fao semantics related projects
TRANSCRIPT
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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: [email protected] Keizer: [email protected]
Dagobert Soergel: [email protected] Kawtrakul: [email protected]
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...