• 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.

  Abstract | PMID:  29295179 | PMCID:  PMC5875427
• 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.

  Abstract | pub8935.pdf | PMID:  25101165 | PMCID:  PMC4120719
• 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
• 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.

  Abstract | PMID:  19394440 | PMCID:  PMC2722378
• 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.

  Abstract | PMID:  23026233 | PMCID:  PMC4031661
• Kilicoglu H, Rogers W. A Hybrid System for Extracting Chemical-Disease Relationships from Scientific Literature. 2015. BioCreative 5 Proceedings.

  Abstract | pub9350.pdf
• 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.

  Abstract | PMID:  22683993 | PMCID:  PMC3438287
• 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/).

  Abstract
• Bodenreider O. A Semantic Navigation Tool for the UMLS AMIA Annu Symp Proc. 2000;: 971.

  Abstract | pub2000035.pdf
• 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.

  Abstract | pub2011023.pdf | PMID:  22126369 | PMCID:  PMC3298549
• Crowell J, Zeng QT, Tse T. A Web Application to Support Consumer Health Vocabulary Development AMIA Annu Symp Proc. 2005:932

  Abstract | pub2005043.pdf
• Burgun A, Bodenreider O. Accessing and Integrating Data and Knowledge for Biomedical Research Yearb Med Inform. 2008:91-101

  Abstract | pub2008027.pdf | PMID:  18660883 | PMCID:  PMC2553094
• 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

  Abstract | pub2007013.pdf | PMID:  17493285 | PMCID:  PMC1892099
• Zhang S, Bodenreider O. Aligning Representations of Anatomy Using Lexical and Structural Methods AMIA Annu Symp Proc. 2003 Nov;:753-757.

  Abstract | pub2003063.pdf | PMID:  14728274 | PMCID:  PMC1480279
• 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

  Abstract | pub2005039.pdf | PMID:  16779163 | PMCID:  PMC1560629
• 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

  Abstract | PMID:  19478019 | PMCID:  PMC2687948
• Peters L, Kapusnik-Uner JE, Nguyen T, Bodenreider O. An approximate matching method for clinical drug names. AMIA Annu Symp Proc. 2011;2011:1117-26. Epub 2011 Oct 22.

  Abstract | pub2011020.pdf | PMID:  22195172 | PMCID:  PMC3243188
• Sahoo S, Bodenreider O, Zeng K, Sheth AP. An Experiment in Integrationg Large Biomedical Knowledge Resources with RDF: Application to Associating Genotype and Phenotype Information Proc Workshop on Health Care and Life Sciences Data Integration for the Semantic Web at WWW2007 (electronic proceedings: http://www2007.org/workshops/paper_149.pdf)

  Abstract | pub2007014.pdf
• Bergun A, Bodenreider O. An ontology of chemical entities helps identify dependence relations among Gene Ontology terms Proc SMBM-2005

  Abstract | pub2005028.pdf
• Wang H, Azuaje F, Bodenreider O. An Ontology-Driven Clustering Method for Supporting Gene Expression Analysis CBMS’2005. 2005:389-394.

  Abstract | pub2005036.pdf
• Mougin FL, Bodenreider O, Burgun A. Analyzing polysemous concepts from a clinical perspective: application to auditing concept categorization in the UMLS. J Biomed Inform. 2009 Jun;42(3):440-51. doi: 10.1016/j.jbi.2009.03.008. Epub 2009 Mar 18.

  Abstract | PMID:  19303057
• Mougin F, Bodenreider O. Approaches to Eliminating Cycles in the UMLS Metathesaurus: Naive vs. Formal AMIA Annu Symp Proc. 2005:550-4

  Abstract | pub2005034.pdf | PMID:  16779100 | PMCID:  PMC1560864
• Vizenor LT, Bodenreider O, McCray AT. Auditing associative relations across two knowledge sources. J Biomed Inform. 2009 Jun;42(3):426-39. doi: 10.1016/j.jbi.2009.01.004.

  Abstract | PMID:  19475724 | PMCID:  PMC2891883
• Cui L, Bodenreider O, Shi J, Zhang GQ. Auditing SNOMED CT hierarchical relations based on lexical features of concepts in non-lattice subgraphs. Biomed Inform. 2018 Feb;78:177-184. doi: 10.1016/j.jbi.2017.12.010. Epub 2017 Dec 20.

  Abstract | PMID:  29274386 | PMCID:  PMC5835197
• Mougin F, Bodenreider O. Auditing the NCI Thesaurus with Semantic Web Technologies AMIA Annu Symp Proc. 2008 Nov 6:500-4

  Abstract | pub2008026.pdf | PMID:  18999265 | PMCID:  PMC2655981

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