Very brief overview of Open Science in *

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A brief overview of Open Science (ODOSOS) solutions applicable to EU-OPENSCREEN solutions.

A brief overview of Open Science (ODOSOS) solutions applicable to EU-OPENSCREEN solutions.

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  • 1. Very brief overview of Open Science in * Egon Willighagen BiGCaT - Maastricht University OpenScreen workshop 2012/09, EBIDepartment of Bioinformatics - BiGCaT 1
  • 2. Message to EU-OPENSCREEN1. 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 problems 1. Can we upgrade them to speed up discovery rather than being an (advanced) hard disk?Department of Bioinformatics - BiGCaT 2
  • 3. Open *• Methods • EU projects – CDK – ToxBank / – Bioclipse OpenTox – Blue Obelisk – Open PHACTS – Linked Data*: drug discovery, toxicology, metabolomics, datawarehouses, molecular modeling, ...Department of Bioinformatics - BiGCaT 3
  • 4. Open Source Cheminformatics• Metabolomics• Drug discovery• ToxicologyDepartment of Bioinformatics - BiGCaT 4
  • 5. CDK applications• OrChem • KNIME workflowsDepartment of Bioinformatics - BiGCaT 5
  • 6. Bioclipse / Brunn (J. Alvarsson, 2011)Department of Bioinformatics - BiGCaT 6
  • 7. Blue Obelisk: Open Data, Open Source,Open Standards (or: interoperability)OBoyle et al., JChemInf, 2011Department of Bioinformatics - BiGCaT 7
  • 8. Linked Open Data (W3C HCLS ig)Samwald et al., JChemInf, 2010Department of Bioinformatics - BiGCaT 8
  • 9. Open PHACTSDepartment of Bioinformatics - BiGCaT 9
  • 10. WikiPathways / PathVisioDepartment of Bioinformatics - BiGCaT 10
  • 11. SEURAT-1 “...replacing animal testing”Department of Bioinformatics - BiGCaT 11
  • 12. OpenTox / ToxBankDepartment of Bioinformatics - BiGCaT 12
  • 13. More info?• egon.willighagen@gmail.com• 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/Department of Bioinformatics - BiGCaT 13