• Adamusiak T, Bodenreider O. Quality assurance in LOINC using Description Logic. AMIA Annu Symp Proc. 2012;2012:1099-108. Epub 2012 Nov 3.

  Abstract | PMID:  23304386 | PMCID:  PMC3540427

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• 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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• An L, Obradovic Z, Smith D, Bodenreider O, Megalooikonomou V. Mining Association Rules among Gene Functions in Clusters of Similar Gene Expression Maps. Workshop proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM09) -- Workshop on Data Mining in Functional Genomics 2009: p. 254-259

  Abstract | PMID:  25635265 | PMCID:  PMC4307020

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• Aronis JM, Cooper GF, Kayaalp M, Buchanan BG. Identifying patient subgroups with simple Bayes'. Proc AMIA Symp. 1999:658-62.

  Abstract | PMID:  10566441 | PMCID:  PMC2232601

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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

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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

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• 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, 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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• Azuaje F, Wang H, Zheng H, Bodenreider O, Chesneau A. Predictive Integration of Gene Ontology-Driven Similarity and Functional Interactions Proc ICDM 2006, Workshop on Data Mining in Bioinformatics: IEEE Computer Society Press; 2006. p. 114 - 119

  Abstract | pub2006064.pdf

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• Azuaje FJ, Bodenreider O, Wang H, Dopazo J. Gene Ontology-Driven Similarity for Gene Expression Correlation Analysis Proceedings of the second conference on Standards and Ontologies for Functional Genomics (SOFG 2) 2004:47.

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• Bahr NJ, Nelson SD, Winnenburg R, Bodenreider O. Eliciting the Intension of Drug Value Sets - Principles and Quality Assurance Applications. Stud Health Technol Inform. 2017;245:843-847.

  Abstract | PMID:  29295218 | PMCID:  PMC5881398

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• Bakker TA, Ryce AN, Logan RA, Tse T, Hutcherson LY. A Consumer Health Informatics (CHI) Toolbox: Challenges and Implications AMIA Annu Symp Proc. 2005:21-5

  Abstract | pub2005071.pdf | PMID:  16778994 | PMCID:  PMC1479846

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• Bangalore A, Thorn KE, Tilley C, Peters L. The UMLS knowledge source server: an object model for delivering UMLS data. AMIA Annu Symp Proc. 2003 Nov;:51-55.

  Abstract | pub2003052.pdf | PMID:  14728132 | PMCID:  PMC1480045

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• 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

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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

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• Beaudoin DE, Rocha RA, Tse T. Enhancing Access to Patient Education Information: A Pilot Usability Study AMIA Annu Symp Proc. 2005:892

  Abstract | pub2005045.pdf | PMID:  16779179 | PMCID:  PMC1560886

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• Ben Abacha A, de Herrera A, Wang Ke, Long LR, Antani SK, Demner-Fushman D. Named entity recognition in functional neuroimaging literature. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Kansas City, MO, 2017, pp. 2218-2220.

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• Bergun A, Bodenreider O. An ontology of chemical entities helps identify dependence relations among Gene Ontology terms Proc SMBM-2005

  Abstract | pub2005028.pdf

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• Bergun A, Bodenreider O, Mougin F. Classifying diseases with respect to anatomy: a study in SNOMED CT AMIA Annu Symp Proc. 2005:91-5

  Abstract | pub2005030.pdf | PMID:  16779008 | PMCID:  PMC1560776

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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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• 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

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• Bodenreider O. Identifying missing hierarchical relations in SNOMED CT from logical definitions based on the lexical features of concept names. Proceedings of the 6th International Conference on Biomedical Ontology (ICBO 2016), 2016: p. (electronic proceedings: http://ceur-ws.org/Vol-1747/IT601_ICBO2016.pdf).

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• Bodenreider O. Multi-lingual features of the Unified Medical Language System. Proc. CLEF-ER 2013 workshop 2013.

  Abstract | 2013-clef_er-ob-abstract.pdf | URL:  http://www.clef2013.org/index.php?page=Pages/proceedings.php

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• Bodenreider O. API: Prescribable

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• Bodenreider O, Peters L, Nguyen T. Browser and application programming interfaces for drug information sources. AMIA Annu Symp Proc, 2011: p. 2129.

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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, Demner-Fushman D. Investigating drug classes in biomedical terminologies from the perspective of clinical decision support. AMIA Annu Symp Proc. 2010 Nov 13;2010:56-60.

  Abstract | pub2010006.pdf | PMID:  21346940 | PMCID:  PMC3041355

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• Bodenreider O, Mougin F, Burgun A. Automatic Determination of Anti-coagulation Status with NDF-RT Proceedings of the 13th ISMB'2010 SIG meeting Bio-ontologies 2010:140-143

  Abstract | pub2010003.pdf

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• Bodenreider O, Burgun A. A framework for comparing phenotype annotations of orthologous genes. Stud Health Technol Inform. 2010;160(Pt 2):1309-13.

  Abstract | pub2010005.pdf | PMID:  20841896

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• Bodenreider O. Using SNOMED CT in combination with MedDRA for reporting signal detection and adverse drug reactions reporting. AMIA Annu Symp Proc. 2009 Nov 14;2009:45-9.

  Abstract | pub2009026.pdf | PMID:  20351820 | PMCID:  PMC2815504

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• Bodenreider O. Provenance information in biomedical knowledge repositories – A use case. Proceedings of the First International Workshop on the role of Semantic Web in Provenance Management (SWPM 2009), 2009: p. (electronic proceedings: http://ceur-ws.org/Vol-526/).

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• 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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• Bodenreider O. Comparing SNOMED CT and the NCI Thesaurus through Semantic Web Technologies Proc. KR-MED 2008

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• Bodenreider O. Ontologies and Data Integration in Biomedicine: Success Stories and Challenging Issues In: Bairoch A, Cohen-Boulakia S, Froidevaux C, editors. Proceedings of the Fifth International Workshop on Data Integration in the Life Sciences (DILS 2008); Berlin Heidelberg New York: Springer; 2008. p. 1-4

  Abstract | pub2008024.pdf

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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, 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/).

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• Bodenreider O. Issues in Mapping LOINC Laboratory Tests to SNOMED CT AMIA Annu Symp Proc. 2008 Nov 6:51-5

  Abstract | PMID:  18999311 | PMCID:  PMC2655945

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• Bodenreider O, Burgun A. Oncologic Pathology in Biomedical Terminologies: Challenges for Data Integration Proc APIII conference on "Anatomic Pathology Informatics and Imaging Support for Translational Medicine", Pittsburgh, Pennsylvania, September 9-12, 2007:Abstract 342.

  Abstract | pub2007050.pdf

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• Bodenreider O, Zhang S. Comparing the Representation of Anatomy in the FMA and SNOMED CT AMIA Annu Symp Proc. 2006:46-50

  Abstract | pub2006054.pdf | PMID:  17238300 | PMCID:  PMC1839313

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• Bodenreider O. Lexical, Terminological and Ontological Resources for Biological Text Mining Ananiadou S, McNaught J, editors. Text mining for biology and biomedicine: Artech House; 2006. p. 43-66.

  Abstract | pub2006007.pdf

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• Bodenreider O, Burgun A. Linking the Gene Ontology to other biological ontologies Proc ISMB'2005 SIG meeting on Bio-ontologies 2005:17-18

  Abstract | pub2005026.pdf

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• Bodenreider O, Aubry M, Burgun A. Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology Pac Symp Biocomput. 2005:91-102

  Abstract | pub2005006.pdf

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• Bodenreider O, Hayamizu TF, Ringwald M, De Coronado S, Zhang S. Of mice and men: aligning mouse and human anatomies. AMIA Annu Symp Proc. 2005:61-5.

  Abstract | pub2005027.pdf | PMID:  16779002 | PMCID:  PMC1560846

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• Bodenreider O, Aubry M, Burgun A. From Functional Similarity Among Gene Products to Dependence Relations Among Gene Ontology Terms Proc SOFG, 2004:53.

  Abstract | pub2004069.pdf

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• Bodenreider O, Azuaje F. Incorporating Ontology-Driven Similarity Knowledge Into Functional Genomics: An Exploratory Study Proceedings of the 2004 IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE-2004) 2004:317-324.

  Abstract | pub2004066.pdf

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• Bodenreider O, Smith B, Burugn A. The Ontology-Epistemology Divide: A Case Study in Medical Terminology Proceedings of the Third International Conference on Formal Ontology in Information Systems (FOIS2004): IOS Press; 2004. p. 185-195.

  Abstract | pub2004064.pdf

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