Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing The AGRICULTURAL ONTOLOGY SERVICE A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating an ontology on Food Safety, Animal and Plant Health (OFsAPH) Johannes Keizer Information Systems Officer Food and Agriculture Organization of the UN AFITA 2002, Beijing28 th October 2002 Team: Boris Lauser Team: Boris Lauser, Allison Poullos, Tanja Wildemann, Frehiwot Fisseha

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 2 FAOs mandate Reducing the quantity of hungry people by 50% within the year 2015 (World Food Summit 1996). WAICENT (World Agricultural Information Center) is FAO’s approach to fight hunger with information FAO itself produces huge amount of content in it’s subject area It is also within FAOs mandate to make available useful information from other information providers FAO collaborates in information networks

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 3 Introduction It has become a triviality to state the difficulty of finding relevant information on the web

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 4 The Search Problem Both parameters are ranking low today! Recall Number of Relevant Documents in the Collection Number of Relevant Documents Identified Precision Number of Relevant Documents Identified Total Number of Documents Identified How to evaluate Search Results?

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 5 State of Search Systems  Full text search engines based on statistical text analysis are inprecise by nature  New system based only on “machine intelligence” do not show too promising results  Recogniton of meaning (semantic analysis) by machines is only possible by using knowledge organization systems agreed metadata schemas Controlled vocabularies Machine readable encoding

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 6 Knowledge Organization Systems: Vocabularies AGROVOC NAL Thesaurus CABI Thesaurus Dedicated KOSs Non-dedicated KOSs e.g., ASFA thesaurus e.g., the Multilingual Forestry Thesaurus e.g., the Sustainable Development website classification e.g., biological taxonomies such as NCBI and ITIS GEMET Other thematic thesauri Existing Thesauri and Knowledge Organization Systems (KOSs)  Common concepts are not declared  No or very limited interoperability  Insufficient subject + language coverage  Severe maintenance problems  Very limited machine readability  Only very simple encoding of semantic relations

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 7 Ontologies?  An ontology is a formal knowledge organization system It contains concepts (and instances) a formal description of the application knowledge Definitions of concepts and instances Relations between concepts and instances possibility of machine processing  Nearly everyone tries to build (inexplicit) ontologies Directory structures, navigation trees Humans can overcome bad organization by intuition Machine have no intuition, Machine need formal information

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 8 What benefits do we expect from Ontologies? Semantic Organization of websites Knowledge maps Guided discovery of knowledge Easy retrievability of information without using complicated Boolean logic Text processing by machines Text Mining on the Web (meaning-oriented access) Automatic indexing and text annotation tools Full text search engines that create meaningful classification (FAO-Schwartz not related to FAO) (semantic clustering) Intelligent search of the Web Building dynamical catalogues from machine readable meta data Natural Language processing Better machine translation Queries using natural language

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 9 The Example: International Portal on Food Safety, Animal and Plant Health Goal: To create an explicit, formal specification of a shared conceptualization of a domain of interest Ontology

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 10 Ontology: conceptual model Concept label synonym stem description Concept relationship

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 11 Ontology: RDFS model, machine readable encoding

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 12 Processes to create a Domain Ontology Ontology acquisition (2 paths) –Creating core ontology from scratch –Automatic extraction of ontological knowledge from base vocabulary and domain specific text sources Merging into one ontology Refinement and Extension Evaluation and Assessment

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 13 Creation of the core ontology 67 concepts 91 relationships Information Resources: Brainstorming Codex Alimentarius SPS Agreement Core Ontology Ontology Editor (SOEP) 3 subject specialists

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 14 1 st Acquisition Approach: Focused Crawling Focused Web Crawling 68 concepts 91 relationships Core Ontology List of extracted main sites: Gateway to Government Food Safety Information Center for Food Safety & Applied Nutrition Canadian Food Inspection Agency Iowa State University - Food Safety Project Iowa State University - Food Safety Consortium United States Department of Agriculture, Food Safety and Inspection Service Foodborne Ilness Education Information Center World Health Organization – Regional Office for Europe Food Safety Programme List of 257 food Safety domain web pages Grouping into Main sites

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 15 Selection of Documents Domain Set: Manual selection –11 documents Codex Alimentarius: Description, Code of Ethics, Food Hygiene, Food Import and Export Report of consultation on risk assessment of microbiological hazards in foods Ensuring food quality and safety, Protecting food quality and safety Domain Set: Focused Crawler Output –5 documents extracted: Generic documents: Manual Selection –8 documents Several documents of the animal feed domain

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 16 2 nd Acquisition Approach: Thesaurus Pruning Food Safety Documents Generic Documents Rice BT … NT … RT … RT … RT … … AGROVOC keywords Automatic Pruning Extracted ontological structure: # of concepts: 504 taxonomic depth: 5 5 evaluation runs 1632 frequent terms

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 17 Merging of Ontologies and Refinement 1632 Terms from pruning process 12 new concepts extracted Ontological structure extracted from AGROVOC 23 new concepts With hierarchical relationships extracted 67 concepts 91 relationships Core Ontology Assembly step 92 new relationships created Food Safety Ontology Prototype 102 concepts 183 relationships

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 18 Final Prototype Food Safety Ontology Prototype 102 concepts 183 relationships 1.79 relationships concept Core Ontology 67 concepts 91 relationships relationships concept 1.36

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide Concepts Agreement of Agriculture ALOP ALOP, Codex ALOP, OIE ALR animal byproducts animal diseases animal fats animal feed additives animal feed contaminants animal feed ingredients animal feeding animal health animal processing animal products animal waste animals antibiotics Bacteria bakery products biological agent CAC Caragene protocol CCFH cereal products cheese chemical agent Codex Committees commodities Consumer health diseases eggs exposure assessment fabrication FAO fishes food food additives food consumption food contaminants food export food import food ingredients food safety food-borne diseases fungi good hygienic practices hazard hazard characterization hazard identification human health human nutrition humans international agreements international food trade international governmental organizations IPPC labelling meat microorganisms microorganisms byproducts microorganisms processing microorganisms products microorganisms waste milk milk products non-pathogens OIE packaging parasites pathogens physical agent plant byproducts plant diseases plant feed additives plant feed contaminants plant feed ingredients plant feeding plant health plant processing plant products plant waste plants processed animal products processed plant products processed products processing risk analysis risk assessment risk characterization risk communication risk management slaughter SPS agreement standards sugar TBT agreement transport viruses WHO WTO

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide Unique Relationships adopts adversely affect are included in are produced by are the source for can be used as constitutes describes determines ensures establishes govern has economical impact on Implies includes influences interacts with is a consequence of is a step in the process is comprised of is established by is protected by originate from refer to requires rule sustains trades uses

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 21 Current project status Ontology creation: 2 nd application of framework Food Safety Ontology Prototype 102 concepts 183 relationships Text To Onto ~ 100 domain Specific documents AGROVOC Revised Ontology Pruner List of frequent terms Pruned Agrovoc: ~3000 concepts Ontology Editor (OIModeler) Merging & Refinement 1 st acquisition approach 2 nd acquisition approach

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 22 Usage Scenario Search: Risk assessment Biosecurity Portal: … … Ontology Enabled Search Application Ontology based search extension Risk characterization Hazard characterization Hazard identification Exposure assessment Risk assessment Risk management Risk communication Risk analysis Is a Step In the process Is a Step In the process Extended Search Mark the terms below, which you might want to include in your search: Interacts with Risk assessment Risk characterization Risk analysis Search: Ontology Doc base Search results

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 23 Current project status Application scenario: 2 use cases Use Case 1: Indexing the subject of a document Use Case 2: Searching information on the portal Risk;… Subject Title … … OFsAPH Risk;… Search … …

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 24 Current project status: Application: Ontology Browser for the Ontology on Food Safety, Animal and Plant Health

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 25 The Project for an Agricultural Ontology Service Only agreed semantic standards guarantee knowledge discovery between different applications The definition of Knowledge Organization systems is resource intensive Therefore FAO started initiatives to bring interested partners together October 2000 Launch of the AGStandards initiative to agree on metadata standards July 2001 concept paper on Agricultural Ontology Service

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 26 What does Agricultural Ontology Service mean? The Agricultural Ontology Service is an approach to organize knowledge organization systems that is  International The Internet must become plurilingual  Multidisciplinary The area of subjects is broad and needs various inputs  Cooperative different expert knowledge has to be associated and used  Distributed no central ownership should be looked for  Coordinated Coordination must ensure reusability and standardization

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 27 AOS: Iterative Knowledge Registration KOS uses components to build an application Discussions and choices for amendments to components Components: terms, definitions, relationships Users search and browse application using components User feedback Agricultural Ontology Service (AOS) Federated storage and description facility Components: terms, definitions, relationships

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 28 Activities up to now The first workshop took place in Rome, November 2001 A launch group was established with participation of –Content providers (FAO, CABI) –Solution providers in the Agricultural Area (ATO -Wageningen, University of Florida) –Ontology development Groups (AIFB Karlsruhe, CNR Italy) Two further workshops were organized in January and May 2002 Ontology protypes are under development

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 29 AOS – a “business model” A consortium of Information Providers A clearinghouse for semantic standards in the relevant subject areas One stop access to agreed standards (Ontologies, Metadataschemas, Vocabularies…) Participation as a consortium in semantic web activities to get funding for specific projects (“Semkos” for EU 6 th framework) Organization of seminars and workshops to further develop and promote the use of semantic standards

Johannes Keizer Food and Agriculture Organization of the UN Library and Documentation Systems Division Semantic Standards for the Web A Comprehensive Framework for Building Multilingual Domain Ontologies: Creating a Prototype Biosecurity Ontology AFITA 2002 Beijing Slide 30 Further Information