Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text

Journal of the American Medical Informatics Association

Volumn 22, Issue e1, 2015, Pages e162-e176

  Bejan, Cosmin Adrian ^a   Wei, Wei Qi ^a   Denny, Joshua C ^a,b  

^a VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^b VANDERBILT UNIVERSITY   (United States)

Author keywords

MEDI; Natural language processing; SemRep; Treatment relation extraction

Indexed keywords

BIOLOGY; EXTRACT; EXTRACTION; HUMAN; HUMAN EXPERIMENT; INFORMATION SCIENCE; NATURAL LANGUAGE PROCESSING; ONTOLOGY; PREDICTION; RECALL; RXNORM; UNIFIED MEDICAL LANGUAGE SYSTEM; VETERAN; ALGORITHM; INFORMATION RETRIEVAL; KNOWLEDGE BASE; PROCEDURES; SEMANTICS;

DRUG;

ALGORITHMS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; KNOWLEDGE BASES; PHARMACEUTICAL PREPARATIONS; RXNORM; SEMANTICS; UNIFIED MEDICAL LANGUAGE SYSTEM;

EID: 84986917859     PISSN: 10675027     EISSN: 1527974X     Source Type: Journal    
DOI: 10.1136/amiajnl-2014-002954     Document Type: Article

References (34)

1. Cebul RD, Love TE, Jain AK, et al. Electronic health records and quality of diabetes care. N Engl J Med. 2011;365:825-33.
2. Ghitza UE, Sparenborg S, Tai B. Improving drug abuse treatment delivery through adoption of harmonized electronic health record systems. Subst Abuse Rehabil. 2011;2011: 125-31.
3. Liu M, Wu Y, Chen Y, et al. Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. J Am Med Inform Assoc. 2012; 19:28-35.
4. Roth CP, Lim YW, Pevnick JM, et al. The challenge of measuring quality of care from the electronic health record. Am J Med Qual. 2009;24:385-94.
5. Roth MT, Weinberger M, Campbell WH. Measuring the quality of medication use in older adults. J Am Geriatr Soc. 2009;57:1096-102.
6. Rindflesch TC, Fiszman M. The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text. J Biomed Inform. 2003;36:462-77.
7. Wei WQ, Cronin RM, Xu H, et al. Development and evaluation of an ensemble resource linking medications to their indications. J Am Med Inform Assoc. 2013;20:954-61.
8. Uzuner Ö, South BR, Shen S, et al. 2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text. J Am Med Inform Assoc. 2011;18:552-6.
9. Rink B, Harabagiu S, Roberts K. Automatic extraction of relations between medical concepts in clinical texts. J Am Med Inform Assoc. 2011;18:594-600.
10. De Bruijn B, Cherry C, Kiritchenko S, et al. Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010. J Am Med Inform Assoc. 2011;18:557-62.
11. Minard AL, Ligozat AL, Ben Abacha A, et al. Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification. J Am Med Inform Assoc. 2011;18:588-93.
12. Patrick JD, Nguyen DHM, Wang Y, et al. A knowledge discovery and reuse pipeline for information extraction in clinical notes. J Am Med Inform Assoc. 2011;18:574-9.
13. Aronson AR. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proceedings AMIA Symposium. 2001:17-21.
14. Fiszman M, Rindflesch TC, Kilicoglu H. Integrating a hypernymic proposition interpreter into a semantic processor for biomedical texts. Proceedings AMIA Symposium 2003:239-43.
15. Rindflesch TC, Pakhomov SV, Fiszman M, et al. Medical facts to support inferencing in natural language processing. Proceedings AMIA Symposium 2005:634-8.
16. Fiszman M, Rindflesch TC, Kilicoglu H. Abstraction summarization for managing the biomedical research literature. HLT-NAACL Workshop on Computational Lexical Semantics 2004:76-83.
17. Wilkowski B, Fiszman M, Miller CM, et al. Graph-based methods for discovery browsing with semantic predications. Proceedings AMIA Symposium 2011:1514-23.
18. Hristovski D, Friedman C, Rindflesch TC, et al. Exploiting semantic relations for literature-based discovery. Proceedings AMIA Symposium 2006:349-53.
19. Liu Y, Bill R, Fiszman M, et al. Using SemRep to label semantic relations extracted from clinical text. Proceedings AMIA Symposium 2012:587-95.
20. Kuhn M, Campillos M, Letunic I, et al. A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol. 2010; 6:343.
21. Denny JC, Smithers JD, Miller RA, et al. 'Understanding' medical school curriculum content using KnowledgeMap. J Am Med Inform Assoc. 2003;10:351-62.
22. Denny JC, Spickard AIII, Miller RA, et al. Identifying UMLS concepts from ECG impressions using KnowledgeMap. Proceedings AMIA Symposium 2005:196-200.
23. Stenetorp P, Pyysalo S, Topić G, et al. BRAT: a web-based tool for NLP-assisted text annotation. Demonstrations Session at EACL 2012:102-7.
24. Noreen EW. Computer-intensive methods for testing hypotheses: an introduction. 1st edn. New York: John Wiley & Sons, 1989.
25. Rindflesch TC, Fiszman M, Libbus B. Semantic interpretation for the biomedical research literature. In: Chen H, Fuller SS, Friedman C, et al., eds. Medical Informatics: Knowledge Management and Data Mining in Biomedicine. New York: Springer, 2005:399-422.
26. Ahlers CB, Fiszman M, Demner-Fushman D, et al. Extracting semantic predications from Medline citations for pharmacogenomics. Pacific Symposium on Biocomputing 2007:209-20.
27. Wei WQ, Mosley JD, Bastarache L, et al. Validation and enhancement of a Computable Medication Indication Resource (MEDI) using a large practice-based dataset. Proceedings AMIA Symposium 2013:1448-56.
28. Ely JW, Osheroff JA, Gorman PN, et al. A taxonomy of generic clinical questions: classification study. BMJ. 2000; 321:429-32.
29. Kho AN, Pacheco JA, Peissig PL, et al. Electronic medical records for genetic research: results of the eMERGE consortium. Sci Transl Med. 2011;3:79re1.
30. Denny JC. Chapter 13: Mining electronic health records in the genomics era. PLoS Comput Biol. 2012;8:e1002823.
31. Newton KM, Peissig PL, Kho AN, et al. Validation of electronic medical record-based phenotyping algorithms: results and lessons learned from the eMERGE network. J Am Med Inform Assoc. 2013;20:147-54.
32. Bejan CA, Vanderwende L, Xia F, et al. Assertion modeling and its role in clinical phenotype identification. J Biomed Inform. 2013;46:68-74.
33. Bejan CA, Xia F, Vanderwende L, et al. Pneumonia identification using statistical feature selection. J Am Med Inform Assoc. 2012;19:817-23.
34. Lin C, Karlson EW, Canhao H, et al. Automatic prediction of rheumatoid arthritis disease activity from the electronic medical records. PLoS One. 2013;8:e69932.