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  • Lin J, Demner-Fushman D. "Bag of words" is not enough for strength of evidence classification AMIA Annu Symp Proc. 2005:1031.
  • Yu Z, Nguyen T, Dhombres F, Johnson T, Bodenreider O. "Hybrid Topics" - Facilitating the Interpretation of Topics Through the Addition of MeSH Descriptors to Bags of Words. Stud Health Technol Inform. 2017;245:662-666.
  • Lin MC, Vreeman DJ, McDonald CJ, Huff SM. A characterization of local LOINC mapping for laboratory tests in three large institutions. Methods Inf Med. 2011;50(2):105-14. doi: 10.3414/ME09-01-0072. Epub 2010 Aug 20.
  • Thomas SM, Overhage JM, Warvel J, McDonald CJ. A comparison of a printed patient summary document with its electronic equivalent: early results. Proc AMIA Symp. 2001:701-5.
  • Hunt S, Cimino J, Koziol DE. A comparison of clinicians' access to online knowledge resources using two types of information retrieval applications in an academic hospital setting. J Med Libr Assoc. 2013 Jan;101(1):26-31. doi: 10.3163/1536-5050.101.1.005.
  • Vreeman DJ, McDonald CJ. A comparison of Intelligent Mapper and document similarity scores for mapping local radiology terms to LOINC. AMIA Annu Symp Proc. 2006:809-13.
  • Overhage JM, Grannis S, McDonald CJ. A comparison of the completeness and timeliness of automated electronic laboritory reporting and spontaneous reporting of notifiable conditions. Am J Public Health. 2008 Feb;98(2):344-50. Epub 2008 Jan 2
  • Kroth PJ, Dexter PR, Overhage JM, Knipe C, Hui SL, Belsito A, McDonald CJ. A computerized decision support system improves the accuracy of temperature capture from nursing personnel at the bedside. AMIA Annu Symp Proc. 2006:444-8.
  • Dexter PR, Perkins S, Overhage JM, Maharry K, Kohler RB, McDonald CJ. A computerized reminder system to increase the use of preventive care for hospitalized patients. N Engl J Med. 2001 Sep 27;345(13):965-70.
  • 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.
  • Winnenburg R, Bodenreider O. A framework for assessing the consistency of drug classes across sources. J Biomed Semantics. 2014 Jul 9;5:30. doi: 10.1186/2041-1480-5-30. eCollection 2014.
  • Bodenreider O, Burgun A. A framework for comparing phenotype annotations of orthologous genes. Stud Health Technol Inform. 2010;160(Pt 2):1309-13.
  • Bodenreider O, Peters LB. A graph-based approach to auditing RxNorm. J Biomed Inform. 2009 Jun;42(3):558-70. doi: 10.1016/j.jbi.2009.04.004. Epub 2009 Apr 24.
  • Cameron D, Bodenreider O, Yalamanchili H, Danh T, Vallabhaneni S, Thirunarayan K, Sheth AP, Rindflesch TC. A graph-based recovery and decomposition of Swanson's hypothesis using semantic predications. J Biomed Inform. 2013 Apr;46(2):238-51. doi: 10.1016/j.jbi.2012.09.004. Epub 2012 Sep 28.
  • Kilicoglu H, Rogers W. A Hybrid System for Extracting Chemical-Disease Relationships from Scientific Literature. 2015. BioCreative 5 Proceedings.
  • Biondich PG, Overhage JM, Dexter PR, Downs SM, Lemmon L, McDonald CJ. A modern optical character recognition system in a real world clinical setting: some accuracy and feasibility observations. Proc AMIA Symp. 2002:56-60.
  • Rance B, Doughty E, Demner-Fushman D, Kann MG, Bodenreider O. A mutation-centric approach to identifying pharmacogenomic relations in text. J Biomed Inform. 2012 Oct;45(5):835-41. doi: 10.1016/j.jbi.2012.05.003. Epub 2012 Jun 7.
  • Laflamme MR, Wilcox DC, Sullivan J, Schadow G, Lindbergh D, Warvel J, Buchanan H, Ising T, Abernathy G, Perkins SM, Daggy J, Frankel RM, Dexter P, McDonald CJ, Weiner M. A pilot study of usefulness of clinician-patient videoconferencing for making routine medical decisions in the nursing home. J Am Geriatr Soc. 2005 Aug;53(8):1380-5.
  • Sorbello A, Ripple AM, Bodenreider O. A pilot study to support prospective detection of emerging adverse drug events [Poster]. AMIA Annu Symp Proc 2015:1699.
  • Weiner M, Stump TE, Callahan CM, Lewis JN, McDonald CJ. A practical method of linking data from Medicare claims and a comprehensive electronic medical records system. Int J Med Inform. 2003 Aug;71(1):57-69.
  • Bodenreider O, Coban ZH, Doganay MC, Erdem E, Kosucu H. A preliminary report on answering complex queries related to drug discovery using answer set programming. Proceedings of the 3rd International Workshop on Applications of Logic Programming to the (Semantic) Web and Web Services (ALPSWS2008), 2008: p. 85-90 (electronic proceedings: http://ceur-ws.org/Vol-434/).
  • Demner-Fushman D, Seckman C, Fisher C, Hauser SE, Clayton J, Thoma GR. A prototype system to support evidence-based practice AMIA Annu Symp Proc. 2008 Nov 6:151-5.
  • Cohen T, Roberts K, Gururaj AE, Chen X, Pournejati S, Alter G, Hersh WR, Demner-Fushman D, Ohno-Machado L, Lu H. A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax061.
  • Overhage JM, Dexter PR, Perkins SM, Cordell WH, McGoff J, McGrath R, McDonald CJ. A randomized, controlled trial of clinical information shared from another institution. Ann Emerg Med. 2002 Jan;39(1):14-23.
  • Zhu X, Fan JW, Baort D, Weng C, Cimino JJ. A review of auditing methods applied to the content of controlled biomedical terminologies. J Biomed Inform. 2009 Jun;42(3):413-25. doi: 10.1016/j.jbi.2009.03.003. Epub 2009 Mar 12.
  • Fontelo P, Liu F. A review of recent publication trends from top publishing countries. Syst Rev. 2018 Sep 27;7(1):147. doi: 10.1186/s13643-018-0819-1.
  • Bodenreider O. A Semantic Navigation Tool for the UMLS AMIA Annu Symp Proc. 2000;: 971.
  • Nelson SJ, Brown SH, Erlbaum MS, Olson N, Powell T, Carlsen B, Carter J, Tuttle MS, Hole WT. A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF. Proc AMIA Symp. 2002:557-61.
  • Zafar A, Mamlin B, Perkins S, Belsito AM, Overhage JM, McDonald CJ. A simple error classification system for understanding sources of error in automatic speech recognition and human transcription. Int J Med Inform. 2004 Sep;73(9-10):719-30.
  • Abhyankar S, Demner-Fushman D. A simple method to extract key maternal data from neonatal clinical notes. AMIA Annu Symp Proc. 2013 Nov 16;2013:2-9. eCollection 2013.
  • Thomas SM, Mamlin B, Schadow G, McDonald CJ. A successful technique for removing names in pathology reports using an augmented search and replace method. Proc AMIA Symp. 2002:777-81.
  • Drake TA, Braun J, Marchevsky A, Kohan IS, Fletcher C, Chueh H, Beckwith B, Berkowicz D, Kuo F, Zeng QT, Balis U, Holzbach A, McMurry A, Gee CE, McDonald C, Schadow G, Davis M, Hattab EM, Blevins L, Hook J, Becich M, Crowley RS, Taube SE, Berman J. A System for Sharing Routine Surgical Pathology Specimens Across Institutions: The Shared Pathology Informatics Network Hum Pathol. 2007 Aug;38(8):1212-25. Epub 2007 May 8
  • Zolnoori M, Fung K, Patrick TB, Fontelo P, Kharrazi H, Faiola A, Wu YSS, Eldredge CE, Luo J, Conway M, Zhu J, Park SK, Xu K, Moayyed H, Goudarzvand S. A systematic approach for developing a corpus of patient reported adverse drug events: A case study for SSRI and SNRI medications. NCBINCBI Logo Skip to main content Skip to navigation Resources How To About NCBI Accesskeys PubMed US National Library of Medicine National Institutes of Health Search databaseSearch term 30611893[uid] Clear inputSearch Create RSSCreate alertAdvancedHelp Result Filters Format: AbstractSend to J Biomed Inform. 2019 Feb;90:103091. doi: 10.1016/j.jbi.2018.12.005. Epub 2019 Jan 4.
  • Sahoo SS, Nguyen V, Bodenreider O, Parikh P, Minning T, Sheth AP. A unified framework for managing provenance information in translational research. BMC Bioinformatics. 2011 Nov 29;12:461. doi: 10.1186/1471-2105-12-461.
  • Goss FR, Lai KH, Topaz M, Acker WW, Kowalski L, Plasek JM, Blumenthal KG, Seger DL, Slight SP, Fung KW, Chang FY, Bates DW, Zhou L. A value set for documenting adverse reactions in electronic health records. J Am Med Inform Assoc. 2018 Jun 1;25(6):661-669. doi: 10.1093/jamia/ocx139.
  • Crowell J, Zeng QT, Tse T. A Web Application to Support Consumer Health Vocabulary Development AMIA Annu Symp Proc. 2005:932
  • Burgun A, Bodenreider O. Accessing and Integrating Data and Knowledge for Biomedical Research Yearb Med Inform. 2008:91-101
  • Hole WT, Carlsen BA, Tuttle MS, Srinivasan S, Lipow SS, Olson NE, Sheretz DD, Humphreys BL. Achieving "source transparency" in the UMLS Metathesaurus. Stud Health Technol Inform. 2004;107(Pt 1):371-5.
  • Fung K, Xue Z, Ameye F, Gutierrez AR, D'Have A. Achieving Logical Equivalence between SNOMED CT and ICD-10-PCS Surgical Procedures. AMIA Annu Symp Proc. 2018 Apr 16;2017:724-733. eCollection 2017.
  • Cimino JJ, Remennick L. Adapting a Clinical Data Repository to ICD-10-CM through the use of a Terminology Repository. AMIA Annu Symp Proc. 2014 Nov 14;2014:405-13. eCollection 2014.
  • Hole WT, Srinivasan S. Adding NeuroNames to the UMLS Metathesaurus. Neuroinformatics. 2003;1(1):61-3.
  • Callaghan F, Demner-Fushman D, Abhyankar S, McDonald CJ. Addressing errors in a retrospective observational ICU database [poster]. AMIA 2011 Fall Symposium.
  • 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.
  • Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Oqbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccaqnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing Translational Research with the Semantic Web BMC Bioinformatics. 2007 May 9;8 Suppl 3:S2
  • McCray AT, Burgun A, Bodenreider O. Aggregating UMLS Semantic Types for Reducing Conceptual Complexity Medinfo. 2001 ;10(Pt 1):216-20.
  • Zhang S, Bodenreider O, Kantz N. Aligning Anatomical Ontologies: The Role of Complex Structural Rules IIAS-Transactions on Systems Research and Cybernetics - Proc InterSymp 2006;VI(2):27-32.
  • Bodenreider O, Burgun A. Aligning Knowledge Sources in the UMLS: Methods, Quantitative Results, and Applications Medinfo. 2004 Sept.;2004:327-331.
  • Zhang S, Bodenreider O. Aligning Representations of Anatomy Using Lexical and Structural Methods AMIA Annu Symp Proc. 2003 Nov;:753-757.
  • Zhang S, Bodenreider O. Alignment of Multiple Ontologies of Anatomy: Deriving Indirect Mappings from Direct Mappings to a Reference AMIA Annu Symp Proc 2005:864-868
  • Schulz S, Beisswanger, van den Hoek L, Bodenreider O, van Mulligen EM. Alignment of the UMLS Semantic Network with BioTop: Methodology and Assessment Bioinformatics 2009;25(12):i69-i76

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