Ontology in Buffalo
June 6, 2013
Barry Smith
Watson’s law of
bioinformatics ontologies
“As the time spent discussing a
particular bioinformatics topic
grows longer, th...
Watson’s Ontology of Bioinformaticians
Top level is
bioinformatician
bioinformation bioinformation
interested in ontology ...
• Stanford University Biomedical Informatics Research
• Mayo Clinic Department of Biomedical Informatics
• University at B...
RELATION
TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
Anatom...
© Ocean Informatics 2005 4.10
Enterprise
Comprehensive Basic
Components
EHR
Multimedia
genetics
workflow
identity
Clinical...
11
Explosion of “biomedical ontology” since 1999
Biomedical Ontologies co-developed at UB
BCO Biocollections Ontology
BFO Basic Formal Ontology
CL Cell Ontology
ENVO Envir...
Biomedical Ontologies co-developed at UB
BCO Biocollections Ontology
BFO Basic Formal Ontology
CL Cell Ontology
ENVO Envir...
http://www.ifomis.org/bfo/users
Biomedical Ontologies co-developed at UB
BCO Biocollections Ontology
BFO Basic Formal Ontology
CL Cell Ontology
ENVO Envir...
Biomedical Ontology in Buffalo
BS, Alan Ruttenberg, Alex Diehl
Philosophy
Dental School,
IHI
Neurology
Werner Ceusters, Dagobert Soergel, Peter Elkin
Psychiatry, IHI
Dental School,
Library and
Information Studies
new Chair of...
IHI: Institute for Healthcare Informatics
IHI Ontology Machine
Strategy
• using BFO, OGMS and their extension ontologies
to provide a consistent framework for the
representation of the ...
Strategy
• using BFO, OGMS and their extension ontologies
to provide a consistent framework for the
representation of the ...
Acknowledgement
• IDO: Immune System Biological Networks: A Case
Study in Improved Data Integration & Analysis (NIH /
NIAI...
Further reading
National Center for Ontological Research
http://ncor.buffalo.edu
Contact
phismith@buffalo.edu
Ontology in-buffalo-2013
Ontology in-buffalo-2013
Ontology in-buffalo-2013
Ontology in-buffalo-2013
Ontology in-buffalo-2013
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Ontology in-buffalo-2013

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Describes current work in ontology in Buffalo, focusing especially on biomedical ontology

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  • 923 Main Street location at the heart of the Medical Campus; 2 blocks from both CTRC and CCR
  • Including individually locked and monitored racks, cold aisle design, dual power
  • Ontology in-buffalo-2013

    1. 1. Ontology in Buffalo June 6, 2013 Barry Smith
    2. 2. Watson’s law of bioinformatics ontologies “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. 3. Watson’s Ontology of Bioinformaticians Top level is bioinformatician bioinformation bioinformation interested in ontology not interested in ontology
    4. 4. • Stanford University Biomedical Informatics Research • Mayo Clinic Department of Biomedical Informatics • University at Buffalo Department of Philosophy Three US partner institutions:
    5. 5. RELATION TO TIME GRANULARITY CONTINUANT OCCURRENT INDEPENDENT DEPENDENT 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)
    6. 6. © Ocean Informatics 2005 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
    7. 7. 11
    8. 8. Explosion of “biomedical ontology” since 1999
    9. 9. Biomedical Ontologies co-developed at 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
    10. 10. Biomedical Ontologies co-developed at 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
    11. 11. http://www.ifomis.org/bfo/users
    12. 12. Biomedical Ontologies co-developed at 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
    13. 13. Biomedical Ontology in Buffalo
    14. 14. BS, Alan Ruttenberg, Alex Diehl Philosophy Dental School, IHI Neurology
    15. 15. Werner Ceusters, Dagobert Soergel, Peter Elkin Psychiatry, IHI Dental School, Library and Information Studies new Chair of Biomedical Informatics
    16. 16. IHI: Institute for Healthcare Informatics
    17. 17. IHI Ontology Machine
    18. 18. 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
    19. 19. 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
    20. 20. Acknowledgement • IDO: Immune System 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)
    21. 21. Further reading National Center for Ontological Research http://ncor.buffalo.edu Contact phismith@buffalo.edu
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