1. Terminology Tools: State of the Art and Practical Lessons James J. Cimino Department of Medical Informatics Columbia University New York, New York, USA

2. Overview Knowledge-based terminologies –what are they? –tools needed for management and use Literature review of terminology tools Experience at Columbia

3. Knowledge-Based Terminologies Concept-based Terms Synonyms Multiple hierarchies Semantic relationships Inheritance

4. Knowledge-Based Tools Browsers - a prerequisite Editors –Collect requisite knowledge –Require referential integrity –Automated classification –Propagate inherited information –Manage change Servers –Term look-up –Answer questions about terms –Class-based queries

5. Literature Review Browsers –MicroMeSH: Lowe et al., SCAMC 1989 –UMLS: Tuttle et al., SCAMC 1991 and 1992 Editors –CMT: Mays et al., SCAMC 1996 –CMT: Campbell et al., SCAMC 1996, Methods 1998 Servers –Meta-1: Sherertz et al., SCAMC 1989 –VOSER: Rocha et al., CBR, 1994 –Galen: Rector et al., Methods 1995 –MED: Forman et al., SCAMC 1995 –InterMED: Gennari et al., SCAMC 1995 –UMLS: Many others

6. Terminology Requirements OMG RFP for terminology services 3M Health System Responded Chute et al. (SCAMC 1999) simplified

7. Experience with Terminology Tools Medical Entities Dictionary MED Editor/Server Architecture KEE MED Editor MUMPS MED Editor Unix shared memory server Qrymed Accessmed Web MED browser Mainframe environment Web MED Editor

8. Experience with Terminology Tools Medical Entities Dictionary

9. CPMC Medical Entities Dictionary Concept-based (60,000) Multiple hierarchy (85,000) Synonyms (149,000) Translations (103,000) Semantic links (114,000) Attributes (136,000)

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

11. Experience with Terminology Tools Medical Entities Dictionary KEE MED Editor

13. Experience with Terminology Tools Medical Entities Dictionary KEE MED Editor MUMPS MED Editor

15. Experience with Terminology Tools Medical Entities Dictionary KEE MED Editor MUMPS MED Editor MED Editor/Server Architecture

16. MED MUMPS Globals Datatree MUMPS MED Editor Functions MED EditorUpdate Programs medlog MED Server Query Functions Command Line Interface MED Browser Translation Tables Unix IBM Unix

17. Experience with Terminology Tools Medical Entities Dictionary KEE MED Editor MUMPS MED Editor MED Editor/Server Architecture Unix shared memory server

18. Unix Shared Memory Server ShMMED MS Acces MED db MedLEE NLP MEDlib MLM compiler Dxplain button Medline button MLM composition tool Integrated results design tool Web MED browser accessMED rpc MEDlib qrymed MED browser MEDviewer Lab upload extract Radiology bupload extract Bloodban upload Integrated results review ICU results display dop Data engine pse WebCIS

19. Experience with Terminology Tools Medical Entities Dictionary KEE MED Editor MUMPS MED Editor MED Editor/Server Architecture Unix shared memory server Qrymed

20. 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.

21. Experience with Terminology Tools Medical Entities Dictionary KEE MED Editor MUMPS MED Editor MED Editor/Server Architecture Unix shared memory server Qrymed Accessmed

25. Experience with Terminology Tools Medical Entities Dictionary KEE MED Editor MUMPS MED Editor MED Editor/Server Architecture Unix shared memory server Qrymed Accessmed Web MED browser

28. Experience with Terminology Tools Medical Entities Dictionary KEE MED Editor MUMPS MED Editor MED Editor/Server Architecture Unix shared memory server Qrymed Accessmed Web MED browser Mainframe environment

29. MED in DB2 on Mainframe 12341234 Entities 10 Name 20 UMLS 30 Part-of 40 Specimen Slots 1 10 2 10 2 20 2 30 Entity-Slots 1 10 Entity 2 10 C0001 2 40 1234 2 50 mg/dl Entity/Slot/Values 1 1 2 1 3 2 3 Ancestry

30. Experience with Terminology Tools Medical Entities Dictionary KEE MED Editor MUMPS MED Editor MED Editor/Server Architecture Unix shared memory server Qrymed Accessmed Web MED browser Mainframe environment Web MED Editor

32. Experience with Terminology Tools Medical Entities Dictionary KEE MED Editor MUMPS MED Editor MED Editor/Server Architecture Unix shared memory server Qrymed Accessmed Web MED browser Mainframe environment Web MED Editor

33. Terminology Requirements for Controlled Data Entry (Chute, 1999) Word normalization Word completion Target terminology specification Spelling correction Lexical matching Term completion Semantic locality Term composition Term decomposition

34. Other Queries For Data Entry Keyword synonyms Class-based queries –“Get me all the terms in class X” –“Is this term in class X?” –Class X may or may not include term X Class-restricted queries –“Get term from class X matching string Y” –Useful for data entry Semantic queries

36. Next Steps Further Web editor development Change management Multieditor environment Server-enable applications

37. Conclusions Knowledge-based terminologies are here to stay Sophisticated tools are needed Terminology-enabled applications need servers Server specifications can be simplified for specific purposes Class-based, class-restricted, and semantic queries are useful