The Future of Ontology in Buffalo Barry Smith ontology.buffalo/smith

1. The Future of Ontology in Buffalo Barry Smith http://ontology.buffalo.edu/smith

2. Uses of ‘ontology’ in PubMed abstracts

3. By far the most successful: GO (The Gene Ontology)

4. Biomedical data is siloed • Lab / pathology data • Electronic Health Record data • Clinical trial data • Patient histories • Medical imaging • Microarray data • Protein chip data • Flow cytometry • Genotype / SNP data

5. Biomedical data is siloed • Data in Pittsburgh • Data in Geneva • Data owned by Medicare • Data owned by the NIH • Data owned by HIV researchers • Data owned by the Cleveland Clinic • Data owned by regional health organizations • Data owned by mouse biologists • Data owned by Dr McFritz • all of which has led to NIH mandates for data reusability

6. NCBO • National Center for Biomedical Ontology • NIH Roadmap Center for Biomedical Computing • Collaboration of: • Stanford Biomedical Informatics Research • Mayo Clinic • Department of Philosophy, University at Buffalo

7. NCOR - Buffalo • National Center for Ontological Research • Core ontologies • Basic Formal Ontology (BFO) • Relation Ontology (RO) • Information Artifact Ontology (IAO) • Environment Ontology (EnvO) • Ontology for Biomedical Investigations (OBI)

8. OBI Collaborating Communities • Environmental Genomics MGED RSBI Group • Genomic Standards Consortium (GSC) • HUPO Proteomics Standards Initiative (PSI) • Immunology Database and Analysis Portal • Immune Epitope Database and Analysis Resource (IEDB) • International Society for Analytical Cytology • Metabolomics Standards Initiative (MSI), • Neurogenetics, Biomedical Informatics Research Network (BIRN) • Nutrigenomics MGED RSBI Group • Toxicogenomics MGED RSBI Group • Transcriptomics MGED Ontology Group

9. Current funded biomedical ontology projects • Protein Ontology (PRO) (NIH/NIGMS) • Infectious Disease Ontology (IDO) (NIH/NIAID) • Gene Ontology (Scientific Advisor) • Cleveland Clinic Semantic Database in Cardiothoracic Surgery (Scientific Advisor) • Ontology for Risks Against Patient Safety (RAPS) • Ontology to support work on revision of DSM V (Diagnostic and Statistical Manual of Mental Disorders)

10. IDO Consortium • MITRE, Mount Sinai, UTSouthwestern – Influenza • IMBB/VectorBase – Vector borne diseases (A. gambiae, A. aegypti, I. scapularis, C. pipiens, P. humanus) • Colorado State University – Dengue Fever • Duke University – Tuberculosis • Cleveland Clinic – Infective Endocarditis • University of Michigan – Brucilosis

11. Unifying goal: integration • within and across domains • across different species • across levels of granularity (organ, organism, cell, molecule) • across different perspectives (physical, biological, clinical) Unification achieved in part through use of the BFO common upper-level ontology

12. Question How to extend the GO to enable intelligent integration of gigantic bodies of heterogeneous data across the entire domain of biology and medicine and beyond? Answer: Open Biomedical Ontologies (OBO) Foundry

13. The Open Biomedical Ontologies (OBO) Foundry

14. How is the OBO Foundry organized? • Core: Basic Formal Ontology (BFO) • serves as starting point for extension modules created in its terms

15. Basic Formal Ontology (BFO) top level mid-level domain level OBO Foundry Modular Organization

16. Principal BFO Types

17. Basic Formal Ontology types Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality .... ..... ....... instances

18. Blinding Flash of the Obvious Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality quality depends on bearer .... ..... .......

19. Blinding Flash of the Obvious Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality, … event depends on participant .... ..... .......

20. Blinding Flash of the Obvious Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality process is change in quality .... ..... .......

21. BFO:continuant

22. BFO:occurrent

23. Ontologies and research groups using BFO • OBO Foundry (60 biomedical ontologies) • National Cancer Institute (BiomedGT) • NIF (NIH Neuroscience Information Framework) • Siemens • AstraZeneca • ACGT Cancer Ontology

24. Universal Core (UCore 2.0) • Department of Defense • Department of Homeland Security • Department of Energy • Department of Justice • Office of the Director of National Intelligence

26. UCore Semantic Layer (UCore-SL)BFO-based common upper level ontology • NCOR • ODNI • Mitre  • NIST (National Institute of Standards and Technology)  (Fabian Neuhaus) • NCI (National Cancer Institute) • ANCDS (US Army Net-Centric Data Strategy) Center of Excellence, Fort Monmouth, NJ

27. Command and Control Ontology

28. Basic Formal Ontology (BFO) top level mid-level domain level OBO Foundry Modular Organization

29. Types of Military Operations Operation Enabling Operation Offensive Operation Support Operation Security Operation Defensive Operation Stability Operation Reconnaissance Operation Movement to Contact Attack Environmental Assistance Operation Peace Operation Area Defensive Operation Mobile Defensive Operation Raid Humanitarian Assistance Operation Ambush Nation Assistance Foreign Internal Defense From: FM 3-0 Operations

30. Modular Ontologies Operation Air Operation Space Operation Land Operation Sea Operation Modular Ontologies will be semantically aligned with the Core C2 Ontology The modular ontologies will semantically aligned with each other

31. Common Upper Ontology Core C2 Ontology Operations Ontology Effects Based Operations Ontology Business Common Upper Ontology Sensors MDA Imagery Data Strategy

32. Joint Common System Functions List (JCSFL) USN USMC USA USAF NCES/NECC Other CPMs Capability Mapping Baseline The “Periodic Table” for Operational Capability Policy Standards Policy Architectures Systems Functions Joint Capability Areas (JCAs) CPM Areas Standards Tier I Analysis Policy Technical Standards Accreditations C2 Portfolio* - Programs of Record - Systems - Sub-systems - New Capabilities Policy Platforms/Weapons Standards Data Bases & Models Policy Joint Staff J7 Mapping Standards Operational Activities Applications/Services Policy JTF OperationalActivities / Tasks / Sub-tasks Networks/Comms UJTLs SN X.X ST X.XX OP X.X.X TA X.X.X.X Standards Policy Assessments Joint Tasks Operational Standards AUTLs, MCTL, NTTL, AFTL Documentation Policy Service Tasks Operational Nodes & Billets Concepts/Plans Standards Joint Warfighter Billets Op Nodes Programmatic PECs-to-JCAs PA&E Mapping Leads to Interoperability, Joint Standards & DOTLMPF COAs Authoritative Sources: * Portfolio Mapping Uses • C2 Focus Areas for POM/PR issues • CENTCOM Best of Breed (BoB) • C2 Core and JTF C2 Equipping/Manning • Cross-CPM Trade Space Analysis TOR

33. SDR UG NC3B NATO PKI Management Authority PKI Advisory Cell NC3 REPS SC/7 IDENT SC SC/5 IS SC SC/1 C3 CC SC SC/8 NAV SC SC/3 FMSC Civ/Mil SC/4 IA SC SC/6 CNS SC SC/3 SM SC/6 CNS SC/5 IIS WG/1 Data Link AHWG/1Security Management Services AHWG/4 NATO Mode 5/Mode S Identification NAVWAR AHWG WG/1 C3 Policy AHWG/1 BLOS Comms WG/1 Policy WG/2 Military Frequency WG/2 Message TextFormats AHWG/5 Air to Surface Identification WG/2 C3 Capabilities Precision Positioning Systems Certification AHWG (Dormant) AHWG/2 Crypto Services AHWG/2 V/UHF Radio AHWG/3 Technical IA Services AHWG/3 Secure Multi-Media Conferencing WG/3 C3 Interoperability WG/3 Technical WG/3 Data Management Services SC/1 = C3 Capabilities Coherence SC/3 = Frequency Management SC/4 = Information Assurance SC/5 = Information Services SC/6 = Communication and Network Services SC/7 = Identification SC/8 = Navigation WG/1 Networking AHWG/4 NATO – Non NATO Cooperation WG/4 NATO Open Systems WG/4 XMLManagement Services AHWG/5 tbd WG/2 SATCOM AHWG/1 Maritime C3 WG/5 Core Enterprise Services Open to Partners (1) Meetings with Partners (2)Currently no meetings with Partners planned NC3B Sub-structure

34. http://icbo.buffalo.edu