ontology (science)

ICBO

International Conference on Biomedical OntologyBuffalo, NY. July 20-26, 2009http://icbo.buffalo.edu

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http://icbo.buffalo.edu/

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Why Ontology Engineering needs

Philosophy

Barry SmithUniversity at Buffalo

http://ontology.buffalo.edu/smith

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Why Biomedical Science needs Ontological

Engineering



Multiple kinds of data in multiple kinds of silos

Lab / pathology dataElectronic Health Record dataClinical trial dataPatient historiesMedical imagingMicroarray dataProtein chip dataFlow cytometry

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Example ontologiesGene Ontology (GO)Environment Ontology (EnvO)Infectious Disease Ontology (IDO)Cell Ontology (CL)Sequence Ontology (SO)Protein Ontology (PRO)Common Anatomy Reference Ontology

(CARO)

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Uses of ‘ontology’ in PubMed abstracts

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MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDV

How to do biology across the genome?

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Gene Ontology

ca. 25,000 nodesorganized in a logical hierarchy

Why is the Gene Ontology so useful

in counteracts silos in biomedical research where so many other ontologies have failed?

1. it was built by biologists2. philosophers play a role in its evolution

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Smith, et al., “Coordinated Evolution of Ontologies to Support Biomedical Data

Integration”, Nature Biotechnology, 25, 2007


Philosophy

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male courtship behavior, orientation prior to leg tapping and wing vibration

Gene Ontologyca. 25,000 nodes

What is an ontology?

universal vs. particularclass vs. instance

(catalog vs. inventory)

(science text vs. diary)

(human being vs. Arnold Schwarzenegger)

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The central distinction

universal vs. particularclass vs. instance

(catalog vs. inventory)

(science text vs. diary)

(human being vs. Arnold Schwarzenegger)

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are representations of universals in reality

= representations of what is general in reality

Science texts, theories

An ontology is a representation of universals

aka kinds, types, categories, species, genera, ...

in reality16

What is an Ontology

siamese

mammal

cat

organism

substance

animal

instances

frog

universals

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An ontology is a representation of universals

We learn about universals from examining the results of scientific experiments

Experiments are performed always on instances

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Whether something is an instance or a universal is not a matter of arbitrary choice

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You can’t take a photograph of a universal

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Why, oh Why, Ontology Engineering needs

Philosophy

The standard engineering methodology

• Pragmatics (‘usefulness’) is everything

• Usefulness = we get to write software which runs on our machines

• People will pay us for writing new ontologies

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• It is easier to write useful software if one works with a simplified model

• (“…we can’t know what reality is like in any case; we only have our concepts…”)

• This looks like a useful model to me• (One week goes by:) This other thing

looks like a useful model to him• Data in Pittsburgh does not interoperate

with data in Paderborn



Pragmatics (‘usefulness’) is everything

Ontology engineering undermines the very promise of ontology to solve the silo problem

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‘agent’ ontologies from the DAML/OIL ontology catalog

ontology engineering needs adult supervision

Ontology Development 101: A Guide to Creating Your First Ontology

Natalya Noy and Deborah McGuinness

Example: The Wine Ontology

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red = instances, black = classes, io = instance of

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Why the Wine Ontology Engineering needs

Philosophy

Terminological problems

Classes describe concepts in the domain. For

example, a class of wines represents all

wines. Specific wines are instances of this

class. The Bordeaux wine in the glass in front

of you … is an instance of the class of

Bordeaux wines.

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Creating Instances… we can create an individual instance Chateau-Morgon-Beaujolais to represent a specific type of Beaujolais wine.Chateau-Morgon-Beaujolais is an instance of the class Beaujolais representing all Beaujolais wines. This instance has the following slot values defined

• Body: light, Color: red, Flavor: delicate, Tannin level: low• Grape: Gamay (instance of the Wine grape class)• Maker: Chateau-Morgon (instance of the Winery class)• Region: Beaujolais (instance of the Wine-Region class)

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The definition of an instance of the Beaujolais classThe instance is Chateaux Morgon Beaujolais from the Beaujolais region, produced from the Gamay grape by the Chateau Morgon winery.

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instance of the class Wine grape

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An instance or a class?

Deciding whether a particular concept [e.g. the Bourgogne region] is a class in an ontology or an individual instance depends on what the potential applications of the ontology are.

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Wines are instancespairing wine with food Sterling Vineyards Merlot as instance in our knowledge base

inventory individual bottles as instances

record different properties for each vintage Sterling Vineyards Merlot 1993 as instance

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What about wine regions

“we may define main wine regions, such as France, United States, Germany, and so on, as classes and specific wine regions within these large regions as instances.

( Bourgogne is an instance of France).

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However, we would also like to say that the Cotes d’Or region is a Bourgogne region. Therefore, Bourgogne region must be a class … However, making Bourgogne region a class and Cotes d’Or region an instance of Bourgogne region seems arbitrary: it is very hard to clearly distinguish which regions are classes and which are instances. Therefore, we define all wine regions as classes. ( Cote d’Or is a class)

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From the Protégé glossary:

Instance: Concrete occurrence of information about a domain that is entered into a knowledge base. For example, Fran Smith might be an instance for a Name slot. An instances is entered via a form generated by Protégé-2000.

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Philosophy

Why build scientific ontologies?

“There are many ways to create ontologies …”Multiple ontologies simply make our data silo problems worse

Q: What is to serve as constraint?A: Reality as revealed by mature experimentally-based science

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Ontological (scientific) realism

• Ontology is ineluctably a multi-disciplinary enterprise – it cannot be left to knowledge engineers

• Find out what the world is like by doing science

• Build representations adequate to this world, not to some simplified model in your laptop

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International Conference on Biomedical OntologyBuffalo, NY. July 20-26, 2009http://icbo.buffalo.edu

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ontology (science)

Education