national center for ontological research University at Buffalo

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national center for ontological research University at Buffalo The Center for the Arts October

national center for ontological research University at Buffalo The Center for the Arts October 27, 2005 http: //ncor. us

national center for ontological research http: //ncor. us

national center for ontological research http: //ncor. us

national center for ontological research Department of Philosophy now largest group of core ontology

national center for ontological research 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 http: //ncor. us 3

national center for ontological research http: //ncor. us 4

national center for ontological research http: //ncor. us 4

national center for ontological research Stanford Medical Informatics, Director: Mark Musen Protégé Applied Ontology

national center for ontological research Stanford Medical Informatics, Director: Mark Musen Protégé Applied Ontology National Center for Biomedical Ontology http: //ncor. us 5

national center for ontological research http: //ncor. us 6

national center for ontological research http: //ncor. us 6

national center for ontological research From chromosome to disease http: //ncor. us 7

national center for ontological research From chromosome to disease http: //ncor. us 7

national center for ontological research genomics proteomics reactomics metabonomics phenomics behavioromics toxicopharmacogenomics … legacy

national center for ontological research genomics proteomics reactomics metabonomics phenomics behavioromics toxicopharmacogenomics … legacy of Human Genome Project http: //ncor. us 8

national center for ontological research -omics data biochemical disease pathway data biomedical image data

national center for ontological research -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 http: //ncor. us 9

a vast new problem of communication national center for ontological research medical researchers, clinical

a vast new problem of communication national center for ontological research medical researchers, clinical practitioners, first responders, customs agencies, pharmaceutical companies, disease control centers need to communicate in ways which involve huge amounts of data http: //ncor. us 10

national center for ontological research Problem how to reason with data from different sources

national center for ontological research Problem how to reason with data from different sources each of which uses its own system of classification http: //ncor. us 11

national center for ontological research Solution: Ontology ! http: //ncor. us 12

national center for ontological research Solution: Ontology ! http: //ncor. us 12

national center for ontological research Ontology (phil. ) The branch of metaphysics that deals

national center for ontological research 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 http: //ncor. us 13

national center for ontological research The need strong general purpose classification hierarchies created by

national center for ontological research The need strong general purpose classification hierarchies created by domain specialists clear, rigorous definitions thoroughly tested in real use cases http: //ncor. us 14

national center for ontological research The actuality (too often) myriad special purpose ‘light’ ontologies,

national center for ontological research The actuality (too often) myriad special purpose ‘light’ ontologies, prepared by ontology engineers and deposited in internet ‘repositories’ or ‘registries’ http: //ncor. us 15

national center for ontological research ontologies for ‘agent’ http: //ncor. us 16

national center for ontological research ontologies for ‘agent’ http: //ncor. us 16

national center for ontological research http: //ncor. us 17

national center for ontological research http: //ncor. us 17

national center for ontological research http: //ncor. us 18

national center for ontological research http: //ncor. us 18

national center for ontological research http: //ncor. us 19

national center for ontological research http: //ncor. us 19

national center for ontological research often do not generalize … repeat work already done

national center for ontological research often do not generalize … repeat work already done by others are not interoperable reproduce the very problems of communication which ontology was designed to solve contain incoherent definitions and incoherent documentation http: //ncor. us 20

national center for ontological research A tragic example “Health Level 7 Reference Information Model”

national center for ontological research A tragic example “Health Level 7 Reference Information Model” (HL 7 RIM) – a standard for exchange of information between clinical information systems http: //ncor. us 21

national center for ontological research The ultimate special purpose ontology A healthcare messaging system

national center for ontological research 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 http: //ncor. us 22

national center for ontological research National Cancer Institute National Biospecimen Network (NBN) “The NBN

national center for ontological research National Cancer Institute National Biospecimen Network (NBN) “The NBN bioinformatics system should be standards-based (e. g. , SNOMED, HL 7, or MIAME for data; Internet for communications) to enable data and information exchange among system components and the researchers who use them. ” http: //ncor. us 23

HL 7 Glossary national center for ontological research Animal Definition: A subtype of Living

HL 7 Glossary national center for ontological research Animal Definition: A subtype of Living Subject representing any animal-of-interest to the Personnel Management domain. Living. Subject Definition: A subtype of Entity representing an organism or complex animal, alive or not. http: //ncor. us 24

HL 7 Glossary national center for ontological research Person Definition: A Living Subject representing

HL 7 Glossary national center for ontological research 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 http: //ncor. us 25

national center for ontological research HL 7’s backbone ‘Act’ class Act Definition: An Act

national center for ontological research HL 7’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” http: //ncor. us 26

HL 7 Incredibly Successful national center for ontological research adopted by Oracle as basis

HL 7 Incredibly Successful national center for ontological research 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 http: //ncor. us 27

national center for ontological research What’s gone wrong? People of good will are making

national center for ontological research 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 http: //ncor. us 28

Glaxo. Smith. Kline * national center for ontological research What we need is “industrial-strength”

Glaxo. Smith. Kline * national center for ontological research 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 Mc. Entire http: //ncor. us 29

Signs of hope national center for ontological research founding of National Center for Biomedical

Signs of hope national center for ontological research founding of National Center for Biomedical Ontology (an NIH Roadmap Center) increased recognition of FMA Open Biomedical Ontologies consortium introduction of rigorous logical tools and scientific methods in the creation of content -rich ontologies for automatic reasoning and seamless integration http: //ncor. us 30

Why NCOR? national center for ontological research NCOR will advance ontology as a discipline

Why NCOR? national center for ontological research 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 http: //ncor. us 31

Why NCOR? national center for ontological research NCOR will provide coordination and support for

Why NCOR? national center for ontological research 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 http: //ncor. us 32

national center for ontological research ontologies are ambitious classification systems they rely on definitions,

national center for ontological research 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 http: //ncor. us 33