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The AGRICULTURAL ONTOLOGY SERVICE. A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating an ontology on Food Safety, Animal and Plant Health (OFsAPH)
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The AGRICULTURAL ONTOLOGY SERVICE. A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating an ontology on Food Safety, Animal and Plant Health (OFsAPH)

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  • 1. SemanticStandards for the WebA Comprehensive Framework for Building The AGRICULTURAL ONTOLOGY SERVICE Multilingual A Comprehensive Framework for Building Multilingual Domain Ontologies: Domain Creating an ontology on Ontologies: Creating a Food Safety, Animal and Plant Health Prototype (OFsAPH) Biosecurity Ontology AFITA 2002 BeijingJohannes Keizer Johannes Keizer Food and Agriculture Information Systems Officer Organization of the UN Food and Agriculture Organization of the UN Library and DocumentationSystems Division Team: Boris Lauser Team: Boris Lauser, Allison Poullos, Tanja Wildemann, Frehiwot Fisseha28-10-2002 AFITA 2002, Beijing 28th October 2002
  • 2. SemanticStandards for FAOs mandate the WebA Comprehensive Framework for Building • Reducing the quantity of hungry people by 50% Multilingual Domain Ontologies: within the year 2015 (World Food Summit 1996). Creating a Prototype Biosecurity • WAICENT (World Agricultural Information Center) Ontology is FAO’s approach to fight hunger with information AFITA 2002 Beijing • FAO itself produces huge amount of content in it’s subject areaJohannes Keizer Food and • It is also within FAOs mandate to make available Agriculture Organization of the UN useful information from other information providers Library and Documentation • FAO collaborates in information networksSystems Division28-10-2002Slide 2
  • 3. Introduction SemanticStandards for the WebA Comprehensive Framework for Building Multilingual Domain Ontologies: It has become a triviality to state the difficulty Creating a Prototype Biosecurity Ontology of finding relevant information on the web AFITA 2002 BeijingJohannes Keizer Food and Agriculture Organization of the UN Library and DocumentationSystems Division28-10-2002Slide 3
  • 4. The Search Problem SemanticStandards for the WebA Comprehensive Framework for How to evaluate Search Results? Building Multilingual Domain Ontologies: Number of Relevant Documents Identified Creating a Prototype Precision Biosecurity Ontology Total Number of Documents Identified AFITA 2002 Beijing Number of Relevant Documents Identified RecallJohannes Keizer Number of Relevant Documents in the Collection Food and Agriculture Organization of the UN Library and DocumentationSystems Division28-10-2002 Both parameters are ranking low today!Slide 4
  • 5. Semantic State of Search SystemsStandards for the WebA Comprehensive Framework for  Full text search engines based on statistical text Building Multilingual Domain analysis are inprecise by nature Ontologies: Creating a Prototype  New system based only on “machine intelligence” Biosecurity Ontology do not show too promising results AFITA 2002  Recogniton of meaning (semantic analysis) by Beijing machines is only possible by using knowledgeJohannes Keizer organization systems Food and Agriculture Organization of the UN  agreed metadata schemas Library and DocumentationSystems Division  Controlled vocabularies  Machine readable encoding28-10-2002Slide 5
  • 6. Knowledge Organization Systems: Vocabularies SemanticStandards for the Web  Insufficientand Knowledge + Existing Thesauri subject Dedicated KOSs Organization Systems (KOSs)A Comprehensive Framework for language coverage e.g., ASFA thesaurus Building e.g., the Multilingual Multilingual Domain  Only very simple encoding Forestry Thesaurus Ontologies: Creating a Prototype of semantic the Sustainable e.g., relations Biosecurity Development Ontology  Common concepts are website classification AFITA 2002 not declared e.g., biological taxonomies such as NCBI and ITIS Beijing  No or very limited Other thematic thesauriJohannes Keizer Food and interoperability Agriculture Non-dedicated KOSs Organization of the UN  Very limited machine CABI Thesaurus Library and Documentation readability AGROVOCSystems Division NAL Thesaurus28-10-2002  Severe maintenance GEMETSlide 6 problems
  • 7. Semantic Ontologies?Standards for the WebA Comprehensive Framework for  An ontology is a formal knowledge organization Building Multilingual Domain system Ontologies: Creating a Prototype  It contains concepts (and instances) Biosecurity Ontology  a formal description of the application knowledge  Definitions of concepts and instances AFITA 2002 Beijing  Relations between concepts and instances  possibility of machine processingJohannes Keizer Food and Agriculture Organization of the UN  Nearly everyone tries to build (inexplicit) ontologies Library and Documentation  Directory structures, navigation treesSystems Division  Humans can overcome bad organization by intuition28-10-2002  Machine have no intuition, Machine need formal informationSlide 7
  • 8. What benefits do we expect from Ontologies? SemanticStandards for the Web • Semantic Organization of websitesA Comprehensive  Knowledge maps Framework for Building Multilingual  Guided discovery of knowledge Domain Ontologies:  Easy retrievability of information without using complicated Creating a Prototype Boolean logic Biosecurity Ontology • Text processing by machines  Text Mining on the Web (meaning-oriented access) AFITA 2002  Automatic indexing and text annotation tools Beijing  Full text search engines that create meaningful classification (FAO-Schwartz not related to FAO) (semantic clustering)Johannes Keizer Food and • Intelligent search of the Web Agriculture Organization of  Building dynamical catalogues from machine readable meta data the UN Library and • Natural Language processing DocumentationSystems Division  Better machine translation  Queries using natural language28-10-2002Slide 8
  • 9. Semantic The Example: International Portal on Food Safety, Animal and Plant HealthStandards for the WebA Comprehensive • Goal: Framework for Building Multilingual Domain Ontologies: Creating a To create an explicit, formal specification of a Prototype Biosecurity Ontology shared conceptualization of a domain of interest AFITA 2002 BeijingJohannes Keizer Food and Agriculture Organization of the UN Library and Documentation OntologySystems Division28-10-2002Slide 9
  • 10. Ontology: conceptual model SemanticStandards for the WebA Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology label Concept AFITA 2002 synonym Beijing relationship ConceptJohannes Keizer stem Food and synonym Agriculture Organization of the UN synonym Library and DocumentationSystems Division description28-10-2002Slide 10
  • 11. Ontology: RDFS model, machine readable encoding SemanticStandards for the WebA Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 BeijingJohannes Keizer Food and Agriculture Organization of the UN Library and DocumentationSystems Division28-10-2002Slide 11
  • 12. Processes to create a Domain Ontology SemanticStandards for the WebA Comprehensive Framework for Building • Ontology acquisition (2 paths) Multilingual Domain Ontologies: – Creating core ontology from scratch Creating a Prototype – Automatic extraction of ontological knowledge from base Biosecurity Ontology vocabulary and domain specific text sources • Merging into one ontology AFITA 2002 Beijing • Refinement and Extension • Evaluation and AssessmentJohannes Keizer Food and Agriculture Organization of the UN Library and DocumentationSystems Division28-10-2002Slide 12
  • 13. Creation of the core ontology SemanticStandards for the WebA Comprehensive Framework for Information Resources: Building Multilingual •Brainstorming Domain Ontologies: •Codex Alimentarius Creating a Prototype Biosecurity •SPS Agreement Ontology AFITA 2002 Beijing 3 subject specialistsJohannes Keizer Core Ontology Food and 67 concepts Agriculture Organization of 91 relationships the UN Library and DocumentationSystems Division Ontology Editor (SOEP)28-10-2002Slide 13
  • 14. 1st Acquisition Approach: Focused Crawling Semantic List of extracted main sites:Standards for http://www.foodsafety.gov/ the Web Gateway to Government Food Safety InformationA Comprehensive http://vm.cfsan.fda.gov/ Framework for Center for Food Safety & Applied Nutrition Building Multilingual Domain http://www.inspection.gc.ca/ Ontologies: Creating a Canadian Food Inspection Agency Prototype Biosecurity Focused Ontology http://www.extension.iastate.edu/foodsafety/ Web Crawling Iowa State University - Food Safety Project AFITA 2002 http://www.foodsafety.iastate.edu Core Ontology Beijing Iowa State University - Food Safety Consortium 68 concepts 91 relationships http://www.fsis.usda.gov/Johannes Keizer List of 257 food United States Department of Agriculture, Food and Safety domain Food Safety and Inspection Service Agriculture Organization of web pages http://www.nal.usda.gov/foodborne/index.html the UN Foodborne Ilness Education Information Center Library and Documentation http://www.euro.who.int/foodsafetySystems Division Grouping into World Health Organization – Regional Office for28-10-2002 Main sites Europe Food Safety ProgrammeSlide 14
  • 15. Selection of Documents SemanticStandards for the WebA Comprehensive • Domain Set: Manual selection Framework for Building – 11 documents Multilingual • Codex Alimentarius: Description, Code of Ethics, Food Hygiene, Food Import and Export Domain • Report of consultation on risk assessment of microbiological hazards in foods Ontologies: • Creating a Ensuring food quality and safety, Protecting food quality and safety Prototype Biosecurity Ontology • Domain Set: Focused Crawler Output – 5 documents extracted: AFITA 2002 • http://vm.cfsan.fda.gov/; • http://www.inspection.gc.ca/; Beijing • http://www.foodsafety.iastate.edu; • http://www.extension.iastate.edu/foodsafety/; • http://www.euro.who.int/foodsafetyJohannes Keizer Food and Agriculture • Generic documents: Manual Selection Organization of the UN – 8 documents • www.nytimes.com Library and • Several documents of the animal feed domain DocumentationSystems Division28-10-2002Slide 15
  • 16. 2nd Acquisition Approach: Thesaurus Pruning SemanticStandards for the WebA Comprehensive Framework for AGROVOC 5 evaluation runs Building Multilingual 27365 keywords Domain Ontologies: Creating a Rice Prototype Biosecurity BT … 1632 frequent Ontology NT … terms AFITA 2002 RT … Automatic Beijing RT … Pruning RT …Johannes Keizer … Food and Agriculture Organization of Food Safety Extracted ontological the UN Documents structure: Library and Documentation # of concepts: 504Systems Division taxonomic depth: 5 Generic28-10-2002 DocumentsSlide 16
  • 17. Merging of Ontologies and Refinement SemanticStandards for the WebA Comprehensive Framework for Building 1632 Terms from Multilingual Domain pruning process 12 new concepts Ontologies: extracted Core Ontology Creating a Prototype 67 concepts Biosecurity Ontology 92 new 91 relationships relationships AFITA 2002 created Assembly Beijing stepJohannes Keizer Food and Agriculture Ontological Organization of structure 23 new concepts the UN extracted from With hierarchical Library and Documentation AGROVOC relationships Food Safety OntologySystems Division extracted Prototype 102 concepts28-10-2002 183 relationshipsSlide 17
  • 18. Final Prototype SemanticStandards for the WebA Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Core Ontology Food Safety OntologyJohannes Keizer 67 concepts Prototype Food and 91 relationships Agriculture Organization of 102 concepts the UN 183 relationships Library and Documentation relationshipsSystems Division 1.36 concept relationships28-10-2002 1.79 conceptSlide 18
  • 19. 102 Concepts SemanticStandards for the Web Agreement of Agriculture chemical agent humans plant feed ingredientsA Comprehensive ALOP Codex Committees international agreements plant feeding Framework for Building ALOP, Codex commodities international food trade plant health Multilingual ALOP, OIE Consumer health international governmental plant processing Domain Ontologies: ALR diseases organizations plant products Creating a animal byproducts eggs IPPC plant waste Prototype Biosecurity animal diseases exposure assessment labelling plants Ontology animal fats fabrication meat processed animal products animal feed additives FAO microorganisms processed plant products animal feed contaminants fishes microorganisms byproducts processed products AFITA 2002 animal feed ingredients food microorganisms processing processing Beijing animal feeding food additives microorganisms products risk analysis animal health food consumption microorganisms waste risk assessment animal processing food contaminants milk risk characterizationJohannes Keizer animal products food export milk products risk communication Food and animal waste food import milk products risk management Agriculture animals food ingredients non-pathogens slaughter Organization of antibiotics food safety OIE SPS agreement the UN Bacteria food-borne diseases packaging standards Library and bakery products fungi parasites sugar DocumentationSystems Division biological agent good hygienic practices pathogens TBT agreement CAC hazard physical agent transport Caragene protocol hazard characterization plant byproducts viruses28-10-2002 CCFH hazard identification plant diseases WHOSlide 19 cereal products human health plant feed additives WTO cheese human nutrition plant feed contaminants
  • 20. 29 Unique Relationships SemanticStandards for the WebA Comprehensive Framework for Building adopts influences Multilingual Domain adversely affect interacts with Ontologies: Creating a are included in is a consequence of Prototype Biosecurity Ontology are produced by is a step in the process are the source for is comprised of AFITA 2002 can be used as is established by Beijing constitutes is protected by describes originate fromJohannes Keizer determines refer to Food and Agriculture ensures requires Organization of the UN establishes rule Library and govern sustains DocumentationSystems Division has economical impact on trades Implies uses28-10-2002 includesSlide 20
  • 21. Current project status Ontology creation: 2nd application of framework SemanticStandards for the WebA Comprehensive Framework for Building Multilingual List of ~100 domain frequent Domain Text To Onto Ontologies: Specific terms Creating a documents Prototype Food Safety Ontology 1st acquisition Biosecurity Prototype Ontology approach 102 concepts 183 relationships AFITA 2002 2nd acquisition approach Beijing Revised Ontology PrunerJohannes Keizer Food and AGROVOC Pruned Agrovoc: Agriculture ~3000 concepts Organization of the UN Library and Documentation Merging &Systems Division Refinement28-10-2002 Ontology EditorSlide 21 (OIModeler)
  • 22. Usage Scenario SemanticStandards for the Web Ontology based search extensionA Comprehensive Framework for Building Biosecurity Portal: Mark the terms below, which you might want to include in Multilingual … your search: Domain Ontologies: Search: Creating a Exposure assessment Is a Prototype Risk assessment Risk characterization Step Biosecurity Ontology … In the Risk assessment Hazard characterization process Hazard identification Is a AFITA 2002 Step Beijing Ontology Interacts In the Enabled with processJohannes Keizer Search Risk communication Risk analysis Food and Application Risk management Agriculture Organization of the UN Search: Risk assessment Risk characterization Risk analysis Library and Documentation Ontology Extended SearchSystems Division Search28-10-2002 Doc base resultsSlide 22
  • 23. Current project status Application scenario: 2 use cases SemanticStandards for the WebA Comprehensive Framework for Building Multilingual Domain Use Case 1: Indexing the subject of a document Ontologies: Creating a … Prototype Biosecurity Title Ontology Subject Risk;… … AFITA 2002 BeijingJohannes Keizer Use Case 2: Searching information on the portal Food and OFsAPH Agriculture Organization of the UN … Library and Search Documentation Risk;…Systems Division …28-10-2002Slide 23
  • 24. Current project status: Application: Ontology Browser for the Ontology on Food Safety, Semantic Animal and Plant HealthStandards for the WebA Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 BeijingJohannes Keizer Food and Agriculture Organization of the UN Library and DocumentationSystems Division28-10-2002Slide 24
  • 25. Semantic The Project for an AgriculturalStandards for the Web Ontology ServiceA Comprehensive Framework for Building Multilingual Domain • Only agreed semantic standards guarantee Ontologies: Creating a Prototype knowledge discovery between different Biosecurity Ontology applications AFITA 2002 • The definition of Knowledge Organization systems Beijing is resource intensiveJohannes Keizer • Therefore FAO started initiatives to bring Food and Agriculture Organization of interested partners together the UN  October 2000 Launch of the AGStandards initiative to agree on Library and Documentation metadata standardsSystems Division  July 2001 concept paper on Agricultural Ontology Service28-10-2002Slide 25
  • 26. What does Agricultural Ontology Service mean? SemanticStandards for the Web The Agricultural Ontology Service is an approach to organizeA Comprehensive Framework for knowledge organization systems that is Building Multilingual Domain Ontologies:  International Creating a Prototype The Internet must become plurilingual Biosecurity Ontology  Multidisciplinary The area of subjects is broad and needs various inputs AFITA 2002 Beijing  Cooperative different expert knowledge has to be associated and usedJohannes Keizer Food and Agriculture  Distributed Organization of no central ownership should be looked for the UN Library and Documentation  CoordinatedSystems Division Coordination must ensure reusability and standardization28-10-2002Slide 26
  • 27. AOS: Iterative Knowledge Registration SemanticStandards for the Web Components: terms, definitions,A Comprehensive Framework for relationships Building KOS uses Multilingual Domain components to build Ontologies: Creating a an application Prototype Biosecurity Ontology Agricultural Ontology AFITA 2002 Service (AOS) Beijing Federated storage and description facilityJohannes Keizer Food and Agriculture Components: terms, Organization of definitions, the UN relationships Library and Users search and browse Documentation application usingSystems Division components Discussions and choices for amendments to28-10-2002 User feedback componentsSlide 27
  • 28. Activities up to now SemanticStandards for the Web • The first workshop took place in Rome, NovemberA Comprehensive Framework for Building Multilingual 2001 • A launch group was established with participation Domain Ontologies: Creating a Prototype Biosecurity Ontology of – Content providers (FAO, CABI) AFITA 2002 – Solution providers in the Agricultural Area (ATO -Wageningen, Beijing University of Florida) – Ontology development Groups (AIFB Karlsruhe, CNR Italy)Johannes Keizer Food and Agriculture Organization of the UN • Two further workshops were organized in January Library and DocumentationSystems Division and May 200228-10-2002 • Ontology protypes are under developmentSlide 28
  • 29. AOS – a “business model” SemanticStandards for the Web • A consortium of Information ProvidersA Comprehensive • A clearinghouse for semantic standards in the Framework for Building Multilingual Domain Ontologies: Creating a relevant subject areas Prototype Biosecurity Ontology • One stop access to agreed standards (Ontologies, AFITA 2002 Metadataschemas, Vocabularies…) Beijing • Participation as a consortium in semantic webJohannes Keizer activities to get funding for specific projects Food and Agriculture (“Semkos” for EU 6th framework) Organization of the UN • Organization of seminars and workshops to further Library and DocumentationSystems Division develop and promote the use of semantic standards28-10-2002Slide 29
  • 30. Further Information SemanticStandards for the WebA Comprehensive http://www.fao.org/agris/AOS Framework for http://www.fao.org/agris/AGMES Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 BeijingJohannes Keizer Food and Agriculture Organization of the UN Library and DocumentationSystems Division28-10-2002Slide 30