ontology in-buffalo-2013
DESCRIPTION
Describes current work in ontology in Buffalo, focusing especially on biomedical ontologyTRANSCRIPT
Ontology in Buffalo
June 6, 2013Barry Smith
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
Watson’s Ontology of Bioinformaticians
Top level is
bioinformatician
bioinformation bioinformationinterested in ontology not interested in ontology
• Stanford University Biomedical Informatics Research • Mayo Clinic Department of Biomedical Informatics• University at Buffalo Department of Philosophy
Three US partner institutions:
RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)Open Biomedical Ontologies (OBO) Foundry
(Gene Ontology marked in yellow)
© Ocean Informatics 2005 4.10
Enterprise
Comprehensive Basic
Components
EHR
Multimediagenetics
workflow
identity
Clinicalref data Clinical
models
terms
Security / access control
realtimegateway
telemedicine
HILS
otherprovider
UPDATEQUERY
demographics
guidelinesprotocolsInteractions
DSLocal
modelling
notifications
DSS
PAS
billing
portal
Alliedhealth
patientPAYER
Msg gateway
Imaging lab
ECG etc
Path lab
LAB
Secondaryusers
Online drug,Interactions DB Online
archetypes
Online terminology
Online Demographic
registries
PatientRecord
with thanks to Thomas Beale
11
Explosion of “biomedical ontology” since 1999
Biomedical Ontologies co-developed at UBBCO Biocollections OntologyBFO Basic Formal OntologyCL Cell OntologyENVO Environment Ontology FMA Foundational Model of AnatomyGO Gene OntologyIDO Infectious Disease OntologyND Neurological Disease OntologyMFO Mental Functioning OntologyNPT Neuropsychological Testing OntologyOBI Ontology for Biomedical InvestigationsOGMS Ontology for General Medical ScienceOHD Oral Health and Disease OntologyPCO Population and Community OntologyPO Plant OntologyPRO Protein Ontology
Biomedical Ontologies co-developed at UBBCO Biocollections OntologyBFO Basic Formal OntologyCL Cell OntologyENVO Environment Ontology FMA Foundational Model of AnatomyGO Gene OntologyIDO Infectious Disease OntologyND Neurological Disease OntologyMFO Mental Functioning OntologyNPT Neuropsychological Testing OntologyOBI Ontology for Biomedical InvestigationsOGMS Ontology for General Medical ScienceOHD Oral Health and Disease OntologyPCO Population and Community OntologyPO Plant OntologyPRO Protein Ontology
http://www.ifomis.org/bfo/users
Biomedical Ontologies co-developed at UBBCO Biocollections OntologyBFO Basic Formal OntologyCL Cell OntologyENVO Environment Ontology FMA Foundational Model of AnatomyGO Gene OntologyIAO Information Artifact OntologyIDO Infectious Disease OntologyND Neurological Disease OntologyMFO Mental Functioning OntologyNPT Neuropsychological Testing OntologyOBI Ontology for Biomedical InvestigationsOGMS Ontology for General Medical SciencePCO Population and Community OntologyPO Plant OntologyPRO Protein Ontology
Biomedical Ontology in Buffalo
BS, Alan Ruttenberg, Alex Diehl
PhilosophyDental School,
IHI Neurology
Werner Ceusters, Dagobert Soergel, Peter Elkin
Psychiatry, IHIDental School,
Library and Information Studies
new Chair of BiomedicalInformatics
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 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
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
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)
Further reading
National Center for Ontological Researchhttp://ncor.buffalo.edu