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Ontology in-buffalo-2013
This document discusses biomedical ontology work being done at the University at Buffalo. It describes three US partner institutions collaborating on biomedical ontologies and lists several biomedical ontologies co-developed at UB, including the Basic Formal Ontology and Foundational Model of Anatomy. It outlines a strategy using these ontologies to provide consistent representation of knowledge in an ontology repository at the Institute for Healthcare Informatics.
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Ontology in-buffalo-2013
- 1. Ontology in Buffalo June6, 2013 Barry Smith
- 2. Watson’s law of bioinformaticsontologies “As the time spent discussing a particular bioinformatics topic grows longer, the probability that someone will suggest the group develops an ontology for that topic approaches 1” http://biomickwatson.wordpress.com
- 3. Watson’s Ontology ofBioinformaticians Top level is bioinformatician bioinformation bioinformation interested in ontology not interested in ontology
- 5. • Stanford UniversityBiomedical Informatics Research • Mayo Clinic Department of Biomedical Informatics • University at Buffalo Department of Philosophy Three US partner institutions:
- 7. RELATION TO TIME GRANULARITY CONTINUANT OCCURRENT 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) Open Biomedical Ontologies (OBO) Foundry (Gene Ontology marked in yellow)
- 10. © Ocean Informatics2005 4.10 Enterprise Comprehensive Basic Components EHR Multimedia genetics workflow identity Clinical ref data Clinical models terms realtime gateway telemedicine HILS other provider UPDATE QUERY demographics guidelines protocols Interactions DS Local modelling notifications DSS PAS billing portal Allied health patient PAYER Msg gateway Imaging lab ECG etc Path lab LAB Secondary users Online drug, Interactions DB Online archetypes Online terminology Online Demographic registries Patient Record with thanks to Thomas Beale
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- 12. Explosion of “biomedicalontology” since 1999
- 13. Biomedical Ontologies co-developedat UB BCO Biocollections Ontology BFO Basic Formal Ontology CL Cell Ontology ENVO Environment Ontology FMA Foundational Model of Anatomy GO Gene Ontology IDO Infectious Disease Ontology ND Neurological Disease Ontology MFO Mental Functioning Ontology NPT Neuropsychological Testing Ontology OBI Ontology for Biomedical Investigations OGMS Ontology for General Medical Science OHD Oral Health and Disease Ontology PCO Population and Community Ontology PO Plant Ontology PRO Protein Ontology
- 14. Biomedical Ontologies co-developedat UB BCO Biocollections Ontology BFO Basic Formal Ontology CL Cell Ontology ENVO Environment Ontology FMA Foundational Model of Anatomy GO Gene Ontology IDO Infectious Disease Ontology ND Neurological Disease Ontology MFO Mental Functioning Ontology NPT Neuropsychological Testing Ontology OBI Ontology for Biomedical Investigations OGMS Ontology for General Medical Science OHD Oral Health and Disease Ontology PCO Population and Community Ontology PO Plant Ontology PRO Protein Ontology
- 16.
- 17. Biomedical Ontologies co-developedat UB BCO Biocollections Ontology BFO Basic Formal Ontology CL Cell Ontology ENVO Environment Ontology FMA Foundational Model of Anatomy GO Gene Ontology IAO Information Artifact Ontology IDO Infectious Disease Ontology ND Neurological Disease Ontology MFO Mental Functioning Ontology NPT Neuropsychological Testing Ontology OBI Ontology for Biomedical Investigations OGMS Ontology for General Medical Science PCO Population and Community Ontology PO Plant Ontology PRO Protein Ontology
- 18. Biomedical Ontology inBuffalo
- 19. BS, Alan Ruttenberg,Alex Diehl Philosophy Dental School, IHI Neurology
- 20. Werner Ceusters, DagobertSoergel, Peter Elkin Psychiatry, IHI Dental School, Library and Information Studies new Chair of Biomedical Informatics
- 21. IHI: Institute forHealthcare Informatics
- 22.
- 23. Strategy • using BFO,OGMS and their extension ontologies to provide a consistent framework for the representation of the types of particulars • developing systematic ways for the consistent tracking of particulars (patients, disorders, encounters …) • putting these together to serve consistent representation of the assertional knowledge in the IHI repository
- 24. Strategy • using BFO,OGMS and their extension ontologies to provide a consistent framework for the representation of the types of particulars • developing systematic ways for the consistent tracking of particulars (patients, disorders, encounters …) • putting these together to serve consistent representation of the assertional knowledge in the IHI repository
- 25. Acknowledgement • IDO: ImmuneSystem Biological Networks: A Case Study in Improved Data Integration & Analysis (NIH / NIAID) • ImmPort: Bioinformatics Integration Support Contract (NIH/NIAID) • Plant Ontology (NSF) • OPMQoL: Ontology for Pain and Related Disability, Mental Health and Quality of Life (NIH/National Institute of Dental and Craniofacial Research) • PRO: A Protein Ontology in Open Biomedical Ontologies (NIH/NIGMS) • NCBO: National Center for Biomedical Ontology (NIH/NHGRI)
- 26. Further reading National Centerfor Ontological Research http://ncor.buffalo.edu Contact phismith@buffalo.edu