Research Issues Related to the Construction and Use of Advanced Controlled Medical Terminologies

Research Issues Related to the Construction and Use of

Advanced Controlled Medical Terminologies

James J. Cimino, M.D.

Department of Medical Informatics

September 12, 2000

The Challenge

Build a central, multipurpose clinical data repository with coded data

Contributing systems have different coding systems

These coding systems change over time

There are no satisfactory standards

Solution: a Central Terminology Repository

K#1 = 4.2K#1 = 3.3

K#2 = 3.2

K#1 = 3.0

K#3 = 2.6

Additional Challenge:Communication of Changes

K#1

K#2 K#3

K#1 = 4.2K#1 = 3.3

K#2 = 3.2

K#1 = 3.0

K#3 = 2.6

Solution: Hierarchical Integration

K#1

K#2 K#3

K

Seeking an Elegant Solution

The DXplain experience

The UMLS experience

The Theory:

"A knowledge-based approach to

vocabulary representation will improve

maintenance and utility."

The Medical Entities Dictionary (MED)

Multiple hierarchy Synonyms Translations Semantic links Attributes Frame-based 65,000 concepts

MED Structure

MedicalEntity

LaboratoryProcedure

CHEM-7PlasmaGlucose

LaboratorySpecimen

PlasmaSpecimen

Substance

Sampled

Part of

Has S

pecimen

Substance Measured

Event

LaboratoryTest

DiagnosticProcedure

Plasma

AnatomicSubstance

Substance

BioactiveSubstance

Glucose

Chemical

Carbo-hydrate




The Theory:







Maintenance Tasks

New Vocabularies (Laboratory)

Changing Vocabularies (Pharmacy)

New Vocabulary: Laboratory

Original lab: 2533 terms

New lab: 5291 terms

Vocabulary delivered: June 15, 1994

“Go live” date: July 24, 1994

Changing Vocabulary: Pharmacy

Started with 2091 drugs

In two years, added 1827 drugs

Classification by:– Ingredients– AHFS Class– Allergy– DEA– Form

Adding New Terms

Identify redundant terms

Put new terms into existing classes

Create new classes where appropriate

Put Terms into Existing Classes

Theory: The attributes of new terms can be used to identify classes

Practice: "Pushing" Terms

“Pushing” a TermMedicalEntity

LaboratoryTest

PlasmaGlucose

Test

BioactiveSubstance

Glucose

Carbo-hydrate

ChemistryTest

Chem-7Glucose

Test

Chem-20Glucose

Test

StatGlucose

Test

Chemical


LaboratoryTest

PlasmaGlucose

Test

BioactiveSubstance

Glucose

Carbo-hydrate

ChemistryTest

Chem-7Glucose

Test

Chem-20Glucose

Test

StatGlucose

Test

StatGlucose

Test

Chemical


LaboratoryTest

PlasmaGlucose

Test

BioactiveSubstance

Glucose

Carbo-hydrate

ChemistryTest

Chem-7Glucose

TestStat

GlucoseTest

Chem-20Glucose

Test

StatGlucose

Test

StatGlucose

Test

Chemical

Create New Classes

Theory: Attribute patterns can be detected which identify potential classes

Practice: Recursive partitioning of existing classes

Finding a New Class

MedicalEntity

LaboratoryTest

Hepatitis BCore Antigen

Chemical

ChemistryTest

CoreAntigenHBC

Antigen

Finding a New Class

MedicalEntity

LaboratoryTest


Chemical

ChemistryTest

CoreAntigen


Test

HBC

Antigen

MedicalEntity

LaboratoryTest


Chemical

ChemistryTest

CoreAntigenHBC

Antigen

Semi-Automated Maintenance

Read formulary file

Identify new drugs

Link new drug to ingredient(s)

Suggest classifying in “preparation” class

Add new drug as per human reviewer

Interactive Classification

Adding "LASIX 20MG TAB"Generic Ingredient "FUROSEMIDE"AHFS Class "DIURETICS"Add to "FUROSEMIDE PREPARATION"? y

Adding "ZAROXOLYN 5MG CAP"Generic Ingredient "METOLAZONE"AHFS Class "DIURETICS"Add to "DIURETICS"? nCreate METOLAZONE PREPARATION" Class? y

Automated ClassificationMedicalEntity

Drug

PharmacologicSubstance

Sulfameth-oxizole

Chemical

Antibiotic

Bactrim"S1", "65"

Trimethoprim/Sulfamethoxizole

PreparationsTrimeth-

oprim

Septra"S1"

Sulfa Allergy"S1"

AllergyClass

TrimethoprimAllergy

"65"

Formulary Correction Statistics

Among original 2091 drugs:– 334 unclassified drugs assigned classes– 289 drugs assigned multiple classes– 173 drugs discovered to be missing allergy codes

Among additional 1827 drugs added:– 25 unclassified drugs assigned classes– 121 drugs assigned multiple classes– 38 drugs discovered to be missing allergy codes

Impact of "Theory into Practice":Better management

Easier to merge new vocabularies

Easier to automate change management

Higher quality through better modeling

The Theory:







Advanced Uses of Coded Data

Primary use Other patient care reuse Financial Management Information transfer (messaging) Clinical research Expert systems Information retrieval Vocabulary discovery

Case Studies

Summary reporting

Case Study:Summary Reporting

Plasma Glucose Test

Serum Glucose TestFingerstick Glucose Test

Lab Test

Intravascular Glucose Test Chem20 Display

Lab Display

DOP Summary

WebCIS Summary

Case Studies

Summary reporting HCFA requirements

Case Study:HCFA Requirements

HCFA won’t pay for lab batteries Individual tests now treated as

orderable procedures Need to appear in database as

procedures and as tests

Lab Procedure

Chem 7

Lab Test

Intravascular Glucose Test

Plasma Glucose Test



Lab Procedure

Chem 7

Lab Test

Intravascular Glucose Test

Plasma Glucose Test


Orderable Test


Case Studies

Summary reporting HCFA requirements Clinical research

Clinical Research

Epidemiology - symptoms, incidence, history of disease

Outcomes - effectiveness of therapy, ideal length of stay

Recruitment - identifying eligible participants

Case Studies

Summary reporting HCFA requirements Clinical research Expert systems

Case Studies

Summary reporting HCFA requirements Clinical research Expert systems Automated decision support

Terminology and Automated Decision Support

Data monitor checks for triggering conditions

Medical Logic Modules decide if warning conditions are present

Message sent to appropriate channel

Example: Tuberculosis culture result

Decision Support Example: TB

Monitors for delayed culture results

Sends message if result not equal to the code “No growth”

One day, dozens of alerts about positive results but no organism was reported

What happened?

How the Lab Fooled the Alert

Alert looked for results = “No Growth”

Lab started reporting “No Growth to Date” “No Growth to Date” “No Growth”

Solution: Use the controlled terminology to map all No-Growth-like lab terms into a single class, and have the alert logic refer to the class.

How We Outsmarted the Lab(Before)

No Growth

Medical Logic Module

No Growth to Date

No Growth after ...

How We Outsmarted the Lab(After)

No Growth

No Growth after 48 Hours


“No Growth” Results


No Growth to Date

Medical Logic Module

Case Studies

Summary reporting HCFA requirements Clinical research Expert systems Automated decision support Linking to on-line information sources

Linking to On-line Resources with Terminology

Clinician reviewing reports will have information needs

On-line information sources can satisfy that need

Data from report can be used to automate the query

Translations with the MED

Gentamicin

EtiologyMeasures

Sensitivity

Substance Measured

InjectableGentamicin

Gentamicn Sensitivity

Test

SerumGentamicin

Level

is-a

IntravascularGentamicin

Tests

GentamicinToxicity

Has ingredient

SummaryReports

DecisionRule

ExpertSystem

DrugInformation

Linking Text Reports to On-line Information Sources

Natural Language Processing

Data representation to support reuse

Codification of information needs

Impact of Better Management:More Useful Vocabulary

MED is up-to-date for ancillary systems

Easier to find terms in the MED

Support for multiple conceptual levels

More accurate database queries

Support for reuse of clinical data

The MED Today

Concept-based (65,000) Multiple hierarchy (85,000) Synonyms (149,000) Translations (103,000) Semantic links (114,000) Attributes (136,000)

MED Editor/Server ArchitectureMED

MUMPS Globals

Datatree

MUMPS

MED Editor Functions

MED Editor Update Programs

medlog

medlog

MED Server

Query Functions

Command Line

Interface

MED Browser

Translation Tables

Unix

IBMUnix

UnixUnix

Unix Shared Memory Server

ShMMED

MS AccesMED db

MedLEENLP

MEDlib

MLMcompiler

Dxplainbutton

Medlinebutton

MLMcomposition

tool

Integratedresults

design tool

Web MEDbrowser

accessMED

rpc MEDlib

qrymed

MEDbrowser

MEDviewer

Lab uploadextract

Radiologybuploadextract

Bloodbanupload

Integratedresultsreview

ICU resultsdisplay

dop

Data engine

pse

WebCIS

Qrymed Functions-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.

MED in DB2 on Mainframe

1234

Entities

10 Name 20 UMLS 30 Part-of

40 Specimen

Slots

1 102 102 202 30

Entity-Slots

1 10 Entity2 10 C00012 40 12342 50 mg/dl

Entity/Slot/Values1 11 21 32 3

Ancestry

Future Directions

Knowledge management system

User interface

Automated maintenance

Expansion of breadth and depth

Research Issues Related to the Construction and Use of Advanced Controlled Medical Terminologies

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