Olivier Bodenreider

228 papers A* 4B 2C 3Misc 80Journal 55Unranked 81

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	A deep learning approach to identify missing J. Am. Medical Informatics Assoc. Rashmie Abeysinghe, Fengbo Zheng, Elmer V. Bernstam, Jay Shi, Olivier Bodenreider, Licong Cui
2023	J	`jnl`	A practical strategy to use the ICD-11 for morbidity coding in the United States without a clinical modification. J. Am. Medical Informatics Assoc. Kin Wah Fung, Julia Xu, Shannon McConnell-Lamptey, Donna Pickett, Olivier Bodenreider
2023	—	`conf`	Solving the Right Problem is Key for Translational NLP: A Case Study in UMLS Vocabulary Insertion. EMNLP (Findings) Bernal Jimenez Gutierrez, Yuqing Mao, Vinh Nguyen, Kin Wah Fung, Yu Su, Olivier Bodenreider
2023	J	`jnl`	Solving the Right Problem is Key for Translational NLP: A Case Study in UMLS Vocabulary Insertion. CoRR Bernal Jimenez Gutierrez, Yuqing Mao, Vinh Nguyen, Kin Wah Fung, Yu Su, Olivier Bodenreider
2023	J	`jnl`	Two complementary AI approaches for predicting UMLS semantic group assignment: heuristic reasoning and deep learning. J. Am. Medical Informatics Assoc. Yuqing Mao, Randolph A. Miller, Olivier Bodenreider, Vinh Nguyen, Kin Wah Fung
2022	A*	`conf`	Context-Enriched Learning Models for Aligning Biomedical Vocabularies at Scale in the UMLS Metathesaurus. WWW Vinh Nguyen, Hong Yung Yip, Goonmeet Bajaj, Thilini Wijesiriwardene, Vishesh Javangula, Srinivasan Parthasarathy, Amit P. Sheth, Olivier Bodenreider
2022	—	`conf`	Evaluating Biomedical Word Embeddings for Vocabulary Alignment at Scale in the UMLS Metathesaurus Using Siamese Networks. Insights@ACL Goonmeet Bajaj, Vinh Nguyen, Thilini Wijesiriwardene, Hong Yung Yip, Vishesh Javangula, Amit P. Sheth, Srinivasan Parthasarathy, Olivier Bodenreider
2022	—	`conf`	Powering Semantic Analysis with Bio-ontologies. WWW (Companion Volume) Olivier Bodenreider
2022	J	`jnl`	UBERT: A Novel Language Model for Synonymy Prediction at Scale in the UMLS Metathesaurus. CoRR Thilini Wijesiriwardene, Vinh Nguyen, Goonmeet Bajaj, Hong Yung Yip, Vishesh Javangula, Yuqing Mao, Kin Wah Fung, Srinivasan Parthasarathy, Amit P. Sheth, Olivier Bodenreider
2022	J	`jnl`	UVA Resources for the Biomedical Vocabulary Alignment at Scale in the UMLS Metathesaurus. CoRR Vinh Nguyen, Olivier Bodenreider
2021	—	`conf`	Adding an Attention Layer Improves the Performance of a Neural Network Architecture for Synonymy Prediction in the UMLS Metathesaurus. MedInfo Vinh Nguyen, Olivier Bodenreider
2021	A*	`conf`	Biomedical Vocabulary Alignment at Scale in the UMLS Metathesaurus. WWW Vinh Nguyen, Hong Yung Yip, Olivier Bodenreider
2021	Misc	`conf`	Can ICD-11 Replace ICD-10-CM for Morbidity Coding in the U.S.? AMIA Kin Wah Fung, Julia Xu, Shannon McConnell-Lamptey, Donna Pickett, Olivier Bodenreider
2021	J	`jnl`	Evaluating Biomedical BERT Models for Vocabulary Alignment at Scale in the UMLS Metathesaurus. CoRR Goonmeet Bajaj, Vinh Nguyen, Thilini Wijesiriwardene, Hong Yung Yip, Vishesh Javangula, Srinivasan Parthasarathy, Amit P. Sheth, Olivier Bodenreider
2021	J	`jnl`	Feasibility of replacing the ICD-10-CM with the ICD-11 for morbidity coding: A content analysis. J. Am. Medical Informatics Assoc. Kin Wah Fung, Julia Xu, Shannon McConnell-Lamptey, Donna Pickett, Olivier Bodenreider
2021	Misc	`conf`	Reproducibility in biomedical natural language processing: A FAIR approach to what we need to know. AMIA Kevin Bretonnel Cohen, Anna M. Ripple, Asma Ben Abacha, Olivier Bodenreider, Orin Hargraves, Karin Verspoor, Pierre Zweigenbaum, Dina Demner-Fushman
2021	—	`conf`	Sequential Mapping - A Novel Approach to Map from ICD-10-CM to ICD-11. MedInfo Julia Xu, Kin Wah Fung, Olivier Bodenreider
2020	J	`jnl`	Assessing the enrichment of dietary supplement coverage in the Unified Medical Language System. J. Am. Medical Informatics Assoc. Jake Vasilakes, Anusha Bompelli, Jeffrey R. Bishop, Terrence J. Adam, Olivier Bodenreider, Rui Zhang
2020	—	`conf`	Siamese KG-LSTM: A deep learning model for enriching UMLS Metathesaurus synonymy. KSE Tien T. T. Tran, Sy V. Nghiem, Van T. Le, Tho Thanh Quan, Vinh Nguyen, Hong Yung Yip, Olivier Bodenreider
2020	J	`jnl`	The new International Classification of Diseases 11th edition: a comparative analysis with ICD-10 and ICD-10-CM. J. Am. Medical Informatics Assoc. Kin Wah Fung, Julia Xu, Olivier Bodenreider
2019	—	`conf`	Automatic Identification of Individual Drugs in Death Certificates. MedInfo Soon Jye Kho, Amit P. Sheth, Olivier Bodenreider
2019	—	`conf`	Comparing the Representation of Medicinal Products in RxNorm and SNOMED CT - Consequences on interoperability. ICBO Jean Noël Nikiema, Olivier Bodenreider
2019	—	`conf`	Construction of UMLS Metathesaurus with Knowledge-Infused Deep Learning. BlockSW/CKG@ISWC Hong Yung Yip, Vinh Nguyen, Olivier Bodenreider
2019	—	`conf`	Normalizing Dietary Supplement Product Names Using the RxNorm Model. MedInfo Jake Vasilakes, Yadan Fan, Rubina F. Rizvi, Anusha Bompelli, Olivier Bodenreider, Rui Zhang
2019	—	`conf`	Singleton Property Graph: Adding A Semantic Web Abstraction Layer to Graph Databases. BlockSW/CKG@ISWC Vinh Nguyen, Hong Yung Yip, Harsh Thakkar, Qingliang Li, Evan Bolton, Olivier Bodenreider
2018	J	`jnl`	Auditing SNOMED CT hierarchical relations based on lexical features of concepts in non-lattice subgraphs. J. Biomed. Informatics Licong Cui, Olivier Bodenreider, Jay Shi, Guo-Qiang Zhang
2018	Misc	`conf`	Historically Comprehensive Medications Metadata for i2b2 Data Warehouses. AMIA Jay Pedersen, Bret J. Gardner, James R. Campbell, Walter S. Campbell, Carol Geary, Lee B. Peters, Olivier Bodenreider, James C. McClay
2018	Misc	`conf`	RxNav-in-a-Box - A locally-installable version of RxNav and related APIs. AMIA Lee B. Peters, Richard Rice, Olivier Bodenreider
2018	—	`conf`	The New SNOMED CT International Medicinal Product Model. ICBO Olivier Bodenreider, Julie James
2018	Misc	`conf`	Using RxNav for drug analytics - How to interpret obsolete drug identifiers? AMIA Olivier Bodenreider, Lee B. Peters
2017	—	`conf`	"Hybrid Topics" - Facilitating the Interpretation of Topics Through the Addition of MeSH Descriptors to Bags of Words. MedInfo Zhiguo Yu, Thang Nguyen, Ferdinand Dhombres, Todd R. Johnson, Olivier Bodenreider
2017	J	`jnl`	Comparison of three commercial knowledge bases for detection of drug-drug interactions in clinical decision support. J. Am. Medical Informatics Assoc. Kin Wah Fung, Joan Kapusnik-Uner, Jean Cunningham, Stefanie Higby-Baker, Olivier Bodenreider
2017	Misc	`conf`	Detecting Adverse Drug Event Safety Signals from MEDLINE Reports: Challenges in Employing Cross-terminology Mapping of MeSH to MedDRA. AMIA Abhivyakti Sawarkar, Alfred Sorbello, Anna Ripple, Olivier Bodenreider
2017	—	`conf`	Eliciting the Intension of Drug Value Sets - Principles and Quality Assurance Applications. MedInfo Nathan J. Bahr, Scott D. Nelson, Rainer Winnenburg, Olivier Bodenreider
2017	Misc	`conf`	Identifying Potentially Missing Hierarchical Relations in SNOMED CT based on Lexical Features - Impact of Synonyms and Lexico-syntactic Constraints. AMIA Satyajeet Raje, Olivier Bodenreider
2017	—	`conf`	Interoperability of Disease Concepts in Clinical and Research Ontologies: Contrasting Coverage and Structure in the Disease Ontology and SNOMED CT. MedInfo Satyajeet Raje, Olivier Bodenreider
2017	—	`conf`	Interoperability of Medication Classification Systems: Lessons Learned Mapping Established Pharmacologic Classes (EPCs) to SNOMED CT. MedInfo Scott D. Nelson, Jaqui Parker, Robert F. Lario, Rainer Winnenburg, Mark S. Erlbaum, Michael J. Lincoln, Olivier Bodenreider
2017	—	`conf`	Investigating the Coverage of Diseases across Biomedical Research and Clinical Ontologies. CRI Satyajeet Raje, Olivier Bodenreider
2017	Misc	`conf`	Mapping U.S. FDA National Drug Codes to Anatomical-Therapeutic-Chemical Classes using RxNorm. AMIA Fabrício S. P. Kury, Olivier Bodenreider
2017	—	`conf`	MetaMap Lite in Excel: Biomedical Named-Entity Recognition for Non-Technical Users. MedInfo Ravi Teja Bhupatiraju, Kin Wah Fung, Olivier Bodenreider
2017	J	`jnl`	Mining non-lattice subgraphs for detecting missing hierarchical relations and concepts in SNOMED CT. J. Am. Medical Informatics Assoc. Licong Cui, Wei Zhu, Shiqiang Tao, James T. Case, Olivier Bodenreider, Guo-Qiang Zhang
2017	Misc	`conf`	RxMix - Use of NLM drug APIs by non-programmers. AMIA Olivier Bodenreider, Lee B. Peters
2017	Misc	`conf`	RxNav 2.0 - A web-based, mobile-responsive RxNorm browser. AMIA Lee B. Peters, Olivier Bodenreider
2017	Misc	`conf`	RxNorm Concept History Service. AMIA Olivier Bodenreider, Lee B. Peters
2017	—	`conf`	Terminology Status APIs - Mapping Obsolete Codes to Current RxNorm, SNOMED CT, and LOINC Concepts. MedInfo Lee B. Peters, Thang Nguyen, Olivier Bodenreider
2017	J	`jnl`	Toward multimodal signal detection of adverse drug reactions. J. Biomed. Informatics Rave Harpaz, William DuMouchel, Martijn J. Schuemie, Olivier Bodenreider, Carol Friedman, Eric Horvitz, Anna Ripple, Alfred Sorbello, Ryen W. White, Rainer Winnenburg, Nigam H. Shah
2017	—	`conf`	Trends in Fetal Medicine: A 10-Year Bibliometric Analysis of Prenatal Diagnosis. MedInfo Ferdinand Dhombres, Olivier Bodenreider
2016	J	`jnl`	A Formal Graph Model for RDF and Its Implementation. CoRR Vinh Nguyen, Jyoti Leeka, Olivier Bodenreider, Amit P. Sheth
2016	Misc	`conf`	Assessing the potential risk in drug prescriptions during pregnancy. AMIA Ferdinand Dhombres, Vojtech Huser, Laritza M. Rodriguez, Olivier Bodenreider
2016	Misc	`conf`	Characterizing the semantic composition of the UMLS Metathesaurus over time. AMIA Olivier Bodenreider, Lee B. Peters
2016	Misc	`conf`	Exploring the Use of ClinicalTrials.gov Trial Results Data for Pharmacovigilance. AMIA Vojtech Huser, Olivier Bodenreider
2016	—	`conf`	Identifying Missing Hierarchical Relations in SNOMED CT from Logical Definitions Based on the Lexical Features of Concept Names. ICBO/BioCreative Olivier Bodenreider
2016	J	`jnl`	Interoperability between phenotypes in research and healthcare terminologies - Investigating partial mappings between HPO and SNOMED CT. J. Biomed. Semant. Ferdinand Dhombres, Olivier Bodenreider
2016	Misc	`conf`	NDC Properties in RxNorm. AMIA Lee B. Peters, Olivier Bodenreider
2016	Misc	`conf`	PubMed 'Early Alerts': Towards Better Precision of Literature Searching for Pharmacovigilance Information based on an Assessment of Relevance Feedback. AMIA Anna Ripple, Alfred Sorbello, Shahrukh Haider, Olivier Bodenreider
2016	Misc	`conf`	Resources for Analyzing Drug Prescription Datasets. AMIA Olivier Bodenreider, Vojtech Huser, Christian G. Reich
2016	—	`conf`	The Drug Data to Knowledge Pipeline: Large-Scale Claims Data Classification for Pharmacologic Insight. CRI Mark L. Homer, Nathan P. Palmer, Olivier Bodenreider, Aurel Cami, Laura Chadwick, Kenneth D. Mandl
2016	J	`jnl`	The digital revolution in phenotyping. Briefings Bioinform. Anika Oellrich, Nigel Collier, Tudor Groza, Dietrich Rebholz-Schuhmann, Nigam Shah, Olivier Bodenreider, Mary Regina Boland, Ivo I. Georgiev, Hongfang Liu, Kevin M. Livingston, Augustin Luna, Ann-Marie Mallon, Prashanti Manda, Peter N. Robinson, Gabriella Rustici, Michelle Simon, Liqin Wang, Rainer Winnenburg, Michel Dumontier
2016	—	`conf`	The national library of medicine pill image recognition challenge: An initial report. AIPR Ziv Yaniv, Jessica Faruque, Sally E. Howe, Kathel Dunn, David Sharlip, Andrew Bond, Pablo Perillan, Olivier Bodenreider, Michael J. Ackerman, Terry S. Yoo
2015	Misc	`conf`	Approaches to Supporting the Analysis of Historical Medication Datasets with RxNorm. AMIA Lee B. Peters, Olivier Bodenreider
2015	J	`jnl`	Context-driven automatic subgraph creation for literature-based discovery. J. Biomed. Informatics Delroy Cameron, Ramakanth Kavuluru, Thomas C. Rindflesch, Amit P. Sheth, Krishnaprasad Thirunarayan, Olivier Bodenreider
2015	J	`jnl`	Evaluating drug-drug interaction information in NDF-RT and DrugBank. J. Biomed. Semant. Lee B. Peters, Nathan J. Bahr, Olivier Bodenreider
2015	J	`jnl`	Exploring adverse drug events at the class level. J. Biomed. Semant. Rainer Winnenburg, Alfred Sorbello, Olivier Bodenreider
2015	—	`conf`	Exposing Provenance Metadata Using Different RDF Models. SWAT4LS Gang Fu, Evan Bolton, Núria Queralt-Rosinach, Laura Inés Furlong, Vinh Nguyen, Amit P. Sheth, Olivier Bodenreider, Michel Dumontier
2015	J	`jnl`	Exposing Provenance Metadata Using Different RDF Models. CoRR Gang Fu, Evan Bolton, Núria Queralt Rosinach, Laura Inés Furlong, Vinh Nguyen, Amit P. Sheth, Olivier Bodenreider, Michel Dumontier
2015	—	`conf`	Extending the coverage of phenotypes in SNOMED CT through post-coordination. MedInfo Ferdinand Dhombres, Rainer Winnenburg, James T. Case, Olivier Bodenreider
2015	Misc	`conf`	Finding Similar Drug Classes using RxClass. AMIA Thang Nguyen, Lee B. Peters, Olivier Bodenreider
2015	—	`conf`	Fingerprinting Biomedical Terminologies - Automatic Classification and Visualization of Biomedical Vocabularies through UMLS Semantic Group Profiles. MedInfo Bastien Rance, Thai Le, Olivier Bodenreider
2015	J	`jnl`	Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies. J. Biomed. Informatics Rainer Winnenburg, Alfred Sorbello, Anna Ripple, Rave Harpaz, Joseph M. Tonning, Ana Szarfman, Henry Francis, Olivier Bodenreider
2015	Misc	`conf`	Navigating between Drug Classes and RxNorm Drugs with RxClass. AMIA Olivier Bodenreider, Lee B. Peters, Thang Nguyen
2015	J	`jnl`	On Reasoning with RDF Statements about Statements using Singleton Property Triples. CoRR Vinh Nguyen, Olivier Bodenreider, Krishnaprasad Thirunarayan, Gang Fu, Evan Bolton, Núria Queralt Rosinach, Laura Inés Furlong, Michel Dumontier, Amit P. Sheth
2015	Misc	`conf`	PubMed 'Early Alerts': A Pilot Study to Support Prospective Detection of Emerging Adverse Drug Events. AMIA Alfred Sorbello, Anna Ripple, Olivier Bodenreider
2015	J	`jnl`	Using description logics to evaluate the consistency of drug-class membership relations in NDF-RT. J. Biomed. Semant. Rainer Winnenburg, Jonathan M. Mortensen, Olivier Bodenreider
2014	J	`jnl`	A framework for assessing the consistency of drug classes across sources. J. Biomed. Semant. Rainer Winnenburg, Olivier Bodenreider
2014	Misc	`conf`	Analyzing U.S. prescription lists with RxNorm and the ATC/DDD Index. AMIA Olivier Bodenreider, Laritza Rodriguez
2014	Misc	`conf`	Automatic coding of Free-Text Medication Data recorded by Research Coordinators. AMIA Laritza Rodriguez, Vojtech Huser, Olivier Bodenreider, James J. Cimino
2014	—	`conf`	Coverage of Rare Disease Names in Clinical Coding Systems and Ontologies and Implications for Electronic Health Records-Based Research. ICBO Rachel L. Richesson, Kin Wah Fung, Olivier Bodenreider
2014	Misc	`conf`	Coverage of Rare Disease Names in Standard Terminologies and Implications for Patients, Providers, and Research. AMIA Kin Wah Fung, Rachel L. Richesson, Olivier Bodenreider
2014	Misc	`conf`	Creating, Maintaining and Publishing Value Sets in the VSAC. AMIA Emir Khatipov, Maureen Madden, Pishing Chiang, Philip Chuang, Duc Nguyen, Ivor D'Souza, Rainer Winnenburg, Olivier Bodenreider, Julia L. Skapik, Robert C. McClure, Steven Emrick
2014	Misc	`conf`	Desiderata for an authoritative Representation of MeSH in RDF. AMIA Rainer Winnenburg, Olivier Bodenreider
2014	A*	`conf`	Don't like RDF reification?: making statements about statements using singleton property. WWW Vinh Nguyen, Olivier Bodenreider, Amit P. Sheth
2014	Misc	`conf`	Facilitating Reconciliation of Inter-Annotator Disagreements. AMIA Johann Stan, Olivier Bodenreider, Kin Wah Fung, Dina Demner-Fushman
2014	—	`conf`	MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and its application to SNOMED CT. IEEE BigData Guo-Qiang Zhang, Wei Zhu, Mengmeng Sun, Shiqiang Tao, Olivier Bodenreider, Licong Cui
2014	Misc	`conf`	RxClass - Navigating between Drug Classes and RxNorm Drugs. AMIA Thang Nguyen, Lee B. Peters, Olivier Bodenreider
2014	—	`conf`	RxClass - Navigating between Drug Classes and RxNorm Drugs. ICBO Olivier Bodenreider, Lee B. Peters, Thang Nguyen
2013	J	`jnl`	A graph-based recovery and decomposition of Swanson's hypothesis using semantic predications. J. Biomed. Informatics Delroy Cameron, Olivier Bodenreider, Hima Yalamanchili, Tu Danh, Sreeram Vallabhaneni, Krishnaprasad Thirunarayan, Amit P. Sheth, Thomas C. Rindflesch
2013	—	`conf`	Aligning Pharmacologic Classes Between MeSH and ATC. VDOS+DO@ICBO Rainer Winnenburg, Laritza Rodriguez, Fiona M. Callaghan, Alfred Sorbello, Ana Szarfman, Olivier Bodenreider
2013	Misc	`conf`	Displaying Drug Classes in RxNav. AMIA Lee B. Peters, Thang Nguyen, Olivier Bodenreider
2013	—	`conf`	Enabling Complex Queries to Drug Information Sources through Functional Composition. MedInfo Lee B. Peters, Jonathan Mortensen, Thang Nguyen, Olivier Bodenreider
2013	—	`conf`	Exploring Pharmacoepidemiologic Groupings of Drugs from a Clinical Perspective. MedInfo Rainer Winnenburg, Olivier Bodenreider
2013	—	`conf`	Leveraging Terminological Resources for Mapping between Rare Disease Information Sources. MedInfo Bastien Rance, Michelle Snyder, Janine Lewis, Olivier Bodenreider
2013	—	`conf`	Medical Concept Representation: The Years Beyond 2000. MedInfo László Balkányi, Stefan Schulz, Ronald Cornet, Olivier Bodenreider
2013	Misc	`conf`	Metrics for assessing the quality of value sets in clinical quality measures. AMIA Rainer Winnenburg, Olivier Bodenreider
2013	—	`conf`	Multi-lingual Features of the Unified Medical Language System. CLEF (Working Notes) Olivier Bodenreider
2013	Misc	`conf`	Network Visualization of UMLS Source Vocabularies using Semantic Groups. AMIA Thai Le, Bastien Rance, Olivier Bodenreider
2013	Misc	`conf`	The NLM Value Set Authority Center at 1 year. AMIA Steven Emrick, Duc Nguyen, Pishing Chiang, Philip Chuang, Maureen Madden, Rainer Winnenburg, Robert C. McClure, Ivor D'Souza, Olivier Bodenreider
2013	—	`conf`	The NLM Value Set Authority Center. MedInfo Olivier Bodenreider, Duc Nguyen, Pishing Chiang, Philip Chuang, Maureen Madden, Rainer Winnenburg, Robert C. McClure, Steven Emrick, Ivor D'Souza
2012	J	`jnl`	A mutation-centric approach to identifying pharmacogenomic relations in text. J. Biomed. Informatics Bastien Rance, Emily Doughty, Dina Demner-Fushman, Maricel G. Kann, Olivier Bodenreider
2012	—	`conf`	Comparing drug-class membership in ATC and NDF-RT. IHI Fleur Mougin, Anita Burgun, Olivier Bodenreider
2012	—	`ed.`	Data Integration in the Life Sciences - 8th International Conference, DILS 2012, College Park, MD, USA, June 28-29, 2012. Proceedings DILS Olivier Bodenreider, Bastien Rance
2012	Misc	`conf`	Issues in Creating and Maintaining Value Sets for Clinical Quality Measures. AMIA Rainer Winnenburg, Olivier Bodenreider
2012	J	`jnl`	Ontologies and terminologies: Continuum or dichotomy? Appl. Ontology Natalia Grabar, Thierry Hamon, Olivier Bodenreider
2012	—	`ed.`	Proceedings of the 2nd International Conference on Biomedical Ontology, Buffalo, NY, USA, July 26-30, 2011 ICBO Olivier Bodenreider, Maryann E. Martone, Alan Ruttenberg
2012	Misc	`conf`	Quality Assurance in LOINC using Description Logic. AMIA Tomasz Adamusiak, Olivier Bodenreider
2012	Misc	`conf`	RxBatch - Batch Operations for RxNorm and NDF-RT APIs. AMIA Lee B. Peters, Olivier Bodenreider, Thang Nguyen
2011	J	`jnl`	A unified framework for managing provenance information in translational research. BMC Bioinform. Satya Sanket Sahoo, Vinh Nguyen, Olivier Bodenreider, Priti Parikh, Todd Minning, Amit P. Sheth
2011	—	`conf`	Semantic Predications for Complex Information Needs in Biomedical Literature. BIBM Delroy Cameron, Ramakanth Kavuluru, Olivier Bodenreider, Pablo N. Mendes, Amit P. Sheth, Krishnaprasad Thirunarayan
2011	—	`conf`	The Knowledge-driven Exploration of Integrated Biomedical Knowledge Sources Facilitates the Generation of New Hypotheses. LISC Vinh Nguyen, Olivier Bodenreider, Todd Minning, Amit P. Sheth
2011	J	`jnl`	The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. J. Biomed. Semant. Joanne S. Luciano, Bosse Andersson, Colin R. Batchelor, Olivier Bodenreider, Tim Clark, Christine K. Denney, Christopher Domarew, Thomas Gambet, Lee Harland, Anja Jentzsch, Vipul Kashyap, Peter J. Kos, Julia Kozlovsky, Timothy Lebo, M. Scott Marshall, Jamie P. McCusker, Deborah L. McGuinness, Chimezie Ogbuji, Elgar Pichler, Robert L. Powers, Eric Prud'hommeaux, Matthias Samwald, Lynn M. Schriml, Peter J. Tonellato, Patricia L. Whetzel, Jun Zhao, Susie Stephens, Michel Dumontier
2011	J	`jnl`	Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature. Bioinform. Emily Doughty, Attila Kertész-Farkas, Olivier Bodenreider, Gary Thompson, Asa Adadey, Thomas A. Peterson, Maricel G. Kann
2010	—	`conf`	A Framework for Comparing Phenotype Annotations of Orthologous Genes. MedInfo Olivier Bodenreider, Anita Burgun
2010	—	`conf`	Combining Relevance Assignment with Quality of the Evidence to Support Guideline Development. MedInfo Marcelo Fiszman, Bruce E. Bray, Dongwook Shin, Halil Kilicoglu, Glen C. Bennett, Olivier Bodenreider, Thomas C. Rindflesch
2010	J	`jnl`	Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG. J. Am. Medical Informatics Assoc. Jyotishman Pathak, Lee B. Peters, Christopher G. Chute, Olivier Bodenreider
2010	—	`conf`	Comparing pharmacologic classes in NDF-RT and SNOMED CT. Semantic Mining in Biomedicine Jonathan Mortensen, Olivier Bodenreider
2010	—	`conf`	Exploiting UMLS Semantics for Checking Semantic Consistency among UMLS concepts. MedInfo Halit Erdogan, Esra Erdem, Olivier Bodenreider
2010	J	`jnl`	Extracting Rx information from clinical narrative. J. Am. Medical Informatics Assoc. James G. Mork, Olivier Bodenreider, Dina Demner-Fushman, Rezarta Islamaj Dogan, François-Michel Lang, Zhiyong Lu, Aurélie Névéol, Lee B. Peters, Sonya E. Shooshan, Alan R. Aronson
2010	A*	`conf`	Finding Semantic Inconsistencies in UMLS using Answer Set Programming. AAAI Halit Erdogan, Olivier Bodenreider, Esra Erdem
2010	—	`conf`	Integrating Consumer-Oriented Vocabularies with Selected Professional Ones from the UMLS Using Semantic Web Technologies. eHealth Elena Cardillo, Genaro Hernández, Olivier Bodenreider
2010	B	`conf`	Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. SSDBM Satya Sanket Sahoo, Olivier Bodenreider, Pascal Hitzler, Amit P. Sheth, Krishnaprasad Thirunarayan
2010	—	`conf`	Using SPARQL to Test for Lattices: Application to Quality Assurance in Biomedical Ontologies. ISWC (2) Guo-Qiang Zhang, Olivier Bodenreider
2010	—	`conf`	Using the Abstraction Network in Complement to Description Logics for Quality Assurance in Biomedical Terminologies - A Case Study in SNOMED CT. MedInfo Duo Helen Wei, Olivier Bodenreider
2009	J	`jnl`	A graph-based approach to auditing RxNorm. J. Biomed. Informatics Olivier Bodenreider, Lee B. Peters
2009	J	`jnl`	Alignment of the UMLS semantic network with BioTop: methodology and assessment. Bioinform. Stefan Schulz, Elena Beisswanger, László van den Hoek, Olivier Bodenreider, Erik M. van Mulligen
2009	J	`jnl`	Analyzing polysemous concepts from a clinical perspective: Application to auditing concept categorization in the UMLS. J. Biomed. Informatics Fleur Mougin, Olivier Bodenreider, Anita Burgun
2009	J	`jnl`	Auditing associative relations across two knowledge sources. J. Biomed. Informatics Lowell Vizenor, Olivier Bodenreider, Alexa T. McCray
2009	—	`conf`	Identifying anatomical concepts associated with ICD10 diseases. TIA Fleur Mougin, Olivier Bodenreider, Anita Burgun
2009	—	`conf`	Provenance Information in Biomedical Knowledge Repositories - A Use Case. SWPM Olivier Bodenreider
2009	J	`jnl`	Special Issue: Biomedical Ontology in Action. Appl. Ontology Olivier Bodenreider
2009	J	`jnl`	The caBIG terminology review process. J. Biomed. Informatics James J. Cimino, Terry F. Hayamizu, Olivier Bodenreider, Brian Davis, Grace A. Stafford, Martin Ringwald
2009	Misc	`conf`	Two approaches to integrating phenotype and clinical information. AMIA Anita Burgun, Fleur Mougin, Olivier Bodenreider
2009	Misc	`conf`	Using SNOMED CT in combination with MedDRA for reporting signal detection and adverse drug reactions reporting. AMIA Olivier Bodenreider
2008	Misc	`conf`	A Framework for Characterizing Drug Information Sources. AMIA Mark Sharp, Olivier Bodenreider, Nina Wacholder
2008	J	`jnl`	An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence. J. Biomed. Informatics Satya Sanket Sahoo, Olivier Bodenreider, Joni L. Rutter, Karen J. Skinner, Amit P. Sheth
2008	Misc	`conf`	Auditing the NCI Thesaurus with Semantic Web Technologies. AMIA Fleur Mougin, Olivier Bodenreider
2008	—	`conf`	Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System. DILS Fleur Mougin, Anita Burgun, Olivier Bodenreider, Julie Chabalier, Olivier Loréal, Pierre Le Beux
2008	—	`conf`	Comparing SNOMED CT and the NCI Thesaurus through Semantic Web Technologies. KR-MED Olivier Bodenreider
2008	Misc	`conf`	Design and Implementation of a Personal Medication Record - AMIA Kelly Zeng, Olivier Bodenreider, Stuart J. Nelson
2008	J	`jnl`	Guest-editorial. Appl. Ontology Olivier Bodenreider
2008	Misc	`conf`	Issues in Mapping LOINC Laboratory Tests to SNOMED CT. AMIA Olivier Bodenreider
2008	—	`conf`	Ontologies and Data Integration in Biomedicine: Success Stories and Challenging Issues. DILS Olivier Bodenreider
2008	J	`jnl`	Ontology Summit 2007 - Ontology, taxonomy, folksonomy: Understanding the distinctions. Appl. Ontology Michael Gruninger, Olivier Bodenreider, Frank Olken, Leo Obrst, Peter Yim
2008	—	`conf`	SNOMED CT: Browsing the Browsers. KR-MED Jeremy Rogers, Olivier Bodenreider
2008	Misc	`conf`	Using the RxNorm Web Services API for Quality Assurance Purposes. AMIA Lee B. Peters, Olivier Bodenreider
2007	J	`jnl`	Advancing translational research with the Semantic Web. BMC Bioinform. Alan Ruttenberg, Tim Clark, William J. Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano, M. Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens, Gwendolyn T. Wong, Elizabeth Wu, Davide Zaccagnini, Tonya Hongsermeier, Eric Neumann, Ivan Herman, Kei-Hoi Cheung
2007	—	`conf`	Combining Lexical and Semantic Methods of Inter-terminology Mapping Using the UMLS. MedInfo Kin Wah Fung, Olivier Bodenreider, Alan R. Aronson, William T. Hole, Suresh Srinivasan
2007	J	`jnl`	Comparing two approaches for aligning representations of anatomy. Artif. Intell. Medicine Songmao Zhang, Peter Mork, Olivier Bodenreider, Philip A. Bernstein
2007	J	`jnl`	Experience in Aligning Anatomical Ontologies. Int. J. Semantic Web Inf. Syst. Songmao Zhang, Olivier Bodenreider
2007	—	`conf`	From "Glycosyltransferase" to "Congenital Muscular Dystrophy": Integrating Knowledge from NCBI Entrez Gene and the Gene Ontology. MedInfo Satya Sanket Sahoo, Kelly Zeng, Olivier Bodenreider, Amit P. Sheth
2007	—	`conf`	From indexing the biomedical literature to coding clinical text: experience with MTI and machine learning approaches. BioNLP@ACL Alan R. Aronson, Olivier Bodenreider, Dina Demner-Fushman, Kin Wah Fung, Vivian K. Lee, James G. Mork, Aurélie Névéol, Lee B. Peters, Willie J. Rogers
2007	—	`conf`	Hybrid Alignment Strategy for Anatomical Ontologies: Results of the 2007 Ontology Alignment Contest. OM Songmao Zhang, Olivier Bodenreider
2007	Misc	`conf`	Identifying Mismatches in Alignments of Large Anatomical Ontologies. AMIA Songmao Zhang, Olivier Bodenreider
2007	J	`jnl`	Investigating subsumption in SNOMED CT: An exploration into large description logic-based biomedical terminologies. Artif. Intell. Medicine Olivier Bodenreider, Barry Smith, Anand Kumar, Anita Burgun
2007	—	`conf`	Lessons Learned from Cross-Validating Alignments between Large Anatomical Ontologies. MedInfo Songmao Zhang, Olivier Bodenreider
2007	—	`conf`	Méthodes de mapping situées aux niveaux instance et schéma pour l'intégration de sources de données hétérogènes. Actes d'IC Fleur Mougin, Julie Chabalier, Olivier Bodenreider, Anita Burgun
2006	—	`conf`	Aligning Multiple Anatomical Ontologies through a Reference. Ontology Matching Songmao Zhang, Olivier Bodenreider
2006	Misc	`conf`	Besides Precision & Recall: Exploring Alternative Approaches to Evaluating an Automatic Indexing Tool for MEDLINE. AMIA Aurélie Névéol, Kelly Zeng, Olivier Bodenreider
2006	J	`jnl`	Bio-ontologies: current trends and future directions. Briefings Bioinform. Olivier Bodenreider, Robert Stevens
2006	Misc	`conf`	Comparing the Representation of Anatomy in the FMA and SNOMED CT. AMIA Olivier Bodenreider, Songmao Zhang
2006	—	`conf`	Data Integration through data elements: Mapping data elements to terminological resources. SMBM Fleur Mougin, Anita Burgun, Olivier Bodenreider
2006	Misc	`conf`	Enhancing Biomedical Ontologies through Alignment of Semantic Relationships: Exploratory Approaches. AMIA Lowell Vizenor, Olivier Bodenreider, Lee B. Peters, Alexa T. McCray
2006	Misc	`conf`	Experience in Reasoning with the Foundational Model of Anatomy in OWL DL. Pacific Symposium on Biocomputing Songmao Zhang, Olivier Bodenreider, Christine Golbreich
2006	—	`ed.`	KR-MED 2006, Formal Biomedical Knowledge Representation, Proceedings of the Second International Workshop on Formal Biomedical Knowledge Representation: "Biomedical Ontology in Action" (KR-MED 2006), Collocated with the 4th International Conference on Formal Ontology in Information Systems (FOIS-2006), Baltimore, Maryland, USA, November 8, 2006 KR-MED Olivier Bodenreider
2006	J	`jnl`	Law and order: Assessing and enforcing compliance with ontological modeling principles in the Foundational Model of Anatomy. Comput. Biol. Medicine Songmao Zhang, Olivier Bodenreider
2006	J	`jnl`	Mapping data elements to terminological resources for integrating biomedical data sources. BMC Bioinform. Fleur Mougin, Anita Burgun, Olivier Bodenreider
2006	—	`conf`	NLM Anatomical Ontology Alignment System. Results of the 2006 Ontology Alignment Contest. Ontology Matching Songmao Zhang, Olivier Bodenreider
2006	—	`conf`	Predictive Integration of Gene Ontology-Driven Similarity and Functional Interactions. ICDM Workshops Francisco Azuaje, Haiying Wang, Huiru Zheng, Olivier Bodenreider, Alban Chesneau
2006	Misc	`conf`	RxNav: A Web Service for Standard Drug Information. AMIA Kelly Zeng, Olivier Bodenreider, John Kilbourne, Stuart J. Nelson
2006	Misc	`conf`	RxNav: Providing Standard Drug Information. AMIA Kelly Zeng, Olivier Bodenreider, John Kilbourne, Stuart J. Nelson
2006	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing K. Bretonnel Cohen, Olivier Bodenreider, Lynette Hirschman
2006	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Robert Stevens, Olivier Bodenreider, Yves A. Lussier
2006	J	`jnl`	The foundational model of anatomy in OWL: Experience and perspectives. J. Web Semant. Christine Golbreich, Songmao Zhang, Olivier Bodenreider
2006	—	`conf`	Using Dependence Relations in MeSH as a Framework for the Analysis of Disease Information in Medline. SMBM Lowell Vizenor, Olivier Bodenreider
2006	Misc	`conf`	Using WordNet to Improve the Mapping of Data Elements to UMLS for Data Sources Integration. AMIA Fleur Mougin, Anita Burgun, Olivier Bodenreider
2005	Misc	`conf`	Alignment of Multiple Ontologies of Anatomy: Deriving Indirect Mappings from Direct Mappings to a Reference. AMIA Songmao Zhang, Olivier Bodenreider
2005	B	`conf`	An Ontology-Driven Clustering Method for Supporting Gene Expression Analysis. CBMS Haiying Wang, Francisco Azuaje, Olivier Bodenreider
2005	Misc	`conf`	Approaches to Eliminating Cycles in the UMLS Metathesaurus: Naïve vs. Formal. AMIA Fleur Mougin, Olivier Bodenreider
2005	Misc	`conf`	Classifying diseases with respect to anatomy: a study in SNOMED CT. AMIA Anita Burgun, Olivier Bodenreider, Fleur Mougin
2005	Misc	`conf`	GenesTrace: Phenomic Knowledge Discovery via Structured Terminology. Pacific Symposium on Biocomputing Michael N. Cantor, Indra Neil Sarkar, Olivier Bodenreider, Yves A. Lussier
2005	—	`conf`	Issues in the Classification of Disease Instances with Ontologies. MIE Anita Burgun, Olivier Bodenreider, Christian Jacquelinet
2005	Misc	`conf`	Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology. Pacific Symposium on Biocomputing Olivier Bodenreider, Marc Aubry, Anita Burgun
2005	Misc	`conf`	Of Mice and Men: Aligning Mouse and Human Anatomies. AMIA Olivier Bodenreider, Terry F. Hayamizu, Martin Ringwald, Sherri de Coronado, Songmao Zhang
2005	—	`conf`	Ontological research and its applications to the biomedical domain. ASIST Miguel E. Ruiz, Olivier Bodenreider, Eric Little, Padmini Srinivasan
2005	Misc	`conf`	RxNav: A Progress Report. AMIA Kelly Zeng, Olivier Bodenreider, Stuart J. Nelson
2005	Misc	`conf`	Session Introduction: Biomedical Ontologies. Pacific Symposium on Biocomputing Olivier Bodenreider, Joyce A. Mitchell, Alexa T. McCray
2005	Misc	`conf`	Utilizing the UMLS for Semantic Mapping between Terminologies. AMIA Kin Wah Fung, Olivier Bodenreider
2004	—	`conf`	Aligning Knowledge Sources in the UMLS: Methods, Quantitative Results, and Applications. MedInfo Olivier Bodenreider, Anita Burgun
2004	—	`conf`	Comparing Associative Relationships among Equivalent Concepts across Ontologies. MedInfo Songmao Zhang, Olivier Bodenreider
2004	C	`conf`	Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships. CIBCB Haiying Wang, Francisco Azuaje, Olivier Bodenreider, Joaquín Dopazo
2004	C	`conf`	Incorporating Ontology-Driven Similarity Knowledge into Functional Genomics: An Exploratory Study. BIBE Francisco Azuaje, Olivier Bodenreider
2004	Misc	`conf`	Investigating Implicit Knowledge in Ontologies with Application to the Anatomical Domain. Pacific Symposium on Biocomputing Songmao Zhang, Olivier Bodenreider
2004	—	`conf`	Investigating subsumption in DL-based terminologies: A Case Study in SNOMED CT . KR-MED Olivier Bodenreider, Barry Smith, Anand Kumar, Anita Burgun
2004	—	`conf`	Lessons learned from aligning two representations of anatomy. KR-MED Songmao Zhang, Peter Mork, Olivier Bodenreider
2004	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Olivier Bodenreider, Joyce A. Mitchell, Alexa T. McCray
2004	J	`jnl`	The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. Olivier Bodenreider
2003	Misc	`conf`	Aligning Representations of Anatomy using Lexical and Structural Methods. AMIA Songmao Zhang, Olivier Bodenreider
2003	—	`conf`	An Evaluation of Hybrid Methods for Matching Biomedical Terminologies: Mapping the Gene Ontology to the UMLS MIE Michael N. Cantor, Indra Neil Sarkar, R. Gelman, Frank W. Hartel, Olivier Bodenreider, Yves A. Lussier
2003	Misc	`conf`	Biomedical Ontologies - Session Introduction. Pacific Symposium on Biocomputing Olivier Bodenreider, Joyce A. Mitchell, Alexa T. McCray
2003	—	`conf`	Evaluation of WordNet as a source of lay knowledge for molecular biology and genetic diseases: A feasibility study. MIE Olivier Bodenreider, Anita Burgun, Joyce A. Mitchell
2003	—	`conf`	Exploring Adjectival Modification in Biomedical Discourse Across Two Genres. BioNLP@ACL Olivier Bodenreider, Sergey V. Pakhomov
2003	J	`jnl`	Exploring semantic groups through visual approaches. J. Biomed. Informatics Olivier Bodenreider, Alexa T. McCray
2003	Misc	`conf`	Graphical Visualization and Navigation of Genetic Disease Information. AMIA Olivier Bodenreider, Joyce A. Mitchell
2003	—	`conf`	Methods for Accurate Retrieval of MEDLINE Citations in Functional Genomics. TREC Mehmet Kayaalp, Alan R. Aronson, Susanne M. Humphrey, Nicholas C. Ide, Lorraine K. Tanabe, Lawrence H. Smith, Dina Demner-Fushman, Russell F. Loane, James G. Mork, Olivier Bodenreider
2003	Misc	`conf`	Strength in Numbers: Exploring Redundancy in Hierarchical Relations across Biomedical Terminologies. AMIA Olivier Bodenreider
2002	J	`jnl`	Assessing the consistency of a biomedical terminology through lexical knowledge. Int. J. Medical Informatics Olivier Bodenreider, Anita Burgun, Thomas C. Rindflesch
2002	Misc	`conf`	Evaluation of the UMLS as a terminology and knowledge resource for biomedical informatics. AMIA Olivier Bodenreider, Joyce A. Mitchell, Alexa T. McCray
2002	Misc	`conf`	From Phenotype to Genotype: Experiences in Navigating the Available Information Resources. AMIA Joyce A. Mitchell, Alexa T. McCray, Olivier Bodenreider
2002	Misc	`conf`	GenNav: Visualizing Gene Ontology as a Graph. AMIA Olivier Bodenreider
2002	Misc	`conf`	Representation of roles in biomedical ontologies: a case study in functional genomics. AMIA Anita Burgun, Olivier Bodenreider, Franck Le Duff, Fouzia Moussouni, Olivier Loréal
2002	Misc	`conf`	The lexical properties of the gene ontology. AMIA Alexa T. McCray, Allen C. Browne, Olivier Bodenreider
2002	—	`conf`	Unsupervised, corpus-based method for extending a biomedical terminology. ACL Workshop on Natural Language Processing in the Biomedical Domain Olivier Bodenreider, Thomas C. Rindflesch, Anita Burgun
2001	—	`conf`	Aggregating UMLS Semantic Types for Reducing Conceptual Complexity. MedInfo Alexa T. McCray, Anita Burgun, Olivier Bodenreider
2001	—	`conf`	An Object-oriented Model for Representing Semantic Locality in the UMLS. MedInfo Olivier Bodenreider
2001	C	`conf`	Aspects of the taxonomic relation in the biomedical domain. FOIS Anita Burgun, Olivier Bodenreider
2001	Misc	`conf`	Circular hierarchical relationships in the UMLS: etiology, diagnosis, treatment, complications and prevention. AMIA Olivier Bodenreider
2001	Misc	`conf`	Evaluating UMLS strings for natural language processing. AMIA Alexa T. McCray, Olivier Bodenreider, James D. Malley, Allen C. Browne
2001	Misc	`conf`	Mapping the UMLS Semantic Network into general ontologies. AMIA Anita Burgun, Olivier Bodenreider
2001	—	`conf`	Methods for Exploring the Semantics of the Relationships between Co-occurring UMLS Concepts. MedInfo Anita Burgun, Olivier Bodenreider
2001	—	`conf`	Natural Language Processing, Medical Terminologies, and Ontological Issues for Patient Records and Biomedical Knowledge. MedInfo Robert H. Baud, Stephen B. Johnson, Christopher G. Chute, Olivier Bodenreider, Jeremy Rogers, Anita Burgun
2000	Misc	`conf`	A Semantic Navigation Tool for the UMLS. AMIA Olivier Bodenreider
2000	Misc	`conf`	The NLM Indexing Initiative. AMIA Alan R. Aronson, Olivier Bodenreider, Florence Chang, Susanne M. Humphrey, James G. Mork, Stuart J. Nelson, Thomas C. Rindflesch, W. John Wilbur
2000	Misc	`conf`	Using UMLS semantics for classification purposes. AMIA Olivier Bodenreider
1999	Misc	`conf`	Automated Assignment of Medical Subject Headings. AMIA Stuart J. Nelson, Alan R. Aronson, Tamas E. Doszkocs, W. John Wilbur, Olivier Bodenreider, H. Florence Chang, James G. Mork, Alexa T. McCray
1998	—	`conf`	A Collaborative Approach to Building a Terminology for Medical Procedures using a Web-based Application : From Specifications to daily use. MedInfo Anita Burgun, Olivier Bodenreider, Patrick Denier, Denis Delamarre, Geneviève Botti, Philippe Oberlin, Jean-Michel Léevêque, Marc Brémond, Marius Fieschi, Pierre Le Beux
1998	Misc	`conf`	Beyond synonymy: exploiting the UMLS semantics in mapping vocabularies. AMIA Olivier Bodenreider, Stuart J. Nelson, William T. Hole, H. Florence Chang
1998	J	`jnl`	Case Report: Evaluation of the Unified Medical Language System as a Medical Knowledge Source. J. Am. Medical Informatics Assoc. Olivier Bodenreider, Anita Burgun, Geneviève Botti, Marius Fieschi, Pierre Le Beux, François Kohler
1998	—	`conf`	From French vocabulary to the Unified Medical Language System: A preliminary study. MedInfo Olivier Bodenreider, Alexa T. McCray
1998	—	`conf`	Integration of the analytical and alphabetical ICD10 in a coding help system. Proposal of a theoretical model for the ICD representation. MedInfo Christine Bouchet, Olivier Bodenreider, François Kohler
1997	J	`jnl`	Application of Information Technology: A Web Terminology Server Using UMLS for the Description of Medical Procedures. J. Am. Medical Informatics Assoc. Anita Burgun, Patrick Denier, Olivier Bodenreider, Geneviève Botti, Denis Delamarre, Bruno Pouliquen, Philippe Oberlin, Jean M. Lévéque, Bertrand Lukacs, François Kohler, Marius Fieschi, Pierre Le Beux