Ontology in Buffalo

Barry Smith

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Ontology (phil.) The science of being

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

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Google hits Mar. 2007 (in millions)

ontology 14.2

ontology + philosophy 1.2

ontology + data 5.0

ontology + medicine 1.3

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where in the body ? where in the cell ?

what kind of disease process ?

how create humanly intelligible + logically tractable systems for annotating data?

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Pleural Cavity

Pleural Cavity

Interlobar recess

Interlobar recess

Mesothelium of Pleura

Mesothelium of Pleura

Pleura(Wall of Sac)

Pleura(Wall of Sac)

VisceralPleura

VisceralPleura

Pleural SacPleural Sac

Parietal Pleura

Parietal Pleura

Anatomical SpaceAnatomical Space

OrganCavityOrganCavity

Serous SacCavity

Serous SacCavity

AnatomicalStructure

AnatomicalStructure

OrganOrgan

Serous SacSerous Sac

MediastinalPleura

MediastinalPleura

TissueTissue

Organ PartOrgan Part

Organ Subdivision

Organ Subdivision

Organ Component

Organ Component

Organ CavitySubdivision

Organ CavitySubdivision

Serous SacCavity

Subdivision

Serous SacCavity

Subdivision

part

_of su

btyp

e

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Ontology (tech.) often marked by intellectual confusions

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US Government Insurance Ontology:

A house contains as part: information about an air conditioning system

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US Government Life Events Taxonomy

Aging Birth Child care Death Divorce Marriage Parenting Retirement Schooling Teenagers

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HL7 (Health Level 7)

every activity is identical with its own documentation

a disease is an act of observationa diagnosis is an observation of an observation

a person is an entity which represents a living subject with an identity document

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(old) Gene Ontology

Definition of Hemolysis:

The processes that cause hemolysis

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Philosophers should not interfere with the sciences

But now computer scientists are interfering in science all the time, and the result is proving a disaster

sometimes involving billions of dollars of wasted investment

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Ontology (science)develops theories of the types of entities

existing in a given domain of reality and of the relations between these types

+ ways of testing such theories

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Systems

respiratorydigestive skeletal circulatorymusculatory immune

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quid? substance quantum? quantity quale? qualityad quid? relationubi? placequando? timein quo situ? status/contextin quo habitu? habitusquid agit? actionquid patitur? passion

What is a System?

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Systems

respiratorydigestive skeletal circulatorymusculatory immune

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Systems

have functions

What is a function?

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Systems

can malfunction

Ontology of disease

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industrial applications

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BS consultant to:

Cleveland Clinic (Cardiovascular Surgery Ontology)

Gene Ontology ConsortiumDuke University Medical School Functional Genomics Investigation Ontology

(FugO)German Ministry of Health World Health Organization

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Resources for Graduate Students

$60,000+ Graduate Fellowships: NSF IGERT grant ($6 mill.)

Humboldt Foundation, Volkswagen Foundation and EU: Graduate Stipendia for Research in Germany ($4.9 mill.)

NIH Protein Ontology: Training workshops ($0.3 mill.)

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National Center for Biomedical Ontology$18.8 mill. NIH Roadmap Center

• Stanford Medical Informatics• University of San Francisco Medical Center• Berkeley Drosophila Genome Project• Cambridge University Department of Genetics• The Mayo Clinic• University at Buffalo Department of Philosophy

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UB2020

Bioinformatics Center

$100,000 for Signature Center in Ontological Research

$1 million start-up funds for new Director of Bioinformatics

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Buffalo philosophers with research focus on ontology

Thomas Bittner

Maureen Donnelly

Randall Dipert

David Hershenov

Barry Smith

Neil Williams