionary - © 2005 - James J. Cimino

qrymed parametersThe commands available are:-mm: sets MED memory model number {must be first option}-allslts: lists all the slots, with their names.-scd: returns the slotcode with string x as its name.-snm: returns the name of slotcode x.-srecip: returns the reciprocal of slotcode x.-stype: returns the type for slotcode x.-cd: returns the medcode with string x as its name (exact match).-find: lists medcodes that have string x in their names (pattern match).-nm: returns the name for medcode x.-pnm: returns the print name for medcode x.-par: lists the parents of medcode x.-child: lists the children of medcode x.-anc: lists the ancestors of medcode x.-desc: lists the descendants of medcode x.-ianc: lists the ancestors of medcode x (including x).-idesc: lists the descendants of medcode x (including x).-slts: lists the slots of medcode x.-sltsval: lists the slots, with their values, for medcode x.-isval: lists the medcodes which have value y in slotcode x.-val: returns the value(s) of slotcode x for medcode y.

The Medical Entities Dictionary - © 2005 - James J. Cimino

Support for Data Reuse

• Generated by one system, used by another

• Different granularities (lumpers and splitters)

• Different semantics (impedance mismatch)

The Medical Entities Dictionary - © 2005 - James J. Cimino

Summary Reporting

Plasma Glucose Test

Serum Glucose TestFingerstick Glucose Test

Lab Test

Intravascular Glucose Test Chem20 Display

Lab Display

The Medical Entities Dictionary - © 2005 - James J. Cimino

DOP Summary

The Medical Entities Dictionary - © 2005 - James J. Cimino

WebCIS Summary

The Medical Entities Dictionary - © 2005 - James J. Cimino

Translations with the MED

Gentamicin

InjectableGentamicin

Gentamicn Sensitivity

Test

SerumGentamicin

Level

GentamicinToxicity

EtiologyMeasures

Sensitivity

Substance Measured Has ingredient

is-a

IntravascularGentamicin

TestsSummaryReports

DecisionRule

ExpertSystem

DrugInformation

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The Medical Entities Dictionary - © 2005 - James J. Cimino

The MED and Cancer Bioinformatics

• Local UMLS for NYP/CUMC

• Ontology-like

• Directed acyclic graph

• Flexible and extensible

• Maintainable