Mapping Clinical Narrative to Mapping Clinical Narrative to LOINC: A Preliminary ReportLOINC: A Preliminary Report

Charles A. Sneiderman, M.D., Ph.D.Charles A. Sneiderman, M.D., Ph.D. Marcelo Fiszman, M.D., Ph.D. Marcelo Fiszman, M.D., Ph.D.

Honglan Jin, Ph.D. Honglan Jin, Ph.D. Thomas C. Rindflesch, Ph.D.Thomas C. Rindflesch, Ph.D.

Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications

IntroductionIntroduction

Pilot projectPilot project Knowledge-intensive NLP for clinical narrativeKnowledge-intensive NLP for clinical narrative

Current limitationsCurrent limitations Identify physiologic functions onlyIdentify physiologic functions only In published clinical case reports [In published clinical case reports [see see CAS_report.pdf]]

Motivation for addressing clinical LOINCMotivation for addressing clinical LOINC Clinical observations less likely structuredClinical observations less likely structured LOINC standard for communicating observationsLOINC standard for communicating observations

Side benefitSide benefit Possibility of semi-automated LOINC codingPossibility of semi-automated LOINC coding

BackgroundBackground

Previous published researchPrevious published research Terminologies mapped to LOINCTerminologies mapped to LOINC No mapping of documents to LOINCNo mapping of documents to LOINC

Limitation of existing NLP methodsLimitation of existing NLP methods MetaMap: Interaction with LOINC in Metathesaurus MetaMap: Interaction with LOINC in Metathesaurus

[see [see CAS_examples.doc]] String matching: LOINC specification not String matching: LOINC specification not

accommodated [accommodated [see see CAS_examples.doc]]

LOINC mapping is knowledge intensiveLOINC mapping is knowledge intensive

Methods: OverviewMethods: Overview

MetaMap to UMLS firstMetaMap to UMLS first Then apply knowledge-based rulesThen apply knowledge-based rules Extension of “Lexically Assign, Logically Refine” Extension of “Lexically Assign, Logically Refine”

strategy of Dolin et al. (1998)strategy of Dolin et al. (1998) Evaluation against coding by FP (CS) checked by Evaluation against coding by FP (CS) checked by

Cardiologist (BB) [Cardiologist (BB) [see see CAS_annotate.txt]]

Methods: KnowledgeMethods: Knowledge

Use canonical document structureUse canonical document structure Physical examination sectionPhysical examination section

• Begin: Lexical cues (e.g. Begin: Lexical cues (e.g. examinationexamination))• End: Semantic types (e.g. Diagnostic Procedure) End: Semantic types (e.g. Diagnostic Procedure)

Use UMLS Semantic typesUse UMLS Semantic types To identify physiologic functions (Physiologic To identify physiologic functions (Physiologic

Function, Organism Function, Clinical Attribute, Function, Organism Function, Clinical Attribute, Organism Attribute)Organism Attribute)

Use syntactic contextUse syntactic context Disambiguation: “BP” followed by quantitative conceptDisambiguation: “BP” followed by quantitative concept

Methods: LOINC structureMethods: LOINC structure

Vital SignsVital Signs Blood pressure Blood pressure system (4th field)=arterial system (4th field)=arterial Respiratory rate Respiratory rate system=respiratory system=respiratory Heart rate Heart rate system=XXX system=XXX Quantitative (QN) in 5th field (scale)Quantitative (QN) in 5th field (scale)

Choose most general LOINCChoose most general LOINC No periods in any fieldNo periods in any field No “^” (other than “^Patient”) in any fieldNo “^” (other than “^Patient”) in any field No “difference” in 2nd fieldNo “difference” in 2nd field

DiscussionDiscussion

Preliminary results [Preliminary results [see see CAS_output.txt]] Initial phaseInitial phase

Assess feasibilityAssess feasibility Note issues facedNote issues faced

Next StepsNext Steps Expand rulesExpand rules Based on structured knowledgeBased on structured knowledge

• What information does LOINC encodeWhat information does LOINC encode• How is it representedHow is it represented

Exploit LOINC information model (Forrey et al. 1996; Exploit LOINC information model (Forrey et al. 1996; Huff et al. 1998; McDonald et al. 2003)Huff et al. 1998; McDonald et al. 2003)

ReferencesReferences

Dolin RH, Huff SM, Rocha RA, Spackman KA, Campbell KE. Evaluation of a “lexically Dolin RH, Huff SM, Rocha RA, Spackman KA, Campbell KE. Evaluation of a “lexically assign, logically refine” strategy for semi-automated integration of overlapping assign, logically refine” strategy for semi-automated integration of overlapping terminologies. J Am Med Inform Assoc. 1998 Mar- Apr;5(2):203- 13. PMID: terminologies. J Am Med Inform Assoc. 1998 Mar- Apr;5(2):203- 13. PMID: 9524353 9524353

Forrey AW, McDonald CJ, DeMoor G, Huff SM, Leavelle D, Leland D, Fiers T, Charles Forrey AW, McDonald CJ, DeMoor G, Huff SM, Leavelle D, Leland D, Fiers T, Charles L, Griffin B, Stalling F, Tullis A, Hutchins K, Baenziger J. Logical observation L, Griffin B, Stalling F, Tullis A, Hutchins K, Baenziger J. Logical observation identifier names and codes (LOINC) database: a public use set of codes and names identifier names and codes (LOINC) database: a public use set of codes and names for electronic reporting of clinical laboratory test results. Clin Chem. 1996 for electronic reporting of clinical laboratory test results. Clin Chem. 1996 Jan;42(1):81-90. PMID: 8565239 Jan;42(1):81-90. PMID: 8565239

Huff SM, Rocha RA, McDonald CJ, De Moor GJ, Fiers T, Bidgood WD Jr, Forrey AW, Huff SM, Rocha RA, McDonald CJ, De Moor GJ, Fiers T, Bidgood WD Jr, Forrey AW, Francis WG, Tracy WR, Leavelle D, Stalling F, Griffin B, Maloney P, Leland D, Francis WG, Tracy WR, Leavelle D, Stalling F, Griffin B, Maloney P, Leland D, Charles L, Hutchins K, Baenziger J. Development of the Logical Observation Charles L, Hutchins K, Baenziger J. Development of the Logical Observation Identifier Names and Codes (LOINC) vocabulary. J Am Med Inform Assoc. 1998 Identifier Names and Codes (LOINC) vocabulary. J Am Med Inform Assoc. 1998 May-Jun;5(3):276-92. PMID: 9609498 May-Jun;5(3):276-92. PMID: 9609498

McDonald CJ, Huff SM, Suico JG, Hill G, Leavelle D, Aller R, Forrey A, Mercer K, McDonald CJ, Huff SM, Suico JG, Hill G, Leavelle D, Aller R, Forrey A, Mercer K, DeMoor G, Hook J, Williams W, Case J, Maloney P. LOINC, a universal standard for DeMoor G, Hook J, Williams W, Case J, Maloney P. LOINC, a universal standard for identifying laboratory observations: a 5-year update. Clin Chem. 2003identifying laboratory observations: a 5-year update. Clin Chem. 2003