nationalcenter for

ontologicalresearch

University at BuffaloThe Center for the Arts

October 27, 2005

nationalcenter for

ontologicalresearch

national center for

ontological research

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nationalcenter for

ontologicalresearch

Department of Philosophy now largest group of core ontology faculty in the world

New York State Center of Excellence in Bioinformatics & Life Science

ORG: The Ontology Research Group

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nationalcenter for

ontologicalresearch

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nationalcenter for

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Stanford Medical Informatics,

Director: Mark Musen

Protégé

Applied Ontology

National Center for Biomedical Ontology

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nationalcenter for

ontologicalresearch

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nationalcenter for

ontologicalresearch

From chromosome

to disease

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nationalcenter for

ontologicalresearch

genomicsproteomicsreactomics metabonomics phenomicsbehavioromicstoxicopharmacogenomics

… legacy of Human Genome Project

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nationalcenter for

ontologicalresearch

-omics data

biochemical disease pathway data

biomedical image data

electronic health record data

hospital management data

hospital insurance data

public health data

Chinese chicken data

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nationalcenter for

ontologicalresearch

a vast new problem of communication

medical researchers, clinical practitioners, first responders, customs agencies, pharmaceutical companies, disease control centers need to communicate in ways which involve huge amounts of data

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nationalcenter for

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Problem

how to reason with data from different sources each of which uses its own system of classification

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nationalcenter for

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Solution:

Ontology !

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nationalcenter for

ontologicalresearch

Ontology (phil.) The branch of metaphysics that deals with the nature of being.

Ontologies (tech.)Standardized classification systems which enable data from different sources to be combined

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nationalcenter for

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The need

strong general purpose classification hierarchies created by domain specialists

clear, rigorous definitions

thoroughly tested in real use cases

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nationalcenter for

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The actuality (too often)

myriad special purpose ‘light’ ontologies, prepared by ontology engineers and deposited in internet ‘repositories’ or ‘registries’

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nationalcenter for

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ontologies for ‘agent’

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nationalcenter for

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often do not generalize …repeat work already done by othersare not interoperablereproduce the very problems of communication which ontology was designed to solvecontain incoherent definitionsand incoherent documentation

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nationalcenter for

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A tragic example

“Health Level 7 Reference Information Model” (HL7 RIM)

– a standard for exchange of information between clinical information systems

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nationalcenter for

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The ultimate special purpose ontology

A healthcare messaging system used as the basis for an entire clinical record architecture, extending as far as core genomic data

Rather like using air-traffic control messaging as starting point for a science of airplane thermodynamics

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National Cancer Institute National Biospecimen Network (NBN)

“The NBN bioinformatics system should be standards-based (e.g., SNOMED, HL7, or MIAME for data; Internet for communications) to enable data and information exchange among system components and the researchers who use them.”

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nationalcenter for

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HL7 Glossary

AnimalDefinition: A subtype of Living Subject

representing any animal-of-interest to the Personnel Management domain.

LivingSubject Definition: A subtype of Entity representing

an organism or complex animal, alive or not.

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nationalcenter for

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Person Definition: A Living Subject representing

single human being [sic] who is uniquely identifiable through one or more legal documents

– impossible to refer to undocumented persons

HL7 Glossary

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HL7’s backbone ‘Act’ class

Act Definition: An Act is the record of an Act

An X is the Y of an X

“There is no difference between an activity and its documentation”

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nationalcenter for

ontologicalresearchHL7 Incredibly

Successful

adopted by Oracle as basis for its Electronic Health Record technology; supported by IBM, GE, Sun ...

embraced as US federal standard

central part of $18 billion program to integrate all UK hospital information systems

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nationalcenter for

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What’s gone wrong? 

People of good will are making mistakes because of lack of expertise

Money is wasted on megasystems that cannot be used

Even large ontologies are built in the spirit of the amateur hobbyist

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nationalcenter for

ontologicalresearchGlaxoSmithKline *

What we need is “industrial-strength” ontologies with a consistent and rich representation formalism that are amenable for use as an integration framework, and support reasoning capabilities. We anticipate that pharma’s need to bring together mountains of data and information and to properly analyse that information all depend on having a stable, well-developed semantic framework that links information/data and that allows reasoning systems to perform some of our more "mundane" analysis work.

*Robin McEntire

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nationalcenter for

ontologicalresearchSigns of hope

founding of National Center for Biomedical Ontology (an NIH Roadmap Center)increased recognition of FMAOpen Biomedical Ontologies consortiumintroduction of rigorous logical tools and scientific methods in the creation of content-rich ontologies for automatic reasoning and seamless integration

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nationalcenter for

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NCOR will

advance ontology as a discipline employing rigorous scientific methods

develop objective, empirical measures of quality for ontologies in ways which will lead to the establishment of best practices

Why NCOR?

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NCOR will

provide coordination and support for investigators working on theoretical ontology and its applications

engage in outreach endeavors designed to foster the goals of high quality ontology in both theory and practice

Why NCOR?

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nationalcenter for

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ontologies are ambitious classification systems

they rely on definitions,

on the logic of relations,

and on theories of high-level categories such as function, process, thing, event, constituent

if you want to build a good ontology …

WORK WITH A PHILOSOPHER