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Barry Smith

August 26, 2013

Ontology: A Basic Introduction

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Barry Smith – who am I?Director: National Center for Ontological Research (Buffalo)Founder: Ontology for the Intelligence Community (OIC, now STIDS) conference seriesOntology work for

Joint-Forces Command Joint Warfighting CenterArmy Net-Centric Data Strategy Center of ExcellenceArmy Intelligence and Information Warfare Directorate (I2WD)

Biomedical initiatives

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•Stanford Medical School•Mayo Clinic•University of California at San Francisco•Cleveland Clinic Semantic Database•Duke University Health System•University of Pittsburgh Medical Center•German Federal Ministry of Health•European Union eHealth Directorate•Plant Genome Research Resource•Protein Information Resource

5http://ncor.us

Ontologists at UB (selected)• Thomas Bittner (Geography, Philosophy)• David Mark (Geography, NCGIA)• Randall Dipert (Philosophy)• Werner Ceusters (IHI, Psychiatry, Bioinformatics)• Alex Diehl (Neurology)• Alan Ruttenberg (Director of Institute for Healthcare

Informatics (IHI) Data Warehouse)• Peter Elkin (Chair, Department of Biomedical Informatics)

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Ontology

= strong semantic indexing (tagging) systembiologymedicinegovernmentmilitary? google? commerce

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Why do people think they need lexicons?

For people (people need to understand each other)• Training (Developing doctrine, …)• Planning (Joint operations, SOPs, …)• Executing (C2, …)• Reporting, Outcomes measurementFor machines• Compiling data (e.g. results of testing …)• Sharing of data (Compiling lessons learned …)• Collective inferencing

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Approaches to the Construction of Lexicons

• Dictionary• Thesaurus• Subject Headings (Library of Congess, National

Library of Medicine)• Ontologies

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Dictionary (Merriam-Webster)

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Thesaurus

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Plan

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Planning

• Definition/Scope: (ADP 3-0) Planning is the art and science of understanding a situation, envisioning a desired future, and laying out effective ways of bringing about that future. Planning consists of two separate but closely related components: a conceptual component and a detailed component. Successful planning requires integrating both these components. Army leaders employ three methodologies for planning after determining the appropriate mix based on the scope of the problem, their familiarity with it, and the time available.

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Planning

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Subject Headings Lists

Broader, Narrower

• Cancer– Cancer, Astrology– Cancer Documentation– Cancer Prevention– Cancer, Tropic of

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Human Disease Ontology

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US DoD Civil Affairs strategy for non-classified information sharing

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The problem of joint / coalition operations

Fire Support

LogisticsAir Operations

Intelligence

Civil-Military Operations

Targeting

Maneuver &Blue Force

Tracking

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The problem with (actually existing) lexicons

• They promote the development of silos (roach motels for data)

• They do not allow us to exploit today’s technologies

• They do not combine natural language understandability with computational adequacy

• They do not scale

Military is 10 years behind the times when it comes to resolving data interoperability problems

–problems of Big Data in biomedicine were recognized already in 1998

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New biology data

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Old biology data

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The Gene Ontology

response to the massive opportunities created by the success of the Human Genome Project

for cross-organism biologyfor intra-organism biologyfor the biology of environments

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How to find your data?

How to reason with data when you find it?How to understand the significance of the data

you collected 3 years earlier?How to integrate with other people’s data?

Part of the solution must involve consensus-based, standardized terminologies and coding schemes

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I2WD = Information and Intelligence Warfare Directorate

DSGS-A = Distributed Common Ground System – ArmyDSC = DSGS-A CloudAIRS Ontology Suite (Ron Rudnicki)

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Ontologies

controlled vocabularies (not lexicons)plus definitions of terms in a logical language

A. for tagging (search, retrieval, …)B. for reasoning (early warning, analysis …)