Babel-fish in Cheminformatics

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Babel-fish in Cheminformatics

• W3C Workshop on
• Semantic Web for Life Sciences
• Cambridge MA 27th-28th October 2004

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The babel fish universal language
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Cheminformatics infinite data formats
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Cheminformatics molecule formats

• Mol, mol2, sd, SMILES, SMIRKS, SMARTS, skc, sdf,
  rlx, ptr, sph, pdb, molen, molin, Shelx, FDAT,
  CSSR, Charmm, CADPAC, Chem3D, Xed, Spartan, MM2,
  MM3, Gromos, Gaussian, GAMESS (various), GSTAT,
  Boogie, Cacao, GROMOS, Hyperchem, Tinker,
  Diagnostics, BGF, Dock, CAChe, Mopac (various),
  Maccs, etc.etc.

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Impact of heterogeneity

• TIME and MONEY
• A very small initiative
• compound collections

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Use Case Compound Collections
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Thinking about the bigger picture
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Return on investment

• Save FTE time
• Real-time updates
• Accurate availabilities and amounts
• Automated ordering
• Compound brokerage
• Save money
• Less delays
• You know what youre getting!

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So why is no one interested?
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Vendors

• Manually normalised collections
• 11,000 per copy per annum
• Tie-in with vendor application
• Repeat fee for file format change
• Always out of date
• Time consuming updates
• Vertical mind set for vertical sales

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And theyre all at itso more formats!
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How do we change this?

• Vendors respond to s
• A group of Big customers weighs more than a 600lb
  gorilla
• The vendor who builds a customer requested
  standard gets bigger market share

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So wheres my Babel-fish?

• Data first, fish second
• Standardisation groups and initiatives
• W3C
• I3C
• OMG LSR
• CSAR
• LSID
• Compound Collections?

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WORKING GROUP CHAIRS at LSR

• Contacts
• juan.esteva_at_intellsolutions.com (Juan Esteva)
• steve_chervitz_at_affymetrix.com (Steve Chervitz)
• richard.scott_at_denovopharma.com (Richard Scott)
• charles_troup_at_agilent.com (Charles Troup)
• senger_at_ebi.ac.uk (Martin Senger)
• t_kano_at_ot.olympus.co.jp (Tokio Kano)

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