Chemical Interoperability - Utrecht / NBIC
Upcoming SlideShare
Loading in...5
×
 

Chemical Interoperability - Utrecht / NBIC

on

  • 1,682 views

Presentation given at a parallel NBIC meeting in Utrecht at 17 Feb 2012. This presentation is not Open; figures are available from cited papers.

Presentation given at a parallel NBIC meeting in Utrecht at 17 Feb 2012. This presentation is not Open; figures are available from cited papers.

Statistics

Views

Total Views
1,682
Views on SlideShare
852
Embed Views
830

Actions

Likes
1
Downloads
7
Comments
0

23 Embeds 830

http://chem-bla-ics.blogspot.com 408
http://pele.farmbio.uu.se 325
http://chem-bla-ics.blogspot.co.uk 15
http://feeds.feedburner.com 13
http://chem-bla-ics.blogspot.in 9
http://chem-bla-ics.blogspot.de 8
http://chem-bla-ics.blogspot.se 8
http://chem-bla-ics.blogspot.nl 7
http://chem-bla-ics.blogspot.kr 7
http://chem-bla-ics.blogspot.com.es 7
http://chem-bla-ics.blogspot.fr 5
http://kris81 3
http://chem-bla-ics.blogspot.com.au 3
http://chem-bla-ics.blogspot.ca 3
http://chem-bla-ics.blogspot.ch 1
http://chem-bla-ics.blogspot.fi 1
http://chem-bla-ics.blogspot.tw 1
http://chem-bla-ics.blogspot.hk 1
http://chem-bla-ics.blogspot.com.ar 1
http://oldweb.farmbio.uu.se 1
http://chem-bla-ics.blogspot.com.br 1
http://webcache.googleusercontent.com 1
https://www.linkedin.com 1
More...

Accessibility

Categories

Upload Details

Uploaded via as Adobe PDF

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

Chemical Interoperability - Utrecht / NBIC Chemical Interoperability - Utrecht / NBIC Presentation Transcript

  • Chemical InteroperabilityEgon WillighagenBiGCaT – Dept of Bioinformatics2012-02-17, Utrecht
  • Interoperability in Chemistry• = Communication, meaning• Why? – Reproducibility – Understanding molecular properties• Interoperability Needs – Open Data, Open Standards, Open Source
  • Whats that Open fetish?• Gives – Collaboration. Credit. Ownership. – Sustainability.• Trough rights – Redistribution (under same rights) – Modification (not with Open Standards) View slide
  • The Blue Obelisk MovementR. Guha et al. J. Chem. Inf. Mod. 2006N. OBoyle et al. J. Cheminf. 2011 View slide
  • 1. Open Standards• Allows: – Software to talk to each other• For: – Well-defined formats – Concepts (aromaticity!) – Practices (licenses, peer review, ...)
  • CML: Exchange of Chemical StructuresP. Murray-Rust et al, J. Chem. Inf. Comput. Sci., 1999E.L. Willighagen, Internet J. Chem., 2000
  • CML in RSS news feedsP. Murray-Rust et al., J. Chem. Inf. Comput. Sci, 2004
  • Resource Description Framework• Family of W3C technologies – RDF / RDFS: basic framework – Serialization formats • RDF/XML, Turtle, RDFa, RDF/JSON – OWL: ontologies (BioPortal, OLS, …) – SPARQL
  • SemanticWeb
  • IUPAC International Chemical IdentifierN. Day. InChI FAQ, http://wwmm.ch.cam.ac.uk/inchifaq/
  • 2. Open Data• What is the average C=N bond length? – Bioinformatics: force fields• What is the LogP of aspirin? – Drug discovery• What metabolite is that? – Metabolomics
  • Linked Open Drug DataM. Samwald et al., J. Cheminf, 2011
  • Blue Obelisk Data Repository● Which two tools calculate the same molecular weight?● Isotope abundancies and weights! ● IUPAC reportsR. Guha et al. J. Chem. Inf. Mod. 2006
  • 3. Open Source• What is aromaticity?
  • Chemistry Development Kit• Cheminformatics – Aromaticity – ...• Many derived tools – Taverna, KNIME, Bioclipse, Cinfony, ...C. Steinbeck et al. J. Chem. Inf. Mod. 2003C. Steinbeck et al. Curr. Pharm. Des. 2006
  • Scripting ...O. Spjuth et al. BMC Bioinf. 2009T. Kuhn et al. BMC Bioinf. 2010
  • Predictive Toxicology IO. Spjuth et al. J. Chem. Inf. Mod. 2011E.L. Willighagen et al. BMC Research Notes. 2011
  • Predictive Toxicology IIE.L. Willighagen et al. J. Biomed Sem. 2011
  • Conclusions• Interoperability via ODOSOS – Open Data – Open Standards – Open Source
  • Thanx / More info• Blue Obelisk movement• CDK developers (Miguel!)• http://scholar.google.com/citations?user=u8SjMZ0AAAAJ• http://chem-bla-ics.blogspot.com/