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  • Peters L, Nguyen T, Bodenreider O. An application programming interface for NDF-RT AMIA Annu Symp Proc 2011:1922
  • Bodenreider O, Peters L, Nguyen T. RxNav: Browser and Application Programming Interfaces for Drug Information Sources [Abstract]. AMIA Annu Symp Proc 2011:2129
  • Rance B, Demner-Fushman D, Rindflesch TC, Bodenreider O. Exploring Automatic Approaches to Extracting Pharmacogenomic Information from the Biomedical Literature Proceedings of the 2011 PSB Workshop on Mining the Pharmacogenomics Literature 2011
  • 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/)
  • Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denny CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schrimi L, Tonellato PJ, Wjetzel JZ, 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 May 17;2 Suppl 2:S1. doi: 10.1186/2041-1480-2-S2-S1.
  • Ripple AM, Mork JG, Humphreys BL, Knecht LS. A retrospective cohort study of structured abstracts in MEDLINE, 1992-2006. J Med Libr Assoc. 2011 Apr;99(2):160-3. doi: 10.3163/1536-5050.99.2.009.
  • Zarin DA, Tse T, Williams RJ, Califf RM, Ide NC. The ClinicalTrials.gov results database--update and key issues. N Engl J Med. 2011 Mar 3;364(9):852-60. doi: 10.1056/NEJMsa1012065.
  • Doughty E, Kirk B, Kann MG, Bodenreider O. Integrating Drug-gene Associations Mined from the Literature with Drug Information Sources - A Comparison with PharmGKB Proceedings of the 2011 PSB Workshop on Mining the Pharmacogenomics Literature 2011
  • 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 point mutations from the biomedical literature. Bioinformatics. 2011 Feb 1;27(3):408-15. doi: 10.1093/bioinformatics/btq667. Epub 2010 Dec 7.
  • Zarin D, Tse T. The effect of funding source on outcome reporting among drug trials [Letter]. Ann Intern Med. 2011 Jan 18;154(2):137-8; author reply 138. doi: 10.7326/0003-4819-154-2-201101180-00020.
  • Beaudoin DE, Longo N, Logan RA, Jones JP, Mitchell JA. Using information prescriptions to refer patients with metabolic conditions to the Genetics Home Reference website. J Med Libr Assoc. 2011 Jan;99(1):70-6. doi: 10.3163/1536-5050.99.1.012.
  • Peters L, Kapusnik-Uner JE, Nguyen T, Bodenreider O. An approximate matching method for clinical drug names. AMIA Annu Symp Proc. 2011;2011:1117-26. Epub 2011 Oct 22.
  • Bodenreider O, Demner-Fushman D. Investigating drug classes in biomedical terminologies from the perspective of clinical decision support. AMIA Annu Symp Proc. 2010 Nov 13;2010:56-60.
  • 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 Nov 13;2010:527-31.
  • Peters L, Kapusnik-Uner JE, Bodenreider O. Methods for managing variation in clinical drug names. AMIA Annu Symp Proc. 2010 Nov 13;2010:637-41.
  • Zhang GQ, Bodenreider O. Large-scale, Exhaustive Lattice-based Structural Auditing of SNOMED CT. AMIA Annu Symp Proc. 2010 Nov 13;2010:922-6.
  • Willams RJ, Tse T, Harlan WR, Zarin DA. Registration of observational studies: is it time? CMAJ. 2010 Oct 19;182(15):1638-42. doi: 10.1503/cmaj.092252. Epub 2010 Jul 19.
  • Bodenreider O, Mougin F, Burgun A. Automatic Determination of Anti-coagulation Status with NDF-RT Proceedings of the 13th ISMB'2010 SIG meeting Bio-ontologies 2010:140-143
  • Dumontier M, Andersson B, Batchelor C, Domarew C, Jentzsch A, Luciano J, 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
  • Sahoo SS, Bodenreider O, Hitzler P, Sheth A, Thirunarayan K. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data SSDBM: Springer, 2010. p. 461-470
  • 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: p. (paper 10579 - electronic proceedings).
  • Bodenreider O, Burgun A. A framework for comparing phenotype annotations of orthologous genes. Stud Health Technol Inform. 2010;160(Pt 2):1309-13.
  • Erdogan H, Erdem E, Bodenreider O. Exploiting UMLS semantics for checking semantic consistency among UMLS concepts. Stud Health Technol Inform. 2010;160(Pt 1):749-53.
  • Fiszman M, Bray B, 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. 2010;160(Pt 1):709-13.
  • 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. 2010;160(Pt 2):1070-4.
  • Williams R, Tse T. ClinicalTrials.gov: A public database of clinical research. Presented at: American Public Health Association 137th Annual Meeting and Expo; November 2009; Philadelphia, PA.
  • 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: p. (electronic proceedings: http://www.irit.fr/TIA09/start_here.htm).
  • Bodenreider O. Using SNOMED CT in combination with MedDRA for reporting signal detection and adverse drug reactions reporting. AMIA Annu Symp Proc. 2009 Nov 14;2009:45-9.
  • Burgun A, Mougin F, Bodenreider O. Two approaches to integrating phenotype and clinical information. AMIA Annu Symp Proc. 2009 Nov 14;2009:75-9.
  • An L, Obradovic Z, Smith D, Bodenreider O, Megalooikonomou V. Mining Association Rules among Gene Functions in Clusters of Similar Gene Expression Maps. Workshop proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM09) -- Workshop on Data Mining in Functional Genomics 2009: p. 254-259
  • Bodenreider O. Provenance information in biomedical knowledge repositories – A use case. Proceedings of the First International Workshop on the role of Semantic Web in Provenance Management (SWPM 2009), 2009: p. (electronic proceedings: http://ceur-ws.org/Vol-526/).
  • Williams R, Tse T, Zarin D. Characterizing sponsor-imposed restrictions on disclosing results of clinical trials. Presented at: Sixth International Congress on Peer Review and Biomedical Publication; September 2009; Vancouver, BC, Canada.
  • Zarin D, Tse T, Williams R. Frequency and nature of changes in primary outcome measures. Presented at: Sixth International Congress on Peer Review and Biomedical Publication; September 2009; Vancouver, BC, Canada.
  • Tse T, Williams RJ, Zarin DA. Reporting "basic results" in ClinicalTrials.gov. Chest. 2009 Jul;136(1):295-303. doi: 10.1378/chest.08-3022.
  • Tse T, Williams RJ, Zarin DA. Update on Registration of Clinical Trials in ClinicalTrials.gov. Chest. 2009 Jul;136(1):304-5. doi: 10.1378/chest.09-1219.
  • Bodenreider O, Peters LB. A graph-based approach to auditing RxNorm. J Biomed Inform. 2009 Jun;42(3):558-70. doi: 10.1016/j.jbi.2009.04.004. Epub 2009 Apr 24.
  • Cimino JJ, Hayamizu TF, Bodenreider O, Davis B, Stafford GA, Ringwald M. The caBIG terminology review process. J Biomed Inform. 2009 Jun;42(3):571-80. doi: 10.1016/j.jbi.2008.12.003. Epub 2008 Dec 25.
  • Mougin FL, Bodenreider O, Burgun A. Analyzing polysemous concepts from a clinical perspective: application to auditing concept categorization in the UMLS. J Biomed Inform. 2009 Jun;42(3):440-51. doi: 10.1016/j.jbi.2009.03.008. Epub 2009 Mar 18.
  • Vizenor LT, Bodenreider O, McCray AT. Auditing associative relations across two knowledge sources. J Biomed Inform. 2009 Jun;42(3):426-39. doi: 10.1016/j.jbi.2009.01.004.
  • Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spounge J, Landsman D. Identification of cis-regulatory Elements in Gene Co-expression Networks Using A-GLAM. Methods Mol Biol. 2009;541:1-22.
  • Schulz S, Beisswanger, van den Hoek L, Bodenreider O, van Mulligen EM. Alignment of the UMLS Semantic Network with BioTop: Methodology and Assessment Bioinformatics 2009;25(12):i69-i76
  • Tse T, Zarin DA. Clinical Trial Registration and Results Reporting: ClinicalTrials.gov and FDAAA FDLI Update. 2009 Jan/Feb;1:18-22
  • Bodenreider O. Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support. Geissbuhler A, Kulikowski C, editors. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med, 2008. 47(Suppl 1): p. 67-79.
  • Bodenreider O. Comparing SNOMED CT and the NCI Thesaurus through Semantic Web Technologies Proc. KR-MED 2008
  • Bodenreider O. Ontologies and Data Integration in Biomedicine: Success Stories and Challenging Issues In: Bairoch A, Cohen-Boulakia S, Froidevaux C, editors. Proceedings of the Fifth International Workshop on Data Integration in the Life Sciences (DILS 2008); Berlin Heidelberg New York: Springer; 2008. p. 1-4
  • Bodenreider O. Semantic Web for Translational Biomedicine: Two Pilot Experiments [Abstract]. Proc. MIA Summit on Translational Bioinformatics 2008:141
  • Burgun A, Bodenreider O. Accessing and Integrating Data and Knowledge for Biomedical Research Yearb Med Inform. 2008:91-101
  • Mougin F, Burgun A, Bodenreider O, Chabalier J, Loreal O, Le Beux P. Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System Proc DILS 2008. Berlin Heidelberg New York: Springer; 2008. p. 61-76
  • Peters L, Bodenreider O. Using the RxNorm Web Services API for Quality Assurance Purposes AMIA Annu Symp Proc. 2008 Nov 6:591-5.

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