Introduction to Biomedical Ontology Barry Smith Saarbrücken November 2008
Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.
-
Upload
darleen-boone -
Category
Documents
-
view
244 -
download
2
Transcript of Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.
![Page 1: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/1.jpg)
1
Barry Smith
August 26, 2013
Ontology: A Basic Introduction
![Page 2: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/2.jpg)
2
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)
![Page 3: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/3.jpg)
Biomedical initiatives
3
•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
![Page 4: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/4.jpg)
![Page 5: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/5.jpg)
5http://ncor.us
![Page 6: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/6.jpg)
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)
![Page 7: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/7.jpg)
7
![Page 8: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/8.jpg)
8
Ontology
= strong semantic indexing (tagging) systembiologymedicinegovernmentmilitary? google? commerce
![Page 9: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/9.jpg)
9
![Page 10: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/10.jpg)
10
![Page 11: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/11.jpg)
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
![Page 12: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/12.jpg)
12
Approaches to the Construction of Lexicons
• Dictionary• Thesaurus• Subject Headings (Library of Congess, National
Library of Medicine)• Ontologies
![Page 13: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/13.jpg)
13
Dictionary (Merriam-Webster)
![Page 14: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/14.jpg)
14
Thesaurus
![Page 15: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/15.jpg)
15
Plan
![Page 16: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/16.jpg)
16
![Page 17: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/17.jpg)
17
![Page 18: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/18.jpg)
18
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.
![Page 19: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/19.jpg)
19
Planning
![Page 20: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/20.jpg)
20
Subject Headings Lists
Broader, Narrower
• Cancer– Cancer, Astrology– Cancer Documentation– Cancer Prevention– Cancer, Tropic of
![Page 21: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/21.jpg)
21
Human Disease Ontology
![Page 22: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/22.jpg)
22
![Page 23: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/23.jpg)
23
![Page 24: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/24.jpg)
US DoD Civil Affairs strategy for non-classified information sharing
24
![Page 25: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/25.jpg)
The problem of joint / coalition operations
Fire Support
LogisticsAir Operations
Intelligence
Civil-Military Operations
Targeting
Maneuver &Blue Force
Tracking
25
![Page 26: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/26.jpg)
26
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
![Page 27: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/27.jpg)
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
27
![Page 28: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/28.jpg)
MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDV
New biology data
28
![Page 29: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/29.jpg)
Old biology data
29/
![Page 30: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/30.jpg)
30
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
![Page 31: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/31.jpg)
31
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
![Page 32: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/32.jpg)
32
I2WD = Information and Intelligence Warfare Directorate
DSGS-A = Distributed Common Ground System – ArmyDSC = DSGS-A CloudAIRS Ontology Suite (Ron Rudnicki)
![Page 33: Barry Smith August 26, 2013 Ontology: A Basic Introduction 1.](https://reader033.fdocuments.net/reader033/viewer/2022061523/56649f435503460f94c636f0/html5/thumbnails/33.jpg)
33
Ontologies
controlled vocabularies (not lexicons)plus definitions of terms in a logical language
A. for tagging (search, retrieval, …)B. for reasoning (early warning, analysis …)