From Biomass to Energy via Semantic Web and Linked data

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The talk provides a high level overview of frameworks for the curation and visualisation of Algal biomass knowledge bases. It was presented at http://www.efita2013.org/web/ …

The talk provides a high level overview of frameworks for the curation and visualisation of Algal biomass knowledge bases. It was presented at http://www.efita2013.org/web/

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  • 1. EFITA 2013, 26th June, TorinoFrom Biomass to Energy throughSemantic Web and Linked dataFrameworks for the curation and visualisation ofbiomass knowledge basesMonika SolankiAston Business SchoolAston University, Birmingham, UKJoint work withJohannes SkarkaKarlsruhe Institute of Technology, ITASm.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 2. EFITA 2013, 26th June, TorinoEnAlgae: Energetic Algae (Since June 2011)Aims to reduce CO2 emissions and dependency onunsustainable energy sources in North West Europe.4 Year Strategic initiative of Interreg IVb NWE programme.19 partners and 14 Observers across 7 EU states.Coordinated set of activities focusing on sharing bestpractice, developing effective stakeholder engagement andencouraging transnational cooperation.http://www.enalgae.eu/m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 3. EFITA 2013, 26th June, TorinoAlgal biomass as biofuelsExtensive research* is being undertaken in the search andproduction of naturally viable and sustainable energysources.The idea that algae biomass based biofuels could serve asan alternative to fossil fuels has been embraced bycouncils across the globe.Major companies, government bodies and dedicated nonprofit organisations* are getting involved.The domain is a rich source of data/information/knowledge.*http://www.algalbiomass.org/*http://www.eaba-association.eu/*http://www.enalgae.eu/m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 4. EFITA 2013, 26th June, TorinoAlgal biomass as biofuels: ObservationsNo systematic analysis of the algae biomass potential forNorth-Western Europe.Most of the knowledge buried in various formats of images,spreadsheets, proprietary data sources and grey literature.Lack of a knowledge level infrastructure that is equippedwith the capabilities to provide semantic grounding to thedatasets for algal biomass.Low levels of motivation among stakeholders, for datasetsto be interlinked, shared and reused within the biomasscommunity.m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 5. EFITA 2013, 26th June, TorinoKnowledge Frameworks for Algal BiomassTransformation and curation of biomass knowledge basesin accordance to Semantic Web and Linked datastandards.Ontology design patterns for building ontologies for thebiomass domain.LEAPS: A framework that enables stakeholders in thealgal biomass domain to interactively explore, via linkeddata, potential algal sites and sources of theirconsumables across regions in North-Western Europe forgeneration of bioenergy.ASPIRE: A content based recommendation engine thatprovides recommendations for algal entities as perstakeholder preference profiles using bespoke proximitysearch algorithms.Visualisations over linked biomass datasets.m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 6. EFITA 2013, 26th June, TorinoSW, Linked data and the Algal Supply Chainm.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 7. EFITA 2013, 26th June, TorinoOntological requirementsOntologies needed to representSpatiality: location of possible algae cultivation sites,location of the sources of consumables (CO2, nutrientsand water).Geometries: area of the cultivation site - extents,polygons, linear and ring arrays.Units and Measurements: conventional measurementunits such as Kgs for quantities and hectares for area,bespoke units of measurements, i.e., Kgs/hectare orKgs/annum.Territorial units for statistics: core concepts of the NUTSsystem.Domain specific knowledge: algae cultivation sites, CO2sources, pipelines.m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 8. EFITA 2013, 26th June, TorinoMinimum Descriptive Language (MDL)m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 9. EFITA 2013, 26th June, TorinoOntology Design PatternStandards Enforcer Pattern (SEP)Enables the ontological modelling of processes, activities,operations and services that enforce guideline(s)recommended by a specific standard and need to explicitlyindicate their conformance to it.Allows the inclusion of minimalistic information regardingthe conformance, while retaining the flexibility to extend theontological primitives as required.m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 10. EFITA 2013, 26th June, TorinoOntology Design PatternStandards Enforcer Pattern (SEP)m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 11. EFITA 2013, 26th June, TorinoOntology Design PatternREactor Pattern (REP)Enables the ontological modelling of reactive processes ina generic way across multiple domains.Targeted towards modelling reactive processes with ablack box view of the process.m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 12. EFITA 2013, 26th June, TorinoOntology Design PatternREactor Pattern (REP)m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 13. EFITA 2013, 26th June, TorinoOntologies for Algal Biomass: Reusem.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 14. EFITA 2013, 26th June, TorinoOntology Development Methodologym.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 15. Ontologies for Algal Biomass: DomainknowledgeOntologies available at http:/purl.org/biomass/ontologies
  • 16. EFITA 2013, 26th June, TorinoLifting XML datasets to Linked dataFirst stepThe first part of the data processing and the potentialcalculation are performed in a GIS-based model which wasdeveloped for this purpose using ArcGIS.Raw datasets with various origins and formats -transformed using bespoke computational algorithms to anArchGIS specific XML format.m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 17. EFITA 2013, 26th June, TorinoLifting XML datasets to Linked dataSecond stepThe original data sources had several limitations and aone-to-one transformation was not possible.A bespoke parser that exploits XPath to selectively querythe XML datasets and generate linked data wasimplemented.It utilises a complex underlying data structure to facilitatethe transformation.m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 18. EFITA 2013, 26th June, TorinoLifting XML datasets to Linked datam.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 19. EFITA 2013, 26th June, TorinoLEAPSLinked Entities for Algal Plant Sitesmotivate the use of Semantic Web technologies and LODfor the algal biomass domain.laying out a set of ontological requirements for knowledgerepresentation that support the publication of algalbiomass data.elaborating on how algal biomass datasets are transformedto their corresponding RDF model representation.interlinking the generated RDF datasets along spatialdimensions with other datasets on the Web of data.visualising the linked datasets via an end user LOD RESTWeb service.The first (known) application of SW/LD to Algal Biomass datasetsm.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 20. EFITA 2013, 26th June, TorinoSystem Architecturem.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 21. EFITA 2013, 26th June, TorinoArchitecture: Main componentsParsing modules: lifting the datafrom their original formats to RDF.Ontologies.Linking engine: producing the linkeddata representation of the datasets.Triple store: OWLIM SE 5.0.REST Web services.SPARQL endpoints.Web Interface.m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 22. EFITA 2013, 26th June, TorinoLEAPS Web applicationwww.semanticwebservices.org/enalgaem.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 23. EFITA 2013, 26th June, TorinoASPIREA content based recommendation service for algal siteentities.Recommendations are made based on stakeholderpreference models defined in their ontological profiles aslinked data.Algal datasets are a combination of continuous andcategorical data entities.An adaption of Gower’s similarity measure is used tocomputed similarities between the entities to proposerecommendations.m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 24. EFITA 2013, 26th June, TorinoBiological taxonomy visualisationAlgaebase is the largest information source of algae on theWeb.The algaebase dataset is not directly available to bedownloaded.The dataset was retrieved using a bespoke informationretrieval algorithm and curated within our triple store aslinked data.The Semantic Import plugin of Gephi has been exploited tovisualise the biological taxonomy of algae.http://www.algaebase.org/https://gephi.org/m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 25. EFITA 2013, 26th June, TorinoBiological taxonomy visualisationm.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data
  • 26. SummaryThe LEAPS framework exploits SW and LD for the algalbiomass community,enabling the screening of data for promising individualplant sites and provides base data for more detailedplanning purposes.proposing a set of domain specific ontologies to be sharedand extended by the community.defining a linked data publishing architecture thattransforms raw data in disparate formats to a uniform XMLrepresentation.using a set of well established and domain specificontologies as metadata to transform it further into linkeddata.providing various data access options such as a SPARQLendpoint, an interactive Google map interface and a RESTAPI for making the data accessible to stakeholders.
  • 27. EFITA 2013, 26th June, TorinoMany Thanks!!!m.solanki@aston.ac.uk From Biomass to Energy through Semantic Web and Linked data