1 / 27

Visualizing Linked Open Data

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

kato
Download Presentation

Visualizing Linked Open Data

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Visualizing LinkedOpen Data Andra Waagmeester

  2. Overview • Context: Pathways • Howto: Linked data • Make sense of linked data • Visualizing linked data

  3. Böhringer Mannheim Poster Gerhard Michal 1974

  4. Pathwayknowledge in theliterature... 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.

  5. Pathway knowledge in databases

  6. PathwayLoom • Plugin for the pathway editor Pathvisio • Using existing knowledge to guide pathway creation (Click-Search-Grow) • Use online and local data resources for interaction data • Searches for known interaction partners for a target element

  7. PathwayLoom

  8. Pathvisio Loom

  9. Caveats • Online resources tend to be volatile • Each Resource comes with its own Webserviceflavour (REST, SOAP, custom made) • The plugin has to deal with multitude of output formats (JSON, CSV, XML, etc)

  10. 5 ★Open Data

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

  12. Guidelines for exposing data as RDF in Open Phacts

  13. Linked Data Elements • The triple • <Subject> <Predicate> <Object> • <Andra> <Lives in> <Antwerp> • <Andra> <Works at> <Maastricht University> • The dereferencable Unified Resource Identfier • <Andra> = http://www.linkedin.com/pub/andra-waagmeester/2/579/478 • <Lives in> = http://www.w3.org/2006/vcard/ns#Home • <Works at> = http://www.w3.org/2006/vcard/ns#Work • <Antwerp> = http://dbpedia.org/resource/Antwerp

  14. Making sense of dereferencable URI’s • Who lives in Antwerp • SPARQL:PREFIX linkedIn: <http://www.linkedin.com/pub/>PREFIX vcard: http://www.w3.org/2006/vcard/ns#PREFIX dbpedia: <http://dbpedia.org/resource/>SELECT * WHERE { ?person vcard:workdbpedia:Antwerp} • Returns a mulitude of the following lines:PREFIX linkedIn ….linkedIn:andra.linkedIn:alex .…… linkedIn:silivius .

  15. Processing LOD output can become cumbersome

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

  17. 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.

  18. Visualbox.org

  19. 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.

  20. Semscape – Visualizing linked data landscapes with Cytoscape • Researchers 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 endpoints

  21. Use case 1: Visualizing SPARQL queries

  22. Use case 2: creating data landscapes

  23. Conclusions • Creating linked data is a process where data is described in triples (subject, predicate, object). • Each element of a triple should be dereferencable URI • SPARQL is a query language for linked data • SPARQL is for the technical savvy • Different visualization techniques allows the integration of Linked Data in various software frameworks, websites, blogs, etc

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

  25. 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)

More Related