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Analysis and visualisation of Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010 RDF resources in Ondex Catherine Canevet catherine.canevet@bbsrc.ac.uk Motivation Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23

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SLIDE 1

Analysis and visualisation of RDF resources in Ondex

Catherine Canevet catherine.canevet@bbsrc.ac.uk

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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SLIDE 2

Motivation

 Biomedical resources provide info on the

Semantic Web

 Potential to advance biomedical research  Need for tools

 Data reduction  Data visualization  Interactive analysis capabilities

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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SLIDE 3

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 positioned

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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Data integration and visualisation in Ondex

Data analysis Data Integration Data Input

Hypothesis New experiments

Ontologies & Free Text Biological Databases Experimental Data Data alignment

  • Concept

mapping

  • Sequence

analysis

  • Text mining

Graph of concepts and relations Parse Expor t

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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SLIDE 5

Data reduction and representation methods

Filter on centrality Filter on confidence

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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SLIDE 6

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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SLIDE 7

Demo

 Interactive importer based on SPARQL  Query-driven construction of datasets  Bring information from different RDF data

resources into Ondex

 Welcome feedback on our prototype

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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SLIDE 8

Data used in demo

integrated by Keywan Hassani-Pak

AHD

Poplar KB

1.

Input

45778 predicted poplar genes

2.

Data Integration

PoplarCyc, Poplar TFDB

3.

Comparative Genomics

BLAST against UniProt Plants HMMer against Pfam Inparanoid to Arabidopsis

4.

  • Autom. Function Prediction

Gene, Plant and Trait Ontology

5.

Text Mining

Co-occurrence of genes and traits in Medline abstracts

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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SLIDE 9

Connecting and querying

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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SLIDE 10

Right-click pre-defined queries

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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SLIDE 11

Filling attributes

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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SLIDE 12

Proteins related to shoot branching

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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Colour proteins by taxonomy ID

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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Scale relation based on BLAST

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010

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Acknowledgements

 Artem Lysenko  Andrea Splendiani  Matthew Pocock  Chris Rawlings

Nature Precedings : doi:10.1038/npre.2010.5430.1 : Posted 23 Dec 2010