1. Barry Smith August 26, 2013 Ontology: A Basic Introduction 1

2. Barry Smith – who am I? Director: National Center for Ontological Research (Buffalo) Founder: Ontology for the Intelligence Community (OIC, now STIDS) conference series Ontology work for Joint-Forces Command Joint Warfighting Center Army Net-Centric Data Strategy Center of Excellence Army Intelligence and Information Warfare Directorate (I2WD) 2

3. Biomedical initiatives 3 Stanford Medical School Mayo Clinic University of California at San Francisco Cleveland Clinic Semantic Database Duke University Health System University of Pittsburgh Medical Center German Federal Ministry of Health European Union eHealth Directorate Plant Genome Research Resource Protein Information Resource

5. http://ncor.us 5

6. Ontologists at UB (selected) Thomas Bittner (Geography, Philosophy) David Mark (Geography, NCGIA) Randall Dipert (Philosophy) Werner Ceusters (IHI, Psychiatry, Bioinformatics) Alex Diehl (Neurology) Alan Ruttenberg (Director of Institute for Healthcare Informatics (IHI) Data Warehouse) Peter Elkin (Chair, Department of Biomedical Informatics)

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8. Ontology = strong semantic indexing (tagging) system biology medicine government military ? google ? commerce 8

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11. Why do people think they need lexicons? For people (people need to understand each other) Training (Developing doctrine, …) Planning (Joint operations, SOPs, …) Executing (C2, …) Reporting, Outcomes measurement For machines Compiling data (e.g. results of testing …) Sharing of data (Compiling lessons learned …) Collective inferencing

12. Approaches to the Construction of Lexicons Dictionary Thesaurus Subject Headings (Library of Congess, National Library of Medicine) Ontologies 12

13. Dictionary (Merriam-Webster) 13

14. Thesaurus 14

15. Plan 15

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18. Planning Definition/Scope: (ADP 3-0) Planning is the art and science of understanding a situation, envisioning a desired future, and laying out effective ways of bringing about that future. Planning consists of two separate but closely related components: a conceptual component and a detailed component. Successful planning requires integrating both these components. Army leaders employ three methodologies for planning after determining the appropriate mix based on the scope of the problem, their familiarity with it, and the time available. 18

19. 19 Planning

20. Subject Headings Lists Broader, Narrower Cancer – Cancer, Astrology – Cancer Documentation – Cancer Prevention – Cancer, Tropic of 20

21. 21 Human Disease Ontology

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24. US DoD Civil Affairs strategy for non-classified information sharing 24

25. The problem of joint / coalition operations Fire Support LogisticsAir Operations Intelligence Civil-Military Operations Targeting Maneuver & Blue Force Tracking 25

26. The problem with (actually existing) lexicons They promote the development of silos (roach motels for data) They do not allow us to exploit today’s technologies They do not combine natural language understandability with computational adequacy They do not scale 26

27. Military is 10 years behind the times when it comes to resolving data interoperability problems –problems of Big Data in biomedicine were recognized already in 1998 27

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29. Old biology data 29/

30. The Gene Ontology response to the massive opportunities created by the success of the Human Genome Project for cross-organism biology for intra-organism biology for the biology of environments 30

31. How to find your data? How to reason with data when you find it? How to understand the significance of the data you collected 3 years earlier? How to integrate with other people’s data? Part of the solution must involve consensus- based, standardized terminologies and coding schemes 31

32. I2WD = Information and Intelligence Warfare Directorate DSGS-A = Distributed Common Ground System – Army DSC = DSGS-A Cloud AIRS Ontology Suite (Ron Rudnicki) 32

33. Ontologies controlled vocabularies (not lexicons) plus definitions of terms in a logical language A.for tagging (search, retrieval, …) B.for reasoning (early warning, analysis …) 33