From Biomass to Energy via Semantic Web and Linked data

EFITA 2013 26th June Torino

From Biomass to Energy throughSemantic Web and Linked data

Frameworks for the curation and visualisation of

biomass knowledge bases

Monika SolankiAston Business School

Aston University Birmingham UK

Joint work withJohannes Skarka

Karlsruhe Institute of Technology ITAS

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

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EnAlgae Energetic Algae (Since June 2011)

Aims to reduce CO2 emissions and dependency onunsustainable energy sources in North West Europe4 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

httpwwwenalgaeeu

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Algal biomass as biofuels

Extensive research is being undertaken in the search andproduction of naturally viable and sustainable energysourcesThe idea that algae biomass based biofuels could serve asan alternative to fossil fuels has been embraced bycouncils across the globeMajor companies government bodies and dedicated nonprofit organisations are getting involvedThe domain is a rich source of datainformationknowledge

httpwwwalgalbiomassorghttpwwweaba-associationeu

httpwwwenalgaeeu

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

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Algal biomass as biofuels Observations

No systematic analysis of the algae biomass potential forNorth-Western EuropeMost of the knowledge buried in various formats of imagesspreadsheets proprietary data sources and grey literatureLack of a knowledge level infrastructure that is equippedwith the capabilities to provide semantic grounding to thedatasets for algal biomassLow levels of motivation among stakeholders for datasetsto be interlinked shared and reused within the biomasscommunity

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

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Knowledge Frameworks for Algal Biomass

Transformation and curation of biomass knowledge basesin accordance to Semantic Web and Linked datastandardsOntology design patterns for building ontologies for thebiomass domainLEAPS 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 bioenergyASPIRE A content based recommendation engine thatprovides recommendations for algal entities as perstakeholder preference profiles using bespoke proximitysearch algorithmsVisualisations over linked biomass datasets

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

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SW Linked data and the Algal Supply Chain

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

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Ontological requirements

Ontologies needed to representSpatiality location of possible algae cultivation siteslocation of the sources of consumables (CO2 nutrientsand water)Geometries area of the cultivation site - extentspolygons linear and ring arraysUnits and Measurements conventional measurementunits such as Kgs for quantities and hectares for areabespoke units of measurements ie Kgshectare orKgsannumTerritorial units for statistics core concepts of the NUTSsystemDomain specific knowledge algae cultivation sites CO2sources pipelines

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

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Minimum Descriptive Language (MDL)

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Ontology Design Pattern

Standards Enforcer Pattern (SEP)

Enables the ontological modelling of processes activitiesoperations and services that enforce guideline(s)recommended by a specific standard and need to explicitlyindicate their conformance to itAllows the inclusion of minimalistic information regardingthe conformance while retaining the flexibility to extend theontological primitives as required

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

EFITA 2013 26th June Torino

Ontology Design PatternStandards Enforcer Pattern (SEP)

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Ontology Design Pattern

REactor Pattern (REP)

Enables the ontological modelling of reactive processes ina generic way across multiple domainsTargeted towards modelling reactive processes with ablack box view of the process

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

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Ontology Design PatternREactor Pattern (REP)

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Ontologies for Algal Biomass Reuse

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Ontology Development Methodology

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Ontologies for Algal Biomass Domainknowledge

Ontologies available at httppurlorgbiomassontologies

EFITA 2013 26th June Torino

Lifting XML datasets to Linked data

First stepThe first part of the data processing and the potentialcalculation are performed in a GIS-based model which wasdeveloped for this purpose using ArcGISRaw datasets with various origins and formats -transformed using bespoke computational algorithms to anArchGIS specific XML format

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

EFITA 2013 26th June Torino

Lifting XML datasets to Linked data

Second stepThe original data sources had several limitations and aone-to-one transformation was not possibleA bespoke parser that exploits XPath to selectively querythe XML datasets and generate linked data wasimplementedIt utilises a complex underlying data structure to facilitatethe transformation

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

EFITA 2013 26th June Torino

Lifting XML datasets to Linked data

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

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LEAPSLinked Entities for Algal Plant Sites

motivate the use of Semantic Web technologies and LODfor the algal biomass domainlaying out a set of ontological requirements for knowledgerepresentation that support the publication of algalbiomass dataelaborating on how algal biomass datasets are transformedto their corresponding RDF model representationinterlinking the generated RDF datasets along spatialdimensions with other datasets on the Web of datavisualising the linked datasets via an end user LOD RESTWeb service

The first (known) application of SWLD to Algal Biomass datasets

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System Architecture

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Architecture 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 50

REST Web services

SPARQL endpoints

Web Interface

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LEAPS Web application

wwwsemanticwebservicesorgenalgae

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

EFITA 2013 26th June Torino

ASPIREA content based recommendation service for algal siteentitiesRecommendations are made based on stakeholderpreference models defined in their ontological profiles aslinked dataAlgal datasets are a combination of continuous andcategorical data entitiesAn adaption of Gowerrsquos similarity measure is used tocomputed similarities between the entities to proposerecommendations

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

EFITA 2013 26th June Torino

Biological taxonomy visualisation

Algaebase is the largest information source of algae on theWebThe algaebase dataset is not directly available to bedownloadedThe dataset was retrieved using a bespoke informationretrieval algorithm and curated within our triple store aslinked dataThe Semantic Import plugin of Gephi has been exploited tovisualise the biological taxonomy of algae

httpwwwalgaebaseorg

httpsgephiorg

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

EFITA 2013 26th June Torino

Biological taxonomy visualisation

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data

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 purposesproposing a set of domain specific ontologies to be sharedand extended by the communitydefining a linked data publishing architecture thattransforms raw data in disparate formats to a uniform XMLrepresentationusing a set of well established and domain specificontologies as metadata to transform it further into linkeddataproviding various data access options such as a SPARQLendpoint an interactive Google map interface and a RESTAPI for making the data accessible to stakeholders

EFITA 2013 26th June Torino

Many Thanks

msolankiastonacuk From Biomass to Energy through Semantic Web and Linked data