COMMIT/ E-FOODLAB

Don Willems don.willems@wur.nl / @oekalegon

What is an Ontology?

COMMIT/ E-FOODLAB

In computer science and information science, an ontology formally represents knowledge as a set of concepts within a domain, and the relationships between pairs of concepts. It can be used to model a domain and support reasoning about concepts.

Source: http://en.wikipedia.org/wiki/Ontology_(information_science)

COMMIT/ E-FOODLAB

In computer science and information science, an ontology formally represents knowledge as a set of concepts within a domain, and the relationships between pairs of concepts. It can be used to model a domain and support reasoning about concepts.

Source: http://en.wikipedia.org/wiki/Ontology_(information_science)

computer science

information science

ontology

knowledge

set of concepts

concepts

domain

relationships reasoning

subject ofsubject ofrepresentation

ofcontains

contains

containscontains description of

makes use of

supports

COMMIT/ E-FOODLAB

Components of an Ontology

Classes(concepts, types, universals)

Apple

COMMIT/ E-FOODLAB

Components of an Ontology

Classes(concepts, types, universals)

Apple

Pomesub class of

Fruitsub class of

Pear

sub class of

Elstar GoldenDelicious

sub class ofsub class of

COMMIT/ E-FOODLAB

Components of an Ontology

Instances(individuals, particulars)

Apple

Pome

Fruit

sub class of

sub class of

Pear

sub class of

Elstar GoldenDelicious

sub class ofsub class of

COMMIT/ E-FOODLAB

Components of an Ontology

Instances(individuals, particulars)

Apple

Pome

Fruit

sub class of

sub class of

Pear

sub class of

Elstar GoldenDelicious

sub class ofsub class of

COMMIT/ E-FOODLAB

Components of an Ontology

Instances(individuals, particulars)

Apple

Pome

Fruit

sub class of

sub class of

Pear

sub class of

Elstar GoldenDelicious

sub class ofsub class of

The apple in my lunch box

type

The apple onthe tree in my garden

type

COMMIT/ E-FOODLAB

Components of an Ontology

Relations

Apple

Pome

Fruit

sub class of

sub class of

Pear

sub class of

Elstar GoldenDelicious

sub class ofsub class of

The apple in my lunch box

type

The apple onthe tree in my garden

type

COMMIT/ E-FOODLAB

Components of an Ontology

Relations

Apple

Pome

Fruit

sub class of

sub class of

Pear

sub class of

Elstar GoldenDelicious

sub class ofsub class of

The apple in my lunch box

type

The apple onthe tree in my garden

type

COMMIT/ E-FOODLAB

Components of an Ontology

Relations

Apple

Pome

Fruit

sub class of

sub class of

Pear

sub class of

Elstar GoldenDelicious

sub class ofsub class of

The apple in my lunch box

type

The apple onthe tree in my garden

type

COMMIT/ E-FOODLAB

Components of an Ontology

Relations

Apple

Pome

Fruit

sub class of

sub class of

Pear

sub class of

Elstar GoldenDelicious

sub class ofsub class of

The apple in my lunch box

type

The apple onthe tree in my garden

type

COMMIT/ E-FOODLAB

Components of an Ontology

Relations

Apple

Pomesub class of

sub class of

Pear

sub class of

Elstar GoldenDelicious

sub class ofsub class of

The apple in my lunch box

type

The apple onthe tree in my garden

type

COMMIT/ E-FOODLAB

Components of an Ontology

Relations

Apple

Pomesub class of

sub class of

Pear

sub class of

Elstar GoldenDelicious

sub class ofsub class of

The apple in my lunch box

type

The apple onthe tree in my garden

type

has colour

red

location

my lunch box

COMMIT/ E-FOODLAB

Ontology Languages

Triples

The apple in my lunch box

Apple

Pomesub class of

sub class of

Pear

sub class of

Elstar GoldenDelicious

sub class ofsub class of

type

The apple onthe tree in my garden

type

has colour

red

location

my lunch box

COMMIT/ E-FOODLAB

Ontology Languages

Triples

The apple in my lunch box has colour red

COMMIT/ E-FOODLAB

Ontology Languages

Triples

The apple in my lunch box has colour red

SUBJECT PREDICATE OBJECT

COMMIT/ E-FOODLAB

Ontology Languages

Triples

SUBJECT PREDICATE OBJECTElstar sub class of AppleElstar label “Elstar”

COMMIT/ E-FOODLAB

Ontology Languages

Triples

SUBJECT PREDICATE OBJECTElstar sub class of AppleElstar label “Elstar”Apple label “Apple”Apple total production 69,569,612

COMMIT/ E-FOODLAB

Ontology Languages

RDF(Resource Description Framework)

SUBJECT PREDICATE OBJECTElstar sub class of AppleElstar label “Elstar”Apple label “Apple”Apple total production 69,569,612

URI (or blank node) URI

URILiteral(number/string)

http://example.com/Elstar http://www.w3.org/2000/01/rdf-schema#subClassOf http://example.com/Appleex:Elstar rdfs:subClassOf ex:Apple

COMMIT/ E-FOODLAB

VocabulariesRDF W3C Conceptual Description Method

RDFS W3C Basic elements for Ontologies

OWL W3C Ontologies

Dublin Core DCMI Metadata Discovery

AgroVoc FAO Food, Nutrition, Fisheries, Forestry, ...

Ontology of Measures FBR Units, Quantities, Scales, ...

Friend Of A Friend FOAF Biographic data, relations, ...

Gene Ontology GO consortium Gene and gene product attributes

Ontology of Astronomical Object Types IVOA Astronomical object Types

COMMIT/ E-FOODLAB

DataDBpedia Data taken from info boxes in

Wikipedia

Geonames Geographical information

BBC Programmes TV Programmes, series, ...

DBLP Computer Science Bibliography Bibliographic metadata

DrugBank Chemical, pharmacological and pharmaceutical data

data.gov.uk Public data related to policy

COMMIT/ E-FOODLAB

Data

And Many More

PUBLIC DATA SETS

and

Not so public data sets

COMMIT/ E-FOODLAB

LINKED OPEN DATA

Remember URIs?

COMMIT/ E-FOODLAB

LINKED OPEN DATA

http://dbpedia.org/page/Nijmegen

Remember URIs?

http://www.w3.org/2002/07/owl#sameAs

http://sws.geonames.org/2750053/

COMMIT/ E-FOODLAB

LINKED OPEN DATA

COMMIT/ E-FOODLAB

WorldFact-book

JohnPeel

(DBTune)

Pokedex

Pfam

US SEC(rdfabout)

LinkedLCCN

Europeana

EEA

IEEE

ChEMBL

SemanticXBRL

SWDogFood

CORDIS(FUB)

AGROVOC

OpenlyLocal

Discogs(Data

Incubator)

DBpedia

yovisto

Tele-graphis

tags2condelicious

NSF

MediCare

BrazilianPoli-

ticians

dotAC

ERA

OpenCyc

Italianpublic

schools

UB Mann-heim

JISC

MoseleyFolk

SemanticTweet

OS

GTAA

totl.net

OAI

Portu-guese

DBpedia

LOCAH

KEGGGlycan

CORDIS(RKB

Explorer)

UMBEL

Affy-metrix

riese

business.data.gov.

uk

OpenData

Thesau-rus

GeoLinkedData

UK Post-codes

SmartLink

ECCO-TCP

UniProt(Bio2RDF)

SSWThesau-

rus

RDFohloh

Freebase

LondonGazette

OpenCorpo-rates

Airports

GEMET

P20

TCMGeneDIT

Source CodeEcosystemLinked Data

OMIM

HellenicFBD

DataGov.ie

MusicBrainz

(DBTune)

data.gov.ukintervals

LODE

Climbing

SIDER

ProjectGuten-berg

MusicBrainz

(zitgist)

ProDom

HGNC

SMCJournals

Reactome

NationalRadio-activity

JP

legislationdata.gov.uk

AEMET

ProductTypes

Ontology

LinkedUser

Feedback

Revyu

GeneOntology

NHS(En-

AKTing)

URIBurner

DBTropes

Eurécom

ISTATImmi-gration

LichfieldSpen-ding

SurgeRadio

Euro-stat

(FUB)

PiedmontAccomo-dations

NewYork

Times

Klapp-stuhl-club

EUNIS

Bricklink

reegle

CO2Emission

(En-AKTing)

AudioScrobbler(DBTune)

GovTrack

GovWILDECS

South-amptonEPrints

KEGGReaction

LinkedEDGAR

(OntologyCentral)

LIBRIS

OpenLibrary

KEGGDrug

research.data.gov.

uk

VIVOCornell

UniRef

WordNet(RKB

Explorer)

Cornetto

medu-cator

DDC DeutscheBio-

graphie

Wiki

Ulm

NASA(Data Incu-

bator)

BBCMusic

DrugBank

Turismode

Zaragoza

PlymouthReading

Lists

education.data.gov.

uk

KISTI

UniPathway

Eurostat(OntologyCentral)

OGOLOD

Twarql

MusicBrainz(Data

Incubator)

GeoNames

PubChem

ItalianMuseums

Good-win

Familyflickr

wrappr

Eurostat

Thesau-rus W

OpenLibrary(Talis)

LOIUS

LinkedGeoData

LinkedOpenColors

WordNet(VUA)

patents.data.gov.

uk

GreekDBpedia

SussexReading

Lists

MetofficeWeatherForecasts

GND

LinkedCT

SISVU

transport.data.gov.

uk

Didac-talia

dbpedialite

BNB

OntosNewsPortal

LAAS

ProductDB

iServe

Recht-spraak.

nl

KEGGCom-pound

GeoSpecies

VIVO UF

LinkedSensor Data(Kno.e.sis)

lobidOrgani-sations

LEM

LinkedCrunch-

base

FTS

OceanDrillingCodices

JanusAMP

ntnusc

WeatherStations

Amster-dam

Museum

lingvoj

Crime(En-

AKTing)

Course-ware

PubMed

ACM

BBCWildlifeFinder

Calames

Chronic-ling

America

data-open-ac-uk

OpenElection

DataProject

Slide-share2RDF

FinnishMunici-palities

OpenEI

MARCCodesList

VIVOIndiana

HellenicPD

LCSH

FanHubz

bibleontology

IdRefSudoc

KEGGEnzyme

NTUResource

Lists

PRO-SITE

LinkedOpen

Numbers

Energy(En-

AKTing)

Roma

OpenCalais

databnf.fr

lobidResources

IRIT

theses.fr

LOV

Rådatanå!

DailyMed

Taxo-nomy

New-castle

GoogleArt

wrapper

Poké-pédia

EURES

BibBase

RESEX

STITCH

PDB

EARTh

IBM

Last.FMartists

(DBTune)

YAGO

ECS(RKB

Explorer)

EventMedia

STW

myExperi-ment

BBCProgram-

mes

NDLsubjects

TaxonConcept

Pisa

KEGGPathway

UniParc

Jamendo(DBtune)

Popula-tion (En-AKTing)

Geo-WordNet

RAMEAUSH

UniSTS

Mortality(En-

AKTing)

AlpineSki

Austria

DBLP(RKB

Explorer)

Chem2Bio2RDF

MGI

DBLP(L3S)

Yahoo!Geo

Planet

GeneID

RDF BookMashup

El ViajeroTourism

Uberblic

SwedishOpen

CulturalHeritage

GESIS

datadcs

Last.FM(rdfize)

Ren.EnergyGenera-

tors

Sears

RAE2001

NSZLCatalog

Homolo-Gene

Ord-nanceSurvey

TWC LOGD

Disea-some

EUTCProduc-

tions

PSH

WordNet(W3C)

semanticweb.org

ScotlandGeo-

graphy

Magna-tune

Norwe-gian

MeSH

SGD

TrafficScotland

statistics.data.gov.

uk

CrimeReports

UK

UniProt

US Census(rdfabout)

Man-chesterReading

Lists

EU Insti-tutions

PBAC

VIAF

UN/LOCODE

Lexvo

LinkedMDB

ESDstan-dards

reference.data.gov.

uk

t4gminfo

Sudoc

ECSSouth-ampton

ePrints

Classical(DB

Tune)

DBLP(FU

Berlin)

Scholaro-meter

St.AndrewsResource

Lists

NVD

Fishesof

TexasScotlandPupils &Exams

RISKS

gnoss

DEPLOY

InterPro

Lotico

OxPoints

Enipedia

ndlna

Budapest

CiteSeer

Media

Geographic

Publications

User-generated content

Government

Cross-domain

Life sciences

As of September 2011

COMMIT/ E-FOODLAB

Thank you!don.willems@wur.nl / @oekalegon