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2023

• Abeysinghe R, Zheng F, Bernstam EV, Shi J, Bodenreider O, Cui L.
  A deep learning approach to identify missing is-a relations in SNOMED CT.
  J Am Med Inform Assoc 2023;30(3):475-484.
   [download PDF]   [PubMed: 36539234]   [PubMedCentral: PMC9933066]  
• Fung KW, Bodenreider O.
  Knowledge representation and ontologies.
  In: Richesson RL, Andrews JE, Fultz Hollis K, editors. Clinical research informatics. 3rd ed. London: Springer International Publishing; 2023. p. 367-388.
   [download PDF]  
• Fung KW, Xu J, McConnell-Lamptey S, Pickett D, Bodenreider O.
  A practical strategy to use the ICD-11 for morbidity coding in the United States without a clinical modification.
  J Am Med Inform Assoc 2023;30(10):1614-1621.
   [download PDF]   [PubMed: 37407272]   [PubMedCentral: PMC10531107]  
• Jiménez Gutiérrez B, Mao Y, Nguyen V, Fung KW, Su Y, Bodenreider O.
  Solving the right problem is key for translational NLP: A case study in UMLS vocabulary insertion.
  Findings of the Association for Computational Linguistics: EMNLP 2023 2023:704-717.
   [download PDF]  
• Mao Y, Miller RA, Bodenreider O, Nguyen V, Fung KW.
  Two complementary AI approaches for predicting UMLS semantic group assignment: Heuristic reasoning and deep learning
  J Am Med Inform Assoc 2023;30(12):1887-1894.
   [download PDF]   [PubMed: 37528056]  

2022

• Bajaj G, Nguyen V, Wijesiriwardene T, Yip HY, Javangula V, Sheth AP, Parthasarathy S, Bodenreider O.
  Evaluating biomedical word embeddings for vocabulary alignment at scale in the UMLS Metathesaurus using Siamese networks.
  Proceedings of the Third Workshop on Insights from Negative Results in NLP 2022:82–87.
   [download PDF]   [PubMed: 36093038]   [PubMedCentral: PMC9455661]  
• Bodenreider O.
  Powering semantic analysis with bio-ontologies. [abstract]
  Companion Proceedings of the Web Conference 2022 (WWW '22) 2022:821.
   [download PDF]  
• Nguyen V, Bodenreider O.
  Adding an attention layer Improves the performance of a neural network architecture for synonymy prediction in the UMLS Metathesaurus.
  Stud Health Technol Inform (Proc Medinfo) 2022:116-119.
   [download PDF]   [PubMed: 35672982]   [PubMedCentral: PMC9484765]  
• Nguyen V, Yip HY, Bajaj G, Wijesiriwardene T, Javangula V, Parthasarathy S, Sheth AP, Bodenreider O.
  Context-enriched learning models for aligning biomedical vocabularies at scale in the UMLS Metathesaurus.
  Proceedings of the 31st The Web Conference (WWW 2022) 2022:1037–1046.
   [download PDF]   [PubMed: 36108322]   [PubMedCentral: PMC9455675]  
• Wijesiriwardene T, Nguyen V, Bajaj G, Yip HY, Javangula V, Mao Y, Fung KW, Parthasarathy S, Sheth AP, Bodenreider O.
  UBERT: A Novel language model for synonymy prediction at scale in the UMLS Metathesaurus.
  arXiv 2022:(pre-print).
   [download PDF]  
• Xu J, Fung KW, Bodenreider O.
  Sequential mapping – a novel approach to map from ICD-10-CM to ICD-11.
  Stud Health Technol Inform (Proc Medinfo) 2022:96-100.
   [download PDF]   [PubMed: 35672978]   [PubMedCentral: PMC9491349]  

2021

• Cohen KB, Ripple A, Ben Abacha A, Bodenreider O, Hargraves, Orin, Karin V, Zweigenbaum P, Demner-Fushman D.
  Reproducibility in biomedical natural language processing: A FAIR approach to what we need to know. [abstract]
  AMIA Annu Symp Proc 2021:1338-1339.
   [download PDF]  
• Fung KW, Xu J, Bodenreider O.
  Can ICD-11 replace ICD-10-CM for morbidity coding in the U.S.? [abstract]
  AMIA Annu Symp Proc 2021:1370-1371.
   [download PDF]  
• Fung KW, Xu J, McConnell-Lamptey S, Pickett D, Bodenreider O.
  Feasibility of replacing ICD-10-CM with ICD-11 for morbidity coding – A content analysis.
  J Am Med Inform Assoc 2021;28(11):2404-2411.
   [download PDF]   [PubMed: 34383897]   [PubMedCentral: PMC8510319]  
• Nguyen V, Yip HY, Bodenreider O.
  Biomedical vocabulary alignment at scale in the UMLS Metathesaurus.
  Proceedings of the 30th The Web Conference (WWW) 2021:(in press).
   [download PDF]  

2020

• Fung KW, Xu J, Bodenreider O.
  The new International Classification of Diseases 11th edition – A comparative analysis with ICD-10 and ICD-10-CM.
  J Am Med Inform Assoc 2020;27(5):738-746.
   [download PDF]   [PubMed: 32364236]   [PubMedCentral: PMC7309235]  

• Tran TTT, Nghiem SV, Le VT, Quan TT, Nguyen V, Yip HY, Bodenreider O.
  Siamese KG-LSTM: A deep learning model for enriching UMLS Metathesaurus synonymy.
  Proceedings of the 12th International Conference on Knowledge and Systems Engineering (KSE) 2020:281-286.
   [download PDF]  

• Vasilakes J, Bompelli A, Bishop JR, Adam TJ, Bodenreider O, Zhang R.
  Assessing the enrichment of dietary supplement coverage in the UMLS.
  J Am Med Inform Assoc 2020:(in press).
   [download PDF]  

2019

• Bodenreider O, Nikiema J-N.
  Comparing the representation of medicinal products in RxNorm and SNOMED CT – Consequences on interoperability. [abstract]
  SNOMED CT Expo 2019:(https://confluence.ihtsdotools.org/pages/viewpage.action?pageId=87042679).
   [download PDF]  

• Kho SJ, Sheth A, Bodenreider O.
  Automatic identification of individual drugs in death certificates.
  Stud Health Technol Inform (Proc Medinfo) 2019;21(264):183-187.
   [download PDF]   [PubMed: 31437910]  

• Nguyen V, Yip HY, Thakkar H, Li Q, Bolton E, Bodenreider O.
  Singleton Property Graph: Adding a Semantic Web abstraction layer to graph databases.
  Proceedings of the Second International Workshop on Contextualized Knowledge Graphs (CKG 2019) 2019:(electronic proceedings: https://wiki.foodmedy.com/index.php?title=File:CKG2019_paper_4.pdf).
   [download PDF]  

• Nikiema J-N, Bodenreider O.
  Comparing the representation of medicinal products in RxNorm and SNOMED CT – Consequences on interoperability.
  Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019) 2019:(electronic proceedings: https://drive.google.com/file/d/1ZTDH-vWUvCqBCyOPY5f97L6L7fb4HRWA/).
   [download PDF]  

• Vasilakes J, Fan Y, Rizvi R, Bompelli A, Zhang R, Bodenreider O.
  Normalizing dietary supplement product names using the RxNorm model.
  Stud Health Technol Inform (Proc Medinfo) 2019;21(264):408-412.
   [download PDF]   [PubMed: 31437955]   [PubMedCentral: PMC6792000]  

• Yip HY, Nguyen V, Bodenreider O.
  Construction of UMLS Metathesaurus with knowledge-infused deep learning.
  Proceedings of the Second International Workshop on Contextualized Knowledge Graphs (CKG 2019) 2019:(electronic proceedings: https://wiki.foodmedy.com/index.php?title=File:CKG2019_paper_3.pdf).
   [download PDF]  

2018

• Bodenreider O.
  Evaluating the quality and interoperability of biomedical terminologies.
  Technical report. Bethesda, Maryland: Lister Hill National Center for Biomedical Communications, National Library of Medicine; April 5, 2018.
   [download PDF]  

• Bodenreider O, Cornet R, Vreeman DJ.
  Recent developments in clinical terminologies – SNOMED CT, LOINC and RxNorm.
  Yearb Med Inform 2018;27(1):129-139.
   [download PDF]   [PubMed: 30157516]   [PubMedCentral: PMC6115234]  

• Bodenreider O, James J.
  The new SNOMED CT international medicinal product model.
  Proceedings of the 7th International Conference on Biomedical Ontology (ICBO 2018) 2018:(electronic proceedings: http://ceur-ws.org/Vol-2285/ICBO_2018_paper_36.pdf).
   [download PDF]  

• Bodenreider O, Peters LB.
  Using RxNav for drug analytics – How to interpret obsolete drug identifiers? [demo]
  AMIA Annu Symp Proc 2018:2229.
   [download PDF]  

• Callahan TJ, Bodenreider O, Kahn MG.
  Towards patient-driven phenotyping and similarity for precision medicine. [abstract]
  AMIA Jt Summits Transl Sci Proc 2018;TBI:261-262.
   [download PDF]  

• Cholan RA, Bodenreider O.
  Interoperability between value sets for clinical research and healthcare: Mapping value sets between the Clinical Data Interchange Standards Consortium (CDISC) and Meaningful Use. [abstract]
  AMIA Jt Summits Transl Sci Proc 2018;CRI:426-427.
   [download PDF]  

• Cui L, Bodenreider O, Shi J, Zhang G-Q.
  Auditing SNOMED CT hierarchical relations based on lexical features of concepts in non-lattice subgraphs.
  Journal of Biomedical Informatics 2018;78:177-184.
   [download PDF]   [PubMed: 29274386]   [PubMedCentral: PMC5835197]  

• Fung KW, Bodenreider O.
  Knowledge representation and ontologies.
  In: Richesson RL, Andrews JE, editors. Clinical research informatics. London: Springer International Publishing; 2018. p. 313-339.
   [download PDF]  

• Pedersen JG, Gardner B, Campbell JR, Campbell WS, Geary C, Peters L, Bodenreider O, McClay JC.
  Historically comprehensive medications metadata for i2b2 data warehouses. [abstract]
  AMIA Annu Symp Proc 2018:1806-1807.
   [download PDF]  

• Peters LB, Rice R, Bodenreider O.
  RxNav-in-a-Box – A locally-installable version of RxNav and related APIs. [poster]
  AMIA Annu Symp Proc 2018:2102.
   [download PDF]  

• Raje S, Bodenreider O.
  Interoperability of disease concepts in clinical and research ontologies – Contrasting coverage and structure in the Disease Ontology and SNOMED CT. [abstract]
  SNOMED CT Expo 2018:(electronic proceedings: https://drive.google.com/file/d/1hRwts7ezsZjThd568G925RC7aB_S5XxN/view).
   [download PDF]  

2017

• Bahr NJ, Nelson SD, Winnenburg R, Bodenreider O.
  Eliciting the intension of drug value sets – Principles and quality assurance applications.
  Stud Health Technol Inform (Proc Medinfo) 2017:843-847.
   [download PDF]   [PubMed: 29295218]   [PubMedCentral: PMC5881398]  

• Bhupatiraju RT, Fung KW, Bodenreider O.
  MetaMapLite in Excel: Biomedical named-entity recognition for non-technical users. [poster]
  Stud Health Technol Inform (Proc Medinfo) 2017:1252.
   [download PDF]   [PubMed: 29295337]   [PubMedCentral: PMC5884681]  

• Bodenreider O.
  Identifying missing hierarchical relations in SNOMED CT from logical definitions based on the lexical features of concept names. [abstract]
  SNOMED CT Expo 2017:(electronic proceedings: https://confluence.ihtsdotools.org/pages/viewpage.action?pageId=47685600&preview=/47685600/47685601/OBO_2017-snomedct_expo-ob-abstract.docx).
   [download PDF]  

• Bodenreider O, Peters LB.
  RxNorm concept history service. [poster]
  AMIA Annu Symp Proc 2017:1955.
   [download PDF]  

• Bodenreider O, Peters LB.
  RxMix – Use of NLM drug APIs by non-programmers. [demo]
  AMIA Annu Symp Proc 2017:2291.
   [download PDF]  

• Cui L, Zhu W, Tao S, Case JT, Bodenreider O, Zhang GQ.
  Mining non-lattice subgraphs for detecting missing hierarchical relations and concepts in SNOMED CT.
  J Am Med Inform Assoc 2017;24(4):788-798.
   [download PDF]   [PubMed: 28339775]   [PubMedCentral: PMC6080685]  

• Dhombres F, Bodenreider O.
  Trends in fetal medicine: A 10-year bibliometric analysis of Prenatal Diagnosis.
  Stud Health Technol Inform (Proc Medinfo) 2017:853-857.
   [download PDF]   [PubMed: 29295220]   [PubMedCentral: PMC5884683]  

• Fung KW, Kapusnik-Uner JE, Cunningham J, Higby-Baker S, Bodenreider O.
  Comparison of three commercial knowledge bases for detection of drug-drug interactions in clinical decision support.
  J Am Med Inform Assoc 2017;24(4):806-812.
   [download PDF]   [PubMed: 28339701]   [PubMedCentral: PMC6080681]  

• Harpaz R, DuMouchel W, Schuemie M, Bodenreider O, Friedman C, Horvitz E, Ripple A, Sorbello A, White RW, Winnenburg R, Shah NH.
  Toward multimodal signal detection of adverse drug reactions.
  Journal of Biomedical Informatics 2017;76:41-49.
   [download PDF]   [PubMed: 29081385]  

• Kury FSP, Bodenreider O.
  Mapping U.S. FDA National Drug Codes to Anatomical-Therapeutic-Chemical classes using RxNorm. [poster]
  AMIA Annu Symp Proc 2017:2070.
   [download PDF]  

• Nelson SD, Parker J, Lario R, Winnenburg R, Erlbaum MS, Lincoln MJ, Bodenreider O.
  Interoperability of medication classification systems: Lessons learned mapping established pharmacologic classes (EPCs) to SNOMED CT.
  Stud Health Technol Inform (Proc Medinfo) 2017:920-924.
   [download PDF]   [PubMed: 29295234]   [PubMedCentral: PMC5881380]  

• Peters LB, Bodenreider O.
  RxNav 2.0 – A web-based, mobile-responsive RxNorm browser. [poster]
  AMIA Annu Symp Proc 2017:2143.
   [download PDF]  

• Peters LB, Nguyen T, Bodenreider O.
  Terminology status APIs – Mapping obsolete codes to current RxNorm, SNOMED CT and LOINC concepts. [poster]
  Stud Health Technol Inform (Proc Medinfo) 2017:1333.
   [download PDF]   [PubMed: 29295414]   [PubMedCentral: PMC5875440]  

• Raje S, Bodenreider O.
  Interoperability of disease concepts in clinical and research ontologies – Contrasting coverage and structure in the Disease Ontology and SNOMED CT.
  Stud Health Technol Inform (Proc Medinfo) 2017:925-929.
   [download PDF]   [PubMed: 29295235]   [PubMedCentral: PMC5881393]  

• Raje S, Bodenreider O.
  Investigating the coverage of diseases across biomedical research and clinical ontologies. [abstract]
  AMIA Jt Summits Transl Sci Proc 2017;CRI:384-385.
   [download PDF]  

• Raje S, Bodenreider O.
  Identifying potentially missing hierarchical relations in SNOMED CT based on lexical features – Impact of synonyms and lexico-syntactic constraints. [abstract]
  AMIA Annu Symp Proc 2017:163-164.
   [download PDF]  

• Sawarkar A, Sorbello A, Ripple A, Bodenreider O.
  Detecting adverse drug event safety signals from MEDLINE reports: Challenges in employing cross-terminology mapping of MeSH to MedDRA. [poster]
  AMIA Annu Symp Proc 2017:2175.
   [download PDF]  

• Sorbello A, Ripple A, Tonning J, Munoz M, Hasan R, Ly T, Francis H, Bodenreider O.
  Harnessing scientific literature reports for pharmacovigilance: Prototype software analytical tool development and usability testing.
  Applied Clinical Informatics 2017;8(1):291-305.
   [download PDF]   [PubMed: 28326432]   [PubMedCentral: PMC5373771]  

• 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 (Proc Medinfo) 2017:662-666.
   [download PDF]   [PubMed: 29295179]   [PubMedCentral: PMC5875427]  

2016

• 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:(electronic proceedings: http://ceur-ws.org/Vol-1747/IT601_ICBO2016.pdf).
   [download PDF]  

• Bodenreider O, Peters LB.
  Characterizing the semantic composition of the UMLS Metathesaurus over time. [poster]
  AMIA Annu Symp Proc 2016:1346.
   [download PDF]  

• Cui L, Zhu W, Tao S, Case JT, Bodenreider O, Zhang GQ.
  Detecting misaligned and missing concepts in SNOMED CT using structural and lexical patterns. [abstract]
  SNOMED CT Expo 2016:(electronic proceedings: https://confluence.ihtsdotools.org/pages/viewpage.action?pageId=29950393&preview=/29950393/29950394/201639_OBO_2016-snomedct_expo-lc-abstract_v2.docx).
   [download PDF]  

• Dhombres F, Bodenreider O.
  Interoperability between phenotypes in research and healthcare terminologies – Investigating partial mappings between HPO and SNOMED CT.
  J Biomed Semantics 2016;7(3).
   [download PDF]   [PubMed: 26865946]   [PubMedCentral: PMC4748471]  

• Dhombres F, Bodenreider O.
  Assessing the potential risk in drug prescriptions during pregnancy. [abstract]
  AMIA Annu Symp Proc 2016:45-46.
   [download PDF]  

• Dhombres F, Bodenreider O.
  Investigating partial mappings between HPO and SNOMED CT. [poster]
  SNOMED CT Expo 2016:(electronic proceedings: https://confluence.ihtsdotools.org/pages/viewpage.action?pageId=29952466&preview=/29952466/29952465/201638_OBO_2016-snomedct_expo-fd-abstract_v2.docx).
   [download PDF]  

• Fung KW, Richesson RL, Smerek M, Pereira KC, Green BB, Patkar A, Clowse M, Bauck A, Bodenreider O.
  Preparing for the ICD-10-CM Transition: Automated methods for translating ICD codes in clinical phenotype definitions.
  eGEMs Journal 2016;4(1):Article 4.
   [download PDF]   [PubMed: 27195309]   [PubMedCentral: PMC4862764]  

• Homer ML, Palmer NP, Bodenreider O, Cami A, Chadwick L, Mandl KD.
  The drug data to knowledge pipeline: Large-scale claims data classification for pharmacologic insight.
  AMIA Jt Summits Transl Sci Proc 2016;CRI:105-110.
   [download PDF]   [PubMed: 27570659]   [PubMedCentral: PMC5001754]  

• Huser V, Bodenreider O.
  Exploring the use of ClinicalTrials.gov trial results data for pharmacovigilance. [poster]
  AMIA Annu Symp Proc 2016:1440.
   [download PDF]  

• Kury FSP, Bodenreider O.
  Desiderata for drug classification systems for their use in analyzing large drug prescription datasets.
  Proceedings of the 3rd Workshop on Data Mining for Medical Informatics (DMMI 2016) 2016.
   [download PDF]  

• Peters LB, Bodenreider O.
  NDC properties in RxNorm. [poster]
  AMIA Annu Symp Proc 2016:1551.
   [download PDF]  

• Ripple A, Sorbello A, Bodenreider O.
  PubMed ‘Early Alerts’: Towards better precision of literature searching for pharmacovigilance information based on an assessment of relevance feedback. [poster]
  AMIA Annu Symp Proc 2016:1569.
   [download PDF]  

• Yaniv Z, Faruque J, Howe S, Dunn K, Sharlip D, Bond A, Perillan P, Bodenreider O, Ackerman MJ, Yoo TS.
  The National Library of Medicine pill image recognition challenge: An initial report.
  Proceedings of the 47th IEEE Applied Imagery Pattern Recognition (AIPR) annual workshop 2016:(electronic proceedings).
   [download PDF]   [PubMed: 29854569]   [PubMedCentral: PMC5973812]  

2015

• Bodenreider O, Peters LB, Nguyen T.
  Navigating between drug classes and RxNorm drugs with RxClass. [demo]
  AMIA Annu Symp Proc 2015:2132.
   [download PDF]  

• Cameron D, Kavuluru R, Rindflesch TC, Sheth AP, Thirunarayan K, Bodenreider O.
  Context-driven automatic subgraph creation for literature-based discovery.
  Journal of Biomedical Informatics 2015;54:141-157.
   [download PDF]   [PubMed: 25661592]   [PubMedCentral: PMC4888806]  

• Dhombres F, Bodenreider O.
  Investigating the lexico-syntactic properties of phenotype terms – Application to interoperability between HPO and SNOMED CT.
  Proceedings of the Joint Bio-Ontologies and BioLINK ISMB'2015 SIG session "Phenotype Day" 2015:8-11.
   [download PDF]  

• Dhombres F, Winnenburg R, Case JT, Bodenreider O.
  Extending the coverage of phenotypes in SNOMED CT through post-coordination.
  Stud Health Technol Inform (Proc Medinfo) 2015:795-799.
   [download PDF]   [PubMed: 26262161]   [PubMedCentral: PMC5875691]  

• Dhombres F, Winnenburg R, Case JT, Bodenreider O.
  Extending the coverage of phenotypes in SNOMED CT through post-coordination. [abstract]
  SNOMED CT Implementation Showcase 2015:(electronic proceedings: https://confluence.ihtsdotools.org/download/attachments/12780103/7_O%20Bodenreider_2015-snomedct_expo-fd-abstract.pdf).
   [download PDF]  

• Fu G, Bolton E, Rosinach NQ, Furlong LI, Nguyen V, Sheth AP, Bodenreider O, Dumontier M.
  Exposing provenance metadata using different RDF models.
  Proceedings of the International Conference on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2015) 2015:(electronic proceedings: http://www.swat4ls.org/wp-content/uploads/2015/10/SWAT4LS_2015_paper_11.pdf).
   [download PDF]  

• Nguyen T, Peters LB, Bodenreider O.
  Finding similar drug classes using RxClass. [poster]
  AMIA Annu Symp Proc 2015:1615.
   [download PDF]  

• Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon A-M, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M.
  The digital revolution in phenotyping.
  Briefings in Bioinformatics 2015;17(5):819-830.
   [download PDF]   [PubMed: 26420780]   [PubMedCentral: PMC5036847]  

• Peters LB, Bahr N, Bodenreider O.
  Evaluating drug-drug interaction information in NDF-RT and DrugBank.
  J Biomed Semantics 2015;6(19).
   [download PDF]   [PubMed: 25964850]   [PubMedCentral: PMC4426554]  

• Peters LB, Bodenreider O.
  Approaches to supporting the analysis of historical medication datasets with RxNorm.
  AMIA Annu Symp Proc 2015:1034-1041.
   [download PDF]   [PubMed: 26958241]   [PubMedCentral: PMC4765580]  

• Rance B, Le T, Bodenreider O.
  Fingerprinting biomedical terminologies – Automatic classification and visualization of biomedical vocabularies through UMLS semantic group profiles.
  Stud Health Technol Inform (Proc Medinfo) 2015:771-775.
   [download PDF]   [PubMed: 26262156]   [PubMedCentral: PMC5881385]  

• Sorbello A, Ripple A, Bodenreider O.
  PubMed ‘Early Alerts’: A pilot study to support prospective detection of emerging adverse drug events. [poster]
  AMIA Annu Symp Proc 2015:1699.
   [download PDF]  

• Tao S, Cui L, Zhu W, Sun M, Bodenreider O, Zhang G-Q.
  Mining relation reversals in the evolution of SNOMED CT.
  AMIA Jt Summits Transl Sci Proc 2015;TBI:46-50.
   [download PDF]   [PubMed: 26306232]   [PubMedCentral: PMC4525241]  

• Winnenburg R, Mortensen J, Bodenreider O.
  Using description logics to evaluate the consistency of drug-class membership relations in NDF-RT.
  J Biomed Semantics 2015;6(13).
   [download PDF]   [PubMed: 25866612]   [PubMedCentral: PMC4392727]  

• Winnenburg R, Sorbello A, Bodenreider O.
  Exploring adverse drug events at the class level.
  J Biomed Semantics 2015;6(18).
   [download PDF]   [PubMed: 25937884]   [PubMedCentral: PMC4416343]  

• Winnenburg R, Sorbello A, Ripple A, Harpaz R, Tonning J, Szarfman A, Francis H, Bodenreider O.
  Leveraging MEDLINE indexing for pharmacovigilance – inherent limitations and mitigation strategies.
  Journal of Biomedical Informatics 2015;57:425–435.
   [download PDF]   [PubMed: 26342964]   [PubMedCentral: PMC4775467]  

2014

• Bodenreider O, Peters LB, Nguyen T.
  RxClass – Navigating between Drug Classes and RxNorm Drugs. [demo]
  Proceedings of the 5th International Conference on Biomedical Ontology 2014:106-107 (electronic proceedings: http://ceur-ws.org/Vol-1327/).
   [download PDF]  

• Bodenreider O, Rodriguez LM.
  Analyzing U.S. prescription lists with RxNorm and the ATC/DDD Index.
  AMIA Annu Symp Proc 2014:297-306.
   [download PDF]   [PubMed: 25954332]   [PubMedCentral: PMC4419961]  

• Bodenreider O, Winnenburg R.
  Drug terminology and ontology – Integration, dissemination, quality assurance and applications.
  Technical report. Bethesda, Maryland: Lister Hill National Center for Biomedical Communications, National Library of Medicine; September 18, 2014.
   [download PDF]  

• Fung KW, Richesson RL, Bodenreider O.
  Coverage of rare disease names in standard terminologies and implications for patients, providers, and research.
  AMIA Annu Symp Proc 2014:564-570.
   [download PDF]   [PubMed: 25954361]   [PubMedCentral: PMC4419993]  

• Harpaz R, Odgers D, Gaskin G, DuMouchel W, Winnenburg R, Bodenreider O, Ripple A, Szarfman A, Sorbello A, Horvitz E, White RW, Shah NH.
  A time-indexed reference standard of adverse drug reactions.
  Nature Scientific Data 2014;1:140043.
   [download PDF]   [PubMed: 25632348]   [PubMedCentral: PMC4306188]  

• Khatipov E, Madden M, Chiang P, Chuang P, Nguyen D, D’Souza I, Winnenburg R, Bodenreider O, Skapik J, McClure R, Emrick S.
  Creating, maintaining and publishing value sets in the VSAC. [poster]
  AMIA Annu Symp Proc 2014:1459.
   [download PDF]  

• Nguyen T, Peters LB, Bodenreider O.
  RxClass - Navigating between drug classes and RxNorm drugs. [poster]
  AMIA Annu Symp Proc 2014:1529.
   [download PDF]  

• Nguyen V, Bodenreider O, Sheth AP.
  Don’t like RDF reification? Making statements about statements using singleton property.
  Proceedings of the 23rd International World Wide Web Conference (WWW 2014) 2014:759-770.
   [download PDF]   [PubMed: 25750938]   [PubMedCentral: PMC4350149]  

• Richesson RL, Fung KW, Bodenreider O.
  Coverage of rare disease names in cinical coding systems and ontologies and implications for electronic health records-based research. [poster]
  Proceedings of the 5th International Conference on Biomedical Ontology 2014:78-80 (electronic proceedings: http://ceur-ws.org/Vol-1327/).
   [download PDF]  

• Rodriguez LM, Huser V, Bodenreider O, Cimino JJ.
  Automatic coding of free-text medication data recorded by research coordinators. [poster]
  AMIA Annu Symp Proc 2014:1565.
   [download PDF]  

• Sorbello A, Harpaz R, Szarfman A, Bodenreider O, Winnenburg R, Ripple A, Tonning J, Francis H.
  Detecting drug-adverse event safety signals through quantitative data mining of MEDLINE indexing terms: A pilot study. [poster]
  Poster presented at the 54th Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC 2014) 2014.
   [download PDF]  

• Stan J, Demner-Fushman D, Fung KW, Bodenreider O.
  Facilitating reconciliation of inter-annotator disagreements. [poster]
  AMIA Annu Symp Proc 2014:1596.
   [download PDF]  

• Winnenburg R, Bodenreider O.
  A framework for assessing the consistency of pharmacological classes across sources.
  J Biomed Semantics 2014;5(30).
   [download PDF]   [PubMed: 25101165]   [PubMedCentral: PMC4120719]  

• Winnenburg R, Bodenreider O.
  Desiderata for an authoritative representation of MeSH in RDF.
  AMIA Annu Symp Proc 2014:1218-1227.
   [download PDF]   [PubMed: 25954433]   [PubMedCentral: PMC4419968]  

• Winnenburg R, Bodenreider O.
  Evaluating the consistency of inferred drug-class membership relations in NDF-RT.
  Proceedings of the 17th ISMB'2014 SIG meeting "Bio-Ontologies" 2014:(electronic proceedings: https://drive.google.com/file/d/0B6AZUdKw1IVHeGVtTVZCRXJhbFk/).
   [download PDF]  

• Winnenburg R, Bodenreider O.
  Coverage of phenotypes in standard terminologies.
  Proceedings of the Joint Bio-Ontologies and BioLINK ISMB'2014 SIG session "Phenotype Day" 2014:41-44.
   [download PDF]  

• Winnenburg R, Bodenreider O.
  Coverage of human phenotypes in SNOMED CT. [abstract]
  SNOMED CT Implementation Showcase 2014:(electronic proceedings: http://ihtsdo.org/show14/abstract_024.pdf).
   [download PDF]  

• Zhang G-Q, Zhu W, Sun M, Tao S, Bodenreider O, Cui L.
  MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and its application to SNOMED CT.
  Proceedings of the IEEE International Conference on Big Data 2014 (IEEE BigData 2014) 2014:754-759.
   [download PDF]   [PubMed: 25705725]   [PubMedCentral: PMC4334137]  

2013

• Balkanyi L, Schulz S, Cornet R, Bodenreider O.
  Medical concept representation, the years beyond 2000. [poster]
  Stud Health Technol Inform (Proc Medinfo) 2013;192:1011.
   [download PDF]   [PubMed: 23920785]   [PubMedCentral: PMC4300111]  

• Bodenreider O.
  Disease ontology.
  In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H, editors. Encyclopedia of Systems Biology: Springer; 2013. p. 578-581.
   [download PDF]  

• Bodenreider O.
  Multi-lingual features of the Unified Medical Language System. [abstract]
  Proceedings of the CLEF-ER 2013 workshop 2013:(electronic proceedings: http://www.clef2013.org/index.php?page=Pages/proceedings.php).
   [download PDF]  

• Bodenreider O, Nguyen D, Chiang P, Chuang P, Madden M, Winnenburg R, McClure R, Emrick S, D’Souza I.
  The NLM value set authority center. [poster]
  Stud Health Technol Inform (Proc Medinfo) 2013;192:1224.
   [download PDF]   [PubMed: 23920998]   [PubMedCentral: PMC4300102]  

• 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.
  Journal of Biomedical Informatics 2013;46(2):238-251.
   [download PDF]   [PubMed: 23026233]   [PubMedCentral: PMC4031661]  

• Emrick S, Nguyen D, Chiang P, Chuang P, Madden M, Winnenburg R, McClure R, D’Souza I, Bodenreider O.
  The NLM Value Set Authority Center at 1 year. [poster]
  AMIA Annu Symp Proc 2013:390.
   [download PDF]  

• Le T, Rance B, Bodenreider O.
  Network visualization of UMLS source vocabularies using semantic groups. [poster]
  AMIA Annu Symp Proc 2013:90.
   [download PDF]  

• Peters LB, Bodenreider O.
  SNOMED CT Status Web Service. [poster]
  SNOMED CT Implementation Showcase 2013:(electronic proceedings: http://ihtsdo.org/show13/abstract47.pdf).
   [download PDF]  

• Peters LB, Mortensen J, Nguyen T, Bodenreider O.
  Enabling complex queries to drug information sources through functional composition.
  Stud Health Technol Inform (Proc Medinfo) 2013;192:692-696.
   [download PDF]   [PubMed: 23920645]   [PubMedCentral: PMC4303373]  

• Peters LB, Nguyen T, Bodenreider O.
  Displaying drug classes in RxNav. [poster]
  AMIA Annu Symp Proc 2013:1134.
   [download PDF]  

• Rance B, Snyder M, Lewis J, Bodenreider O.
  Leveraging terminological resources for mapping between rare disease information sources.
  Stud Health Technol Inform (Proc Medinfo) 2013;192:529-533.
   [download PDF]   [PubMed: 23920611]   [PubMedCentral: PMC4296515]  

• Schulz S, Balkanyi L, Cornet R, Bodenreider O.
  From concept representations to ontologies: A paradigm shift in health informatics?
  Healthcare Informatics Research 2013;19(4):235-242.
   [download PDF]   [PubMed: 24523987]   [PubMedCentral: PMC3920035]  

• Winnenburg R, Bodenreider O.
  Exploring pharmacoepidemiologic groupings of drugs from a clinical perspective.
  Stud Health Technol Inform (Proc Medinfo) 2013;192:827-831.
   [download PDF]   [PubMed: 23920673]   [PubMedCentral: PMC4304656]  

• Winnenburg R, Bodenreider O.
  Metrics for assessing the quality of value sets in clinical quality measures.
  AMIA Annu Symp Proc 2013:1497-1505.
   [download PDF]   [PubMed: 24551422]   [PubMedCentral: PMC3900160]  

• Winnenburg R, Bodenreider O.
  Criteria and metrics for assessing the quality of SNOMED CT value sets in clinical quality measures. [poster]
  SNOMED CT Implementation Showcase 2013:(electronic proceedings: http://ihtsdo.org/show13/abstract54.pdf).
   [download PDF]  

• Winnenburg R, Rodriguez LM, Callaghan F, Sorbello A, Szarfman A, Bodenreider O.
  Aligning pharmacologic classes between MeSH and ATC.
  Proceedings of the International Workshop on Vaccine and Drug Ontology Studies (VDOS 2013) 2013:(electronic proceedings: http://www2.unb.ca/csas/data/ws/semantic-trilogy-workshops/papers/ICBO-Workshops.pdf).
   [download PDF]  

2012

• Adamusiak T, Bodenreider O.
  Quality assurance in LOINC using description logic.
  AMIA Annu Symp Proc 2012:1099-1108.
   [download PDF]   [PubMed: 23304386]   [PubMedCentral: PMC3540427]  

• Fung KW, Bodenreider O.
  Knowledge representation and ontologies.
  In: Richesson RL, Andrews JE, editors. Clinical research informatics. London: Springer-Verlag; 2012. p. 255-275.
   [download PDF]  

• Grabar N, Hamon T, Bodenreider O.
  Ontologies and terminologies: Continuum or dichotomy. [editorial]
  Applied Ontology 2012;7(4):375-386.
   [download PDF]  

• Mougin F, Burgun A, Bodenreider O.
  Comparing drug-class membership in ATC and NDF-RT.
  Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2012) 2012:437-443.
   [download PDF]  

• Nguyen V, Bodenreider O, Rindflesch TC, Sheth AP.
  iExplore: A provenance-based application for exploring biomedical knowledge. [poster]
  Poster Proceedings of the Eighth International Conference on Data Integration in the Life Sciences (DILS 2012) 2012:18.
   [download PDF]  

• Peters LB, Nguyen T, Bodenreider O.
  RxBatch – Batch operations for RxNorm and NDF-RT APIs. [poster]
  AMIA Annu Symp Proc 2012:1897.
   [download PDF]  

• Rance B, Bodenreider O.
  A multi-factor approach to identifying missed synonymy in the UMLS. [poster]
  Poster Proceedings of the Eighth International Conference on Data Integration in the Life Sciences (DILS 2012) 2012:20.
   [download PDF]  

• Rance B, Doughty E, Demner-Fushman D, Kann MG, Bodenreider O.
  A mutation-centric approach to identifying pharmacogenomic relations in text.
  Journal of Biomedical Informatics 2012;45(5):835-841.
   [download PDF]   [PubMed: 22683993]   [PubMedCentral: PMC3438287]  

• Winnenburg R, Bodenreider O.
  Issues in creating and maintaining value sets for clinical quality measures.
  AMIA Annu Symp Proc 2012:988-996.
   [download PDF]   [PubMed: 23304374]   [PubMedCentral: PMC3540585]  

• Winnenburg R, Bodenreider O.
  Mapping drug entities between the European and American standards, ATC and RxNorm. [poster]
  Poster Proceedings of the Eighth International Conference on Data Integration in the Life Sciences (DILS 2012) 2012:22.
   [download PDF]  

2011

• Bodenreider O, Peters LB, Nguyen T.
  RxNav: Browser and application programming interfaces for drug information sources. [demo]
  AMIA Annu Symp Proc 2011:2129.
   [download PDF]  

• Cameron D, Kavuluru R, Bodenreider O, Mendes PN, Sheth AP, Thirunarayan K.
  Semantic predications for complex information needs in biomedical literature.
  Proceedings of the 5th IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011) 2011:512-519.
   [download PDF]   [PubMed: 25699291]   [PubMedCentral: PMC4330970]  

• Doughty E, Kertesz-Farkas A, Bodenreider O, Thompson G, Adadey A, Peterson T, Kann MG.
  Toward an automatic method for extracting cancer- and other disease-related mutations from the biomedical literature.
  Bioinformatics 2011;27(3):408-415.
   [download PDF]   [PubMed: 21138947]   [PubMedCentral: PMC3031038]  

• Doughty E, Kirk B, Kann MG, Bodenreider O.
  Integrating drug-gene associations mined from the literature with drug information sources -- A comparison with PharmGKB. [abstract]
  Proceedings of the 2011 PSB Workshop on Mining the Pharmacogenomics Literature 2011:(electronic proceedings).
   [download PDF]  

• Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall MS, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M.
  The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside.
  J Biomed Semantics 2011;2(2(Suppl 2)):S1.
   [download PDF]   [PubMed: 21624155]   [PubMedCentral: PMC3102889]  

• Nguyen V, Bodenreider O, Minning T, Sheth AP.
  The knowledge-driven exploration of integrated biomedical knowledge sources facilitates the generation of new hypotheses.
  Proceedings of the First International Workshop on Linked Science (LISC 2011) 2011:(electronic proceedings: http://ceur-ws.org/Vol-783/).
   [download PDF]  

• Peters LB, Kapusnik-Uner JE, Nguyen T, Bodenreider O.
  An approximate matching method for clinical drug names.
  AMIA Annu Symp Proc 2011:1117-1126.
   [download PDF]   [PubMed: 22195172]   [PubMedCentral: PMC3243188]  

• Peters LB, Nguyen T, Bodenreider O.
  An application programming interface for NDF-RT. [poster]
  AMIA Annu Symp Proc 2011:1922.
   [download PDF]  

• Rance B, Demner-Fushman D, Rindflesch TC, Bodenreider O.
  Exploring automatic approaches to extracting pharmacogenomic information from the biomedical literature. [abstract]
  Proceedings of the 2011 PSB Workshop on Mining the Pharmacogenomics Literature 2011:(electronic proceedings).
   [download 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;29(12).
   [download PDF]   [PubMed: 22126369]   [PubMedCentral: PMC3298549]  

2010

• Bodenreider O.
  Quality assurance in biomedical terminologies and ontologies.
  Technical report. Bethesda, Maryland: Lister Hill National Center for Biomedical Communications, National Library of Medicine; April 8, 2010.
   [download PDF]  

• Bodenreider O, Burgun A.
  A framework for comparing phenotype annotations of orthologous genes.
  Stud Health Technol Inform (Proc Medinfo) 2010;160:1309-1313.
   [download PDF]   [PubMed: 20841896]   [PubMedCentral: PMC4300101]  

• Bodenreider O, Demner-Fushman D.
  Investigating drug classes in biomedical terminologies from the perspective of clinical decision support.
  AMIA Annu Symp Proc 2010:56-60.
   [download PDF]   [PubMed: 21346940]   [PubMedCentral: PMC3041355]  

• Bodenreider O, Mougin F, Burgun A.
  Automatic determination of anticoagulation status with NDF-RT.
  Proceedings of the 13th ISMB'2010 SIG meeting "Bio-ontologies" 2010:140-143.
   [download PDF]  

• Bodenreider O, Peters LB.
  RxNav: Browser and application programming interfaces for RxNorm. [demo]
  AMIA Annu Symp Proc 2010:1330.
   [download PDF]  

• Cardillo E, Hernandez Jr G, Bodenreider O.
  Integrating consumer-oriented vocabularies with selected professional ones from the UMLS using Semantic Web Technologies.
  Proceedings of the eHealth 2010 conference 2010:(paper 10579 - electronic proceedings).
   [download PDF]  

• Dumontier M, Andersson B, Batchelor C, Domarew C, Jentzsch A, Luciano JS, Pichler E, Prud'hommeaux E, Whetzel PL, Bodenreider O, Clark T, Harland L, Kashyap V, Kos P, Kozlovsky J, McGurk J, Ogbuji C, Samwald M, Schriml L, Tonellato PJ, Zhao J, Stephens S.
  The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench.
  Proceedings of the 13th ISMB'2010 SIG meeting "Bio-ontologies" 2010:120-123.
   [download PDF]  

• Erdoğan H, Bodenreider O, Erdem E.
  Finding semantic inconsistencies in UMLS using Answer Set Programming. [poster]
  Proceedings of the Twenty-Fourth AAAI Conference on Artificial Intelligence 2010:1927-1928.
   [download PDF]  

• Erdoğan H, Erdem E, Bodenreider O.
  Exploiting UMLS semantics for checking semantic consistency among UMLS concepts.
  Stud Health Technol Inform (Proc Medinfo) 2010;160:749-753.
   [download PDF]   [PubMed: 20841786]   [PubMedCentral: PMC4303374]  

• Fiszman M, Bray BE, Shin D, Kilicoglu H, Bennett GC, Bodenreider O, Rindflesch TC.
  Combining relevance assignment with quality of the evidence to support guideline development.
  Stud Health Technol Inform (Proc Medinfo) 2010;160:709-713.
   [download PDF]   [PubMed: 20841778]   [PubMedCentral: PMC4296513]  

• Mork JG, Bodenreider O, Demner-Fushman D, Dogan RI, Lang F-M, Lu Z, Névéol A, Peters LB, Shooshan SE, Aronson AR.
  Extracting Rx Information from clinical narrative.
  J Am Med Inform Assoc 2010;17(5):536-239.
   [download PDF]   [PubMed: 20819859]   [PubMedCentral: PMC2995679]  

• Mortensen J, Bodenreider O.
  Comparing pharmacologic classes in NDF-RT and SNOMED CT.
  Proceedings of the Fourth International Symposium on Semantic Mining in Biomedicine (SMBM 2010) 2010:116-121 (electronic proceedings: http://ceur-ws.org/Vol-714/).
   [download PDF]  

• Mougin F, Bodenreider O, Burgun A.
  Looking for anemia (and other disorders) in SNOMED CT: Comparison of three approaches and practical implications.
  AMIA Annu Symp Proc 2010:527-531.
   [download PDF]   [PubMed: 21347034]   [PubMedCentral: PMC3041405]  

• Pathak J, Peters LB, Chute CG, Bodenreider O.
  Comparing and evaluating terminology services APIs: RxNav, UMLSKS, and LexBIG.
  J Am Med Inform Assoc 2010;17(6):714-719.
   [download PDF]   [PubMed: 20962136]   [PubMedCentral: PMC3000749]  

• Peters LB, Bodenreider O.
  RESTful services for accessing RxNorm. [poster]
  AMIA Annu Symp Proc 2010:983.
   [download PDF]  

• Peters LB, Kapusnik-Uner JE, Bodenreider O.
  Methods for managing variation in clinical drug names.
  AMIA Annu Symp Proc 2010:638-641.
   [download PDF]   [PubMed: 21347056]   [PubMedCentral: PMC3041346]  

• Sahoo SS, Bodenreider O, Hitzler P, Sheth AP, Thirunarayan K.
  Provenance Context Entity (PaCE): Scalable provenance tracking for scientific RDF data.
  In: Gertz M, Ludascher B, editors. Proceedings of the 22nd International Scientific and Statistical Database Management (SSDBM) Conference. Heidelberg, Germany: Springer; 2010. p. 461-470.
   [download PDF]   [PubMed: 25621321]   [PubMedCentral: PMC4303908]  

• Wei D, Bodenreider O.
  Using the Abstraction Network in complement to Description Logics for quality assurance in biomedical terminologies - A case study in SNOMED CT.
  Stud Health Technol Inform (Proc Medinfo) 2010;160:1070-1074.
   [download PDF]   [PubMed: 20841848]   [PubMedCentral: PMC4303368]  

• Whetzel PL, Batchelor C, Denney CK, Pichler E, Andersson B, Bodenreider O, Clark T, Domarew C, Dumontier M, Jentzsch A, Kashyap V, Kozlovsky J, Luciano JS, Ogbuji C, Samwald M, Zhao J, Stephens S.
  Translational Medicine Ontology: A patient-centric ontology for drug development and clinical practice. [poster]
  AMIA Jt Summits Transl Sci Proc 2010;TBI:74.
   [download PDF]  

• Zhang G-Q, Bodenreider O.
  Large-scale, exhaustive lattice-based structural auditing of SNOMED CT.
  AMIA Annu Symp Proc 2010:922-926.
   [download PDF]   [PubMed: 21347113]   [PubMedCentral: PMC3041382]  

• Zhang G-Q, Bodenreider O.
  Using SPARQL to test for lattices: application to quality assurance in biomedical ontologies.
  In: Patel-Schneider PF, Pan Y, Hitzler P, Mika P, Zhang L, Pan JZ, et al., editors. Proceedings of the 9th International Semantic Web Conference (ISWC 2010), Shanghai, China, November 7-11, 2010. Berlin, Heidelberg: Springer; 2010. p. 273-288.
   [download PDF]   [PubMed: 25699294]   [PubMedCentral: PMC4330995]  

2009

• 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 2009:254-259.
   [download PDF]   [PubMed: 25635265]   [PubMedCentral: PMC4307020]  

• Bodenreider O.
  Biomedical ontology in action. [editorial]
  Applied Ontology 2009;4(1):1-4.
   [download PDF]  

• Bodenreider O.
  Using SNOMED CT in combination with MedDRA for reporting signal detection and adverse drug reactions reporting.
  AMIA Annu Symp Proc 2009:45-49.
   [download PDF]   [PubMed: 20351820]   [PubMedCentral: PMC2815504]  

• 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:(electronic proceedings: http://ceur-ws.org/Vol-526/).
   [download PDF]  

• Bodenreider O, Burgun A.
  Desiderata for an ontology of diseases for the annotation of biological datasets.
  Proceedings of the First International Conference on Biomedical Ontology (ICBO 2009) 2009:39-42.
   [download PDF]  

• Bodenreider O, Peters LB.
  A graph-based approach to auditing RxNorm.
  Journal of Biomedical Informatics 2009;42(3):558-570.
   [download PDF]   [PubMed: 19394440]   [PubMedCentral: PMC2722378]  

• Burgun A, Mougin F, Bodenreider O.
  Two approaches to integrating phenotype and clinical information.
  AMIA Annu Symp Proc 2009:75-79.
   [download PDF]   [PubMed: 20351826]   [PubMedCentral: PMC2815427]  

• Cimino JJ, Hayamizu TF, Bodenreider O, Davis B, Stafford GA, Ringwald M.
  The caBIG terminology review process.
  Journal of Biomedical Informatics 2009;42(3):571-580.
   [download PDF]   [PubMed: 19154797]   [PubMedCentral: PMC2729758]  

• Denney CK, Batchelor C, Bodenreider O, Cheng S, Hart J, Hill J, Madden J, Musen MM, Pichler E, Samwald M, Szalma S, Schriml L, Sedlock D, Soldatova L, Sonoda K, Statham D, Whetzel PL, Wu E, Stephens S.
  Creating a translational medicine ontology. [poster]
  Proceedings of the First International Conference on Biomedical Ontology (ICBO 2009) 2009:164.
   [download PDF]  

• Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spounge JL, Landsman D.
  Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.
  Methods Mol Biol 2009;541:1-22.
   [download PDF]   [PubMed: 19381547]   [PubMedCentral: PMC2719765]  

• Mougin F, Bodenreider O, Burgun A.
  Analyzing polysemous concepts from a clinical perspective: Application to auditing concept categorization in the UMLS.
  Journal of Biomedical Informatics 2009;42(3):440-451.
   [download PDF]   [PubMed: 19303057]   [PubMedCentral: PMC4303376]  

• Mougin F, Bodenreider O, Burgun A.
  Identifying anatomical concepts associated with ICD10 diseases.
  Proceedings of the 8th Conference on Terminology and Artificial Intelligence (TIA 2009) 2009:(electronic proceedings: http://www.irit.fr/TIA09/start_here.htm).
   [download PDF]  

• Pathak J, Peters LB, Chute CG, Bodenreider O.
  Comparing and evaluating terminology services APIs: RxNav, UMLSKS, and LexBIG. [abstract]
  AMIA Annu Symp Proc 2009:515.
   [download PDF]  

• Schulz S, Beisswanger E, 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.
   [download PDF]   [PubMed: 19478019]   [PubMedCentral: PMC2687948]  

• Vizenor LT, Bodenreider O, McCray AT.
  Auditing associative relations across two knowledge sources.
  Journal of Biomedical Informatics 2009;42(3):426-439.
   [download PDF]   [PubMed: 19475724]   [PubMedCentral: PMC2891883]  

2008

• Bodenreider O.
  Comparing SNOMED CT and the NCI Thesaurus through Semantic Web technologies.
  Proceedings of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008) 2008:37-43 (electronic proceedings: http://ceur-ws.org/Vol-410/).
   [download PDF]  

• Bodenreider O.
  Issues in mapping LOINC laboratory tests to SNOMED CT.
  AMIA Annu Symp Proc 2008:51-55.
   [download PDF]   [PubMed: 18999311]   [PubMedCentral: PMC2655945]  

• Bodenreider O.
  Biomedical ontologies in action: role in knowledge management, data integration and decision support.
  Yearb Med Inform 2008:67-79.
   [download PDF]   [PubMed: 18660879]   [PubMedCentral: PMC2592252]  

• Bodenreider O.
  Ontologies and data integration in biomedicine: Success stories and challenging issues. [abstract]
  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.
   [download PDF]  

• Bodenreider O.
  Towards a metaontology for the biomedical domain [editorial]
  Applied Ontology 2008;3(4):201-203.
   [download PDF]  

• 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) 2008:85-90 (electronic proceedings: http://ceur-ws.org/Vol-434/).
   [download PDF]  

• Bodenreider O, Sahoo SS.
  Semantic Web for translational biomedicine: Two pilot experiments. [poster]
  Proceedings of the AMIA Summit on Translational Bioinformatics 2008:141.
   [download PDF]  

• Burgun A, Bodenreider O.
  Accessing and integrating data and knowledge for biomedical research.
  Yearb Med Inform 2008:91-99.
   [download PDF]   [PubMed: 18660883]   [PubMedCentral: PMC2553094]  

• Gruninger M, Bodenreider O, Olken F, Obrst L, Yim P.
  Ontology Summit 2007 – Ontology, taxonomy, folksonomy: Understanding the distinctions. [Communiqué]
  Applied Ontology 2008;3(3):191-200.
   [download PDF]  

• Mougin F, Bodenreider O.
  Auditing the NCI thesaurus with Semantic Web technologies.
  AMIA Annu Symp Proc 2008:500-504.
   [download PDF]   [PubMed: 18999265]   [PubMedCentral: PMC2655981]  

• Mougin F, Burgun A, Bodenreider O, Chabalier J, Loréal O, Le Beux P.
  Automatic methods for integrating biomedical data sources in a mediator-based system.
  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. 61-76.
   [download PDF]  

• Nelson SJ, Zeng K, Bodenreider O.
  MyMedicationList: Integrating personal medication records with resources. [demo]
  AMIA Annu Symp Proc 2008:1228.
   [download PDF]   [PubMed: 18998987]  

• Peters LB, Bodenreider O.
  Using the RxNorm web services API for quality assurance purposes.
  AMIA Annu Symp Proc 2008:591-595.
   [download PDF]   [PubMed: 18999038]   [PubMedCentral: PMC2656097]  

• Rogers J, Bodenreider O.
  SNOMED CT: Browsing the browsers.
  Proceedings of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008) 2008:30-36 (electronic proceedings: http://ceur-ws.org/Vol-410/).
   [download PDF]  

• Sahoo SS, Bodenreider O, Rutter JL, Skinner KJ, Sheth AP.
  An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence.
  Journal of Biomedical Informatics 2008;41:752-765.
   [download PDF]   [PubMed: 18395495]   [PubMedCentral: PMC2766186]  

• Sharp M, Bodenreider O, Wacholder N.
  A framework for characterizing drug information sources.
  AMIA Annu Symp Proc 2008:662-666.
   [download PDF]   [PubMed: 18999182]   [PubMedCentral: PMC2656044]  

• Tharakaraman K, Bodenreider O, Landsman D, Spounge JL, Mariño-Ramírez L.
  The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.
  Nucleic Acids Res 2008;36(8):2777–2786.
   [download PDF]   [PubMed: 18367472]   [PubMedCentral: PMC2377430]  

• Zeng K, Bodenreider O, Kilbourne JT, Nelson SJ.
  Standards, security and usability: Experience with MyMedicationList. [abstract]
  Proceedings of the AMIA Spring Congress 2008.
   [download PDF]  

• Zeng K, Bodenreider O, Nelson SJ.
  Design and implementation of a personal medication record--MyMedicationList.
  AMIA Annu Symp Proc 2008:844-848.
   [download PDF]   [PubMed: 18998962]   [PubMedCentral: PMC2656100]  

2007

• Aronson AR, Bodenreider O, Demner-Fushman D, Fung KW, Lee VK, Mork JG, Névéol A, Peters LB, Rogers WJ.
  From indexing the biomedical literature to coding clinical text: Experience with MTI and machine learning approaches.
  Proceedings of the ACL'2007 Workshop "BioNLP" 2007:105-112.
   [download PDF]  

• Bodenreider O, Burgun A.
  Oncologic pathology in biomedical terminologies: Challenges for data integration. [abstract]
  Proceedings of the APIII conference on "Anatomic Pathology Informatics and Imaging Support for Translational Medicine", Pittsburgh, Pennsylvania, September 9-12, 2007 2007:Abstract 342.
   [download PDF]  

• Bodenreider O, Smith B, Kumar A, Burgun A.
  Investigating subsumption in SNOMED CT: An exploration into large Description Logic-based biomedical terminologies.
  Artificial Intelligence in Medicine 2007;39(3):183-195.
   [download PDF]   [PubMed: 17241777]   [PubMedCentral: PMC2442845]  

• Burgun A, Bodenreider O.
  Issues in integrating epidemiology and research information in oncology: Experience with ICD-O3 and the NCI Thesaurus.
  AMIA Annu Symp Proc 2007:85-89.
   [download PDF]   [PubMed: 18693803]  

• Fung KW, Bodenreider O, Aronson AR, Hole WT, Srinivasan S.
  Combining lexical and semantic methods of inter-terminology mapping using the UMLS.
  Stud Health Technol Inform (Proc Medinfo) 2007;129(Pt 1):605-609.
   [download PDF]   [PubMed: 17911788]   [PubMedCentral: PMC2430093]  

• 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.
   [download PDF]  

• Mougin F, Chabalier J, Bodenreider O, Burgun A.
  Méthodes de mapping situées aux niveaux instance et schéma pour l'intégration de sources de données hétérogènes [Instance-level mapping methods for heterogeneous data sources integration].
  In: Trichet F, editor. Proceedings of the 18th Journées Francophones d'Ingénierie des Connaissances (IC 2007); Toulouse: Cépaduès; 2007. p. 37-48.
   [download PDF]  

• Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano JS, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung K-H.
  Advancing translational research with the Semantic Web.
  BMC Bioinformatics 2007;8(Suppl 3):S2.
   [download PDF]   [PubMed: 17493285]   [PubMedCentral: PMC1892099]  

• Sahoo SS, Bodenreider O, Zeng K, Sheth AP.
  An experiment in integrating large biomedical knowledge resources with RDF: Application to associating genotype and phenotype information.
  Proceedings of the workshop on Health Care and Life Sciences Data Integration for the Semantic Web at the 16th International World Wide Web Conference (WWW2007) 2007:(electronic proceedings: http://www2007.org/workshops/paper_149.pdf).
   [download PDF]  

• Sahoo SS, Zeng K, Bodenreider O, Sheth AP.
  From "glycosyltransferase" to "congenital muscular dystrophy": Integrating knowledge from NCBI Entrez Gene and the Gene Ontology.
  Stud Health Technol Inform (Proc Medinfo) 2007;129(Pt 1):1260-1264.
   [download PDF]   [PubMed: 17911917]   [PubMedCentral: PMC2562001]  

• Zeng K, Bodenreider O.
  Experience in integrating large RDF-based biomedical knowledge resources with Oracle. [abstract]
  Proceedings of the 8th International Oracle Life Sciences User Group Meeting 2007:(electronic proceedings: http://www.olsug.org/wiki/images/d/d1/Kelly_Zheng.pdf).
   [download PDF]  

• Zeng K, Bodenreider O.
  Integrating the UMLS into an RDF-based biomedical knowledge repository. [poster]
  AMIA Annu Symp Proc 2007:1170.
   [download PDF]   [PubMed: 18694266]  

• Zeng K, Bodenreider O, Kilbourne JT, Nelson SJ.
  RxNav: Towards an integrated view on drug information. [poster]
  Medinfo 2007:P386.
   [download PDF]  

• Zeng K, Bodenreider O, Kilbourne JT, Nelson SJ.
  RxNav: An integrated view on drug information. [demo]
  AMIA Annu Symp Proc 2007:1202.
   [download PDF]  

• Zhang S, Bodenreider O.
  Experience in aligning anatomical ontologies.
  International Journal on Semantic Web and Information Systems 2007;3(2):1-26.
   [download PDF]   [PubMed: 18974854]   [PubMedCentral: PMC2575410]  

• Zhang S, Bodenreider O.
  Lessons learned from cross-validating alignments between large anatomical ontologies.
  Stud Health Technol Inform (Proc Medinfo) 2007;129(Pt 1):822-826.
   [download PDF]   [PubMed: 17911831]   [PubMedCentral: PMC2408442]  

• Zhang S, Bodenreider O.
  Identifying mismatches in alignments of large anatomical ontologies.
  AMIA Annu Symp Proc 2007:851-855.
   [download PDF]   [PubMed: 18693957]   [PubMedCentral: PMC2655858]  

• Zhang S, Bodenreider O.
  Hybrid alignment strategy for anatomical ontologies: Results of the 2007 ontology alignment contest.
  Proceedings of the Ontology Alignment Evaluation Initiative 2007 Campaign (OAEI 2007) 2007:139-149 (electronic proceedings: http://CEUR-WS.org/Vol-304/).
   [download PDF]  

• Zhang S, Bodenreider O, Mork P, Bernstein PA.
  Comparing two approaches for aligning representations of anatomy.
  Artificial Intelligence in Medicine 2007;39(3):227-236.
   [download PDF]   [PubMed: 17250997]   [PubMedCentral: PMC1973160]  

2006

• Azuaje FJ, Wang H, Zheng H, Bodenreider O, Chesneau A.
  Predictive integration of Gene Ontology-driven similarity and functional interactions.
  In: Proceedings of IEEE International Conference on Data Mining (ICDM) 2006, Workshop on Data Mining in Bioinformatics: IEEE Computer Society Press; 2006. p. 114 -119.
   [download PDF]   [PubMed: 25698910]   [PubMedCentral: PMC4331034]  

• Bodenreider O.
  Lexical, terminological and ontological resources for biological text mining.
  In: Ananiadou S, McNaught J, editors. Text mining for biology and biomedicine. Boston: Artech House; 2006. p. 43-66.
   [download PDF]  

• Bodenreider O, editor.
  Proceedings of the Second International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2006) "Biomedical Ontology in Action", Baltimore, Maryland, November 8, 2006: (electronic proceedings: http://ceur-ws.org/Vol-222/); 2006
   [download PDF]  

• Bodenreider O, Rindflesch TC.
  Advanced library services: Developing a biomedical knowledge repository to support advanced information management applications.
  Technical report. Bethesda, Maryland: Lister Hill National Center for Biomedical Communications, National Library of Medicine; September 14, 2006.
   [download PDF]  

• Bodenreider O, Stevens R.
  Bio-ontologies: Current trends and future directions.
  Briefings in Bioinformatics 2006;7(3):256-274.
   [download PDF]   [PubMed: 16899495]   [PubMedCentral: PMC1847325]  

• Bodenreider O, Zhang S.
  Comparing the representation of anatomy in the FMA and SNOMED CT.
  AMIA Annu Symp Proc 2006:46-50.
   [download PDF]   [PubMed: 17238300]   [PubMedCentral: PMC1839313]  

• Bretonnel Cohen K, Bodenreider O, Hirschman L.
  Linking biomedical information through text mining. [editorial]
  In: Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE, editors. Pacific Symposium on Biocomputing 2006: World Scientific; 2006. p. 1-3.
   [download PDF]  

• Golbreich C, Zhang S, Bodenreider O.
  The Foundational Model of Anatomy in OWL: Experience and perspectives.
  Journal of Web Semantics: Science, Services and Agents on the World Wide Web 2006;4(3):181-195.
   [download PDF]   [PubMed: 18360535]   [PubMedCentral: PMC2270940]  

• Mariño-Ramírez L, Bodenreider O, Kantz N, Jordan IK.
  Co-evolutionary rates of functionally-related yeast genes.
  Evolutionary Bioinformatics Online 2006;2:295–300.
   [download PDF]   [PubMed: 18345352]   [PubMedCentral: PMC2674680]  

• Mougin F, Bodenreider O.
  Eliminer les cycles dans les systèmes terminologiques: Comparaison de deux approches [Comparing two approaches to eliminating cycles from terminological systems].
  Proceedings of the 15th conference on Pattern Recognition and Artificial Intelligence (RFIA 2006) 2006:(electronic proceedings).
   [download PDF]  

• Mougin F, Burgun A, Bodenreider O.
  Data integration through data elements: Mapping data elements to terminological resources.
  Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM-2006) 2006:52-59 (electronic proceedings: http://ceur-ws.org/Vol-177/).
   [download PDF]  

• Mougin F, Burgun A, Bodenreider O.
  Using WordNet to improve the mapping of data elements to UMLS for data sources integration.
  AMIA Annu Symp Proc 2006:574-578.
   [download PDF]   [PubMed: 17238406]   [PubMedCentral: PMC1839757]  

• Mougin F, Burgun A, Bodenreider O.
  Mapping data elements to terminological resources for integrating biomedical data sources.
  BMC Bioinformatics 2006;7(Suppl 3):S6.
   [download PDF]   [PubMed: 17134479]   [PubMedCentral: PMC1764450]  

• Névéol A, Zeng K, Bodenreider O.
  Besides precision & recall: Exploring alternative approaches to evaluating an automatic indexing tool for MEDLINE.
  AMIA Annu Symp Proc 2006:589-593.
   [download PDF]   [PubMed: 17238409]   [PubMedCentral: PMC1839480]  

• Sahoo SS, Bodenreider O, Zeng K, Sheth AP.
  Adapting resources to the Semantic Web: Experience with Entrez Gene. [abstract]
  Proceedings of the workshop on Semantic Web Health Care & Life Sciences at ISWC 2006 2006:(electronic proceedings).
   [download PDF]  

• Stevens R, Bodenreider O, Lussier YA.
  Semantic webs for life sciences. [editorial]
  In: Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE, editors. Pacific Symposium on Biocomputing 2006: World Scientific; 2006. p. 112-115.
   [download PDF]   [PubMed: 17094232]   [PubMedCentral: PMC2920338]  

• Tsaparas P, Mariño-Ramírez L, Bodenreider O, Koonin EV, Jordan IK.
  Global similarity and local divergence in human and mouse gene co-expression networks.
  BMC Evol Biol 2006;6(1):70.
   [download PDF]   [PubMed: 16968540]   [PubMedCentral: PMC1601971]  

• Vizenor LT, Bodenreider O.
  Using dependence relations in MeSH as a framework for the analysis of disease information in Medline.
  Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM-2006) 2006:76-83 (electronic proceedings: http://ceur-ws.org/Vol-177/).
   [download PDF]  

• Vizenor LT, Bodenreider O, Peters LB, McCray AT.
  Enhancing biomedical ontologies through alignment of semantic relationships: Exploratory approaches.
  AMIA Annu Symp Proc 2006:804-808.
   [download PDF]   [PubMed: 17238452]   [PubMedCentral: PMC1839588]  

• Zeng K, Bodenreider O, Kilbourne JT, Nelson SJ.
  RxNav: A web service for standard drug information. [poster]
  AMIA Annu Symp Proc 2006:1198.
   [download PDF]   [PubMed: 17238775]   [PubMedCentral: PMC1839335]  

• Zeng K, Bodenreider O, Kilbourne JT, Nelson SJ.
  RxNav: Providing standard drug information. [demo]
  AMIA Annu Symp Proc 2006:1156.
   [download PDF]   [PubMedCentral: PMC1839369]  

• Zhang S, Bodenreider O.
  Law and order: Assessing and enforcing compliance with ontological modeling principles.
  Computers in Biology and Medicine 2006;36(6-7):674-693.
   [download PDF]   [PubMed: 16144698]   [PubMedCentral: PMC1784072]  

• Zhang S, Bodenreider O.
  Aligning anatomical ontologies: The role of complex structural rules.
  IIAS-Transactions on Systems Research and Cybernetics -- Proceedings of the 18th International Conference on Systems Research, Informatics and Cybernetics (InterSymp 2006) 2006;VI(2):27-32.
   [download PDF]  

• Zhang S, Bodenreider O.
  Aligning multiple anatomical ontologies through a reference.
  Proceedings of the International Workshop on Ontology Matching (OM 2006) 2006:201-205 (electronic proceedings: http://ceur-ws.org/Vol-225/).
   [download PDF]  

• Zhang S, Bodenreider O.
  NLM anatomical ontology alignment system: Results of the 2006 ontology alignment contest.
  Proceedings of the Ontology Alignment Evaluation Initiative 2006 Campaign (OAEI 2006) 2006:153-164 (electronic proceedings: http://ceur-ws.org/Vol-225/).
   [download PDF]  

• Zhang S, Bodenreider O, Golbreich C.
  Experience in reasoning with the Foundational Model of Anatomy in OWL DL.
  In: Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE, editors. Pacific Symposium on Biocomputing 2006: World Scientific; 2006. p. 200-211.
   [download PDF]   [PubMed: 17094240]   [PubMedCentral: PMC4349213]  

2005

• Azuaje FJ, 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.
   [download PDF]  

• Bodenreider O, Aubry M, Burgun A.
  Non-lexical approaches to identifying associative relations in the Gene Ontology.
  In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2005: World Scientific; 2005. p. 91-102.
   [download PDF]   [PubMed: 15759617]   [PubMedCentral: PMC2224899]  

• Bodenreider O, Burgun A.
  Biomedical ontologies.
  In: Chen H, Fuller S, Hersh WR, Friedman C, editors. Medical informatics: Advances in knowledge management and data mining in biomedicine. New York: Springer-Verlag; 2005. p. 211-236.
   [download PDF]  

• Bodenreider O, Burgun A.
  Linking the Gene Ontology to other biological ontologies.
  Proceedings of the ISMB'2005 SIG meeting on Bio-ontologies 2005:17-18.
   [download PDF]  

• Bodenreider O, Hayamizu TF, Ringwald M, de Coronado S, Zhang S.
  Of mice and men: Aligning mouse and human anatomies.
  AMIA Annu Symp Proc 2005:61-65.
   [download PDF]   [PubMed: 16779002]   [PubMedCentral: PMC1560846]  

• Bodenreider O, Mitchell JA, McCray AT.
  Biomedical ontologies. [editorial]
  In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2005: World Scientific; 2005. p. 76-78.
   [download PDF]   [PubMed: 15759615]   [PubMedCentral: PMC4300097]  

• Burgun A, Bodenreider O.
  An ontology of chemical entities helps identify dependence relations among Gene Ontology terms.
  Proceedings of the First International Symposium on Semantic Mining in Biomedicine (SMBM-2005) 2005:(electronic proceedings: http://ceur-ws.org/Vol-148/).
   [download PDF]  

• Burgun A, Bodenreider O, Jacquelinet C.
  Issues in the classification of disease instances with ontologies.
  Stud Health Technol Inform (Proc MIE) 2005;116:695-700.
   [download PDF]   [PubMed: 16160339]   [PubMedCentral: PMC1784521]  

• Burgun A, Bodenreider O, Mougin F.
  Classifying diseases with respect to anatomy: a study in SNOMED CT.
  AMIA Annu Symp Proc 2005:91-95.
   [download PDF]   [PubMed: 16779008]   [PubMedCentral: PMC1560776]  

• Cantor MN, Sarkar IN, Bodenreider O, Lussier YA.
  GenesTrace: Phenomic knowledge discovery via structured terminologies.
  In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2005: World Scientific; 2005. p. 103-114.
   [download PDF]   [PubMed: 15759618]   [PubMedCentral: PMC2894422]  

• Fung KW, Bodenreider O.
  Utilizing the UMLS for semantic mapping between terminologies.
  AMIA Annu Symp Proc 2005:266-270.
   [download PDF]   [PubMed: 16779043]   [PubMedCentral: PMC1560893]  

• Golbreich C, Zhang S, Bodenreider O.
  Migrating the FMA from Protégé to OWL.
  Proceedings of the Eighth International Protégé Conference 2005:108-111.
   [download PDF]  

• Golbreich C, Zhang S, Bodenreider O.
  The Foundational Model of Anatomy in OWL: Experience and perspectives.
  Proceedings of the Workshop on "OWL: Experiences and Directions" (OWLED 2005) 2005:(electronic proceedings).
   [download PDF]  

• Mougin F, Bodenreider O.
  Approaches to eliminating cycles in the UMLS Metathesaurus: Naïve vs. formal.
  AMIA Annu Symp Proc 2005:550-554.
   [download PDF]   [PubMed: 16779100]   [PubMedCentral: PMC1560864]  

• Verspoor KM, Joslyn CA, Ambrosiano J, Backer A, Bodenreider O, Hirschman L, Karp P, Kelly H, Loranger S, Musen MM, Sriram R, Wroe C.
  Knowledge integration for bio-threat response.
  Technical report. Los Alamos, New Mexico: Los Alamos National Laboratory, 2005.
   [download PDF]  

• Wang H, Azuaje FJ, Bodenreider O.
  An ontology-driven clustering method for supporting gene expression analysis.
  Proceedings of the 18th IEEE International Symposium on Computer-Based Medical Systems (CBMS'2005) 2005:389-394.
   [download PDF]  

• Zeng K, Bodenreider O, Nelson SJ.
  Implementing RxNav, a RxNorm browser. [poster]
  Proceedings of Medical Informatics Europe 2005 (CD-ROM) 2005:1268.
   [download PDF]  

• Zeng K, Bodenreider O, Nelson SJ.
  RxNav: A progress report. [poster]
  AMIA Annu Symp Proc 2005:1168.
   [download PDF]   [PubMed: 16779454]   [PubMedCentral: PMC1560640]  

• 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.
   [download PDF]   [PubMed: 16779163]   [PubMedCentral: PMC1560629]  

2004

• Azuaje FJ, Bodenreider O.
  Incorporating ontology-driven similarity knowledge into functional genomics: An exploratory study.
  Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE-2004) 2004:317-324.
   [download PDF]   [PubMed: 25635264]   [PubMedCentral: PMC4307019]  

• Azuaje FJ, Bodenreider O, Wang H, Dopazo J.
  Gene Ontology-driven similarity for gene expression correlation analysis. [abstract]
  Proceedings of the second conference on Standards and Ontologies for Functional Genomics (SOFG 2) 2004:47.
   [download PDF]  

• Bodenreider O.
  The Unified Medical Language System (UMLS): Integrating biomedical terminology.
  Nucleic Acids Res 2004;32 Database issue:D267-70.
   [download PDF]   [PubMed: 14681409]   [PubMedCentral: PMC308795]  

• Bodenreider O, Aubry M, Burgun A.
  From functional similarity among gene products to dependence relations among Gene Ontology terms. [poster]
  Proceedings of the second conference on Standards and Ontologies for Functional Genomics (SOFG 2) 2004:53.
   [download PDF]  

• Bodenreider O, Burgun A.
  Aligning knowledge sources in the UMLS: Methods, quantitative results, and applications.
  Stud Health Technol Inform (Proc Medinfo) 2004;107(Pt 1):327-331.
   [download PDF]   [PubMed: 15360828]   [PubMedCentral: PMC4303371]  

• Bodenreider O, Mitchell JA, McCray AT.
  Biomedical ontologies. [editorial]
  In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2004: World Scientific; 2004. p. 164-165.
   [download PDF]  

• Bodenreider O, Nelson SJ.
  RxNav: A semantic navigation tool for clinical drugs. [poster]
  Medinfo 2004:1530.
   [download PDF]  

• Bodenreider O, Smith B, Burgun A.
  The ontology-epistemology divide: A case study in medical terminology.
  In: Varzi AC, Vieu L, editors. Proceedings of the Third International Conference on Formal Ontology in Information Systems (FOIS 2004): IOS Press; 2004. p. 185-195.
   [download PDF]   [PubMed: 25745641]   [PubMedCentral: PMC4346778]  

• Bodenreider O, Smith B, Kumar A, Burgun A.
  Investigating subsumption in DL-based terminologies: A case study in SNOMED CT.
  In: Hahn U, Schulz S, Cornet R, editors. Proceedings of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004); 2004. p. 12-20 (electronic proceedings: http://ceur-ws.org/Vol-102/).
   [download PDF]  

• Burgun A, Bodenreider O, Aubry M, Mosser J.
  Dependence relations in Gene Ontology: A preliminary study.
  Workshop on The Formal Architecture of the Gene Ontology - Leipzig, Germany, May 28-29, 2004 2004:(electronic proceedings).
   [download PDF]  

• Kumar Sehgal A, Srinivasan P, Bodenreider O.
  Gene names and English words: An ambiguous mix.
  Proceedings of the SIGIR 2004 Workshop on Search and Discovery in Bioinformatics 2004:(electronic proceedings).
   [download PDF]  

• Sarkar IN, Cantor MN, Bodenreider O, Lussier YA.
  GenesTrace(TM): Biological knowledge discovery via structured terminology. [poster]
  Medinfo 2004:1842.
   [download PDF]  

• Tringali M, Rindflesch TC, Kilicoglu H, Fiszman M, Bodenreider O.
  Strategies for mapping concepts in gastrointestinal endoscopy reports to the UMLS Metathesaurus. [poster]
  Medinfo 2004:1885.
   [download PDF]  

• Wang H, Azuaje FJ, Bodenreider O, Dopazo J.
  Gene expression correlation and gene ontology-based similarity: An assessment of quantitative relationships.
  Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'2004) 2004:25-31.
   [download PDF]   [PubMed: 25664345]   [PubMedCentral: PMC4317290]  

• Zhang S, Bodenreider O.
  Investigating implicit knowledge in ontologies with application to the anatomical domain.
  In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2004: World Scientific; 2004. p. 250-261.
   [download PDF]   [PubMed: 14992508]   [PubMedCentral: PMC4351965]  

• Zhang S, Bodenreider O.
  Comparing associative relationships among equivalent concepts across ontologies.
  Stud Health Technol Inform (Proc Medinfo) 2004;107(Pt 1):459-463.
   [download PDF]   [PubMed: 15360855]   [PubMedCentral: PMC4299595]  

• Zhang S, Mork P, Bodenreider O.
  Lessons learned from aligning two representations of anatomy.
  In: Hahn U, Schulz S, Cornet R, editors. Proceedings of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004); 2004. p. 102-108 (electronic proceedings: http://ceur-ws.org/Vol-102/).
   [download PDF]  

2003

• Bodenreider O.
  Strength in numbers: Exploring redundancy in hierarchical relations across biomedical terminologies.
  AMIA Annu Symp Proc 2003:101-105.
   [download PDF]   [PubMed: 14728142]   [PubMedCentral: PMC1480297]  

• Bodenreider O, Burgun A, Mitchell JA.
  Evaluation of WordNet as a source of lay knowledge for molecular biology and genetic diseases: A feasibility study.
  Stud Health Technol Inform (Proc MIE) 2003;95:379-384.
   [download PDF]   [PubMed: 14664016]   [PubMedCentral: PMC1893008]  

• Bodenreider O, McCray AT.
  Exploring semantic groups through visual approaches.
  Journal of Biomedical Informatics 2003;36(6):414-432.
   [download PDF]   [PubMed: 14759816]   [PubMedCentral: PMC1997308]  

• Bodenreider O, Mitchell JA.
  Graphical visualization and navigation of genetic disease information. [poster]
  AMIA Annu Symp Proc 2003:792.
   [download PDF]   [PubMed: 14728297]   [PubMedCentral: PMC1479900]  

• Bodenreider O, Mitchell JA, McCray AT.
  Biomedical ontologies. [editorial]
  In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2003: World Scientific; 2003. p. 562-564.
   [download PDF]  

• Bodenreider O, Pakhomov S.
  Exploring adjectival modification in biomedical discourse across two genres.
  Proceedings of the ACL'2003 Workshop "Natural Language Processing in Biomedicine" 2003:105-112.
   [download PDF]  

• Bodenreider O, Zhang S.
  Semantic Integration in Biomedicine.
  Proceedings of the Semantic Integration Workshop at the Second International Semantic Web Conference (ISWC 2003) 2003:156-157.
   [download PDF]  

• Cantor MN, Sarkar IN, Hartel F, Bodenreider O, Lussier YA.
  An evaluation of hybrid methods for matching biomedical terminologies: Mapping the Gene Ontology to the UMLS.
  Stud Health Technol Inform (Proc MIE) 2003:62-67.
   [download PDF]   [PubMed: 14663964]   [PubMedCentral: PMC1796946]  

• Kayaalp M, Aronson AR, Humphrey SM, Ide NC, Tanabe LK, Smith LH, Demner-Fushman D, Loane RR, Mork JG, Bodenreider O.
  Methods for accurate retrieval of MEDLINE citations in functional genomics.
  Proceedings of the Text Retrieval Conference (TREC-2003) 2003:175-184.
   [download PDF]  

• Mitchell JA, McCray AT, Bodenreider O.
  From phenotype to genotype: Issues in navigating the available information resources.
  Methods of Information in Medicine 2003;42(5):557-563.
   [download PDF]   [PubMed: 14654891]   [PubMedCentral: PMC1800828]  

• Zhang S, Bodenreider O.
  Knowledge augmentation for aligning ontologies: An evaluation in the biomedical domain. [poster]
  Proceedings of the Semantic Integration Workshop at the Second International Semantic Web Conference (ISWC 2003) 2003:109-114.
   [download PDF]  

• Zhang S, Bodenreider O.
  Aligning representations of anatomy using lexical and structural methods.
  AMIA Annu Symp Proc 2003:753-757.
   [download PDF]   [PubMed: 14728274]   [PubMedCentral: PMC1480279]  

2002

• Bodenreider O.
  GenNav: Visualizing Gene Ontology as a graph. [poster]
  Proceedings of AMIA Annual Symposium 2002:978.
   [download PDF]   [PubMedCentral: PMC2244208]  

• Bodenreider O.
  Experiences in visualizing and navigating biomedical ontologies and knowledge bases.
  Proceedings of the ISMB'2002 SIG meeting "Bio-ontologies" 2002:29-32.
   [download PDF]  

• Bodenreider O, Burgun A.
  Characterizing the definitions of anatomical concepts in WordNet and specialized sources.
  Proceedings of the First Global WordNet Conference 2002:223-230.
   [download PDF]  

• Bodenreider O, Burgun A, Rindflesch TC.
  Assessing the consistency of a biomedical terminology through lexical knowledge.
  International Journal of Medical Informatics 2002;67(1-3):85-95.
   [download PDF]   [PubMed: 12460634]  

• Bodenreider O, Mitchell JA, McCray AT.
  Evaluation of the UMLS as a terminology and knowledge resource for biomedical informatics.
  Proceedings of AMIA Annual Symposium 2002:61-65.
   [download PDF]   [PubMed: 12463787]   [PubMedCentral: PMC2244306]  

• Bodenreider O, Rindflesch TC, Burgun A.
  Unsupervised, corpus-based method for extending a biomedical terminology.
  Proceedings of the ACL'2002 Workshop "Natural Language Processing in the Biomedical Domain" 2002:53-60.
   [download PDF]  

• Burgun A, Bodenreider O, Le Duff F, Mounssouni F, Loréal O.
  Representation of roles in biomedical ontologies: a case study in functional genomics.
  Proceedings of AMIA Annual Symposium 2002:86-90.
   [download PDF]   [PubMed: 12463792]   [PubMedCentral: PMC2244301]  

• McCray AT, Bodenreider O.
  A conceptual framework for the biomedical domain.
  In: Green R, Bean CA, Myaeng SH, editors. The semantics of relationships: an interdisciplinary perspective. Dordrecht; Boston: Kluwer Academic Publishers; 2002. p. 181-198.
   [download PDF]  

• McCray AT, Browne AC, Bodenreider O.
  The lexical properties of the Gene Ontology (GO).
  Proceedings of AMIA Annual Symposium 2002:504-508.
   [download PDF]   [PubMed: 12463875]   [PubMedCentral: PMC2244431]  

• Mitchell JA, McCray AT, Bodenreider O.
  From phenotype to genotype: Navigating the available information resources. [poster]
  Proceedings of AMIA Annual Symposium 2002:1109.
   [download PDF]   [PubMedCentral: PMC2244561]  

• Srinivasan P, Mitchell JA, Bodenreider O, Pant G, Menczer F.
  Web crawling agents for retrieving biomedical information.
  In: Proceedings of the International Workshop on Bioinformatics and Multi-Agent Systems (BIXMAS 2002), Bologna, Italy, July 15, 2002; 2002. p. (electronic proceedings).
   [download PDF]  

• Travers D, Bodenreider O.
  Identifying medical concepts in free text chief complaint data. [abstract]
  Academic Emergency Medicine 2002;9(5):511.
   [download PDF]  

2001

• Bodenreider O.
  An object-oriented model for representing semantic locality in the UMLS.
  Stud Health Technol Inform (Proc Medinfo) 2001;84(Pt 1):161-165.
   [download PDF]   [PubMed: 11604725]   [PubMedCentral: PMC4296525]  

• Bodenreider O.
  Circular hierarchical relationships in the UMLS: Etiology, diagnosis, treatment, complications and prevention.
  Proceedings of AMIA Annual Symposium 2001:57-61.
   [download PDF]   [PubMed: 11825155]   [PubMedCentral: PMC2243677]  

• Bodenreider O.
  Medical Ontology Research.
  Technical report. Bethesda, Maryland: Lister Hill National Center for Biomedical Communications, National Library of Medicine; May 17, 2001.
   [download PDF]  

• Bodenreider O, Bean CA.
  Relationships among knowledge structures: Vocabulary integration within a subject domain.
  In: Bean CA, Green R, editors. Relationships in the organization of knowledge. Dordrecht; Boston: Kluwer Academic Publishers; 2001. p. 81-98.
   [download PDF]  

• Bodenreider O, Burgun A, Rindflesch TC.
  Lexically-suggested hyponymic relations among medical terms and their representation in the UMLS.
  Proceedings of TIA'2001 "Terminology and Artificial Intelligence" 2001:11-21.
   [download PDF]  

• Burgun A, Bodenreider O.
  Methods for exploring the semantics of the relationships between co-occurring UMLS concepts.
  Stud Health Technol Inform (Proc Medinfo) 2001;84(Pt 1):171-175.
   [download PDF]   [PubMed: 11604727]   [PubMedCentral: PMC4299664]  

• Burgun A, Bodenreider O.
  Comparing terms, concepts and semantic classes in WordNet and the Unified Medical Language System.
  Proceedings of the NAACL'2001 Workshop, "WordNet and Other Lexical Resources: Applications, Extensions and Customizations" 2001:77-82.
   [download PDF]  

• Burgun A, Bodenreider O.
  Aspects of the taxonomic relation in the biomedical domain.
  In: Welty C, Smith B, editors. Collected papers from the Second International Conference "Formal Ontology in Information Systems": ACM Press; 2001. p. 222-233.
   [download PDF]   [PubMed: 25635263]   [PubMedCentral: PMC4307028]  

• Burgun A, Bodenreider O.
  Mapping the UMLS Semantic Network into general ontologies.
  Proceedings of AMIA Annual Symposium 2001:81-85.
   [download PDF]   [PubMed: 11833483]   [PubMedCentral: PMC2243467]  

• McCray AT, Bodenreider O, Malley JD, Browne AC.
  Evaluating UMLS strings for natural language processing.
  Proceedings of AMIA Annual Symposium 2001:448-452.
   [download PDF]   [PubMed: 11825228]   [PubMedCentral: PMC2243606]  

• McCray AT, Burgun A, Bodenreider O.
  Aggregating UMLS semantic types for reducing conceptual complexity.
  Stud Health Technol Inform (Proc Medinfo) 2001;84(Pt 1):216-220.
   [download PDF]   [PubMed: 11604736]   [PubMedCentral: PMC4300099]  

2000

• Aronson AR, Bodenreider O, Chang HF, Humphrey SM, Mork JG, Nelson SJ, Rindflesch TC, Wilbur WJ.
  The NLM Indexing Initiative.
  Proceedings of AMIA Annual Symposium 2000:17-21.
   [download PDF]   [PubMed: 11079836]   [PubMedCentral: PMC2243970]  

• Bodenreider O.
  Using UMLS semantics for classification purposes.
  Proceedings of AMIA Annual Symposium 2000:86-90.
   [download PDF]   [PubMed: 11079850]   [PubMedCentral: PMC2243905]  

• Bodenreider O.
  A semantic navigation tool for the UMLS. [poster]
  Proceedings of AMIA Annual Symposium 2000:971.
   [download PDF]   [PubMedCentral: PMC2244094]  

• Bodenreider O.
  Comment les usagers accèdent à l'information médicale aux USA: l'exemple de MEDLINEplus [How consumers access health information in the USA: MEDLINEplus as an example].
  Innovation et Technologie en Biologie et Médecine 2000;21(5):286-290.
   [download PDF]  

• Bodenreider O, Zweigenbaum P.
  Stratégies d'identification des noms propres à partir de nomenclatures médicales parallèles [Strategies for identifying proper names in parallel medical terminologies].
  Traitement Automatique des Langues 2000;41(3):727-757.
   [download PDF]  

• Bodenreider O, Zweigenbaum P.
  Identifying proper names in parallel medical terminologies.
  Stud Health Technol Inform (Proc MIE) 2000;77:443-7.
   [download PDF]   [PubMed: 11187591]   [PubMedCentral: PMC1790050]  

• Botti G, Bodenreider O, Burgun A, Le Beux P, Fieschi M.
  De la classification à la connaissance des maladies: une réflexion à partir de la Classification Internationale des Maladies [From classification to knowledge about diseases: Thoughts about the International Classification of Diseases].
  Innovation et Technologie en Biologie et Médecine 2000;21(5):291-297.
   [download PDF]  

• Jacquelinet C, Bodenreider O, Burgun A.
  Modelling syllepse in medical knowledge bases with application in the domain of organ failure and transplantation.
  Proceedings of OntoLex 2000 (Workshop on Ontologies and Lexical Knowledge Bases) 2000.
   [download PDF]  

1999

• Nelson SJ, Aronson AR, Doszkocs TE, Wilbur WJ, Bodenreider O, Chang HF, Mork JG, McCray AT.
  Automated assignment of Medical Subject Headings. [poster]
  Proceedings of AMIA Annual Symposium 1999:1127.
   [download PDF]   [PubMedCentral: PMC2232883]  

1998

• Bodenreider O, Burgun A, Botti G, Fieschi M, Le Beux P, Kohler F.
  Evaluation of the Unified Medical Language System as a medical knowledge source.
  J Am Med Inform Assoc 1998;5(1):76-87.
   [download PDF]   [PubMed: 9452987]   [PubMedCentral: PMC61277]  

• Bodenreider O, McCray AT.
  From French vocabulary to the Unified Medical Language System: a preliminary study.
  Stud Health Technol Inform (Proc Medinfo) 1998;52(Pt 1):670-4.
   [download PDF]   [PubMed: 10384539]   [PubMedCentral: PMC4296523]  

• Bodenreider O, Nelson SJ, Hole WT, Chang HF.
  Beyond synonymy: exploiting the UMLS semantics in mapping vocabularies.
  Proceedings of AMIA Annual Symposium 1998:815-9.
   [download PDF]   [PubMed: 9929332]   [PubMedCentral: PMC2232139]  

• Bouchet C, Bodenreider O, Kohler F.
  Integration of the analytical and alphabetical ICD10 in a coding help system. Proposal of a theoretical model for the ICD representation.
  Stud Health Technol Inform (Proc Medinfo) 1998;52(Pt 1):176-9.
   [download PDF]   [PubMed: 10384443]   [PubMedCentral: PMC4303372]  

• Burgun A, Bodenreider O, Denier P, Delamarre D, Botti G, Oberlin P, Levêque J-M, Brémond M, Fieschi M, Le Beux P.
  A collaborative approach to building a terminology for medical procedures using a Web-based application: from specifications to daily use.
  Stud Health Technol Inform (Proc Medinfo) 1998;52(Pt 1):596-9.
   [download PDF]   [PubMed: 10384524]   [PubMedCentral: PMC4300115]  

• Guichet JM, Braillon P, Bodenreider O, Lascombes P.
  Role of periosteum and bone marrow in lengthening: A quantitative study in rabbits using DEXA. [abstract]
  Journal of Biomechanics 1998;31(Supplement 1):124.
   [download PDF]  

• Guichet JM, Braillon P, Bodenreider O, Lascombes P.
  Periosteum and bone marrow in bone lengthening: a DEXA quantitative evaluation in rabbits.
  Acta Orthop Scand 1998;69(5):527-31.
   [download PDF]   [PubMed: 9855238]  

1997

• Burgun A, Denier P, Bodenreider O, Botti G, Delamarre D, Pouliquen B, Oberlin P, Levêque J-M, Lukacs B, Kohler F, Fieschi M, Le Beux P.
  A Web terminology server using UMLS for the description of medical procedures.
  J Am Med Inform Assoc 1997;4(5):356-63.
   [download PDF]   [PubMed: 9292841]   [PubMedCentral: PMC61253]  

• Gillois P, Garin H, Bodenreider O, Kohler F.
  Case mix of elderly in-patients in the 29 hospitals in Lorraine in 1994 and 1995.
  Stud Health Technol Inform (Proc MIE) 1997;43(Pt A):455-9.
   [PubMed: 10179590]  

1996

• Burgun A, Botti G, Bodenreider O, Delamarre D, Levêque J-M, Lukacs B, Mayeux D, Brémond M, Kohler F, Fieschi M, Le Beux P.
  Methodology for using the UMLS as a background knowledge for the description of surgical procedures.
  Int J Biomed Comput 1996;43(3):189-202.
   [download PDF]   [PubMed: 9032008]  

1995

• Burgun A, Bodenreider O, Denier P, Delamarre D, Botti G, Lukacs B, Mayeux D, Brémond M, Kohler F, Fieschi M.
  Knowledge acquisition from the UMLS sources: application to the description of surgical procedures.
  Proc Medinfo 1995;8(Pt 1):75-9.
   [PubMed: 8591317]  

1994

• Grasser B, Pinelli G, Carteaux J-P, Bodenreider O, Sadoul N, Aliot E, Villemot J-P.
  Chirurgie coronaire après 70 ans : analyse des facteurs de risque de mortalité opératoire [Coronary artery surgery after 70 years: an analysis of the risk factors of operative mortality].
  Arch. Mal. Coeur Vaiss. 1994;87(9):1169-75.
   [PubMed: 7646230]  

1993

• Faller B, Genestier S, Bodenreider O, Brignon P, Boess G.
  Experience regarding reduction of peritonitis rates in continuous ambulatory peritoneal dialysis. [abstract]
  Peritoneal Dialysis International 1993;13(suppl. 2):319-321.
   [PubMed: 8399598]