Analysis and visualisation of RDF resources in Ondex

Catherine Canevetcatherine.canevet@bbsrc.ac.uk

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Motivation

Biomedical resources provide info on the Semantic Web 

Potential to advance biomedical research  Need for tools 

Data reduction Data visualization Interactive analysis capabilities

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Ondex: a platform to exploit the Semantic Web

1) all information can be represented as a graph

2) all elements of the graph can be annotated with ontologies

3) data model conformant to Semantic Web framework,           in particular to RDF

 Ondex ideally positionedNat

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Data integration and visualisation in Ondex

Data analysisData Integration

Data Input

HypothesisNew experiments

Ontologies & Free Text

Biological Databases

Experimental DataData alignment

• Concept mapping

• Sequence analysis

• Text mining

Graph of concepts and 

relations 

Parse Export

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Data reduction and representation methods

Filter on centrality

Filter on confidence

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Demo

Interactive importer based on SPARQL Query­driven construction of datasets Bring information from different RDF data 

resources into Ondex

Welcome feedback on our prototype

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Data used in demointegrated by Keywan Hassani-Pak

AHD

Poplar KB

1. Input 45778 predicted poplar genes 

2. Data IntegrationPoplarCyc, Poplar TFDB

3. Comparative GenomicsBLAST against UniProt PlantsHMMer against PfamInparanoid to Arabidopsis

4. Autom. Function PredictionGene, Plant and Trait Ontology

5. Text MiningCo­occurrence of genes and traits in Medline abstracts

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Connecting and queryingN

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Right-click pre-defined queriesN

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Filling attributesN

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Proteins related to shoot branchingN

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Colour proteins by taxonomy IDN

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Scale relation based on BLASTN

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Acknowledgements

Artem Lysenko

Andrea Splendiani

Matthew Pocock

Chris RawlingsNat

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