O Bodenreider

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Using SNOMED CT in combination with MedDRA for reporting signal detection and adverse drug reactions reporting
    Olivier Bodenreider
    National Library of Medicine, Bethesda, Maryland, USA
    AMIA Annu Symp Proc 2009:45-9. 2009
  2. pmc Issues in mapping LOINC laboratory tests to SNOMED CT
    Olivier Bodenreider
    National Library of Medicine, Bethesda, MD, USA
    AMIA Annu Symp Proc . 2008
  3. pmc Using UMLS semantics for classification purposes
    O Bodenreider
    National Library of Medicine, Bethesda, Maryland, USA
    Proc AMIA Symp . 2000
  4. pmc Of mice and men: aligning mouse and human anatomies
    Olivier Bodenreider
    National Library of Medicine, Bethesda, USA
    AMIA Annu Symp Proc . 2005
  5. pmc Biomedical ontologies in action: role in knowledge management, data integration and decision support
    O Bodenreider
    National Library of Medicine, 8600 Rockville Pike MS 3841 Bldg 38A, Rm B1N28U, Bethesda, MD 20894, USA
    Yearb Med Inform . 2008
  6. pmc Circular hierarchical relationships in the UMLS: etiology, diagnosis, treatment, complications and prevention
    O Bodenreider
    National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Proc AMIA Symp . 2001
  7. pmc Comparing the representation of anatomy in the FMA and SNOMED CT
    Olivier Bodenreider
    National Library of Medicine, NIH, Bethesda, Maryland, USA
    AMIA Annu Symp Proc . 2006
  8. pmc Strength in numbers: exploring redundancy in hierarchical relations across biomedical terminologies
    Olivier Bodenreider
    U S National Library of Medicine, Bethesda, Maryland National Institutes of Health and Human Services, USA
    AMIA Annu Symp Proc . 2003
  9. pmc Non-lexical approaches to identifying associative relations in the gene ontology
    Olivier Bodenreider
    US National Library of Medicine, Bethesda, Maryland 20894, USA
    Pac Symp Biocomput . 2005
  10. pmc A unified framework for managing provenance information in translational research
    Satya S Sahoo
    Department of Computer Science and Engineering, Wright State University, Dayton, OH, USA
    BMC Bioinformatics 12:461. 2011

Collaborators

Detail Information

Publications40

  1. pmc Using SNOMED CT in combination with MedDRA for reporting signal detection and adverse drug reactions reporting
    Olivier Bodenreider
    National Library of Medicine, Bethesda, Maryland, USA
    AMIA Annu Symp Proc 2009:45-9. 2009
    ..To investigate the feasibility of using SNOMED CT as an entry point for coding adverse drug reactions and map them automatically to MedDRA for reporting purposes and interoperability with legacy repositories...
  2. pmc Issues in mapping LOINC laboratory tests to SNOMED CT
    Olivier Bodenreider
    National Library of Medicine, Bethesda, MD, USA
    AMIA Annu Symp Proc . 2008
    ..However, a large proportion of LOINC codes could not be mapped to SNOMED CT through this approach, because of underspecified definitions in SNOMED CT and a lack of fine-grained, pre-coordinated concepts in SNOMED CT...
  3. pmc Using UMLS semantics for classification purposes
    O Bodenreider
    National Library of Medicine, Bethesda, Maryland, USA
    Proc AMIA Symp . 2000
    ..135 (7%) failed to be classified and 14 (.77%) were misclassified. The limits of this method are discussed, as well as the reuse of existing components, and the tuning required to achieve automatic classification...
  4. pmc Of mice and men: aligning mouse and human anatomies
    Olivier Bodenreider
    National Library of Medicine, Bethesda, USA
    AMIA Annu Symp Proc . 2005
    ..715 and 781 mappings were identified by each method respectively, of which 639 are common to both and all valid. The applications of the map-ping are discussed from the perspective of biology and from that of ontology...
  5. pmc Biomedical ontologies in action: role in knowledge management, data integration and decision support
    O Bodenreider
    National Library of Medicine, 8600 Rockville Pike MS 3841 Bldg 38A, Rm B1N28U, Bethesda, MD 20894, USA
    Yearb Med Inform . 2008
    ..To provide typical examples of biomedical ontologies in action, emphasizing the role played by biomedical ontologies in knowledge management, data integration and decision support...
  6. pmc Circular hierarchical relationships in the UMLS: etiology, diagnosis, treatment, complications and prevention
    O Bodenreider
    National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Proc AMIA Symp . 2001
    ..Then, we discuss methods to identify and remove these relationships. Finally, we briefly discuss the consequences of these relationships for applications based on the UMLS, and we propose some prevention measures...
  7. pmc Comparing the representation of anatomy in the FMA and SNOMED CT
    Olivier Bodenreider
    National Library of Medicine, NIH, Bethesda, Maryland, USA
    AMIA Annu Symp Proc . 2006
    ....
  8. pmc Strength in numbers: exploring redundancy in hierarchical relations across biomedical terminologies
    Olivier Bodenreider
    U S National Library of Medicine, Bethesda, Maryland National Institutes of Health and Human Services, USA
    AMIA Annu Symp Proc . 2003
    ....
  9. pmc Non-lexical approaches to identifying associative relations in the gene ontology
    Olivier Bodenreider
    US National Library of Medicine, Bethesda, Maryland 20894, USA
    Pac Symp Biocomput . 2005
    ..The application to quality assurance of annotation databases is also discussed...
  10. pmc A unified framework for managing provenance information in translational research
    Satya S Sahoo
    Department of Computer Science and Engineering, Wright State University, Dayton, OH, USA
    BMC Bioinformatics 12:461. 2011
    ....
  11. pmc The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside
    Joanne S Luciano
    Rensselaer Polytechnic Institute, Troy, NY, USA
    J Biomed Semantics 2:S1. 2011
    ..Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery...
  12. pmc Global similarity and local divergence in human and mouse gene co-expression networks
    Panayiotis Tsaparas
    Basic Research Unit, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
    BMC Evol Biol 6:70. 2006
    ..Expression profiles were resolved into species-specific coexpression networks, and the topological properties of the networks were compared between species...
  13. pmc Advancing translational research with the Semantic Web
    Alan Ruttenberg
    Millennium Pharmaceuticals, Cambridge, MA, USA
    BMC Bioinformatics 8:S2. 2007
    ....
  14. pmc Mapping data elements to terminological resources for integrating biomedical data sources
    Fleur Mougin
    EA 3888, IFR 140, Faculte de Medecine, Universite de Rennes I, France
    BMC Bioinformatics 7:S6. 2006
    ..Data elements (DEs) in particular play an important role in data integration. We combine schema- and instance-based approaches to mapping DEs to terminological resources in order to facilitate data sources integration...
  15. pmc Aligning knowledge sources in the UMLS: methods, quantitative results, and applications
    Olivier Bodenreider
    U S National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MS 43, Bethesda, MD 20894, USA
    Stud Health Technol Inform 107:327-31. 2004
    ..The relative contribution and limitations of the two methods used for the alignment are also discussed...
  16. pmc A graph-based approach to auditing RxNorm
    Olivier Bodenreider
    Lister Hill National Center for Biomedical Communications, National Library of Medicine, Bethesda, MD 20894, USA
    J Biomed Inform 42:558-70. 2009
    ..In this paper, we audit relations in RxNorm for consistency and completeness through the systematic analysis of the graph of its concepts and relationships...
  17. pmc A framework for comparing phenotype annotations of orthologous genes
    Olivier Bodenreider
    US National Library of Medicine, NIH, Bethesda, USA
    Stud Health Technol Inform 160:1309-13. 2010
    ..The objective of this paper is to propose a framework for comparing phenotype annotations of orthologous genes based on the Medical Subject Headings (MeSH) indexing of biomedical articles in which these genes are discussed...
  18. pmc An object-oriented model for representing semantic locality in the UMLS
    O Bodenreider
    U S National Library of Medicine, Bethesda, MD 20894, USA
    Stud Health Technol Inform 84:161-5. 2001
    ..Additional semantic methods for reducing the complexity of the hierarchical relationships represented in the UMLS are proposed. Implementation details are presented, as well as examples of use. The interest of this approach is discussed...
  19. pmc Investigating subsumption in SNOMED CT: an exploration into large description logic-based biomedical terminologies
    Olivier Bodenreider
    U S National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Artif Intell Med 39:183-95. 2007
    ..The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles...
  20. ncbi request reprint Assessing the consistency of a biomedical terminology through lexical knowledge
    Olivier Bodenreider
    US National Library of Medicine, 8600 Rockville Pike, MS 43, Bethesda, MD 20894, USA
    Int J Med Inform 67:85-95. 2002
    ..We investigate the use of adjectival modification as a way of assessing the systematic use of linguistic phenomena to represent similar lexical or semantic features in the constituent terms of a vocabulary...
  21. pmc Evaluation of WordNet as a source of lay knowledge for molecular biology and genetic diseases: a feasibility study
    Olivier Bodenreider
    University of Rennes I, France
    Stud Health Technol Inform 95:379-84. 2003
    ..This paper evaluates whether concepts needed for molecular biology and genetic diseases are present in WordNet, the electronic lexical database...
  22. pmc Bio-ontologies: current trends and future directions
    Olivier Bodenreider
    National Library of Medicine, Bethesda, MD 20894, USA
    Brief Bioinform 7:256-74. 2006
    ..With this and the institutionalization of ontology has come greater formality. We review this trend and what benefits it might bring to ontologies and their use within biomedicine...
  23. pmc The Unified Medical Language System (UMLS): integrating biomedical terminology
    Olivier Bodenreider
    Lister Hill Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:D267-70. 2004
    ..All vocabularies are available at no fee for research purposes within an institution, but UMLS users are required to sign a license agreement. The UMLS knowledge sources are distributed on CD-ROM and by FTP...
  24. pmc Exploring semantic groups through visual approaches
    Olivier Bodenreider
    Department of Health and Human Services, National Institutes of Health, National Library of Medicine, Lister Hill National Center for Biomedical Communications, MS 43, Bldg 38A Rm B1N28U, 8600 Rockville Pike, Bethesda, MD 20894, USA
    J Biomed Inform 36:414-32. 2003
    ..They make outliers immediately apparent, and, thus, serve as a tool for auditing and validating both the semantic network and the semantic groups...
  25. pmc Aggregating UMLS semantic types for reducing conceptual complexity
    A T McCray
    National Library of Medicine, Bethesda, Maryland, 20894, USA
    Stud Health Technol Inform 84:216-20. 2001
    ..We present some of the difficulties we encountered and the consequences of the decisions we have made. We discuss some possible uses of the semantic groups, and we conclude with implications for future work...
  26. pmc Methods for exploring the semantics of the relationships between co-occurring UMLS concepts
    A Burgun
    U S National Library of Medicine, Bethesda, MD 20894, USA
    Stud Health Technol Inform 84:171-5. 2001
    ..To characterize the relationships among UMLS concepts that co-occur as MeSH descriptors in MEDLINE citations (1990-1999)...
  27. pmc Combining lexical and semantic methods of inter-terminology mapping using the UMLS
    Kin Wah Fung
    National Library of Medicine, Bethesda, Maryland 20894, USA
    Stud Health Technol Inform 129:605-9. 2007
    ..The combined method outperformed both methods, achieving coverage of 91%, recall of 43% and precision of 27%. It is also possible to customize the method of combination to optimize performance according to the task at hand...
  28. pmc The caBIG terminology review process
    James J Cimino
    National Institutes of Health, Laboratory for Informatics Development, Clinical Center, Room 6 2551, 10 Center Drive, Bethesda, MD 20892, USA
    J Biomed Inform 42:571-80. 2009
    ..The resulting caBIG criteria are presented as a matrix that may be applicable to any terminology standardization effort...
  29. pmc Comparing associative relationships among equivalent concepts across ontologies
    Songmao Zhang
    U S National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Stud Health Technol Inform 107:459-66. 2004
    ..The various types of matches identified are discussed as well as the application of this method to detecting inconsistencies across the ontologies...
  30. pmc From phenotype to genotype: issues in navigating the available information resources
    J A Mitchell
    Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
    Methods Inf Med 42:557-63. 2003
    ..As part of an investigation of connecting health professionals and the lay public to both disease and genomic information, we assessed the availability and nature of the data from the Human Genome Project relating to human genetic diseases...
  31. pmc Law and order: assessing and enforcing compliance with ontological modeling principles in the Foundational Model of Anatomy
    Songmao Zhang
    U S National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Comput Biol Med 36:674-93. 2006
    ..Reasons for non-compliance are analyzed and suggestions are made for implementing effective enforcement mechanisms in ontology development environments. The limitations of this study are also discussed...
  32. pmc Extracting Rx information from clinical narrative
    James G Mork
    US National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    J Am Med Inform Assoc 17:536-9. 2010
    ....
  33. pmc Mapping the UMLS Semantic Network into general ontologies
    A Burgun
    National Library of Medicine, National Institutes of Health, Bethsda, Maryland, USA
    Proc AMIA Symp . 2001
    ..WordNet, as a general language-oriented ontology is a source of lay knowledge, particularly important for consumer health applications...
  34. pmc Identifying proper names in parallel medical terminologies
    O Bodenreider
    U.S. National Library of Medicine, Bethesda, MD, USA
    Stud Health Technol Inform 77:443-7. 2000
    ..A combination of five criteria achieved 86% precision and 88% recall on the 16,401 word forms of the International Classification of Diseases...
  35. pmc Identification of cis-regulatory elements in gene co-expression networks using A-GLAM
    Leonardo Mariño-Ramírez
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
    Methods Mol Biol 541:1-22. 2009
    ..Using this approach, we analyze the cell-cycle co-expression network of the yeast Saccharomyces cerevisiae, showing that this approach correctly identifies cis-regulatory elements present in clusters of co-expressed genes...
  36. pmc The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site
    Kannan Tharakaraman
    Computational Biology Branch, National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, MSC 6075 Bethesda, MD 20894 6075, USA
    Nucleic Acids Res 36:2777-86. 2008
    ..By exploiting the phenomenon of positional regulation, it uses position to differentiate the biological functions of subsets of TFBSs sharing a common sequence motif...
  37. pmc Combining relevance assignment with quality of the evidence to support guideline development
    Marcelo Fiszman
    National Library of Medicine, NIH, Bethesda, MD, USA
    Stud Health Technol Inform 160:709-13. 2010
    ..5-score 0.75). We suggest that this system can potentially improve the efficiency of the literature review process in guideline development...
  38. pmc From "glycosyltransferase" to "congenital muscular dystrophy": integrating knowledge from NCBI Entrez Gene and the Gene Ontology
    Satya S Sahoo
    Kno e sis Center, Department of Computer Science and Engineering, Wright State University, Dayton, OH, USA
    Stud Health Technol Inform 129:1260-4. 2007
    ..We illustrate the effectiveness of our approach by answering a real-world biomedical query linking a specific molecular function, glycosyltransferase, to the disorder congenital muscular dystrophy...
  39. pmc Comparing two approaches for aligning representations of anatomy
    Songmao Zhang
    Institute of Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, PR China
    Artif Intell Med 39:227-36. 2007
    ..To analyze the comparison, through their results, of two distinct approaches applied to aligning two representations of anatomy...
  40. pmc Lessons learned from cross-validating alignments between large anatomical ontologies
    Songmao Zhang
    Institute of Mathematics, Academy of Mathematics and Systems Science Chinese Academy of Sciences, Beijing, PR China
    Stud Health Technol Inform 129:822-6. 2007
    ....