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 Assoc2020:(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 Expo2019:(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]
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, 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 Proc2018:2229. [download PDF]
Callahan TJ, Bodenreider O, Kahn MG. Towards patient-driven phenotyping and similarity for precision medicine. [abstract] AMIA Jt Summits Transl Sci Proc2018;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 Proc2018;CRI:426-427. [download PDF]
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 Proc2018:1806-1807. [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 Proc2018:2102. [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 Expo2018:(electronic proceedings: https://drive.google.com/file/d/1hRwts7ezsZjThd568G925RC7aB_S5XxN/view). [download PDF]
Bodenreider O. Identifying missing hierarchical relations in SNOMED CT from logical definitions based on the lexical features of concept names. [abstract] SNOMED CT Expo2017:(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 Proc2017:1955. [download PDF]
Bodenreider O, Peters LB. RxMix – Use of NLM drug APIs by non-programmers. [demo] AMIA Annu Symp Proc2017:2291. [download PDF]
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 Assoc2017;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 Informatics2017;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 Proc2017:2070. [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 Proc2017:2143. [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. 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 Proc2017;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 Proc2017:163-164. [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 Proc2017:2175. [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 Informatics2017;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 Proc2016:1346. [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 Expo2016:(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. Assessing the potential risk in drug prescriptions during pregnancy. [abstract] AMIA Annu Symp Proc2016:45-46. [download PDF]
Dhombres F, Bodenreider O. Investigating partial mappings between HPO and SNOMED CT. [poster] SNOMED CT Expo2016:(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 Journal2016;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 Proc2016;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 Proc2016:1440. [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 Proc2016:1551. [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 Proc2016:1569. [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 workshop2016:(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 Proc2015:2132. [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 Informatics2015;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. [abstract] SNOMED CT Implementation Showcase2015:(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 Proc2015:1615. [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 Bioinformatics2015;17(5):819-830. [download PDF] [PubMed: 26420780] [PubMedCentral: PMC5036847]
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 Proc2015:1699. [download PDF]
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 Informatics2015;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 Ontology2014:106-107 (electronic proceedings: http://ceur-ws.org/Vol-1327/). [download PDF]
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]
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 Data2014;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 Proc2014:1459. [download PDF]
Nguyen T, Peters LB, Bodenreider O. RxClass - Navigating between drug classes and RxNorm drugs. [poster] AMIA Annu Symp Proc2014:1529. [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 Ontology2014:78-80 (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 Proc2014:1565. [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 Proc2014:1596. [download PDF]
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 Showcase2014:(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]
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 workshop2013:(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 Informatics2013;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 Proc2013:390. [download PDF]
Le T, Rance B, Bodenreider O. Network visualization of UMLS source vocabularies using semantic groups. [poster] AMIA Annu Symp Proc2013:90. [download PDF]
Peters LB, Bodenreider O. SNOMED CT Status Web Service. [poster] SNOMED CT Implementation Showcase2013:(electronic proceedings: http://ihtsdo.org/show13/abstract47.pdf). [download PDF]
Winnenburg R, Bodenreider O. Criteria and metrics for assessing the quality of SNOMED CT value sets in clinical quality measures. [poster] SNOMED CT Implementation Showcase2013:(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]
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 Ontology2012;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 Proc2012:1897. [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]
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 Proc2011:2129. [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. Bioinformatics2011;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 Literature2011:(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 Semantics2011;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, Nguyen T, Bodenreider O. An application programming interface for NDF-RT. [poster] AMIA Annu Symp Proc2011:1922. [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 Literature2011:(electronic proceedings). [download PDF]
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, 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 Proc2010:1330. [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 conference2010:(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 Intelligence2010:1927-1928. [download PDF]
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 Assoc2010;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]
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 Proc2010;TBI:74. [download PDF]
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 Ontology2009;4(1):1-4. [download PDF]
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]
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]
Mougin F, Bodenreider O, Burgun A. Analyzing polysemous concepts from a clinical perspective: Application to auditing concept categorization in the UMLS. Journal of Biomedical Informatics2009;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 Proc2009:515. [download PDF]
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. 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 Ontology2008;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 Bioinformatics2008:141. [download PDF]
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 Proc2008:1228. [download PDF] [PubMed: 18998987]
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 Informatics2008;41:752-765. [download PDF] [PubMed: 18395495] [PubMedCentral: PMC2766186]
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 Res2008;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 Congress2008. [download PDF]
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, 20072007: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 Medicine2007;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 Proc2007:85-89. [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 Bioinformatics2007;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 Meeting2007:(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 Proc2007:1170. [download PDF] [PubMed: 18694266]
Zeng K, Bodenreider O, Kilbourne JT, Nelson SJ. RxNav: Towards an integrated view on drug information. [poster] Medinfo2007:P386. [download PDF]
Zeng K, Bodenreider O, Kilbourne JT, Nelson SJ. RxNav: An integrated view on drug information. [demo] AMIA Annu Symp Proc2007:1202. [download PDF]
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]
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 Web2006;4(3):181-195. [download PDF] [PubMed: 18360535] [PubMedCentral: PMC2270940]
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]
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 20062006:(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]
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]
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-ontologies2005:9-10. [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-ontologies2005:17-18. [download PDF]
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]
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]
Golbreich C, Zhang S, Bodenreider O. Migrating the FMA from Protégé to OWL. Proceedings of the Eighth International Protégé Conference2005:108-111. [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]
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]
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, 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, 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] Medinfo2004:1530. [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, 20042004:(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 Bioinformatics2004:(electronic proceedings). [download PDF]
Sarkar IN, Cantor MN, Bodenreider O, Lussier YA. GenesTrace(TM): Biological knowledge discovery via structured terminology. [poster] Medinfo2004:1842. [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] Medinfo2004:1885. [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, 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]
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, 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]
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]
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 Conference2002:223-230. [download PDF]
Bodenreider O, Burgun A, Rindflesch TC. Assessing the consistency of a biomedical terminology through lexical knowledge. International Journal of Medical Informatics2002;67(1-3):85-95. [download PDF] [PubMed: 12460634]
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]
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]
Mitchell JA, McCray AT, Bodenreider O. From phenotype to genotype: Navigating the available information resources. [poster] Proceedings of AMIA Annual Symposium2002:1109. [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 Medicine2002;9(5):511. [download PDF]
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. 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]
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 Médecine2000;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 Langues2000;41(3):727-757. [download PDF]
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 Médecine2000;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 Symposium1999:1127. [download PDF] [PubMedCentral: PMC2232883]
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 Biomechanics1998;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 Scand1998;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 Assoc1997;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 Comput1996;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 Medinfo1995;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 International1993;13(suppl. 2):319-321. [PubMed: 8399598]