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On the 21st of November 2013, Yannis Tzitzikas, FORTH, presented the Integrating heterogeneous and distributed information about marine species through a top level ontology paper at the 7th Metadata and Semantic Research Conference in Thessaloniki, Greece.


  • 1. Yannis Tzitzikas et al., MTSR 2013, Thessaloniki1Integrating Heterogeneous and Distributed Information about Marine Species through a Top Level OntologyY. Tzitzikas 1,2 , C. Alloca 1 , C. Bekiari 1 , Y. Marketakis 1 , P. Fafalios 1,2 , M. Doerr 1 , N. Minadakis 1 , T.Patkos 1 , L. Candela 3 1 Institute of Computer Science, FORTH-ICS 2 Computer Science Department, University of Crete, GREECE 3 Consiglio Nazionale delle Ricerche, CNR-ISTI, Pisa, Italy7th Metadata and Semantics Research Conference (MTSR), Thessaloniki, Nov 19-22, 20131

2. Outline Context, Problem, Objectives Main Approaches for Integration The Followed Approach The Ontology MarineTLO Objectives, Benefits, Architecture The MarineTLO-based Warehouse Exploitation Scenarios Concluding RemarksYannis Tzitzikas et al., MTSR 2013, Thessaloniki3Context: iMarine Id: It is an FP7 Research Infrastructure Project (2011-2014) Final goal: launch an initiative aimed at establishing and operating an einfrastructure supporting the principles of the Ecosystem Approach to fisheries management and conservation of marine living resources. Partners:Yannis Tzitzikas et al., MTSR 2013, Thessaloniki42 3. Problem and objectives The Problem There are several sources of the marine domain, but each of them stores complementary information structured according to its needs. Our objective Harmonize and integrate (link, connect) information of the marine domain Specific motivating scenario and use cases will be given at the endYannis Tzitzikas et al., MTSR 2013, Thessaloniki5Marine Information: in several sources WoRMS: World Register of Marine Species Registers more than 200K species ECOSCOPE- A Knowledge Base About Marine Ecosystems (IRD, France) FLOD (Fisheries Linked Data) of Food and Agriculture Organization (FAO) of the United Nations FishBase: Probably the largest and most extensively accessed online database of fish species. DBpedia Yannis Tzitzikas et al., MTSR 2013, Thessaloniki63 4. Marine Information: in several sourcesStoringTaxonomic informationcomplementary informationEcosystem information (e.g. which fish eats which fish)Commercial codesGeneral information, occurrence data, including information from other sourcesGeneral information, figures Yannis Tzitzikas et al., MTSR 2013, ThessalonikiMarine Information: in several sources7Using and accessed throughdifferent technologiesWeb services (SOAP/WSDL)RDF + OWL filesSPARQL EndpointRelational DatabaseSPARQL Endpoint Yannis Tzitzikas et al., MTSR 2013, Thessaloniki84 5. Main approaches for Integration In general there are two main approaches for integration Warehouse approach (materialized integration) Design Phase: The underlying sources (and their parts) have to be selected Creation Phase: Process for getting and creating the warehouse Maintenance Phase: Ability to create the warehouse from scratch, and/or ability to update parts of it Mappings are exploited to extract information from data sources, to transform it to the target model and then to store it at the central repository Mediator approach (virtual integration) The mediator receives a query formulated in terms of the unified model/schema. The mappings are used to enable query translation. The derived sub-queries are sent to the wrappers of the individual sources, which transform them into queries over the underlying sources. The results of these sub-queries are sent back to the mediator where they are assembled to form the final answer Yannis Tzitzikas et al., MTSR 2013, Thessaloniki9Main approaches for integration (cont.) Warehouse Mediator Benefit: Flexibility in transformation logic (including ability to curate and fix problems) Benefit: Decoupling of the release management of the integrated resource from the management cycles of the underlying sources Benefit: Decoupling of access load from the underlying sources. Benefit: Faster responses (in query answering but also in other tasks, e.g. if one wants to use it for applying an entity matching technique).Benefit: One advantage (but in some cases disadvantage) of virtual integration is the real-time reflection of source updates in integrated access Comment: The higher complexity of the system (and the quality of service demands on the sources) is only justified if immediate access to updates is indeed required.Shortcomings You have to pay the cost for hosting the warehouse. You have to refresh periodically the warehouse Yannis Tzitzikas et al., MTSR 2013, Thessaloniki105 6. Main approaches for integration (cont.) In both cases we need a unified model/schemaYannis Tzitzikas et al., MTSR 2013, Thessaloniki11The ontology MarineTLO (Marine Top Level Ontology)6 7. MarineTLO: Objectives MarineTLO aims at being a global core model that provides a common, agreed-upon and understanding of the concepts and relationships holding in the marine domain to enable knowledge sharing, information exchanging and integration between heterogeneous sources covers with suitable abstractions the marine domain to enable the most fundamental queries, can be extended to any level of detail on demand, and allows data originating from distinct sources to be adequately mapped and integrated MarineTLO is not supposed to be the single ontology covering the entirety of what exists Yannis Tzitzikas et al., MTSR 2013, Thessaloniki13MarineTLO: Benefits from a Top-Level Ontology The adoption of a global core model has various benefits: reduced effort for improving and evolving the focus is given on one model, rather than many (the results are beneficial for the entire community reduced effort for constructing mappings this approach avoids the inevitable combinatorial explosion and complexities that results from pair-wise mappings between individual metadata formats and/or ontologiesYannis Tzitzikas et al., MTSR 2013, Thessaloniki147 8. MarineTLO: Key Design Principles Formulation It is an object-oriented semantic model, expressed to a form comprehensible to both documentation experts and information scientists while readily can be converted to machine-readable formats such as RDF Schema, OWL, etc Metaclasses certain types of inference about classes is supported in an analogous way as classes support certain types of inference about instances Monotonicity It aims to be monotonic in the sense of Domain Theory: the existing constructs and the deductions made from them should remain valid and well-formed, even as new constructs are added to the MarinTLOYannis Tzitzikas et al., MTSR 2013, Thessaloniki15MarineTLO: Query capabilities It allows formulating complex queries, e.g.:1.Given the scientific name of a species, find its predators with the related taxon-rank classification and with the different codes that the organizations use to refer to them. 2. Given the scientific name of a species, find the ecosystems, waterareas and countries that this species is native to, and the common names that are used for this species in each of the countriesYannis Tzitzikas et al., MTSR 2013, Thessaloniki168 9. The notion of competence queries as driver #Query For a scientific name of a species (e.g. Thunnus Albacares or Poromitra Crassiceps), find/give me Q1the biological environments (e.g. ecosystems) in which the species has been introduced and more general descriptive information of it (such as the country)Q2its common names and their complementary info (e.g. languages and countries where they are used)Q3 Q4 Q5 Q6the water areas and their FAO codes in which the species is native the countries in which the species lives the water areas and the FAO portioning code associated with a country the presentation w.r.t Country, Ecosystem, Water Area and Exclusive Economical Zone (of the water area)Q7the projection w.r.t. Ecosystem and Competitor, providing for each competitor the identification information (e.g. several codes provided by different organizations)Q8a map w.r.t. Country and Predator, providing for each predator both the identification information and the biological classificationQ9who discovered it, in which year, the biological classification, the identification information, the common names - providing for each common name the language, the countries where it is used in. Yannis Tzitzikas et al., MTSR 2013, Thessaloniki17MarineTLO as Product The full version of MarineTLO (Version3.0.0) aims at covering any part of the marine domain contains 70 classes and 41 properties The operational version, for the needs of iMarine(Version 3.0.0) used for building MarineTLO Warehouse (Version 3.0.0) contains 92 classes and 41 properties applied for integrating data mainly from FLOD, ECOSCOPE, part of WoRMS and FISHBASE sources URL: Tzitzikas et al., MTSR 2013, Thessaloniki189 10. Class Level (excerpt)S-Class Level (Version 3.0.0) Temporal PhenomenonCountry Code AssignmentCountryEcosystem Code AssignmentEcosystem Event Human ActivityExclusive Economic ZoneTLO EntityScientific Name AssignmentAttribute AssignmentCommon Name AssignmentPhysical Man Made ThingMan Made Object Water Area Code AssignmentMan Made Thing ActorPersistent ItemConceptual ObjectVesselCodification System IdentifierEEZCodePhysical ThingAreaFAOGearTypeIdentifierSub AreaWater AreaFAOVesselTypeIdentifierDivision Sub DivisionYannis Tzitzikas et al., MTSR 2013, Thessaloniki FORTH, i-Marine, Ostend, January 201319 19Meta Class Level (excerpt)Meta Class Level (Version 3.0.0) Marine Ecosystem Type Temporal Phenomen on TypeEcosystem TypeEvent TypeHuman Activity TypeAttribute Assignment TypeTLO Entity Type Digital Object typeActor TypePersistent Item TypeIdentifier TypeConceptual Object TypeGear Type Physical Thing TypeEquipment TypeBiotic Element TypeECOSCOPE Marine Animal Type FLOD Marine Animal Type WoRMS Marine Animal TypeVessel Type Marine Animal TypeFish Base Marine Animal Type DBpedia Marine Animal TypeYannis Tzitzikas et al., MTSR 2013, Thessaloniki FORTH, i-Marine, Ostend, January 20132


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