Bio AID Knowledge extraction for a Virtual Laboratory for e -Science Marco Roos , Scott Marshall , Sophia Katrenko, Edgar Meij, Willem van Hage, Pieter Adriaans ISMB/ECCB2007 – AIDA demonstration 10/06/09 BioAID AIDA = Adaptive Information Disclosure Application

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Biomedical knowledge repository 10/06/09 BioAID PubMed statistics http://www.ncbi.nlm.nih.gov/entrez >17 million citations >400,000 added/year ~70,000 searches/month … Does not compute Does not fit

Text mining 10/06/09 BioAID Biology Customized or personalized experiment Extracted knowledge I want to do it my way, use my models Carole Goble’s me-scientist

Bioinformatics and e-science 10/06/09 BioAID Single purpose, black box application Customized experiments with reusable components My component Your component My component Your component My component

The AIDA toolbox for knowledge extraction and knowledge management in a Virtual Laboratory for e-Science

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Components of the AIDA toolbox used for Life Science knowledge extraction

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Bio AID ‘watskeburt’ workflow 10/06/09 BioAID AIDA AIDA OMIM service (Japan) AIDA ‘ Taverna shim’ Taverna ‘shim’

Bio AID ‘watskeburt’ running 10/06/09 BioAID

Bio AID ‘watskeburt’ results 10/06/09 BioAID

Proto-ontology (Protégé Jambalaya plugin) 10/06/09 BioAID

Enriched ontology (snapshot) 10/06/09 BioAID

Components of the AIDA toolbox used for Food Informatics

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Food AID thesaurus workflow 10/06/09 BioAID

Food AID thesaurus workflow 10/06/09 BioAID

10/06/09 BioAID For my research on crispiness of food products I need pictures of bread structure RMS

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Food Resource Management System using AIDA services 10/06/09 BioAID

Food Resource Management System using AIDA services 10/06/09 BioAID

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Conclusions We have demonstrated an e-science approach to text mining: Application to knowledge extraction (EZH2) Application to rapid prototyping and synonym support (Food Informatics) Application that logs the trail to evidence (EZH2++) The use of web services and semantic web: Application by non-text miners Collaboration, information sharing 10/06/09 BioAID

We have demonstrated an e-science approach to text mining:

Application to knowledge extraction (EZH2)

Application to rapid prototyping and synonym support (Food Informatics)

Application that logs the trail to evidence (EZH2++)

The use of web services and semantic web:

Application by non-text miners

Collaboration, information sharing

Acknowledgements AIDA developers team: Sophia Katrenko, Edgar Meij, Willem van Hage, Frans Verster, Guus Schreiber, Maarten de Rijke, Pieter Adriaans Jan Top, Nicole Koenderink, Food informatics, Wageningen University Martijn Schuemie, Erasmus University Rotterdam myGrid team, especially Katy Wolstencroft, Stian Soiland, Stuart Owen, Andy Gibson, Alan Rector, Robert Stevens, Carole Goble W3C Semantic Web Health Care and Life Sciences Interest Group http:// adaptivedisclosure.org Work supported by VL-e and BioRange projects (BSIK grants) 10/06/09 BioAID

AIDA developers team: Sophia Katrenko, Edgar Meij, Willem van Hage, Frans Verster,

Guus Schreiber, Maarten de Rijke, Pieter Adriaans

Jan Top, Nicole Koenderink, Food informatics, Wageningen University

Martijn Schuemie, Erasmus University Rotterdam

myGrid team, especially Katy Wolstencroft, Stian Soiland, Stuart Owen, Andy Gibson, Alan Rector, Robert Stevens, Carole Goble

W3C Semantic Web Health Care and Life Sciences Interest Group

http:// adaptivedisclosure.org

Work supported by VL-e and BioRange projects (BSIK grants)

Further information and resources AID information and resources http:// adaptivedisclosure.org W3C Semantic Web Health Care and Life Sciences Interest Group http://www.w3.org/2001/sw/hcls/ 10/06/09 BioAID Workflows available from myExperiment.org going online August 2007

AID information and resources

http:// adaptivedisclosure.org

W3C Semantic Web Health Care and Life Sciences Interest Group

http://www.w3.org/2001/sw/hcls/

On line demo movies Demo movies online (hyperlinks) EZH2 demo (101Mb) [flash version] EZH2 highlights ( 81Mb) [flash version] 10/06/09 BioAID

Demo movies online (hyperlinks)

EZH2 demo (101Mb) [flash version]

EZH2 highlights ( 81Mb) [flash version]

End of presentation... 10/06/09 BioAID