very brief overview of open science in *
DESCRIPTION
A brief overview of Open Science (ODOSOS) solutions applicable to EU-OPENSCREEN solutions.TRANSCRIPT
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Department of Bioinformatics - BiGCaT 1
Very brief overview of
Open Science in *
Egon WillighagenBiGCaT - Maastricht University
OpenScreen workshop 2012/09, EBI
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Department of Bioinformatics - BiGCaT 2
Message to EU-OPENSCREEN
1. Many solutions (fact: we all have different deadlines and different objectives)
2. Standardize solutions or interoperability?1. Where is the API?2. Where is the communication standard? (e.g. ontology)
3. Focus on practical problems and not on our scientific problems1. Can we upgrade them to speed up discovery rather than
being an (advanced) hard disk?
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Department of Bioinformatics - BiGCaT 3
Open *
• Methods–CDK–Bioclipse–Blue Obelisk–Linked Data
• EU projects–ToxBank /
OpenTox–Open PHACTS
*: drug discovery, toxicology, metabolomics, data warehouses, molecular modeling, ...
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Department of Bioinformatics - BiGCaT 4
Open Source Cheminformatics
• Metabolomics• Drug discovery• Toxicology
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Department of Bioinformatics - BiGCaT 5
CDK applications
• OrChem • KNIME workflows
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Department of Bioinformatics - BiGCaT 6
Bioclipse / Brunn (J. Alvarsson, 2011)
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Department of Bioinformatics - BiGCaT 7
O'Boyle et al., JChemInf, 2011
Blue Obelisk: Open Data, Open Source, Open Standards (or: interoperability)
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Department of Bioinformatics - BiGCaT 8
Linked Open Data (W3C HCLS ig)
Samwald et al., JChemInf, 2010
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Department of Bioinformatics - BiGCaT 9
Open PHACTS
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Department of Bioinformatics - BiGCaT 10
WikiPathways / PathVisio
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Department of Bioinformatics - BiGCaT 11
SEURAT-1 “...replacing animal testing”
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Department of Bioinformatics - BiGCaT 12
OpenTox / ToxBank
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Department of Bioinformatics - BiGCaT 13
More info?
• http://www.blueobelisk.org/
• http://wiki.bioclipse.net/index.php?title=Brunn
• http://cdk.sf.net/
• http://opentox.org/
• http://openphacts.org/
or @egonwillighagenor http://chem-bla-ics.blogspot.com/