Biomedical question answering using semantic relations

BMC Bioinformatics

Volumn 16, Issue 1, 2015, Pages

  Hristovski, Dimitar ^a   Dinevski, Dejan ^b   Kastrin, Andrej ^c   Rindflesch, Thomas C ^d  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

^b UNIVERSITY OF MARIBOR   (Slovenia)

^c Faculty of Information Studies   (Slovenia)

^d NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INFORMATION RETRIEVAL; SEARCH ENGINES; SEMANTICS; WEB SERVICES; WEBSITES;

AUTOMATIC QUESTION ANSWERING; BIOMEDICAL LITERATURE; BIOMEDICAL QUESTION ANSWERING; INNOVATIVE METHODOLOGIES; KNOWLEDGE EXTRACTION; RELATIONAL DATABASE; SCIENTIFIC LITERATURE; WEB-BASED APPLICATIONS;

NATURAL LANGUAGE PROCESSING SYSTEMS;

ALGORITHM; COMPUTER PROGRAM; DNA MICROARRAY; DOCUMENTATION; FACTUAL DATABASE; HUMAN; INFORMATION RETRIEVAL; NATURAL LANGUAGE PROCESSING; PHARMACOGENETICS; SEMANTICS;

ABSTRACTING AND INDEXING AS TOPIC; ALGORITHMS; DATABASES, FACTUAL; HUMANS; INFORMATION STORAGE AND RETRIEVAL; NATURAL LANGUAGE PROCESSING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHARMACOGENETICS; SEMANTICS; SOFTWARE;

EID: 84923864995     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-014-0365-3     Document Type: Article

References (32)

1. Sackett DL, Rosenberg WM, Gray JA, Haynes RB, Richardson WS: Evidence based medicine: what it is and what it isn't. BMJ 1996, 312:71-72.
2. Smith R: What clinical information do doctors need? BMJ 1996, 313:1062-1068.
3. Ely JW, Osheroff JA, Ebell MH, Bergus GR, Levy BT, Chambliss ML, Evans ER: Analysis of questions asked by family doctors regarding patient care. BMJ 1999, 319:358-361.
4. Ely JW, Osheroff JA, Chambliss ML, Ebell MH, Rosenbaum ME: Answering physicians' clinical questions: obstacles and potential solutions. J Am Med Inform Assoc 2005, 12:217-224.
5. Hersh WR, Crabtree MK, Hickam DH, Sacherek L, Friedman CP, Tidmarsh P, Mosbaek C, Kraemer D: Factors associated with success in searching MEDLINE and applying evidence to answer clinical questions. J Am Med Inform Assoc 2002, 9:283-293.
6. Cordero F, Botta M, Calogero RA: Microarray data analysis and mining approaches. Brief Funct Genomic Proteomic 2007, 6:265-281.
7. Vallin A, Magnini B, Giampiccolo D, Aunimo L, Ayache C, Osenova P, Peñas A, De RM, Sacaleanu B, Santos D, Sutcliffe R: Overview of the CLEF 2005 Multilingual Question Answering Track. In Access Multiling Inf Repos. Volume 4022. Edited by Peters C, Gey FC, Gonzalo J, Müller H, Jones GJF, Kluck M, Magnini B, de Rijke M. Berlin: Springer; 2006 [Lecture Notes in Computer Science].
8. Kando N: Overview of the Fifth NTCIR Workshop. In Proceedings of Fifth NTCIR Workshop Meeting on Evaluation of Information Access Technologies: 6-9 Decenber 2005; Tokyo. Tokyo: National Institute of Informatics; 2005:i-vii.
9. Athenikos SJ, Han H: Biomedical question answering: a survey. Comput Methods Programs Biomed 2010, 99:1-24.
10. Mollá D, Vicedo JL: Question Answering in Restricted Domains: An Overview. Comput Linguist 2007, 33:41-61.
11. Zweigenbaum P: Question Answering in Biomedicine. In Proceedings of the Workshop on Natural Language Processing for Question Answering: 14 April 2003; Budapest. Edited by De RM, Webber B. Budapest: Association for Computational Linguistics; 2003:1-4.
12. Jacquemart P, Zweigenbaum P: Towards a medical question-answering system: a feasibility study. Stud Health Technol Inform 2003, 95:463-468.
13. Niu Y, Hirst G, McArthur G, Rodriguez-Gianolli P: Answering clinical questions with role identification. In Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine: 11 July 2003; Sapporo, Japan. Edited by Ananiadou S, Tsujii J. Morristown, NJ: Association for Computational Linguistics; 2003:73-80. 13.
14. Demner-Fushman D, Lin J: Answering Clinical Questions with Knowledge-Based and Statistical Techniques. Comput Linguist 2007, 33:63-103.
15. Weiming W, Hu D, Feng M, Wenyin L: Automatic Clinical Question Answering Based on UMLS Relations. In Proceedings of the Third International Conference on Semantics, Knowledge and Grid (SKG 2007): 29-31 October 2007; Xi'an, China. Edited by Zhuge H. Los Alamitos, CA: IEEE Computer Society; 2007:495-498.
16. Humphreys BL, Lindberg DA: The UMLS project: making the conceptual connection between users and the information they need. Bull Med Libr Assoc 1993, 81:170-177.
17. 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, 36:462-477.
18. Aronson AR: Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. In Proceedings of American Medical Informatics Association Annual Symposium (AMIA): 3-7 November 2001; Washington, DC. Edited by Bakken S. Washington, DC: American Medical Informatics Association; 2001:17-21.
19. Hersh W, Voorhees E: TREC genomics special issue overview. Inf Retrieval 2009, 12:1-15.
20. Cao Y, Liu F, Simpson P, Antieau L, Bennett A, Cimino JJ, Ely J, Yu H: AskHERMES: An online question answering system for complex clinical questions. J Biomed Inform 2011, 44:277-288.
21. Lopez V, Unger C, Cimiano P, Motta E: Evaluating question answering over linked data. J Web Semant 2013, 21:3-13.
22. Shatkay H, Edwards S, Wilbur WJ, Boguski M: Genes, themes and microarrays: using information retrieval for large-scale gene analysis. In Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (ISMB): 16-23 August 2000; La Jolla, CA. Edited by Bourne PE, Gribskov M, Altman RB, Jensen N, Hope D, Lengauer T, Mitchell JC, Scheeff E, Smith C, Strande S, Weissig H. Menlo Park, CA: AAAI Press; 2000:317-328. 8.
23. Blaschke C, Oliveros JC, Valencia A: Mining functional information associated with expression arrays. Funct Integr Genomics 2001, 1:256-268.
24. Yang J, Cohen AM, Hersh W: Automatic summarization of mouse gene information by clustering and sentence extraction from MEDLINE abstracts. In Proceedings of American Medical Informatics Association Annual Symposium (AMIA): 10-14 November 2007; Chicago, IL. Edited by Teich JM, Suermondt J, Hripcsak G. Chicago, IL: American Medical Informatics Association; 2007:831-835.
25. Leach SM, Tipney H, Feng W, Baumgartner WA, Kasliwal P, Schuyler RP, Williams T, Spritz RA, Hunter L: Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol 2009, 5:e1000215.
26. Jelier R, 't Hoen PAC, Sterrenburg E, Den Dunnen JT, Van Ommen G-JB, Kors JA, Mons B: Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease. BMC Bioinformatics 2008, 9:291.
27. Burkart MF, Wren JD, Herschkowitz JI, Perou CM, Garner HR: Clustering microarray-derived gene lists through implicit literature relationships. Bioinformatics 2007, 23:1995-2003.
28. McCray AT, Srinivasan S, Browne AC: Lexical methods for managing variation in biomedical terminologies. In Proceedings of the Eighteenth Annual Symposium on Computer Application in Medical Care: 5-9 November 1994; Washington, DC. Edited by Ozbolt JG. Philadelphia, PA: Hanley & Belfus; 1994:235-239.
29. Smith L, Rindflesch T, Wilbur WJ: MedPost: a part-of-speech tagger for bioMedical text. Bioinformatics 2004, 20:2320-2321.
30. Ahlers CB, Fiszman M, Demner-Fushman D, Lang F-M, Rindflesch TC: Extracting semantic predications from Medline citations for pharmacogenomics. In Pacific Symposium on Biocomputing: 3-7 January 2007; Maui, Hawaii. Edited by Altman RB, Dunker AK, Hunter L, Murray T, Klein TE. Singapore: World Scientific Publishing Co. Inc; 2007:209-220.
31. Hirschman L, Gaizauskas R: Natural language question answering: the view from here. Nat Lang Eng 2002, 7:275-300.
32. Masseroli M, Kilicoglu H, Lang F-M, Rindflesch TC: Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease. BMC Bioinformatics 2006, 7:291.