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. Watson’s Ontology of Bioinformaticians
Top level is
bioinformatician
bioinformation bioinformation
interested in ontology not interested in ontology
4.
5. • Stanford University Biomedical Informatics Research
• Mayo Clinic Department of Biomedical Informatics
• University at Buffalo Department of Philosophy
Three US partner institutions:
6.
7. 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)
13. 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
14. 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
17. 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
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: 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)