Visualizing Linked Open Data

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Visualizing Linked Open Data. Andra Waagmeester. Overview. Context: Pathways Howto : Linked data Make sense of linked data Visualizing linked data. Bhringer Mannheim Poster. Gerhard Michal 1974. Pathway knowledge in the literature. - PowerPoint PPT Presentation

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Visualizing LinkedOpen DataAndra Waagmeester1OverviewContext: PathwaysHowto: Linked dataMake sense of linked dataVisualizing linked data

Gerhard Michal 1974Bhringer Mannheim Poster Pathways are much more complicated now and come in many different flavors. New high-throughput measurements are being fed into interactomes, condition-specific signaling pathways,pathways of development, of disease and of drug action.

And pathways are now more than just static images; they can be used as research tools for data visualization and data analysis.Pathway knowledge in the literature...

Insulin inactivates liver phosphorylase, the principal enyzme that causes liver glycogen to split into glucose. This prevents breakdown of the glycogen that has been stored in the liver.Pathway knowledge in databases

PathwayLoomPlugin for the pathway editor PathvisioUsing existing knowledge to guide pathway creation (Click-Search-Grow)Use online and local data resources for interaction dataSearches for known interaction partners for a target elementPathwayLoom

Pathvisio Loom

CaveatsOnline resources tend to be volatileEach Resource comes with its own Webservice flavour (REST, SOAP, custom made)The plugin has to deal with multitude of output formats (JSON, CSV, XML, etc)5 Open Data

The Linking Open Data cloud diagrammaintained by Richard Cyganiak (DERI, NUI Galway) and Anja Jentzsch (HPI) http://lod-cloud.net

Guidelines for exposing data as RDF in Open Phacts

Linked Data ElementsThe triple The dereferencable Unified Resource Identfier = http://www.linkedin.com/pub/andra-waagmeester/2/579/478 = http://www.w3.org/2006/vcard/ns#Home = http://www.w3.org/2006/vcard/ns#Work = http://dbpedia.org/resource/Antwerp

Making sense of dereferencable URIsWho lives in AntwerpSPARQL:PREFIX linkedIn: PREFIX vcard: http://www.w3.org/2006/vcard/ns#PREFIX dbpedia: SELECT * WHERE { ?person vcard:work dbpedia:Antwerp }Returns a mulitude of the following lines:PREFIX linkedIn .linkedIn:andra .linkedIn:alex . linkedIn:silivius .

Processing LOD output can become cumbersome

Find compounds, targets and enzmes. Viewing provenance, filtering by species or activity and searching by structure are only a click or two away.

Within the OpenPHACTS Explorer data from Chemspider, drugbank, chembl and other sources are combined in an easy to use interface. Download your results as a spreadsheet to your own computer.

Visualbox.org

With Interaction available as Linked data Online resources remains volatile, but having the data in downloadable format allows local usage.There is a uniform webservice (SPARQL query).The plugin requires only a SPARQL wrapper to consume data.

Semscape Visualizing linked data landscapes with CytoscapeResearchers need to easily and intuitively exploit and query the wealth of data that is available behind SPARQL endpoints.SemScape, a semantic-web enabled plugin for Cytoscape.Allows visualizing Sparql queries in cytoscape.Allows creating link data landscapes, which linked data schemas of distributed SPARQL endpointsUse case 1: Visualizing SPARQL queries

Use case 2: creating data landscapes

ConclusionsCreating linked data is a process where data is described in triples (subject, predicate, object).Each element of a triple should be dereferencable URISPARQL is a query language for linked dataSPARQL is for the technical savvyDifferent visualization techniques allows the integration of Linked Data in various software frameworks, websites, blogs, etc

Google Summer of code 2013NRNB Google Summer of Code (http://nrnb.org/gsoc/)IDEA 28: Visualizing Pathway RDF with VisualboxIDEA 42: User Interaction on Biomedical Linked Data

Acknowledgments

Yigang Zhou (GSOC student)Andrea Splendiani (DERI, Galway)Carina Haupt (Bonn-Aachen Institute for Information Technology)Helena Deus (DERI, Galway)Ian Dunlop (Manchester University)Alvaro Graves (Rensselaer Polytechnic Institute)