The Future of Ontology in Buffalo Barry Smith 1

Uses of ‘ontology’ in PubMed abstracts 2

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

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 4

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 5

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 6

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) 7

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 8

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) 9

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 10

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 11

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 12

RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) The Open Biomedical Ontologies (OBO) Foundry 13

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

Anatomy Ontology (FMA*, CARO) Environment Ontology (EnvO) Infectious Disease Ontology (IDO*) Biological Process Ontology (GO*) Cell Ontology (CL) Cellular Component Ontology (FMA*, GO*) Phenotypic Quality Ontology (PaTO) Subcellular Anatomy Ontology (SAO) Sequence Ontology (SO*) Molecular Function (GO*) Protein Ontology (PRO*) OBO Foundry Modular Organization 15 top level mid-level domain level Information Artifact Ontology (IAO) Ontology for Biomedical Investigations (OBI) Spatial Ontology (BSPO) Basic Formal Ontology (BFO)

Principal BFO Types 16 CONTINUANT (endures through time  UCore “Entity”) OCCURRENT (occurs in time  UCore “Event”) INDEPENDENTDEPENDENTSPATIALPROCESSTEMPORAL Object: Person, Rock, Vehicle Attribute: Quality, Role, Capability Spatial Region Speaking, Walking, Flying Temporal Interval, Spatiotemporal Region

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

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

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

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

continuant independent continuant portion of material object fiat object part object aggregate object boundary site dependent continuant generically dependent continuant information artifact specifically dependent continuant quality realizable entity function role disposition spatial region 0D-region 1D-region 2D-region 3D-region BFO:continuant 21

occurrent processual entity process fiat process part process aggregate process boundary processual context spatiotemporal region scattered spatiotemporal region connected spatiotemporal region spatiotemporal instant spatiotemporal interval temporal region scattered temporal region connected temporal region temporal instant temporal interval BFO:occurrent 22

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 23

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 24

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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 26

national center for ontological research Command and Control Ontology

Anatomy Ontology (FMA*, CARO) Environment Ontology (EnvO) Infectious Disease Ontology (IDO*) Biological Process Ontology (GO*) Cell Ontology (CL) Cellular Component Ontology (FMA*, GO*) Phenotypic Quality Ontology (PaTO) Subcellular Anatomy Ontology (SAO) Sequence Ontology (SO*) Molecular Function (GO*) Protein Ontology (PRO*) OBO Foundry Modular Organization 28 top level mid-level domain level Information Artifact Ontology (IAO) Ontology for Biomedical Investigations (OBI) Spatial Ontology (BSPO) Basic Formal Ontology (BFO)

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

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

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

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

NATO HQ C 3 Staff 33 NC3B Sub-structure

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