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Terminology Tools: State of the Art and Practical Lessons

Terminology Tools: State of the Art and Practical Lessons. James J. Cimino Department of Medical Informatics Columbia University New York, New York, USA. Overview. Knowledge-based terminologies what are they? tools needed for management and use Literature review of terminology tools

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Terminology Tools: State of the Art and Practical Lessons

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

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

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

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

  14. Datatree MUMPS MED Editor Functions MED Editor Update Programs medlog Unix medlog Unix IBM MED Server Query Functions Unix Unix Command Line Interface MED Browser Translation Tables MED Editor/Server Architecture MED MUMPS Globals

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

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

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

  18. 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.

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

  20. 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

  21. 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

  22. Slots Entities 1 2 3 4 10 Name 20 UMLS 30 Part-of 40 Specimen Entity-Slots Ancestry Entity/Slot/Values 1 10 Entity 2 10 C0001 2 40 1234 2 50 mg/dl 1 10 2 10 2 20 2 30 1 1 1 2 1 3 2 3 MED in DB2 on Mainframe

  23. 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

  24. 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

  25. 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

  26. 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

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

  28. 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

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