the medical entities dictionary - © 2005 - james j. cimino the columbia university/ newyork...
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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