1. The Medical Entities Dictionary - © 2005 - James J. Cimino The Columbia University/ NewYork Presbyterian Hospital Medical Entities Dictionary (The MED) Ontology and Cancer Bioinformatics October 14, 2005

2. 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

3. The Medical Entities Dictionary - © 2005 - James J. Cimino New York Presbyterian Hospital Clinical Information Systems Architecture Clinical Database Medical Entities Dictionary Database Monitor Medical Logic Modules Database Interface Research Administrative Alerts & Reminders Results Review... Radiology Laboratory Discharge Summaries Reformatter

4. The Medical Entities Dictionary - © 2005 - James J. Cimino Medical Entities Dictionary: A Central Terminology Repository

5. The Medical Entities Dictionary - © 2005 - James J. Cimino K#1 = 4.2 K#1 = 3.3 K#2 = 3.2 K#1 = 3.0 Communicating Terminology Changes K#1 K#2 K#3 = 2.6 K#3

6. The Medical Entities Dictionary - © 2005 - James J. Cimino K#1 = 4.2 K#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

7. The Medical Entities Dictionary - © 2005 - James J. Cimino MED Structure Medical Entity Laboratory Procedure CHEM-7 Plasma Glucose Laboratory Specimen Plasma Specimen Substance Sampled Part of Has Specimen Event Laboratory Test Diagnostic Procedure Substance Measured Glucose Plasma Anatomic Substance Bioactive Substance Chemical Carbo- hydrate

8. 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

9. 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)

10. 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 2 NYH 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

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

14. 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…?

15. The Medical Entities Dictionary - © 2005 - James J. Cimino Using the MED MED QueryMED Translation Table Interface Engine WebCIS Decision Support

16. The Medical Entities Dictionary - © 2005 - James J. Cimino The MED and Messaging Ancillary System Local Codes MED Codes Clinical Data Repository Other Subscribers Interface Engine Translation Table

17. The Medical Entities Dictionary - © 2005 - James J. Cimino qrymed parameters The 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.

18. 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)

19. 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

20. The Medical Entities Dictionary - © 2005 - James J. Cimino DOP Summary

21. The Medical Entities Dictionary - © 2005 - James J. Cimino WebCIS Summary

22. The Medical Entities Dictionary - © 2005 - James J. Cimino Translations with the MED Gentamicin Injectable Gentamicin Gentamicn Sensitivity Test Serum Gentamicin Level Gentamicin Toxicity Etiology Measures Sensitivity Substance Measured Has ingredient is-a Intravascular Gentamicin Tests Summary Reports Decision Rule Expert System Drug Information

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

34. The MED and Cancer Bioinformatics Local UMLS for NYP/CUMC Ontology-like Directed acyclic graph Flexible and extensible Maintainable