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Semantic Technologies at FAO

Bioversity International, Maccarese, Roma, Italy

Margherita Sini20 April 2009

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Few words about myself

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Just a very rapid introduction• What?

– semantic, semantic web, semantic technologies– ontologies, Knowledge Organization Systems, – metadata

• Why?– interoperability, exchange, share– user orientation, precision and recall– multilinguality, cultural views, context

• Who?– everybody, all domains, all countries, all .org

• Which instruments?– experts, NLP, methodologies and techniques

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Outline• Semantic projects involving FAO

– AOS– IPFSAPH, FNA, CWR, Fisheries, Food & nutrition,

Geopolitical ontology, AGROVOC Concept Server– Thai Rice Onto, Agropedia Indica

• Methods and Methodologies– Ontology models (AGROVOC Concept Server, LIR, ...)– Modeling considerations

• What’s next– networked ontologies– ontology-based applications– collaborations

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Semantic projects involving FAO

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Why AOS

vessel? craft? boat?

bateaux?barco?

Terminology brokering

Semantic navigation,Clustering, Ranking, ...

Intelligent query expansion

InferencingReasoningMachine learning

Interoperabilityship

orcontainer

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• Built from AGROVOC • Domain concepts• Categories

AGROVOCConcept Server

Agricultural Ontology Service• an FAO initiative for

more coherence in Agricultural Information Systems

• multiple partners• need of a semantic approach• AOS elements:

– AGROVOC Concept Server– KOS registry– Mapping registries– Metadata standards– Tools (refinement tool, WB, ...)

Ontology registrySub-domainontologies

Metadataontologies

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IPFSAPH

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IPFSAPH

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The Ontology

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Creation of the core ontology

1600 concepts3 languages

Information Resources•Brainstorming•Codex Alimentarius•SPS Agreement

Ontology

subjectspecialists

AGROVOC

Food SafetyDocuments

GenericDocuments

Ontology Editor(OI-Modeler)

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Features: Concept Search

The same records will be retrieved regardless of the specific synonyms or singular/plural forms that the user uses to refer to a concept.

Related concepts

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Features: Multilinguality

The system is also able to understand a concept even when different languages are used.

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Features: Check spelling

Spelling errors are corrected: e.g. “desease” into “disease”

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Features: Paraphrasing

“mad cow disease symptoms” or

“clinical signs of bovine spongiform encephalopathy”

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give the same results, which are ranked.

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Features: Semantic Navigation of Knowledge

parent concept(s)

children concept(s)

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FNA

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FNA

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Creation of the core ontologyFAO

BIBLIOGRAPHICDATABASE

FAO CORPORATEDOCUMENT

REPOSITORYDATABASE

MERGERECORDS

+TRANSFORM

TO RDFS

Ontology Editor(OI-Modeler)

maintain

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The ontology concepts• Publication• Issue• Work

• Article• Subject Term• Category• Author• Region• Language• Year

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Ontology Relationships

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The ontology instances

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Features• Multilingual concept resolution• Get suggestions for the navigation

(e.g. synonyms)• Guided query formulation• Easy navigation of the objects by following the

semantic links

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RDFa

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Features (cont.)

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CWR

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The project• International partners (BGCI, Bioversity International,

BLE, FAO, IUCN, UNEP WCMC)• Developed in harmony with CWR descriptor list• First version (English only) available by December 2006• About 800 core terms + acronyms + spelling variants• Clearly definition of concepts (AGROVOC + other

sources)• Relationships: hierarchical + causative

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The Ontology• OWL Full• http://www.fao.org/aims/aos/cwr.owl

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More semantics

Term: wild plants

subclass of plants superclass of crop wild relatives

adapted by domestication benefits from resource conservation

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Ontology properties (1/2)

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Ontology properties (2/2)

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Fisheries

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The projectOneFish

FIGIS

AGROVOC

Aquaculture

BrackishwaterAquaculture

MarineAquaculture

AquacultureDevelopment

AquacultureFacilities

BROADERTERM

BROADERTERM

RELATEDTERM

RELATEDTERM

FreshwaterAquaculture

AquacultureEconomics

AquacultureEngineering

BROADERTERM

RELATEDTERM

RELATEDTERM

Aquaculture Resource

Water Area

land

strainsSpecieslife cycle

Farming system

management system

Production center

Spawning technique

Breeding technique

Hatchery technique

Expl. form

Regulation

Farming

technique

Environment

Institution

Health monitoring technique

diseases

suppliers

ASFA

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Basic activities in FOS

Catalog building

PRECEDESPRECEDESPRECEDES OntologyMerging

Wrapping

TerminologyRe-

engineering

Formatting Union Mapping

Interfacing

Exploitation

Matching

DiscoveryConsistency checking

Formalization

ConceptualIntegration

Analysis

ImportingDescriptorsTermsRelationsScope notesSubjectsIdentifiersCodesDB specific links

ConceptsRelationsAxiomsRulesLexicalizationAnnotations

@ CNR

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The Ontology

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Features1. Form versus meaning:

a) Traditional Searchb) Concept Search

2. Implemented functionalities:a) synonym searchb) multilingual capabilityc) terminology brokeringd) disambiguatione) related conceptsf) query expansion

3. Basic natural language queries

4. Semantic navigation of bibliographical metadata

5. Semantic Navigation of Knowledgea) Alphabetic list ...b) Core Fishery

Concepts ...

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Ontology properties|Fishing Grounds@ag| PARTICIPANT-IN |Fishing Operations@ag||Sponges@ag| PARTICIPANT-IN |Sponge Fisheries@ag||Pearls@ag| PARTICIPANT-IN |Pearl Culture@ag||Pearls@ag| PARTICIPANT-IN |Pearl Fisheries@ag||Silk@ag| PARTICIPANT-IN |Sericulture@ag||Small Enterprises@ag| PARTICIPANT-IN |Artisanal Fisheries@ag||Dairy Farms@ag| PARTICIPANT-IN |Milk Production@ag||Fish Farms@ag| PARTICIPANT-IN |Aquaculture@ag||Fish Farms@ag| PARTICIPANT-IN |Fish Feeding@ag||Fish Farms@ag| PARTICIPANT-IN |Fisheries@ag||Natural Resources@ag| PARTICIPANT-IN |Resource Conservation@ag|

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Example"tell me what vessels from a nearby country are

currently in the marine area 50N060W within Atlantic Ocean, provided that also some Thunnus

alalunga stock can be fished by those vessels, through allowed techniques"

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Using multilingual lexicalizations ENGLISH

SPANISH

FRENCH

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Using hierarchically related concepts

hierarchically related concept

Polyvalent Trawlers

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Using non-hierarchically related concepts

non-hierarchically related concept

gears

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Help the user formulate queries

Original query: bateau de pêcheTo refine your query, click on the concepts you are interested in. They will appear to the left.

Search:

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Reconcile different vocabularies

“navire de pêche”, “fishing

vessel”, “embarcaciones

de pesca”

AGROVOC or ASFA or

other“fishing vessels,”

“fishing boat,”

AGROVOC: “fishing vessels”, “barco”, etc...ASFA: “fishing

vessels”

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Semantic Navigation of Knowledge: Thesaurus based

Highlighting the originator thesaurus. User can select a specific thesaurus to look for.

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Geopolitical ontology

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Geopolitical ontology• Incorporate geopolitical data• Will serve as a bridge to allow communication

between the various systems

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PropertiesisValidFromhasOfficialNamehasCodeisSuccessorOfhasBorderWithdependsOn

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Nutrition Ontology

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Procedure

=CONCATENATE("<owl:Class rdf:ID=""",J2,"""><rdfs:subClassOf><owl:Class rdf:ID=""c_",B2,"""/></rdfs:subClassOf><rdfs:label xml:lang=""en""><![CDATA[",D2,"]]></rdfs:label><code><![CDATA[",J2,"]]></code><TAGNAME><![CDATA[",J2,"]]></TAGNAME>",S2, T2,"</owl:Class>")

<?xml version="1.0"?><rdf:RDF xmlns="http://www.fao.org/aos/infoods#" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:daml="http://www.daml.org/2001/03/daml+oil#" xmlns:dc="http://purl.org/dc/elements/1.1/" xml:base="http://www.fao.org/aos/infoods"> <owl:Ontology rdf:about=""> <owl:imports rdf:resource="http://protege.stanford.edu/plugins/owl/protege"/> <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >Revision 4.0</owl:versionInfo> <protege:defaultLanguage rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >en</protege:defaultLanguage> <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >International Network of Food Data Systems (INFOODS) was established in 1984 on the basis of the recommendations of an international group convened under the auspices of the United Nations University (UNU). Its goal was to .....</rdfs:comment> </owl:Ontology> <owl:Class rdf:ID="c_0413"> <code rdf:datatype="http://www.w3.org/2001/XMLSchema#string" >0413</code> <rdfs:subClassOf> <owl:Class rdf:ID="c_041"/> </rdfs:subClassOf> <rdfs:label xml:lang="en">Vitamin D</rdfs:label> </owl:Class>

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AGROVOC

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TerminologyWorkbench

AGROVOCOWL

AOS Core: the Concept Server

Export

AGROVOCRDFS formats

(e.g. SKOS)and

TagTextISO2709

Other thesauriand

terminologies

integration

ABACA NT1 Food NT2 AppleANIMAL BT Organ NT ....

mapping

Other thesauri & terminologies

ABACA NT1 Food NT2 AppleANIMAL BT Organ NT ....

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Concept Server project• Refine semantics and enrich data pool and lexicon• Develop a workbench for terminology and ontology

development and maintenance• Support information management specialists in the

development, maintenance, and quality assurance of the AGROVOC CS

• Global knowledge vs Local knowledge

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AGROVOC Concept Server• AGROVOC cleaning and refinement

CurrentAGROVOC

MySQL

ImprovedAGROVOC

MySQL

AGROVOC OWLRevision

andRefinement

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Modeling• Conversion to UTF-8• Incorporated AGRIS/CARIS classification scheme

(multilingual) and the mapping with AGROVOC keywords

• Modified structure to store multiple classification schemes

• Export to OWL format (v0.8a)• Export to SKOS format (v0.8a)• Revised RDBMS scheme for ontology representation• Identified the ontological model + represent in OWL

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Thai Rice Ontology

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Thai Rice Onto

metadatarepository

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http://www.fao.org/aims/Plant ontology: Relationship typesTaxon <hasSuperclass> Taxon

Taxon <has GrowthType> GrowthType

Taxon <hasPropagationMethod> PropagationMethod

Taxon <occursIn> Environment

Taxon <hasPest> Taxon

Taxon <hasDisease> Disease

Disease <causedBy> Taxon

TaxonPart <isa> AnatomicalPart

TaxonPart <isa> AnatomicalTypeOfFruit

TaxonPart <partOf> Taxon

TaxonPart <usedAs> Use

TaxonPart <usedToMake> ProductType

Taxon <hasDescription> Text

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Thai plant ontology: ExampleMangifera indica Linn. <hasSuperclass> Mangifera

Mangifera indica Linn. <hasGrowthType> tree

Mangifera indica Linn. <hasPropagationMethod> seedling

Mangifera indica Linn <hasDescription> "leaves ...., flower ...... “

Mangifera indica Linn <occursIn> dry soil

Mangifera indica Linn. <hasPest> Scirtothrips dosalis Hood

Mangifera indica Linn <hasPest> Oidium mangiferae

OR, instead of the last statement or in addition to it

Mangifera indica Linn <hasDisease> Powdery Mildew

Powdery mildew <caused by> Oidium mangiferae

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Agropedia Indica

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Agropedia Indica• http://www.slideshare.net/marghe_rita/1-pantnag

ar• http://www.slideshare.net/marghe_rita/2-pantnag

ar-w-guidelines• http://www.slideshare.net/marghe_rita/3-pantnag

ar-w-exercices

• http://agropedia.iitk.ac.in/ • Guidelines

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Retrieval

Navigate KMJAVA+JENA

this is a documentabout rice and its

pests.....Once the rice ap-

pearin the world .....

Mad Cow Disea-se is the commonly

used name for Bovine

Spongiform Encephalopathy

(BSE) ....

results.....

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And also...

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Other projects• Language ontology

– http://www.fao.org/aims/aos/languagecode.owl • AGRIS metadata ontology• ...

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Ontology Construction Methodologies / Methods

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Several points to consider• Start from existing KOS• Incorporate Terminology/Concepts from sources• Different data models to homogenize / link /

merge• From RDBMS/excel to RDFS/OWL• Make use of existing standards (Dublin Core)• From unstructured data to formalized data• Available tools

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Modeling• Identify use cases / Application needs• Competency questions• Identify the ontological model + Evaluate standards

– AGROVOC– NeOn LIR– Others

• Identify tools / APIs– Performances!– Development team!– Maintenance team (domain experts)!

• Process – Conversion to UTF-8– Merging schemes / data– Automatic tools expert revision!

• Guidelines

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Ontology models: AGROVOC

Concept

Relationshipsbetweenconcepts

Lexicalization/Term

String

Relationshipsbetweenstrings

Relationshipsbetweenterms

designated by

manifested asOther information:language/culture

subvocabulary/scopeaudiencetype, etc.

Note

annotation relationship

Relationship

RelationshipsbetweenRelationships

All terms are created as instances of the class o_terms. All at the same level. Only one language per term.

term levelstring level

concept level

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LIR

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Modeling (cont.)• concepts from descriptors• Synonym

<owl:DatatypeProperty rdf:ID="synonym">

• Acronyms <owl:AnnotationProperty rdf:about="http://www.fao.org/aos/agrovoc/2005#acronym">

<owl:Class rdf:about=" http://www.fao.org/aos/agrovoc/2005#c_3"> <rdfs:label xml:lang="en">ABA</rdfs:label> <rdfs:label xml:lang="fr">ABA</rdfs:label> <rdfs:label xml:lang="es">ABA</rdfs:label> <rdfs:label xml:lang="ar">آبا</rdfs:label> <rdfs:label xml:lang="zh">脱è½é…¸</rdfs:label>� <synonym xml:lang="en">[8565] Abscisic acid</synonym> <rdfs:subClassOf rdf:resource=" http://www.fao.org/aos/agrovoc/2005#c_3397"/> <rdfs:subClassOf rdf:resource=" http://www.fao.org/aos/agrovoc/2005#c_32543"/></owl:Class>

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Modeling (cont.):Registries concepts, relationships

subclass of subclassOf

Y <subclass_of> X. Y has all the features of X plus additional ones which make it more specific than X. E.g. { cow's milk } <subclass_of> { milk }.

superclass of superclassOf

X <superclass_of> Y. X is more general than Y in the sense that X is characterized by having a subset of the features of Y. E.g. { milk } <superclass_of> { cow's milk }.

part of partOf

Y <part_of> X. Part Y is a constituent of entity X. Use this relationship when none of the other partitivity relations (<component>, <composed_of>, <portion>, <member>, <includes_subprocess>) apply. E.g. in a plant ontology: {PlantPart} <part_of> {taxon}

part part

X <part> Y. A composite entity X that can be identified as having one or more parts Y. Use this relationship when none of the other partitivity relations (<component>, <composed_of>, <portion>, <member>, <includes_subprocess>) apply.

used as <used_as

X <used_as> Y. Thus far, restricted to plant domain, i.e., {Taxon} <used_as> {use}, and for uses of chemicals i.e., {chemical substance} <used_as> {use}. E.g.: "apple" <used_as> "fruit"; "alcohol" <used_as> "cleaner"; "ddt" <used_as> "pesticide".

is use of <is_use_of>

Y <is_use_of> X. For use within the plant domain, {Use} <is_use_of> {Taxon},. and for chemical substances {use} <is_use_of> {chemical substance}. E.g.: "fruit" <is_use_of> "apple"; "cleaner" <is_use_of> "alcohol"; "pesticide" <is_use_of> "ddt";

pest of <pest_of>X <pest_of> Y. An organism X causes harm to organism Y. E.g. "Bactrocera dorsalis" <pest_of> "Litchi chinensis";

pest <pest>Y <pest> X. An organism Y can be harmed by organism X. E.g. "Litchi chinensis" <pest> "Bactrocera dorsalis";

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What’s next

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Networked ontologies: AOS

Market Ontolgy@IITK

general PestOntology@IITK

Application Specific Layer

OtherSpecific

Ontologies

Domain Specific Layer

AgriculturalDomain Specific

Ontologies

(may

)

impo

rt

(may

)

impo

rt

RiceOntology@FAO

RiceOntology@IITK

general PestOntology@FAO

PlantOntology@FAO

RiceOntology@KU

IndianRiceOntology@IITK

Indian RiceCultivationOntology@IITK

PestactivityOntology@IITK

sam

e U

RI

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Ontology-based applications• Better exploitation of the potentiality at the

application level: powerful IR, reasoning• No more words but URIs in IS• Ontology Web services (OWS)

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Ontology-based Application

Search for:Search for:

Providers MetadataLayer Ontology Layer Web Interface

<dc:title/>< />< />< />< />

<dc:title/>< />< />< />< />

<dc:title/>< />< />< />< />

<dc:title/>< />< />< />< />

<dc:title/>< />< />< />< />

<dc:title/>< />< />< />< />

<dc:title/>< />< />< />< />

<dc:title/>< />< />< />< />

<dc:title/>< />< />< />< />

<OWL .....>

</OWL>

dc:title

dc:subject

dc:author

<OWL .....>

</OWL>

rights

gmo

Search for:

ok

StemmingDisambiguationCheck-spelling

...

conceptsresolution

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AGROVOC CSWorkbench

HEALTH CSWorkbench

internet

My Personal CS Workbench

My Personal CS Workbench

My Personal CS Workbench

Future AOS Ontologies GridNetworked CS ontologies

....organismssubstances

....healthmedicine

Health Modules

Thai Agriculture Ontology

CS Workbench

....ricecornpara rubbersugarcane

....ricemangosorghum

IITK Modules

Agropedia IndicaWorkbench

CS Modules

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Collaborations• With AOS partners• Mapping projects• NeOn• SEMIC.EU• GBIF Global Biodiversity Information Facility

secretariat• JRC + BGS• Ecoterm

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Take-home message• There are many uses for terminology +

ontology systems in food and agriculture, both for information access and information processing

• FAO has several projects using such systems

• FAO and partners are deploying the Agricultural Ontology Server (AOS)as a global resource

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Questions?

Thanks

Margherita Sini: margherita.Sini@fao.orgJohannes Keizer: Johannes.Keizer@fao.org

Dagobert Soergel: dsoergel@umd.eduAsanee Kawtrakul: asanee_naist@yahoo.com

But Also: Gudrun Johannsen, Boris Lauser, Claudio Baldassarre, Gauri Salokhe, Marta Iglesias, Caterina

Caracciolo, Sachit Rajbhandari, Jeetendra Singh, Mary Redahan, Shrestha, Prashanta, Ton, Imm, Thanapth, Trakul,

and many others...