• Ahlers C, Fiszman M, Demner-Fushman D, Lang F, Rindflesch TC. Extracting Semantic Predications from MEDLINE Citations for Pharmacogenomics Pacific Symposium on Biocomputing 2007 12:209-220

  Abstract | pub2007002.pdf | PMID:  17990493

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• Ahlers CB, Hristovski D, Kilicoglu H, Rindflesch TC. Using the Literature-based Discovery Paradigm to Investigate Drug Mechanisms AMIA Annu Symp Proc. 2007 Oct 11:6-10

  Abstract | PMID:  18693787 | PMCID:  PMC2655783

  Abstract
• Anne A, Bagayoko C, Fontelo P. Evaluation de BabelMeSH en Francais. IRBM 2009. DOI: 10.1016/j.irbm.2009.06.006.

  Abstract | pub2009048.pdf

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• Apostolova E, Channin DS, Demner-Fushman D, Furst J, Lytinen S, Raicu D. Automatic segmentation of clinical texts. 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Minneapolis, MN, 2009, pp. 5905-5908. doi: 10.1109/IEMBS.2009.5334831

  Abstract | PMID:  19965054

  Abstract
• Aronson AR, Mork J, Lang FM, Rogers W, Jimeno-Yepes A, Sticco JC. The NLM Indexing Initiative: Current Status and Role in Improving Access to Biomedical Information April 2012 Technical Report to the LHNCBC Board of Scientific Counselors.

  Abstract | tr2012001.pdf

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• Aronson AR, Lang FM. An overview of MetaMap: historical perspective and recent advances. J Am Med Inform Assoc. 2010 May-Jun;17(3):229-36. doi: 10.1136/jamia.2009.002733.

  Abstract | pub2010033.pdf | PMID:  20442139 | PMCID:  PMC2995713

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• Aronson AR, Lang FM. The Evolution of MetaMap, a Concept Search Program for Biomedical Text AMIA Annu Symp Proc. 2009 Nov:22

  Abstract | pub2009041.pdf

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• Aronson AR, Mork JG, Neveol A, Shooshan SE, Demner-Fushman D. Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing AMIA Annu Symp Proc. 2008 Nov 6:21-5

  Abstract | PMID:  18998883 | PMCID:  PMC2655934

  Abstract
• Aronson AR, Mork JG, Lang FM, Rogers WJ, Neveol A. NLM Medical Text Indexer: A Tool for Automatic and Assisted Indexing April 2008 Technical Report to the LHNCBC Board of Scientific Counselors.

  Abstract | tr2008002.pdf

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• Aronson AR, Bodenreider O, Demner-Fushman D, Fung KW, Lee VK, Mork JG, Névéol A, Peters L, Rogers WJ. From indexing the biomedical literature to coding clinical text: experience with MTI and machine learning approaches. Proc 2007 Workshop BioNL'07, June 2007, pp. 105-112, Prague, Czech Republic.

  Abstract | pub2007040.pdf

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• Aronson AR. API: Semantic Knowledge Representation

  Abstract

  Abstract
• Aronson AR, Demner-Fushman D, Humphrey SM, Lin J, Liu H, Ruch P, Ruiz ME, Smith LH, Tanabe LK, Wilbur WJ. Fusion of Knowledge-intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents Proc TREC 2005, 36-45

  Abstract | pub2005072.pdf

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• Aronson AR, Demner-Fushman D, Humphrey SM, Ide NC, Kim W, Liu H, Loane RF, Mork JG, Smith LH, Tanabe LK, Wilbur WJ, Xie N. Knowledge-intensive and statistical approaches to the retrieval and annotation of genomics MEDLINE citations. The Thirteenth Text Retrieval Conference (TREC 2004). 2004:503-11.

  Abstract | pub2004-076.pdf

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• Aronson AR, Mork JG, Gay CW, Humphrey SM, Rogers W. The NLM Indexing Initiative's Medical Text Indexer. Stud Health Technol Inform. 2004;107(Pt 1):268-72.

  Abstract | pub2004-077.pdf | PMID:  15360816

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• Aronson AR. Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program Proc AMIA Symp. 2001:17-21.

  Abstract | pub2001032.pdf | PMID:  11825149 | PMCID:  PMC2243666

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• Aronson AR, Bodenreider O, Chang HF, Humphrey SM, Mork JG, Nelson SJ, Rindflesch TC, Wilbur WJ. The NLM Indexing Initiative. Proc AMIA Symp. 2000:17-21.

  Abstract | pub2000033.pdf | PMID:  11079836 | PMCID:  PMC2243970

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• Balkanyi L, Schulz S, Cornet R, Bodenreider O. Medical concept representation: the years beyond 2000 [Poster]. Stud Health Technol Inform. 2013;192:1011.

  Abstract | PMID:  23920785 | PMCID:  PMC4300111

  Abstract
• Bangalore A, Browne AC, Divita G. UMLSKS SUGGEST: an auto-complete feature for the UMLSKS interface using AJAX. AMIA Annu Symp Proc. 2006:851.

  Abstract | PMID:  17238471 | PMCID:  PMC1839508

  Abstract
• Bangalore AK, Divita G, Humphrey SM, Browne AC, Thorn KE. Automatic Categorization of Google Search Results for Medical Queries using JDI Medinfo 2007: Proc. of the 11th World Congress on Health (Medical) Informatics

  Abstract

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• Bashyam V, Divita G, Bennett DB, Browne AC, Taira RK. A normalized lexical lookup approach to identifying UMLS concepts in free text. Stud Health Technol Inform. 2007;129(Pt 1):545-9.

  Abstract | PMID:  17911776

  Abstract
• Ben Abacha A, Demner-Fushman D. On the role of question summarization and information source restriction in consumer health question answering. In Proceedings of the AMIA 2019 Informatics Summit, San Francisco, CA, USA, 2019.

  Abstract | pub9917.pdf

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• Ben Abacha A, Long LR, Seco de Herrera AG, Antani SK, Wang K, Demner-Fushman D. Named Entity Recognition in Functional Neuroimaging Literature. BIBM 2017

  Abstract | URL:  https://ieeexplore.ieee.org/document/8218002

  AbstractExternal link
• Ben Abacha A, Demner-Fushman D. Recognizing Question Entailment for Medical Question Answering. AMIA Annu Symp Proc. 2017 Feb 10;2016:310-318. eCollection 2016.

  Abstract | pub9500.pdf | PMID:  28269825 | PMCID:  PMC5333286

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• Ben Abacha A, Demner-Fushman D. NLM_NIH at SemEval-2017 Task 3: from Question Entailment to Question Similarity for Community Question Answering. In Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval@ACL) 2017: 349-352.

  Abstract | pub9538.pdf

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• Ben Abacha A, Demner-Fushman D. Meta-Learning with Selective Data Augmentation for Medical Entity Recognition. International Journal of Computational Linguistics and Applications (IJCLA) 7(2): 167-182 (2016)

  Abstract | 1_IJCLA.pdf

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• Bernhardt PJ, Humphrey SM, Rindflesch TC. Determining Prominent Subdomains in Medicine. AMIA Annu Symp Proc. 2005:46-50.

  Abstract | pub2005052.pdf | PMID:  16778999 | PMCID:  PMC1560510

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• Bernhardt PJ, Rindflesch TC, Kilicoglu H, Tringali M. Identifying Anatomical Concepts in Biomedical Text for Automatic Selection of Images Medinfo. 2004 Sept.;2004: 1521.

  Abstract | pub2004036.pdf

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• Bhupatiraju R, Fung K, Bodenreider O. MetaMapLite in Excel: Biomedical named-entity recognition for non-technical users. Stud Health Technol Inform (Proc Medinfo): 1252.

  Abstract | PMID:  29295337 | PMCID:  PMC5884681

  Abstract
• Blake C, Rindflesch TC. Leveraging syntax to better capture the semantics of elliptical coordinated compound noun phrases. J Biomed Inform. 2017 Aug;72:120-131. doi: 10.1016/j.jbi.2017.07.001. Epub 2017 Jul 4.

  Abstract | PMID:  28687199

  Abstract
• Bodenreider O, Peters L, Nguyen T. RxClass – Navigating between Drug Classes and RxNorm Drugs (Demo). Prc. ICBO 2014

  Abstract | URL:  http://ceur-ws.org/Vol-1327/icbo2014_paper_49.pdf

  AbstractExternal link
• Bodenreider O, Burgun A. Desiderata for an Ontology of Diseases for the Annotation of Biological Datasets Proc ICBO 2009:39-42

  Abstract | pub2009023.pdf

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• Brennan PF, Rindflesch TC. Towards Linking Patients and Clinical Information: Detecting UMLS Concepts in E-mail J Biomed Inform. 2003 Aug-Oct;36(4-5):334-41

  Abstract | pub2003070.pdf

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• Brown AC, Divita G, Lu C, McCreedy L, Nace D. Lexical Systems: A Report to the Board of Scientific Counselors September 2003 Technical Report to the LHNCBC Board of Scientific Counselors.

  Abstract | tr2003003.pdf

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• Browne AC, Kayaalp M, Dodd Z, Sagan, P, McDonald CJ. The Challenges of Creating a Gold Standard for De-identification Research. AMIA Annu Symp Proc. 2014 Nov 14;2014:353-8. eCollection 2014.

  Abstract | pub8927.pdf | PMID:  25954338 | PMCID:  PMC4420002

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• Browne AC, Divita Guy, Aronson AR, McCray AT. Language and Vocabulary Tools AMIA Annu Symp Proc. 2003:798.

  Abstract | pub2003051.pdf | PMID:  14728303 | PMCID:  PMC1480270

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• Burgun A, Bodenreider O. Issues in Integrating Epidemiology and Research Information in Oncology: Experience with ICD-O3 and the NCI Thesaurus AMIA Annu Symp Proc. 2007 Oct 11:85-9

  Abstract | pub2007084.pdf | PMID:  18693803

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• Cairelli M, Rindflesch TC. Identifying Potential Biomarkers for Mild Traumatic Brain Injury by Mining Semantic Relations from MEDLINE Citations [Poster[. 2011 Trauma Spectrum Conference, Bethesda, MD, December 9, 2011.

  Abstract

  Abstract
• Cairelli M, Rindflesch TC. Hierarchical Summarization of Concepts for Visual Discovery Browsing - a Pilot Study [abstract and demo]. Procedings of the IEEE VisWeek Workshop on Visual Analytics in Healthcare, October 23, 2011, Providence, RI, 37-40.

  Abstract | URL:  http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CD0QFjAA&url...

  AbstractExternal link
• Cairelli MJ, Fiszman M, Zhang H, Rindflesch TC. Networks of neuroinjury semantic predications to identify biomarkers for mild traumatic brain injury. J Biomed Semantics. 2015 May 18;6:25. doi: 10.1186/s13326-015-0022-4. eCollection 2015.

  Abstract | PMID:  25992264 | PMCID:  PMC4436163

  Abstract
• Cairelli MJ, Miller CM, Fiszman M, Workman TE, Rindflesch TC. Semantic MEDLINE for discovery browsing: using semantic predications and the literature-based discovery paradigm to elucidate a mechanism for the obesity paradox. AMIA Annu Symp Proc. 2013 Nov 16;2013:164-73. eCollection 2013.

  Abstract | PMID:  24551329 | PMCID:  PMC3900170

  Abstract
• Cameron D, Kavuluru R, Rindflesch TC, Sheth AP, Thirunarayan K, Bodenreider O. Context-driven automatic subgraph creation for literature-based discovery. J Biomed Inform. 2015 Apr;54:141-57. doi: 10.1016/j.jbi.2015.01.014. Epub 2015 Feb 7.

  Abstract | PMID:  25661592 | PMCID:  PMC4888806

  Abstract
• Chapman WW, Fiszman M, Dowling JN, Chapman BE, Rindflesch TC. Identifying Respiratory Findings in Emergency Department Reports for Biosurveillance using MetaMap Medinfo. 2004 Sept.;2004: 487-491.

  Abstract | pub2004035.pdf

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• Cho D, Mork JG, Aronson A, Demner-Fushman D, Schmidt S, Ozga D, Pash J, Kilbourne J. MeSH on demand: an easy way to identify relevant MeSH terms and related articles from text [Poster]. National Cancer Institute (NCI) Symposium "RNA Biology 2015".

  Abstract | pub9358.pdf

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• Choi J, Han SB, Kim S, Hole WT, Srinivasan S. Challenges for Integrating Korean Medical Vocabulary into the UMLS MedInfo. 2004 Sept.;2004: 1554.

  Abstract | pub2004046.pdf

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• Cohen KB, Demner-Fushman D. Biomedical Natural Language Processing John Benjamins Publishing Company, 2014. DOI: 10.1075/nlp.11

  Abstract

  Abstract
• Cohen T, Widdows D, Stephan C, Zinner R, Kim J, Rindflesch TC, Davies P. Predicting high-throughput screening results with scalable literature-based discovery methods. CPT Pharmacometrics Syst Pharmacol. 2014 Oct 8;3:e140. doi: 10.1038/psp.2014.37.

  Abstract | PMID:  25295575 | PMCID:  PMC4474167

  Abstract
• Cohen T, Widdows D, Rindflesch TC. Expansion-by-analogy: A vector symbolic approach to semantic search. AAAI-Fall 2014 Symposium on Quantum Informatics for Cognitive, Social, and Semantic Processes.

  Abstract

  Abstract
• Cohen T, Widdows D, Schvaneveldt RW, Rindflesch TC. Logical Leaps and Quantum Connectives: Forging Paths through Predication Space AAAI-Fall 2010 Symposium on Quantum Informatics for Cognitive, Social, and Semantic Processes

  Abstract | pub2010028.pdf

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• Cohen T, Schvaneveldt R, Rindflesch TC. Predication-based semantic indexing: permutations as a means to encode predications in semantic space. AMIA Annu Symp Proc. 2009 Nov 14;2009:114-8.

  Abstract | pub2009044.pdf | PMID:  20351833 | PMCID:  PMC2815384

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• Culbertson A, Fiszman M, Shin D, Rindflesch TC. Semantic processing to identify adverse drug event information from black box warnings. AMIA Annu Symp Proc. 2014 Nov 14;2014:442-8. eCollection 2014.

  Abstract | PMID:  25954348 | PMCID:  PMC4419903

  Abstract

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