The Future of Ontology in BuffaloBarry Smith
http://ontology.buffalo.edu/smith
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Uses of ‘ontology’ in PubMed abstracts
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By far the most successful: GO (The Gene Ontology)
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Biomedical data is siloedLab / pathology dataElectronic Health Record dataClinical trial dataPatient historiesMedical imagingMicroarray dataProtein chip dataFlow cytometryGenotype / SNP data
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Biomedical data is siloedData in PittsburghData in GenevaData owned by MedicareData owned by the NIHData owned by HIV researchersData owned by the Cleveland ClinicData owned by regional health organizations Data owned by mouse biologistsData owned by Dr McFritz
all of which has led to NIH mandates for data reusability
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NCBO National Center for Biomedical Ontology
NIH Roadmap Center for Biomedical Computing
Collaboration of:Stanford Biomedical Informatics ResearchMayo ClinicDepartment of Philosophy, University at Buffalo
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NCOR - Buffalo
National Center for Ontological Research
Core ontologies
Basic Formal Ontology (BFO)Relation Ontology (RO)Information Artifact Ontology (IAO)Environment Ontology (EnvO)Ontology for Biomedical Investigations (OBI)
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OBI Collaborating Communities
Environmental Genomics MGED RSBI GroupGenomic Standards Consortium (GSC)HUPO Proteomics Standards Initiative (PSI)Immunology Database and Analysis PortalImmune Epitope Database and Analysis Resource (IEDB)International Society for Analytical CytologyMetabolomics Standards Initiative (MSI), Neurogenetics, Biomedical Informatics Research Network
(BIRN)Nutrigenomics MGED RSBI GroupToxicogenomics MGED RSBI GroupTranscriptomics MGED Ontology Group 8
Current funded biomedical ontology projects
Protein Ontology (PRO) (NIH/NIGMS)
Infectious Disease Ontology (IDO) (NIH/NIAID)
Gene Ontology (Scientific Advisor)
Cleveland Clinic Semantic Database in Cardiothoracic Surgery (Scientific Advisor)
Ontology for Risks Against Patient Safety (RAPS)
Ontology to support work on revision of DSM V (Diagnostic and Statistical Manual of Mental Disorders)
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IDO ConsortiumMITRE, Mount Sinai, UTSouthwestern –
InfluenzaIMBB/VectorBase – Vector borne diseases (A.
gambiae, A. aegypti, I. scapularis, C. pipiens, P. humanus)
Colorado State University – Dengue FeverDuke University – TuberculosisCleveland Clinic – Infective EndocarditisUniversity of Michigan – Brucilosis
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Unifying goal: integration
– within and across domains– across different species– across levels of granularity (organ,
organism, cell, molecule)– across different perspectives (physical,
biological, clinical)
Unification achieved in part through use of the BFO common upper-level ontology
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Question
How to extend the GO to enable intelligent integration of gigantic bodies of heterogeneous data across the entire domain of biology and medicine and beyond?
Answer: Open Biomedical Ontologies (OBO) Foundry
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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)
The Open Biomedical Ontologies (OBO) Foundry13
How is the OBO Foundry organized?
Core: Basic Formal Ontology (BFO)serves as starting point for extension
modules created in its terms
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Anatomy Ontology(FMA*, CARO)
Environment
Ontology(EnvO)
Infectious Disease
Ontology(IDO*)
Biological Process
Ontology (GO*)
Cell Ontology
(CL)
CellularComponentOntology
(FMA*, GO*) Phenotypic Quality
Ontology(PaTO)
Subcellular Anatomy Ontology (SAO)Sequence Ontology
(SO*) Molecular Function
(GO*)Protein Ontology(PRO*) OBO Foundry Modular Organization 15
top level
mid-level
domain level
Information Artifact Ontology
(IAO)
Ontology for Biomedical
Investigations(OBI)
Spatial Ontology(BSPO)
Basic Formal Ontology (BFO)
Principal BFO Types
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CONTINUANT (endures through time UCore “Entity”)
OCCURRENT (occurs in time UCore
“Event”)
INDEPENDENT DEPENDENT SPATIAL PROCESS TEMPORAL
Object: Person, Rock,
Vehicle
Attribute: Quality,
Role, Capability
Spatial Region
Speaking, Walking, Flying
Temporal Interval,
Spatiotemporal Region
Basic Formal Ontology
Continuant Occurrent
process, eventIndependentContinuant
thing
DependentContinuant
quality
.... ..... .......
types
instances 17
Blinding Flash of the Obvious
Continuant Occurrent
process, eventIndependentContinuant
thing
DependentContinuant
quality
.... ..... .......quality dependson bearer
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Blinding Flash of the Obvious
Continuant Occurrent
process, eventIndependentContinuant
thing
DependentContinuant
quality, …
.... ..... .......event dependson participant
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Blinding Flash of the Obvious
ContinuantOccurrent
process, eventIndependentContinuant
thing
DependentContinuant
quality
.... ..... .......process is change in quality
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BFO:continuant
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BFO:occurrent
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Ontologies and research groups using BFO
– OBO Foundry (60 biomedical ontologies)– National Cancer Institute (BiomedGT)– NIF (NIH Neuroscience Information Framework)– Siemens– AstraZeneca– ACGT Cancer Ontology
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Universal Core (UCore 2.0)
Department of DefenseDepartment of Homeland SecurityDepartment of EnergyDepartment of JusticeOffice of the Director of National Intelligence
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UCore Semantic Layer (UCore-SL)BFO-based common upper level ontology
NCORODNIMitre NIST (National Institute of Standards and
Technology) (Fabian Neuhaus)NCI (National Cancer Institute) ANCDS (US Army Net-Centric Data Strategy) Center
of Excellence, Fort Monmouth, NJ
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nationalcenter for
ontologicalresearch
Command and Control Ontology
Anatomy Ontology(FMA*, CARO)
Environment
Ontology(EnvO)
Infectious Disease
Ontology(IDO*)
Biological Process
Ontology (GO*)
Cell Ontology
(CL)
CellularComponentOntology
(FMA*, GO*) Phenotypic Quality
Ontology(PaTO)
Subcellular Anatomy Ontology (SAO)Sequence Ontology
(SO*) Molecular Function
(GO*)Protein Ontology(PRO*) OBO Foundry Modular Organization28
top level
mid-level
domain level
Information Artifact Ontology
(IAO)
Ontology for Biomedical
Investigations(OBI)
Spatial Ontology(BSPO)
Basic Formal Ontology (BFO)
Types of Military Operations
Operation
Offensive Operation
Defensive Operation
Stability Operation
Support Operation
Enabling Operation
Area Defensive Operation
Mobile Defensive Operation
Peace Operation
Humanitarian Assistance Operation
Movement to Contact
Attack Environmental Assistance Operation
Raid
AmbushNation
Assistance
Reconnaissance Operation
From: FM 3-0 Operations Foreign Internal Defense
Security Operation
Modular Ontologies
Operation
Land Operation
Space Operation
Air Operation
Modular Ontologies will be semantically aligned with the Core C2 Ontology
The modular ontologies will semantically aligned with each other
Sea Operation
Common Upper
Ontology
Common Upper
OntologySensorsSensors
Business
Business
Operations
Operations
Ontology
Ontology
ImageryImagery
Core C2Core C2OntologyOntology Effects Based Operations
Effects Based Operations
Ontology
Ontology
MDAMDA
Data Strategy
Operational ActivitiesOperational Activities
Systems FunctionsSystems Functions
Joint StaffJ7 Mapping
Architectures
Analysis
Accreditations
Platforms/Weapons
Concepts/Plans
Applications/Services
Data Bases & Models
Networks/Comms
Assessments
Policy
Standards
Policy
Standards
Policy
Standards
Policy
Standards
Policy
Standards
Policy
Standards
Operational
Programmatic
Technical
Documentation
Policy
Standards
Leads to Interoperability,
Joint Standards & DOTLMPF COAs
Policy
Standards
Joint Capability Areas (JCAs)Joint Capability Areas (JCAs)
• C2 Focus Areas for POM/PR issues• CENTCOM Best of Breed (BoB) • C2 Core and JTF C2 Equipping/Manning• Cross-CPM Trade Space Analysis
* Portfolio Mapping Uses
Joint TasksJoint Tasks
Service TasksService Tasks
Other CPMs
C2 Portfolio*C2 Portfolio*
- Programs of Record - Systems - Sub-systems - New Capabilities
PECs-to-JCAs
PA&EMapping
CPM AreasCPM Areas
Capability Mapping BaselineCapability Mapping BaselineThe “Periodic Table” for Operational CapabilityThe “Periodic Table” for Operational Capability
NCES/NECC
USAFUSA
USMC
USN
Joint CommonSystem Functions
List (JCSFL)
Operational Nodes & Billets Operational Nodes & Billets
JTF OperationalActivities / Tasks / Sub-tasks
Tier I
UJTLsSN X.XST X.XXOP X.X.XTA X.X.X.X
OpNodes
Joint Warfighter Billets
Authoritative Sources:
AUTLs, MCTL, NTTL, AFTL
TOR
NATO HQ
C3 Staff
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NC3B Sub-structure
AHWG/4 NATO Mode 5/Mode S
Identification
AHWG/2 Crypto Services
AHWG/4 NATO – Non NATO
Cooperation
NC3B
NC3 REPS
SC/3 SM SC/5 IIS SC/6 CNS
NAVWAR AHWG
SC/5 IS SC
SC/7 IDENT SC
SC/1 C3 CC SC
AHWG/1 Security Management
Services
WG/1Policy
WG/2Military Frequency
WG/3Technical
AHWG/1BLOS Comms
AHWG/3 Secure Multi-Media
Conferencing
AHWG/3 Technical IA
Services
AHWG/2V/UHF Radio
AHWG/5 tbd
Precision Positioning Systems Certification
AHWG (Dormant)
WG/1C3 Policy
WG/3 C3 Interoperability
WG/2C3 Capabilities
AHWG/5 Air to Surface
Identification
NCSA
N
V
Y
SC/3 FMSC Civ/Mil
SC/6 CNS SC
SC/8 NAV SC
SC/4 IA SC
WG/4 NATO Open
Systems
WG/1 Networking
WG/2 SATCOMAHWG/1
Maritime C3
SDR UG
NATO PKI Management
Authority
SC/1 = C3 Capabilities Coherence SC/3 = Frequency ManagementSC/4 = Information Assurance
SC/5 = Information ServicesSC/6 = Communication and Network ServicesSC/7 = IdentificationSC/8 = Navigation
PKI Advisory
Cell
WG/5 Core
Enterprise Services
WG/4 XML
Management Services
WG/3 Data
Management Services
WG/2 Message
TextFormats
WG/1Data Link
Open to Partners (1) Meetings with Partners (2)
Currently no meetings with Partners planned
34http://icbo.buffalo.edu