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MED History

The Columbia University/ NewYork Presbyterian Hospital Medical Entities Dictionary (The MED) Ontology and Cancer Bioinformatics October 14, 2005. MED History. 1997 – Paul Clayton charged with developing clinical information system

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MED History

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  1. The Columbia University/ NewYork Presbyterian Hospital Medical Entities Dictionary(The MED)Ontology and Cancer BioinformaticsOctober 14, 2005

  2. 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. Medical Logic Modules Clinical Database Alerts & Reminders Database Monitor Results Review Database Interface Administrative Medical Entities Dictionary Research Reformatter Reformatter Reformatter . . . . . . Radiology Discharge Summaries Laboratory New York Presbyterian HospitalClinical Information Systems Architecture

  4. Medical Entities Dictionary: A Central Terminology Repository

  5. K#1 = 4.2 K#1 = 3.3 K#2 = 3.2 K#1 = 3.0 K#3 = 2.6 K#1 K#2 K#3 Communicating Terminology Changes

  6. K#1 = 4.2 K#1 = 3.3 K#2 = 3.2 K#1 = 3.0 K#3 = 2.6 K K#3 Solution: Hierarchical Integration K#1 K#2

  7. Substance Laboratory Specimen Event Chemical Anatomic Substance Plasma Specimen Diagnostic Procedure Substance Sampled Plasma Laboratory Test Laboratory Procedure Has Specimen Carbo- hydrate Bioactive Substance Part of Glucose Substance Measured MED Structure Medical Entity CHEM-7 Plasma Glucose

  8. 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 MED Today • “Concept”-based (98,028) • Multiple hierarchy (145,553) • Synonyms (244,072) • Translations (141,972) • Semantic links (233,454) • Attributes (227,820)

  10. Medical Entity Pharmacy Item Display Information Sample Entity Physical Object Specimen Display Types Cardiovascular Drugs Sampleable Entity Substance Digimedex CPMC Formulary Drug Items Body Substance Specimen Laboratory Results Spreadsheet Cardiac Drugs Physical Anatomic Substance Intravascular Fluid Specimen Therapeutic Drug Level Display Digoxin Preparations Anatomic Substance Serum Specimen Intravascular Chemistry Specimen Digoxin Tablets Body Substance Laboratory Diagnostic Procedure Serum Chemistry Specimen Measurable Entity Digoxin 0.25mg Tablet Intravascular Fluid Laboratory Diagnostic Battery Single Result Laboratory Test NYH Serum Specimen Chemical CPMC Drug: Digoxin 0.25mg Tab Serum Serum Antiarrhythmic Drug Level Tests Chemical Viewed Structurally NYH Laboratory Diagnostic Battery NYH Single Result Laboratory Test Chemical Viewed Functionally Serum Digoxin Test Organic Chemical Pharmacologic Substance Biologically Active Substance Rogosin Profile 2 Carbohydrate Steroid NYH Lab Procedure: Digoxin Digoxin

  11. 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…?

  12. WebCIS QueryMED Translation Table Interface Engine Decision Support Using the MED MED

  13. Clinical Data Repository Interface Engine Translation Table Local Codes MED Codes Other Subscribers The MED and Messaging Ancillary System

  14. 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. qrymed parameters

  15. Support for Data Reuse • Generated by one system, used by another • Different granularities (lumpers and splitters) • Different semantics (impedance mismatch)

  16. Lab Display Lab Test Intravascular Glucose Test Summary Reporting Chem20 Display Fingerstick Glucose Test Serum Glucose Test Plasma Glucose Test

  17. DOP Summary

  18. WebCIS Summary

  19. Intravascular Gentamicin Tests Summary Reports is-a Has ingredient Substance Measured Decision Rule Measures Sensitivity Etiology Drug Information Expert System Translations with the MED Injectable Gentamicin Serum Gentamicin Level Gentamicin Gentamicn Sensitivity Test Gentamicin Toxicity

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

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