Ontology in Buffalo Barry Smith

2 Ontology (phil.) The science of being Ontologies (tech.) Standardized classification systems which enable data from different sources to be combined and applied to new uses

3 Google hits Mar (in millions) ontology 14.2 ontology + philosophy 1.2 ontology + data 5.0 ontology + medicine1.3

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5 where in the body ? where in the cell ? what kind of disease process ? how create humanly intelligible + logically tractable systems for annotating data?

6 Pleural Cavity Pleural Cavity Interlobar recess Interlobar recess Mesothelium of Pleura Mesothelium of Pleura Pleura(Wall of Sac) Pleura(Wall of Sac) Visceral Pleura Visceral Pleura Pleural Sac Parietal Pleura Parietal Pleura Anatomical Space Organ Cavity Organ Cavity Serous Sac Cavity Serous Sac Cavity Anatomical Structure Anatomical Structure Organ Serous Sac Mediastinal Pleura Mediastinal Pleura Tissue Organ Part Organ Subdivision Organ Subdivision Organ Component Organ Component Organ Cavity Subdivision Organ Cavity Subdivision Serous Sac Cavity Subdivision Serous Sac Cavity Subdivision part_of subtype

7 Ontology (tech.) often marked by intellectual confusions

8 US Government Insurance Ontology: A house contains as part: information about an air conditioning system

9 US Government Life Events Taxonomy Aging Birth Child care Death Divorce Marriage Parenting Retirement Schooling Teenagers

10 HL7 (Health Level 7) every activity is identical with its own documentation a disease is an act of observation a diagnosis is an observation of an observation a person is an entity which represents a living subject with an identity document

11 (old) Gene Ontology Definition of Hemolysis: The processes that cause hemolysis

12 Philosophers should not interfere with the sciences But now computer scientists are interfering in science all the time, and the result is proving a disaster sometimes involving billions of dollars of wasted investment

13 Ontology (science) develops theories of the types of entities existing in a given domain of reality and of the relations between these types +ways of testing such theories

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15 Systems respiratorydigestive skeletal circulatory musculatory immune

16 quid? substance quantum? quantity quale? quality ad quid? relation ubi? place quando? time in quo situ? status/context in quo habitu? habitus quid agit? action quid patitur? passion What is a System?

17 Systems respiratorydigestive skeletal circulatory musculatory immune

18 Systems have functions What is a function?

19 Systems can malfunction Ontology of disease

20 industrial applications

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24 BS consultant to: Cleveland Clinic (Cardiovascular Surgery Ontology) Gene Ontology Consortium Duke University Medical School Functional Genomics Investigation Ontology (FugO) German Ministry of Health World Health Organization

25 Resources for Graduate Students $60,000+ Graduate Fellowships: NSF IGERT grant ($6 mill.) Humboldt Foundation, Volkswagen Foundation and EU: Graduate Stipendia for Research in Germany ($4.9 mill.) NIH Protein Ontology: Training workshops ($0.3 mill.)

26 National Center for Biomedical Ontology $18.8 mill. NIH Roadmap Center Stanford Medical Informatics University of San Francisco Medical Center Berkeley Drosophila Genome Project Cambridge University Department of Genetics The Mayo Clinic University at Buffalo Department of Philosophy

27 UB2020 Bioinformatics Center $100,000 for Signature Center in Ontological Research $1 million start-up funds for new Director of Bioinformatics

28 Buffalo philosophers with research focus on ontology Thomas Bittner Maureen Donnelly Randall Dipert David Hershenov Barry Smith Neil Williams