1. New York State Center of Excellence in Bioinformatics & Life Sciences Biomedical Ontology in Buffalo Part I: The Gene Ontology Barry Smith and Werner Ceusters

2. New York State Center of Excellence in Bioinformatics & Life Sciences Ontology: An antidote to silos 2 Department of Philosophy 135 Park Hall University at Buffalo Buffalo NY 14260 Department of Philosophy 135 Park Hall University at Buffalo Buffalo NY 14260 promoting: information retrieval information consistency, and thus continuity and cumulation information integration reasoning

3. New York State Center of Excellence in Bioinformatics & Life Sciences Uses of ‘ontology’ in PubMed abstracts 3

4. New York State Center of Excellence in Bioinformatics & Life Sciences By far the most successful: GO (The Gene Ontology)

5. New York State Center of Excellence in Bioinformatics & Life Sciences Biomedical Ontology in BuffaloPart 3: What we do

6. New York State Center of Excellence in Bioinformatics & Life Sciences The GO is amazingly successful in overcoming silo problems but it covers only generic biological entities of three sorts: –cellular components –molecular functions –biological processes and it does not provide representations of diseases, symptoms, … 6

7. New York State Center of Excellence in Bioinformatics & Life Sciences The core of biomedical ontology in Buffalo – extending the methodology of high quality ontologies to other domains of biology and medicine, and to EHRs and coding systems – combining ontology with referent tracking 7

8. 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 8

9. New York State Center of Excellence in Bioinformatics & Life Sciences NCBO NIH Roadmap Center for Biomedical Computing Collaboration of: Stanford Biomedical Informatics Research Mayo Clinic University at Buffalo National Center for Biomedical Ontology (NCBO) 9

10. New York State Center of Excellence in Bioinformatics & Life Sciences National Center for Ontological Research (NCOR) Army Net-Centric Data Strategy Center of Excellence –Biometrics Ontology –Command and Control Ontology –Universal Core Semantic Layer 10

11. New York State Center of Excellence in Bioinformatics & Life Sciences Current funded biomedical ontology projects Protein Ontology (PRO) (NIH/NIGMS) Infectious Disease Ontology (IDO) (NIH/NIAID) Realism-Based Versioning for Biomedical Ontologies (SNOMED) (NIH/NLM) Ontology for Risks Against Patient Safety (RAPS) (EU) DSM Ontology (to support work on revision of Diagnostic and Statistical Manual of Mental Disorders Cleveland Clinic Semantic Database in Cardiothoracic Surgery 11

12. New York State Center of Excellence in Bioinformatics & Life Sciences 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 12

13. New York State Center of Excellence in Bioinformatics & Life Sciences “Better Information” must cover … EHR-EMR-ENR-… PHR Various modality-related databases –Lab, imaging, … Textbooks Classification systems Terminologies Ontologies Patient-specific information Scientific “knowledge” 1 2 3 13

14. New York State Center of Excellence in Bioinformatics & Life Sciences Ontologies Keeping track of what is general (diabetes, malaria, nasal bone, nose …) 14

15. New York State Center of Excellence in Bioinformatics & Life Sciences Referent tracking Keeping track of what is particular (this particular nasal bone, this particular fracture, this particular swimming pool, this particular image …) 15

16. New York State Center of Excellence in Bioinformatics & Life Sciences eyeGENE 16

17. New York State Center of Excellence in Bioinformatics & Life Sciences Ontology for Risks Against Patient Safety 17

18. New York State Center of Excellence in Bioinformatics & Life Sciences REMINE: RT-based adverse event analysis 18