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