Biomedical Informatics

Introduction to OntologyLiqin Wang, MS

SWE Workshop 2011

Aug 10th, 2011

Biomedical InformaticsOutline• What is ontology• Ontology Language• How to create an ontology• Ontology Reasoning• Evaluation of Ontology• Application of Ontology• Institutes & People• Processing Tools & Triple Store• Resources• Practice

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Biomedical InformaticsWhat is ontology?• Def. in Philosophy

– A foundational discipline of philosophy, which has its origins in ancient Greece.

– About “existence”

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Biomedical InformaticsWhat is ontology? (Cont.)• Def. in Information Science

– A formal, explicit specification of a conceptualization.– A model for describing the world

• Concepts• Properties• Constraints• Individuals

– Also as a domain-specific knowledge base that is machine interpretable, reusable and sharable

T. R. Gruber. A translation approach to portable ontologies. Knowledge Acquisition, 5(2):199-220, 1993.

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Biomedical InformaticsWith ontology, we are able…• To share common understanding of the

structure of information among people or software agents

• To enable reuse of domain knowledge• To make domain assumptions explicit• To analyze domain knowledge• To separate domain knowledge from the

operational knowledge

Natalya F. Noy, Deborah McGuinness. Ontology Development 101: A Guide to Creating Your First Ontology

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Biomedical InformaticsOntology Language• In order to facilitate the

create, reading, writing, query and sharing of the ontology, it is a necessary to have ontology language(s).

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Semantic Web Stackby Tim Berners-Lee

Biomedical InformaticsOntology Language (Cont.)• By syntax:

– RDF/XML• Interchange (can be written and read by all conformant OWL

2 software)

– OWL/XML• Easier to process using XML tools

– Functional Syntax• Easier to see the formal structure of ontologies

– Manchester syntax• Easier to read/write DL ontologies

– Turtle• Easier to read/write RDF triples

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Go to protégé and Notepad++

Biomedical InformaticsOWL• OWL (Web Ontology Language)

– W3C standard– OWL is built on top of RDF, and written in XML– OWL has three sublanguages

• DL, Lite, Full

– Hard to read by people– Interpretable by computers

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Biomedical InformaticsThree Variants of OWL• OWL Full

– an extension of RDF– allows for classes as instances, modification of RDF and

OWL vocabularies

• OWL DL– the part of OWL Full that fits in the Description Logic

framework– known to have decidable reasoning

• OWL Lite– a subset of OWL DL– easier for frame-based tools to transition to– easier reasoning

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Biomedical InformaticsOWL Example

<owl:Class  rdf:about=''firstYearCourse''>

  <rdfs:subClassOf>

    <owl:Restriction>

      <owl:onProperty  rdf:resource=''isTaughtBy''/>

<owl:allValuesFrom  rdf:resource=''#Professor''/>

    </owl:Restriction>

  </rdfs:subClassOf>

</owl:Class>

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Biomedical InformaticsManchester OWL syntax• Restrictions

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Biomedical InformaticsManchester OWL syntax• Boolean Class Constructors

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Biomedical InformaticsExample

Person and hasChild some (Person and (hasChild only Man) and (hasChild some Person))

Describes the set of people who have at least one child that has some children that are only men (i.e. grandparents that only have grandsons)

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Biomedical InformaticsOWL vs. RDF• OWL and RDF are much of the same thing, but

OWL is a stronger language with greater machine interpretability than RDF.

• OWL comes with a larger vocabulary and stronger syntax than RDF.

• OWL supports the identification of inconsistencies (e.g. disjoint classes man & woman, instances and classes cannot be both)

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Biomedical InformaticsExample of Ontology

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Biomedical InformaticsHow to create an ontology?• Determine the scope of the ontology• Consider reusing existing ontologies• Enumerate important terms in the ontology• Define the classes and the class hierarchy• Define the properties of classes-slots• Define the constraints of the slots• Create instances

• In reality, there is no order for these process…

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Biomedical InformaticsDetermine the scope• What is the domain that the ontology will cover?

• For what we are going to use the ontology?

• For what types of questions the information in the ontology should provide answers?

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Biomedical InformaticsDetermine the scope• What is the domain that the ontology will cover?• e.g. Cardiology, food…• For what we are going to use the ontology?• e.g. Question answering, information extraction• For what types of questions the information in

the ontology should provide answers?• e.g. what is the treatment for patient of cognitive

heart failure?

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Biomedical InformaticsWhat to reuse?• Domain specific ontologies

– UMLS Semantic Network• Semantic type and Relationship

– SNOMED CT– National Drug File – Reference Term

• IEEE Upper Ontology– Suggested Upper Merged Ontology

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Biomedical InformaticsWhere to get important terms?• From

– your mind if you are domain experts– Other persons

• From– Books– Guidelines– Literatures– etc.

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Biomedical InformaticsClasses• Classes usually constitute a taxonomic

hierarchy (a subclass-superclass hierarchy)• A class hierarchy is usually an IS-A hierarchy

– an instance of a subclass is an instance of a superclass

• If you think of a class as a set of elements a subclass is a subset

• Multiple inheritance, (A is a B), (A is a C)

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Biomedical InformaticsProperties• rdf:Property

– owl:ObjectProperty• Link individuals to individuals• hasParent

– owl:DatatypeProperty• Link individuals to data values

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Go to protégé, see NDF-RT.owl

Biomedical InformaticsProperty restrictions• Value constraints

– Put constraints on value range for a particular property

• Cardinality constraints– Constraints on the number of values for a particular

property

• e.g. hasParent– Value constraints: allValuesFrom “Human”– Cardinality constraints: maxCardinality “2”

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Biomedical InformaticsOntology Reasoning• Determine the consistency of ontology• Identify subsumption relationships between

classes• Reasoners:

– RacerPro– FaCT++

• C++-based reasoner

– Pellet– HermiT

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Biomedical InformaticsEvaluation of Ontology• Assessment by human against a set of criteria• Natural language evaluation techniques• Evaluate use of ontology in an application• Comparison of ontology against a source of

domain data• Using reality as benchmark• Ontology accreditation, certification, maturity

model

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Biomedical InformaticsApplications of Ontology•  Global Health Monitor

– BioCaster

• Question answering– QALL-ME

• NLP/IE– Extended Syndrome Surveillance Ontology

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Biomedical InformaticsInstitutes & People• W3C web ontology• ONTOLOG• Stanford

– Thomas R. Gruber– Mark A. Musen, M.D., Ph.D

• Buffalo ontology site– Barry Smith

• University of Manchester– e.g. Alan Rector

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Biomedical InformaticsProcessing Tools & Triple Store• Ontology Engineering Environments

– Ontolingua

– Protégé

– Altova SemanticWorks (Commercial)

• Parser/Serializer– Rapper: Raptor RDF parsing and serializing utility

• SPARQL Query– Jena ARQ

• Triple Store– Jena SDB

– http://www.w3.org/wiki/LargeTripleStores

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Biomedical InformaticsResources all about OWL• OWL Web Ontology Language Overview

• OWL Web Ontology Language Guide

• OWL Web Ontology Language Reference

• OWL Web Ontology Language Semantics and Abstract Syntax

• OWL Web Ontology Language Test Cases

• OWL Web Ontology Language Use Cases and Requirements

• OWL Web Ontology Language XML Presentation Syntax 

• OWL Web Ontology Language Parsing OWL in RDF/XML 

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Biomedical InformaticsBiomedical Informatics

QUESTIONS?

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Biomedical InformaticsPractice• Protégé

– How to work with Protégé

• Jena SDB Triple Store– Load the RDF file into triple store

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Biomedical InformaticsBiomedical Informatics

PROTÉGÉ

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Biomedical InformaticsProtégé - Windows• Ontology metrics

• Preference Render– Show the classes in different way

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Biomedical InformaticsInverse Properties• Each object property may have a corresponding

inverse property.• If some property links individual a to individual

b, then its inverse property will link individual b to individual a.

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Biomedical InformaticsFunctional Properties• If a property is functional, for a given individual,

there can only be at most one individual to be related via this property.– For a given domain, range must be unique

• Functional properties are also known as single valued properties.

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Biomedical InformaticsInverse Functional Properties• If a property is inverse functional, then its

inverse property is functional.– For a given range, domain must be unique.

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Biomedical InformaticsFunctional vs. inverse functional properties• FunctionalProperty vs InverseFunctionalProperty

domain range example

Functional

Property

For a given domain

Range is unique

hasFather: A hasFather B, A hasFather C B=C

InverseFunctionalProperty

Domain is unique

For a given range

hasID: A hasID B, C hasID B A=C

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Biomedical InformaticsTransitive Properties• If a property is transitive, and the property related individual a

to individual b, and also individual b to individual c, then we can infer that individual a is related to individual c via property P.

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Biomedical InformaticsProtégé – DL Query• Quickly test definitions of classes to see that

they subsume the appropriate subclasses. • Or check for class membership of arbitrary

descriptions without having to create named class placeholders.

• Follow Manchester OWL Syntax• http://protegewiki.stanford.edu/wiki/DLQueryTab• Example

– For pizza.owl– Pizza and hasTopping only VegetarianTopping

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Biomedical InformaticsProtégé - OWLViz• http://protegewiki.stanford.edu/wiki/OWLViz• Graphviz

– Installation– Set path

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Biomedical InformaticsBiomedical Informatics

TRIPLE STORE

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Biomedical InformaticsInstall• Mysql server• Latest mysql connector jar file• Jena SDB• Cygwin

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Biomedical InformaticsBiomedical Informatics

THANK YOU!

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