Barry Smith PhD FACMI
Barry Smith
PhD FACMI
Distinguished Professor of Philosophy; Affiliate Professor of Biomedical Informatics, Computer Science, and Neurology
Professional Summary:
Barry Smith is a prominent contributor to both theoretical and applied research in ontology, especially in the biomedical domain. He is the author of some 500 publications on ontology with some 30,000 citations. 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 and Director of the National Center for Ontological Research in the University at Buffalo (UB). He is also Affiliate Professor in the UB Departments of Biomedical Informatics, Computer Science and Neurology.
Smith’s pioneering work on the science of ontology led to the formation of the OBO (Open Biomedical Ontologies) Foundry, a suite of resources designed to support information-driven research in biology and biomedicine. He is ontology lead for the NIAID ImmPort project, one of the principal scientists of the National Center for Biomedical Ontology, a Scientific Advisor to the Gene Ontology Consortium, and a PI on the Protein Ontology and Infectious Disease Ontology projects.
Since 2009 Smith has also served as ontology consultant to Hernando de Soto of the Institute of Liberty and Democracy (ILD) supporting the work of the ILD on creating modern legal frameworks that help the poor of the developing and ex-communist world access property and business rights.
Education and Training:
- PhD, Philosophy, University of Manchester (1976)
- MA, Mathematics and Philosophy, Oxford University (1975)
- BA, Mathematics and Philosophy, Oxford University (1973)
Employment:
- Distinguished Professor, Philosophy, University at Buffalo (1994-present)
- Professor, International Academy for Philosophy (1989–1994)
- Professor, Philosophy, University of Manchester (1979–1989)
- Post Doctoral Fellow, Philosophy, University of Sheffield (1976–1979)
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.
- 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.
- Ceusters W, Smith B. (2018) On Defining Bruxism. Stud Health Technol Inform (Jan), 247: 551-555.
- 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.
- 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.
- 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.
- 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.
- 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.
- Ai J, Smith B, Wong DT. (2010) Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base. BMC Bioinformatics (Jun), 11: 302-302.
- 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.
- 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.
- 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.
- 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.
- 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, 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.
- Smith B, Williams J, Schulze-Kremer S. (2003) The ontology of the gene ontology. AMIA Annu Symp Proc (Jan)609-613.