Barry Smith

Summary

Affiliation: University at Buffalo
Country: USA

Publications

  1. ncbi request reprint Establishing and harmonizing ontologies in an interdisciplinary health care clinical research environment
    Barry Smith
    University at Buffalo, Buffalo, NY 14260, USA
    Stud Health Technol Inform 134:219-33. 2008
  2. pmc The representation of protein complexes in the Protein Ontology (PRO)
    Carol J Bult
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    BMC Bioinformatics 12:371. 2011
  3. pmc Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base
    Jiye Ai
    University of California at Los Angeles School of Dentistry, University of California, Los Angeles, CA 90095 1668, USA
    BMC Bioinformatics 11:302. 2010
  4. pmc Framework for a protein ontology
    Darren A Natale
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven St, NW, Washington, DC 20007, USA
    BMC Bioinformatics 8:S1. 2007
  5. pmc Survey-based naming conventions for use in OBO Foundry ontology development
    Daniel Schober
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 10:125. 2009
  6. pmc TGF-beta signaling proteins and the Protein Ontology
    Cecilia N Arighi
    Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 10:S3. 2009
  7. pmc Gene Ontology annotations: what they mean and where they come from
    David P Hill
    The Jackson Laboratory, Bar Harbor, ME, USA
    BMC Bioinformatics 9:S2. 2008
  8. pmc Quality control for terms and definitions in ontologies and taxonomies
    Jacob Köhler
    Biomathematics and Bioinformatics Division, Rothamsted Research, Harpenden, UK
    BMC Bioinformatics 7:212. 2006
  9. pmc An improved ontological representation of dendritic cells as a paradigm for all cell types
    Anna Maria Masci
    Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
    BMC Bioinformatics 10:70. 2009
  10. pmc Putting biomedical ontologies to work
    B Smith
    Institute of Formal Ontology and Medical Information Science IFOMIS, Universitat des Saarlandes, Campus A2 4, 66123 Saarbrucken, Germany
    Methods Inf Med 49:135-40. 2010

Collaborators

Detail Information

Publications39

  1. ncbi request reprint Establishing and harmonizing ontologies in an interdisciplinary health care clinical research environment
    Barry Smith
    University at Buffalo, Buffalo, NY 14260, USA
    Stud Health Technol Inform 134:219-33. 2008
    ..An example of such harmonization within the ACGT project is described, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research...
  2. pmc The representation of protein complexes in the Protein Ontology (PRO)
    Carol J Bult
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    BMC Bioinformatics 12:371. 2011
    ....
  3. pmc Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base
    Jiye Ai
    University of California at Los Angeles School of Dentistry, University of California, Los Angeles, CA 90095 1668, USA
    BMC Bioinformatics 11:302. 2010
    ..SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO)...
  4. pmc Framework for a protein ontology
    Darren A Natale
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven St, NW, Washington, DC 20007, USA
    BMC Bioinformatics 8:S1. 2007
    ..Here we describe the initial development of PRO, illustrated using human and mouse proteins involved in the transforming growth factor-beta and bone morphogenetic protein signaling pathways...
  5. pmc Survey-based naming conventions for use in OBO Foundry ontology development
    Daniel Schober
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 10:125. 2009
    ....
  6. pmc TGF-beta signaling proteins and the Protein Ontology
    Cecilia N Arighi
    Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 10:S3. 2009
    ..Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO...
  7. pmc Gene Ontology annotations: what they mean and where they come from
    David P Hill
    The Jackson Laboratory, Bar Harbor, ME, USA
    BMC Bioinformatics 9:S2. 2008
    ....
  8. pmc Quality control for terms and definitions in ontologies and taxonomies
    Jacob Köhler
    Biomathematics and Bioinformatics Division, Rothamsted Research, Harpenden, UK
    BMC Bioinformatics 7:212. 2006
    ..As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way...
  9. pmc An improved ontological representation of dendritic cells as a paradigm for all cell types
    Anna Maria Masci
    Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
    BMC Bioinformatics 10:70. 2009
    ..This approach limits the CL's utility for computation and for cross-species data integration...
  10. pmc Putting biomedical ontologies to work
    B Smith
    Institute of Formal Ontology and Medical Information Science IFOMIS, Universitat des Saarlandes, Campus A2 4, 66123 Saarbrucken, Germany
    Methods Inf Med 49:135-40. 2010
    ..How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage?..
  11. pmc The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    Barry Smith
    Department of Philosophy and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York 14203, USA
    Nat Biotechnol 25:1251-5. 2007
    ..We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved...
  12. ncbi request reprint HL7 RIM: an incoherent standard
    Barry Smith
    Department of Philosophy, University at Buffalo, Buffalo NY, USA
    Stud Health Technol Inform 124:133-8. 2006
    ..We offer evidence that these obstacles are insurmountable and that the time has come to abandon an unworkable paradigm...
  13. ncbi request reprint Sixteen days
    Barry Smith
    Institute for Formal Ontology and Medical Information Science, Faculty of Medicine, University of Leipzig, Leipzig, Germany
    J Med Philos 28:45-78. 2003
    ..Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the relation between fetus and mother (connection, parthood, dependence)...
  14. pmc Relations in biomedical ontologies
    Barry Smith
    Institute for Formal Ontology and Medical Information Science, Saarland University, D 66041 Saarbrucken, Germany
    Genome Biol 6:R46. 2005
    ..The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena...
  15. ncbi request reprint From concepts to clinical reality: an essay on the benchmarking of biomedical terminologies
    Barry Smith
    Department of Philosophy and National Center for Biomedical Ontology, University at Buffalo, Buffalo, NY 14260, USA
    J Biomed Inform 39:288-98. 2006
    ..We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support...
  16. ncbi request reprint Referent tracking: the problem of negative findings
    Werner Ceusters
    Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, NY 14023, USA
    Stud Health Technol Inform 124:741-6. 2006
    ..This relation is found to be able to accommodate nearly all occurrences of negative findings in the examined sample, in ways which involve no reference to negative entities...
  17. ncbi request reprint Strategies for referent tracking in electronic health records
    Werner Ceusters
    European Centre for Ontological Research, Univerisität des Saarlandes, Postfach 151150, D 66041 Saarbrucken, Germany
    J Biomed Inform 39:362-78. 2006
    ....
  18. doi request reprint Ontologies of cellular networks
    Robert Arp
    National Center for Biomedical Ontology, University at Buffalo, Buffalo, NY 14260, USA
    Sci Signal 1:mr2. 2008
    ..The meeting focused on three questions: What is an ontology? What is a pathway? What is a cellular network?..
  19. ncbi request reprint Functional anatomy: a taxonomic proposal
    Ingvar Johansson
    Institute for Formal Ontology and Medical Information Science, University of Saarland, Saarbrucken, Postfach 151150, D 66041, Germany
    Acta Biotheor 53:153-66. 2005
    ..We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences...
  20. pmc Negative findings in electronic health records and biomedical ontologies: a realist approach
    Werner Ceusters
    Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, NY 14203, USA
    Int J Med Inform 76:S326-33. 2007
    ..The purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT...
  21. pmc A unified framework for biomedical terminologies and ontologies
    Werner Ceusters
    Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
    Stud Health Technol Inform 160:1050-4. 2010
    ..We propose a framework for such analysis that is designed to maximize the degree to which legacy terminologies and the data coded with their aid can be successfully used for information-driven clinical and translational research...
  22. ncbi request reprint The role of foundational relations in the alignment of biomedical ontologies
    Barry Smith
    Institute for Formal Ontology and Medical Information Service, University of Leipzig, Härtelstrasse 16 18, 04107 Leipzig, Germany
    Stud Health Technol Inform 107:444-8. 2004
    ..We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies...
  23. ncbi request reprint Formal ontology for natural language processing and the integration of biomedical databases
    Jonathan Simon
    IFOMIS, Saarland University, Saarbrucken, Germany
    Int J Med Inform 75:224-31. 2006
    ..Montayne, J. Flanagan, Formal Ontology: The Foundation for Natural Language Processing, 2003. http://www.landcglobal.com/]...
  24. pmc Foundations for a realist ontology of mental disease
    Werner Ceusters
    Ontology Research Group, Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203, USA
    J Biomed Semantics 1:10. 2010
    ....
  25. ncbi request reprint Bodily systems and the spatial-functional structure of the human body
    Barry Smith
    Institute for Formal Ontology and Medical Information Science, Faculty of Medicine, University of Leipzig, Leipzig, Germany
    Stud Health Technol Inform 102:39-63. 2004
    ..In our analysis we will accordingly provide the framework for a formal definition of bodily system and of associated notions...
  26. pmc An evolutionary approach to the representation of adverse events
    Werner Ceusters
    New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, NY 14203, USA
    Stud Health Technol Inform 150:537-41. 2009
    ..We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project...
  27. ncbi request reprint Biodynamic ontology: applying BFO in the biomedical domain
    Pierre Grenon
    Institute for Formal Ontology and Medical Information Science, University of Leipzig
    Stud Health Technol Inform 102:20-38. 2004
    ..We outline an approach which allows them to be combined together, and provide examples of its application in biomedicine...
  28. ncbi request reprint Mistakes in medical ontologies: where do they come from and how can they be detected?
    Werner Ceusters
    Language and Computing nv, Hazenakkerstraat 20a, B 9520 Zonnegem, Belgium
    Stud Health Technol Inform 102:145-63. 2004
    ..We conclude by outlining the results of applying the methodology in the form of a taxonomy different types of errors and potential errors detected in SNOMED-CT...
  29. 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...
  30. pmc Wrestling with SUMO and bio-ontologies
    Mark A Musen
    Nat Biotechnol 24:21; author reply 23. 2006
  31. ncbi request reprint Towards new information resources for public health--from WordNet to MedicalWordNet
    Christiane Fellbaum
    Department of Psychology, Princeton University Green Hall, Washington Rd, Princeton, NJ 08544, United States
    J Biomed Inform 39:321-32. 2006
    ..The work described here has been tested in a small pilot experiment and awaits large-scale implementation...
  32. ncbi request reprint Using cross-lingual information to cope with underspecification in formal ontologies
    Werner Ceusters
    Language and Computing nv, Zonnegem, Beligium
    Stud Health Technol Inform 95:391-6. 2003
    ..By using a specific experimental design, we are able to quantify the impact of cross-lingual information in coping with underspecification in formal ontologies...
  33. ncbi request reprint Ontology-based error detection in SNOMED-CT
    Werner Ceusters
    VP Research, Language and Computing nv, Het Moorhof, Hazenakkerstraat 20a, B9520 Zonnegem, Belgium
    Stud Health Technol Inform 107:482-6. 2004
    ..Analysis of the results provides evidence for the thesis that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies...
  34. pmc Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Chris F Taylor
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 26:889-96. 2008
  35. ncbi request reprint Context-based task ontologies for clinical guidelines
    Anand Kumar
    LMI, Department of Computer Science, University of Pavia, Italy
    Stud Health Technol Inform 102:81-94. 2004
    ....
  36. ncbi request reprint An ontological framework for the implementation of clinical guidelines in health care organizations
    Anand Kumar
    LMI, Department of Computer Science, University of Pavia, Italy
    Stud Health Technol Inform 102:95-107. 2004
    ....
  37. ncbi request reprint National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge
    Daniel L Rubin
    Stanford Medical Informatics, Stanford University, Stanford, California 94305, USA
    OMICS 10:185-98. 2006
    ....
  38. ncbi request reprint Bridging the gap between medical and bioinformatics: an ontological case study in colon carcinoma
    Anand Kumar
    IFOMIS, University of Saarland, Saarbruecken, Germany
    Comput Biol Med 36:694-711. 2006
    ..In this paper, we describe a large multi-granular datasource built by using ontological principles and focusing on the case of colon carcinoma...
  39. pmc Development of FuGO: an ontology for functional genomics investigations
    Patricia L Whetzel
    Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    OMICS 10:199-204. 2006
    ....