Visualizing LinkedOpen DataAndra Waagmeester

Overview

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

Gerhard Michal 1974

Böhringer Mannheim Poster

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

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

PathwayLoom

Pathvisio Loom

Caveats

• Online resources tend to be volatile• Each 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 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

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: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 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

Use case 1: Visualizing SPARQL queries

Use case 2: creating data landscapes

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

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

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)