national center for ontological research University at Buffalo The Center for the Arts October 27, 2005

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

national center for ontological research

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

national center for ontological research

national center for ontological research From chromosome to disease

national center for ontological research genomics proteomics reactomics metabonomics phenomics behavioromics toxicopharmacogenomics … legacy of Human Genome Project

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

national center for ontological research 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

national center for ontological research Problem how to reason with data from different sources each of which uses its own system of classification

national center for ontological research Solution: Ontology !

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

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

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’

national center for ontological research ontologies for ‘agent’

national center for ontological research

national center for ontological research

national center for ontological research

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

national center for ontological research A tragic example “Health Level 7 Reference Information Model” (HL7 RIM) – a standard for exchange of information between clinical information systems

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

national center for ontological research 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.”

national center for ontological research HL7 Glossary Animal Definition: 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.

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 HL7 Glossary

national center for ontological research 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”

national center for ontological research HL7 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

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

national center for ontological research GlaxoSmithKline * 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

national center for ontological research Signs of hope 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

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 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 Why NCOR?

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