| National Library of Medicine

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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Azuaje F, Wang H, Bodenreider O. Ontology-driven Similarity Approaches to Supporting Gene Functional Assessment Proceedings of the ISMB'2005 SIG meeting on Bio-ontologies 2005:9-10

Abstract | pub2005024.pdf

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Bodenreider O. Evaluating the Quality and Interoperability of Biomedical Terminologies Technical Report to the LHNCBC Board of Scientific Counselors April 2018

Abstract | pub9754.pdf

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Bodenreider O, Winnenburg R. Drug Terminology and Ontology Integration -- Dissemination, Quality Assurance and Applications. September 2014 Technical Report to the LHNCBC Board of Scientific Counselors.

Abstract | Tech_Report_Sep14.pdf

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Bodenreider O. Disease Ontologies In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H, editors. Encyclopedia of Systems Biology: Springer; 2013. p. 578-581.

Abstract | pub2011017.pdf

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Bodenreider O, Peters L, Nguyen T. RxNav: Browser and Application Programming Interfaces for Drug Information Sources [Abstract]. AMIA Annu Symp Proc 2011:2129

Abstract | pub2011018.pdf

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Bodenreider O. Quality Assurance in Biomedical Terminologies and Ontologies April 2010 Technical Report to the LHNCBC Board of Scientific Counselors.

Abstract | tr2010001.pdf

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Bodenreider O. Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support. Geissbuhler A, Kulikowski C, editors. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med, 2008. 47(Suppl 1): p. 67-79.

Abstract | PMID: 18660879 | PMCID: PMC2592252

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Bodenreider O. Semantic Web for Translational Biomedicine: Two Pilot Experiments [Abstract]. Proc. MIA Summit on Translational Bioinformatics 2008:141

Abstract | pub2008025.pdf

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Bodenreider O, Rindflesch TC. Advanced Library Services: Developing a Biomedical Knowledge Repository to Support Advanced Information Management Applications September 2006 Technical Report to the LHNCBC Board of Scientific Counselors.

Abstract | tr2006001.pdf

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Bodenreider O, Bean CA. Relationships Among Knowledge Structures: Vocabulary Integration Within a Subject Domain. In: Bean A, Green R, editors. Relationships in the organization of knowledge. Springer; 2001. pp. 81-98.

Abstract | pub2001024.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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Cohen KB, Demner-Fushman D. Biomedical Natural Language Processing John Benjamins Publishing Company, 2014. DOI: 10.1075/nlp.11

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Demner-Fushman D. Clinical, Consumer Health, and Visual Question Answering. Springer Nature Switzerland AG 2019. J. A. Lossio-Ventura et al. (Eds.): SIMBig 2018, CCIS 898, pp. 1–6, 2019.

Abstract | URL: https://link.springer.com/chapter/10.1007%2F978-3-030-11680-4_1

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Demner-Fushman D, Elhadad N. Aspiring to Unintended Consequences of Natural Language Processing: A Review of Recent Developments in Clinical and Consumer-Generated Text Processing. IMIA Yearbook of Medical Informatics 2016.

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Demner-Fushman D, Antani SK, Chachra S, Kushnir M, Gayen S. Open-i Imaging informatics, natural language processing and multi-modal information retrieval - research and development Technical Report to the LHNCBC Board of Scientific Counselors September 2016

Abstract | pub9414.pdf

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Demner-Fushman D, Mork JG. NLM Medical Text Indexer Technical Report to the LHNCBC Board of Scientific Counselors April 2016

Abstract | pub9359.pdf

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Demner-Fushman D, Kilicoglu H, Roberts K, Masterton K, Deardorff A. Consumer Health Question Answering to Automatically Support NLM Customer Services September2015 Technical Report to the LHNCBC Board of Scientific Counselors

Abstract | pub9264.pdf

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Demner-Fushman D, Antani SA, Simpson M, Rahman MM. Combining Text and Visual Features for Biomedical Information Retrieval and Ontologies. September 2010 Technical Report to the LHNCBC Board of Scientific Counselors.

Abstract | tr2010002.pdf

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Fung KW, Bodenreider O. Knowledge representation and ontologies. Richesson RL, Andrews JE (Eds.). Clinical Research Informatics, Health Informatics, DOI 10.1007/978-1-84882-448-5_14, Springer-Verlag London Limited Publishing 2012.

Abstract | pub2012015.pdf

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He Y, Kayaalp M. A Comparison of 13 Tokenizers on MEDLINE December 2006 Technical Report.

Abstract | tr2006003.pdf

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Hristovski D, Kastrin A, Peterlin B, Rindflesch TC. Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation Lecture Notes in Bioinformatics. Springer

Abstract | pub2009060.pdf

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Kayaalp M, Dodd Z, Browne AC, Sagan, P, McDonald CJ. Software: NLM-Scrubber

Abstract | URL: https://scrubber.nlm.nih.gov/

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Kayaalp M, Browne AC, Dodd Z, Sagan P, McDonald CJ. Clinical Text De-Identification Research September 2013 Technical Report to the LHNCBC Board of Scientific Counselors

Abstract | 6932.pdf

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Kayaalp M. Separation of Data, Interpreters and Likelihood March 2007 Technical Report to the LHNCBC Board of Scientific Counselors.

Abstract | tr2007001.pdf

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Kilicoglu H. Software: Bio-SCoRes

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Long LR, Antani SK, Thoma GR, Deserno TM. Content-based Image Retrieval For Advancing Medical Diagnostics, Treatment, and Education New Technologies for Advancing Healthcare and Clinical Practices. June 2011:1-17.

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Lu C, Humphrey SM, Rogers W, Browne AC. Development of a semantic type based WSD tool [Abstract]. AMIA Annu Symp Proc 2009:943.

Abstract | pub2009067.pdf

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Lussier YA, Bodenreider O. Clinical Ontologies for Discovery Applications In: Baker CJO, Cheung K-H, editors. Semantic Web: Revolutionizing knowledge discovery in the life sciences. New York: Springer; 2007. p. 101-119.

Abstract | pub2007012.pdf

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McCray AT, Bodenreider O. A Conceptual Framework for the Biomedical Domain The Semantics of Relationships: An Interdisciplinary Perspective. Boston: Kluwer Academic Publishers. 2002;:181-198.

Abstract | pub2002029.pdf

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Mork JG, Aronson AR. The Medical Text Indexer (MTI) system for indexing biomedical literature. book chapter submitted to monograph Indexing Specialities: Medicine. Edited by L. Pilar Wyman. Medford, NJ: Information Today, Inc., in association with the American Society of Indexers, Phoenix, AZ. 2010.

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Pearson G. Methods to Store Metadata within Motion JPEG 2000 Files. Technical Report Preprint. May 2005.

Abstract | pub-2005-104.pdf

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Rindflesch TC, Fiszman M, Kilicoglu H, Rosemblat G, Shin D, Cairelli M, Chen G, Miller CM, Workman E. Semantic Knowledge Representation Project: Advanced Information Management for Biomedical Research September 2012 Technical Report to the LHNCBC Board of Scientific Counselors.

Abstract | tr2012002.pdf

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Ripple AM, Tse T, Zarin D. ClinicalTrials.gov scope expanded NLM Tech Bull. 2005 Jul-Aug;(345):e6.

Abstract | URL: http://www.nlm.nih.gov/pubs/techbull/ja05/ja05_clinical_trials.html

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Simpson MS, Demner-Fushman D. Biomedical Text Mining: A Survey of Recent Progress. In Charu C. Aggarwal and ChengXiang Zhai, Editors. Mining Text Data. (Springer) 2011.

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Sneiderman C, Rosemblat G, Bray B, Fiszman M, Rindflesch TC. Matching Clinical Observations in Published Cardiology Case Reports to LOINC [Abstract]. AMIA Annu Symp Proc; 2009 Nov 14-18; San Francisco. p. 1036.

Abstract | pub2009056.pdf

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Thoma GR, Ford G, Demner-Fushman D, Antani SK, Chung M. Software: Panorama

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Thoma GR, Antani S, Ford GL, Chung M, Vasudevan K. Interactive Publications Research: A Report to the Board of Scientific Counselors September 2005 Technical Report to the LHNCBC Board of Scientific Counselors.

Abstract | tr2005005.pdf

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Tse T, Zarin D, Williams R, Ide N. The role and importance of clinical trial registries and results databases In: Gallin JI, Ognibene FP, eds, Principles and Practice of Clinical Research. 3rd ed. Amsterdam: Academic Press; 2012: 171-81.

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Tse T, Johnson SO, Ripple AM. Update: Expanded ClinicalTrials.gov search capabilities NLM Tech Bull. 2002 Jul-Aug;(327):e5.

Abstract | URL: http://www.nlm.nih.gov/pubs/techbull/ja02/ja02_ctgov.html

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Tse T. Searching ClinicalTrials.gov. NLM Tech Bull. 2000 Sep-Oct;(316):e1.

Abstract | URL: http://www.nlm.nih.gov/pubs/techbull/so00/so00_clinicaltrials_js.html

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Zarin DA, Williams RJ, Bergeris AM, Dobbins H, Ide NC, Loane RF, Robbins A, Tse T. ClinicalTrials.gov and Related Projects: Improving Access to Information about Clinical Trials April 2013 Technical Report to the LHNCBC Board of Scientific Counselors

Abstract | tr2013001r.pdf

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Zeng K, Bodenreider O, Kilbourne J, Nelson SJ. Standards, Security and Usability: Experience with MyMedicationList [Abstract]. Proc. AMIA Spring Congress 2008

Abstract | pub2008035.pdf

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Zeng K, Bodenreider O. Experience in Integrating Large RDF-based Biomedical Knowledge Resources with Oracle [Abstract]. Proc 8th International Oracle Life Sciences User Group Meeting 2007:(electronic proceedings: http://www.olsug.org/wiki/images/d/d1/Kelly_Zheng.pdf)

Abstract | pub2007008.pdf

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Zweigenbaum P, Demner-Fushman D. Advanced Literature-Mining Tools. In Edwards D, Stajich J, and Hansen D. (Editors). Bioinformatics: Tools and Applications. Springer 2009.

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Zweigenbaum P, Demner-Fushman D. Bioinformatics: Tools and Applications. Springer 2009.

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