University at Buffalo (UB)
Barry Smith PhD FACMI
Barry Smith
PhD FACMI
Professor
Department of Biomedical Informatics
Specialty/Research Focus
Artificial Intelligence; Biomedical Informatics; Biomedical Ontology; Pain
Professional Summary:
Barry Smith is a prominent contributor to both theoretical and applied research in ontology, contributing especially in the biomedical domain. He is the author of some 500 publications on ontology, with some 48,000 citations and an h-index of 103. His research has been funded by the National Institutes of Health, the US, Swiss and Austrian National Science Foundations, the US Department of Defense, the Volkswagen Foundation, and the European Union. In 2002 he received the 2 million Euro Wolfgang Paul Award of the Alexander von Humboldt Foundation and in 2010 he was awarded the first Paolo Bozzi Prize in Ontology by the University of Turin.
Smith is SUNY Distinguished Professor in the Department of Philosophy in the University at Buffalo (UB) and Affiliate Professor in the UB Departments of Biomedical Informatics and Computer Science and Engineering. He is also Director of the National Center for Ontological Research and national Co-Director of the Clinical and Translational Science Ontology Group (CTSOG). He has served as ontology lead for the NIAID ImmPort project, as lead for dissemination and ontology best practices for the National Center for Biomedical Ontology, as a Scientific Advisor to the Gene Ontology Consortium, and as a PI on the Protein Ontology and Infectious Disease Ontology projects.
Smith’s pioneering work on the science of ontology led to the formation in 2004 of the OBO (Open Biomedical Ontologies) Foundry, a suite of ontology resources designed to support information-driven research in biology and biomedicine. Basic Formal Ontology (BFO), the capstone ontology in the OBO Foundry suite, was approved in 2021 as international standard ISO/ICE 21838-2. It is now used by some 500 ontology development groups around the world.
Education and Training:
- PhD, Philosophy, University of Manchester (1976)
- MA, Mathematics and Philosophy, Oxford University (1975)
- BA, Mathematics and Philosophy, Oxford University (1973)
Employment:
- Director, Philosophy, National Center for Ontological Research (2002-present)
- Distinguished Professor, Philosophy, University at Buffalo (1994-present)
- Director, UB Center for Brain and Behavior Informatics (CBBI) (2009–2012)
- Professor, International Academy for Philosophy (1989–1994)
- Professor, Philosophy, University of Manchester (1979–1989)
- Post Doctoral Fellow, Philosophy, University of Sheffield (1976–1979)
Awards and Honors:
- Wolfgang Paul Award (2022)
- Paolo Bozzi Prize (2010)
- Carl Linnaeus Lecturer (2005)
- SUNY Chancellor’s Award for Excellence in Scholarship (2002)
- Fellow of the American Philosophical Society (1999)
- Fellow of the American College of Medical Informatics (FACMI)
Research Centers:
- Center of Excellence in Bioinformatics and Life Sciences
- Clinical and Translational Research Center (CTRC)
UB 2020 Strategic Strengths:
- Health and Wellness Across the Lifespan
- Information and Computing Technology
Grants and Sponsored Research:
- August 2015–March 2019
Clinical and Translational Science Award: Buffalo Clinical and Translational Research Center
National Center for Advancing Translational Sciences
Role: Co-Investigator
$13,151,902 - January 2017–July 2018
Coordinated Holistic Alignment of Manufacturing Processes
DMDII
Role: Principal Investigator
$1,254,004 - October 2012–September 2017
Bioinformatics Integration Support Contract
NIH
Role: Principal Investigator
$1,028,815
Journal Articles:
- Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L. Whetzel, Suzanna Lewis. (2007) The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration. Nature Biotechnology (Nov), 25(11): 1251-1255.
- He Y, Yu H, Huffman A, Lin AY, Natale DA, Beverley J, Zheng L, Perl Y, Wang Z, Liu Y, Ong E, Wang Y, Huang P, Tran L, Du J, Shah Z, Shah E, Desai R, Huang HH, Tian Y, Merrell E, Duncan WD, Arabandi S, Schriml LM, Zheng J, Masci AM, Wang L, Liu H, Smaili FZ, Hoehndorf R, Pendlington ZM, Roncaglia P, Ye X, Xie J, Tang YW, Yang X, Peng S, Zhang L, Chen L, Hur J, Omenn GS, Athey B, Smith B. (2022) A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. Journal of biomedical semantics (Oct), 13(1): 25. doi:10.1186/s13326-022-00279-z
- Yu H, Li L, Huffman A, Beverley J, Hur J, Merrell E, Huang HH, Wang Y, Liu Y, Ong E, Cheng L, Zeng T, Zhang J, Li P, Liu Z, Wang Z, Zhang X, Ye X, Handelman SK, Sexton J, Eaton K, Higgins G, Omenn GS, Athey B, Smith B, Chen L, He Y. (2022) A new framework for host-pathogen interaction research. Frontiers in immunology (Jan), 13: 1066733. doi:10.3389/fimmu.2022.1066733
- Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley DM, Duncan WD, Harris NL, Haendel MA, Lewis SE, Natale DA, Osumi-Sutherland D, Ruttenberg A, Schriml LM, Smith B, Stoeckert CJ, Vasilevsky NA, Walls RL, Zheng J, Mungall CJ, Peters B. (2021) OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database : the journal of biological databases and curation (Oct), 2021. doi:10.1093/database/baab069
- Babcock S, Beverley J, Cowell LG, Smith B. (2021) The Infectious Disease Ontology in the age of COVID-19. Journal of biomedical semantics (Jul), 12(1): 13. doi:10.1186/s13326-021-00245-1
- Lin AY, Gebel S, Li QL, Madan S, Darms J, Bolton E, Smith B, Hofmann-Apitius M, He YO, Kodamullil AT. (2020) CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView. CEUR workshop proceedings (Sep), 2807.
- Kolyvakis P, Kalousis A, Smith B, Kiritsis D. (2018) Biomedical ontology alignment: an approach based on representation learning. J Biomed Semantics (Aug), 9(1): 21-21.
- Bhattacharya S, Dunn P, Thomas CG, Smith B, Schaefer H, Chen J, Hu Z, Zalocusky KA, Shankar RD, Shen-Orr SS, Thomson E, Wiser J, Butte AJ. (2018) ImmPort, toward repurposing of open access immunological assay data for translational and clinical research. Sci Data (Feb), 5: 180015-180015.
- Cooper L, Meier A, Laporte MA, Elser JL, Mungall C, Sinn BT, Cavaliere D, Carbon S, Dunn NA, Smith B, Qu B, Preece J, Zhang E, Todorovic S, Gkoutos G, Doonan JH, Stevenson DW, Arnaud E, Jaiswal P. (2018) The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Res (Jan), 46(D1): 1168-1180.
- Ceusters W, Smith B. (2018) On Defining Bruxism. Stud Health Technol Inform (Jan), 247: 551-555.
- Smith B, Dubovsky SL, Smith BA. (2017) Pharmacotherapy of mood disorders and psychosis in pre- and post-natal women. Expert Opin Pharmacother (Nov), 18(16): 1703-1719.
- Moore N, Moreno Gonzales M, Bonner K, Smith B, Park W, Stegall M, Bonner KP. (2017) Impact of CXCR4/CXCL12 Blockade on Normal Plasma Cells In Vivo. Am J Transplant (Jun), 17(6): 1663-1669.
- Gurcan MN, Tomaszewski J, Overton JA, Doyle S, Ruttenberg A, Smith B. (2017) Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. J Biomed Inform (Feb), 66: 129-135.
- Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. (2017) Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res (Jan), 45(D1): 339-346.
- Gurcan, MN, Tomaszewski JE, Overton, JA, Doyle ST, Ruttenberg, A, Smith B. (2016) Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. Epub (Dec), 12(006).
- Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. (2016) Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res (Nov).
- Zheng J, Harris MR, Masci AM, Lin Y, Hero A, Smith B, He Y. (2016) The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. J Biomed Semantics (Sep), 7(1): 53-53.
- Huang J, Gutierrez F, Strachan HJ, Dou D, Huang W, Smith B, Blake JA, Eilbeck K, Natale DA, Lin Y, Wu B, Silva ND, Wang X, Liu Z, Borchert GM, Tan M, Ruttenberg A. (2016) OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. J Biomed Semantics (May), 7: 25-25.
- Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M. (2016) The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. J Biomed Semantics (May), 7: 24-24.
- Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. (2016) The Ontology for Biomedical Investigations. PLoS One (Apr), 11(4): 0154556-0154556.
- Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, de Silva N, Kasukurthi MV, Jha VK, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M. (2016) The development of non-coding RNA ontology. Int J Data Min Bioinform (Jan), 15(3): 214-232.
- Smith B, Arabandi S, Brochhausen M, Calhoun M, Ciccarese P, Doyle S, Gibaud B, Goldberg I, Kahn CE, Overton J, Tomaszewski J, Gurcan M, Doyle ST. (2015) Biomedical imaging ontologies: A survey and proposal for future work. J Pathol Inform (Jun), 6: 37-37.
- Arighi C, Shamovsky V, Masci AM, Ruttenberg A, Smith B, Natale DA, Wu C, D'Eustachio P, Ruttenberg AH. (2015) Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework. PLoS One (Apr), 10(3): 0122978-0122978.
- Ceusters W, Smith B. (2015) Biomarkers in the ontology for general medical science. Stud Health Technol Inform (Jan), 210: 155-159.
- Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P, Ruttenberg AH. (2015) Finding our way through phenotypes. PLoS Biol (Jan), 13(1): 1002033-1002033.
- He Y, Sarntivijai S, Lin Y, Xiang Z, Guo A, Zhang S, Jagannathan D, Toldo L, Tao C, Smith B. (2014) OAE: The Ontology of Adverse Events. J Biomed Semantics (Jul), 5: 29-29.
- Hastings J, Frishkoff GA, Smith B, Jensen M, Poldrack RA, Lomax J, Bandrowski A, Imam F, Turner JA, Martone ME. (2014) Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies. Front Neuroinform (Jun), 8: 62-62.
- Walls RL, Deck J, Guralnick R, Baskauf S, Beaman R, Blum S, Bowers S, Buttigieg PL, Davies N, Endresen D, Gandolfo MA, Hanner R, Janning A, Krishtalka L, Matsunaga A, Midford P, Morrison N, Ó Tuama É, Schildhauer M, Smith B, Stucky BJ, Thomer A, Wieczorek J, Whitacre J, Wooley J. (2014) Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. PLoS One (Mar), 9(3): 89606-89606.
- Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Çelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH. (2014) Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res (Jan), 42(Datab): 415-421.
- Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE. (2013) The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics (Dec), 4(1): 43-43.
- Jensen M, Cox AP, Chaudhry N, Ng M, Sule D, Duncan W, Ray P, Weinstock-Guttman B, Smith B, Ruttenberg A, Szigeti K, Diehl AD. (2013) The neurological disease ontology. Journal of biomedical semantics (Dec), 4(1): 42. doi:10.1186/2041-1480-4-42
- Fuellen G, Boerries M, Busch H, de Grey A, Hahn U, Hiller T, Hoeflich A, Jansen L, Janssens GE, Kaleta C, Meinema AC, Schäuble S, Simm A, Schofield PN, Smith B, Sühnel J, Vera J, Wagner W, Wönne EC, Wuttke D. (2013) In silico approaches and the role of ontologies in aging research. Rejuvenation Res (Dec), 16(6): 540-546.
- Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P. (2013) The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol (Feb), 54(2): 1-1.
- Smith B. (2012) CLASSIFYING PROCESSES: AN ESSAY IN APPLIED ONTOLOGY. Ratio (Oxf) (Dec), 25(4): 463-488.
- Smith B. (2012) Classifying Processes: An Essay in Applied Ontology. Ratio (Oxf) (Dec), 25(4): 463-488.
- Walls RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall CJ, Preece J, Rensing S, Smith B, Stevenson DW. (2012) Ontologies as integrative tools for plant science. American journal of botany (Aug), 99(8): 1263-75. doi:10.3732/ajb.1200222
- Ai JY, Smith B, Wong DT. (2012) Bioinformatics advances in saliva diagnostics. International journal of oral science (Jun), 4(2): 85-7. doi:10.1038/ijos.2012.26
- Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B. (2012) The National Center for Biomedical Ontology. J Am Med Inform Assoc (Mar), 19(2): 190-195.
- Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A, D'Eustachio P, Smith B, Blake JA, Wu C. (2011) The representation of protein complexes in the Protein Ontology (PRO). BMC Bioinformatics (Sep), 12: 371-371.
- Goldfain A, Smith B, Cowell LG. (2011) Towards an ontological representation of resistance: the case of MRSA. Journal of biomedical informatics (Feb), 44(1): 35-41. doi:10.1016/j.jbi.2010.02.008
- Kalra D, Musen M, Smith B, Ceusters W, De Moor G. (2011) ARGOS policy brief on semantic interoperability. Studies in health technology and informatics (Jan), 170: 1-15.
- Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Zhang J, Wu CH. (2011) The Protein Ontology: a structured representation of protein forms and complexes. Nucleic Acids Res (Jan), 39(Datab): 539-545.
- Ceusters W, Smith B. (2010) Foundations for a realist ontology of mental disease. Journal of biomedical semantics (Dec), 1(1): 10. doi:10.1186/2041-1480-1-10
- Smith B, Ceusters W. (2010) Ontological realism: A methodology for coordinated evolution of scientific ontologies. Applied ontology (Nov), 5(3-4): 139-188. doi:10.3233/AO-2010-0079
- Ai J, Smith B, Wong DT. (2010) Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base. BMC Bioinformatics (Jun), 11: 302-302.
- Klein GO, Smith B. (2010) Concept Systems and Ontologies: Recommendations for Basic Terminology. Transactions of the Japanese Society for Artificial Intelligence = Jinko Chino Gakkai ronbunshi (Jan), 25(3): 433-441. doi:10.1527/tjsai.25.433
- Ceusters W, Smith B. (2010) A unified framework for biomedical terminologies and ontologies. Studies in health technology and informatics (Jan), 160(Pt 2): 1050-4.
- Arighi CN, Liu H, Natale DA, Barker WC, Drabkin H, Blake JA, Smith B, Wu CH. (2009) TGF-beta signaling proteins and the Protein Ontology. BMC Bioinformatics (May), 10 Su: 3-3.
- Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA. (2009) Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinformatics (Apr), 10: 125-125.
- Koepsell D, Arp R, Fostel J, Smith B. (2009) Creating a controlled vocabulary for the ethics of human research: towards a biomedical ethics ontology. J Empir Res Hum Res Ethics (Mar), 4(1): 43-58.
- Schulz S, Stenzhorn H, Boeker M, Smith B. (2009) Strengths and limitations of formal ontologies in the biomedical domain. Revista electronica de comunicacao, informacao & inovacao em saude : RECIIS (Mar), 3(1): 31-45. doi:10.3395/reciis.v3i1.241en
- Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG. (2009) An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC bioinformatics (Feb), 10: 70. doi:10.1186/1471-2105-10-70
- Blobel B, Kalra D, Koehn M, Lunn K, Pharow P, Ruotsalainen P, Schulz S, Smith B. (2009) The role of ontologies for sustainable, semantically interoperable and trustworthy EHR solutions. Studies in health technology and informatics (Jan), 150: 953-7.
- Ceusters W, Capolupo M, Smith B, De Moor G. (2009) An evolutionary approach to the representation of adverse events. Studies in health technology and informatics (Jan), 150: 537-41.
- Hill DP, Smith B, McAndrews-Hill MS, Blake JA. (2008) Gene Ontology annotations: what they mean and where they come from. BMC Bioinformatics (Apr), 9 Sup: 2-2.
- Smith B, Brochhausen M. (2008) Establishing and harmonizing ontologies in an interdisciplinary health care clinical research environment. Studies in health technology and informatics (Jan), 134: 219-33.
- Stenzhorn H, Schulz S, Boeker M, Smith B. (2008) Adapting Clinical Ontologies in Real-World Environments. Journal of universal computer science : J. UCS (Jan), 14(22): 3767-3780. doi:10.3217/jucs-014-22-3767
- Ceusters W, Elkin P, Smith B. (2007) Negative findings in electronic health records and biomedical ontologies: a realist approach. International journal of medical informatics (Dec), 76 Suppl 3(Supplement 3): S326-33. doi:10.1016/j.ijmedinf.2007.02.003
- Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH. (2007) Framework for a protein ontology. BMC Bioinformatics (Nov), 8 Sup: 1-1.
- Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, , Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature biotechnology (Nov), 25(11): 1251-5. doi:10.1038/nbt1346
- Ceusters WM, Spackman KA, Smith B. (2007) Would SNOMED CT benefit from realism-based ontology evolution?. AMIA ... Annual Symposium proceedings. AMIA Symposium (Oct), 2007: 105-9.
- Bodenreider O, Smith B, Kumar A, Burgun A. (2007) Investigating subsumption in SNOMED CT: an exploration into large description logic-based biomedical terminologies. Artificial intelligence in medicine (Mar), 39(3): 183-95. doi:10.1016/j.artmed.2006.12.003
- Ceusters W, Smith B. (2006) Referent tracking for treatment optimisation in schizophrenic patients: A case study in applying philosophical ontology to diagnostic algorithms. Web semantics (Online) (Sep), 4(3): 229-236. doi:10.1016/j.websem.2006.05.002
- Smith B. (2006) From concepts to clinical reality: an essay on the benchmarking of biomedical terminologies. Journal of biomedical informatics (Jun), 39(3): 288-98.
- Köhler J, Munn K, Rüegg A, Skusa A, Smith B. (2006) Quality control for terms and definitions in ontologies and taxonomies. BMC bioinformatics (Apr), 7: 212. doi:10.1186/1471-2105-7-212
- Simon J, Dos Santos M, Fielding J, Smith B. (2006) Formal ontology for natural language processing and the integration of biomedical databases. Int J Med Inform (Mar), 75(3-4): 224-231.
- Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert CJ, Taylor C, White J, Wood A. (2006) Development of FuGO: an ontology for functional genomics investigations. OMICS (Jan), 10(2): 199-204.
- Ceusters W, Smith B. (2006) A realism-based approach to the evolution of biomedical ontologies. AMIA ... Annual Symposium proceedings. AMIA Symposium (Jan), 2006: 121-5.
- Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Day-Richter J, Noy NF, Musen MA. (2006) National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS (Jan), 10(2): 185-198.
- Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C. (2005) Relations in biomedical ontologies. Genome Biol (Apr), 6(5): 46-46.
- Kumar A, Yip YL, Smith B, Marwede D, Novotny D. (2005) An ontology for carcinoma classification for clinical bioinformatics. Stud Health Technol Inform (Jan), 116: 635-640.
- Smith B, Ceusters W. (2005) An ontology-based methodology for the migration of biomedical terminologies to electronic health records. AMIA ... Annual Symposium proceedings. AMIA Symposium (Jan), 2005: 704-8.
- Johansson I, Smith B, Munn K, Tsikolia N, Elsner K, Ernst D, Siebert D. (2005) Functional anatomy: a taxonomic proposal. Acta biotheoretica (Jan), 53(3): 153-66.
- Smith B, Kumar A, Ceusters W, Rosse C. (2005) On carcinomas and other pathological entities. Comparative and functional genomics (Jan), 6(7-8): 379-87. doi:10.1002/cfg.497
- Rosse C, Kumar A, Mejino JL, Cook DL, Detwiler LT, Smith B. (2005) A strategy for improving and integrating biomedical ontologies. AMIA ... Annual Symposium proceedings. AMIA Symposium (Jan), 2005: 639-43.
- Smith B, Ceusters W, Temmerman R. (2005) Wüsteria. Stud Health Technol Inform (Jan), 116: 647-652.
- Bodenreider O, Smith B, Burgun A. (2004) The Ontology-Epistemology Divide: A Case Study in Medical Terminology. Form Ontol Inf Syst (Jan), 2004: 185-195.
- Ceusters W, Smith B, Kumar A, Dhaen C. (2004) Mistakes in medical ontologies: where do they come from and how can they be detected?. Studies in health technology and informatics (Jan), 102: 145-63.
- Kumar A, Smith B, Pisanelli DM, Gangemi A, Stefanelli M. (2004) An ontological framework for the implementation of clinical guidelines in health care organizations. Studies in health technology and informatics (Jan), 102: 95-107.
- Kumar A, Smith B, Novotny DD. (2004) Biomedical informatics and granularity. Comparative and functional genomics (Jan), 5(6-7): 501-8. doi:10.1002/cfg.429
- Kumar A, Ciccarese P, Smith B, Piazza M. (2004) Context-based task ontologies for clinical guidelines. Studies in health technology and informatics (Jan), 102: 81-94.
- Smith B, Munn K, Papakin I. (2004) Bodily systems and the spatial-functional structure of the human body. Studies in health technology and informatics (Jan), 102: 39-63.
- Grenon P, Smith B, Goldberg L. (2004) Biodynamic ontology: applying BFO in the biomedical domain. Studies in health technology and informatics (Jan), 102: 20-38.
- Ceusters W, Smith B, Kumar A, Dhaen C. (2004) Ontology-based error detection in SNOMED-CT. Studies in health technology and informatics (Jan), 107(Pt 1): 482-6.
- Smith B, Rosse C. (2004) The role of foundational relations in the alignment of biomedical ontologies. Studies in health technology and informatics (Jan), 107(Pt 1): 444-8.
- Smith B, Brogaard B. (2003) Sixteen days. The Journal of medicine and philosophy (Feb), 28(1): 45-78.
- Ceusters W, Desimpel I, Smith B, Schulz S. (2003) Using cross-lingual information to cope with underspecification in formal ontologies. Studies in health technology and informatics (Jan), 95: 391-6.
- Smith B, Williams J, Schulze-Kremer S. (2003) The ontology of the gene ontology. AMIA Annu Symp Proc (Jan)609-613.