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Babel-fish in Cheminformatics

Babel-fish in Cheminformatics. W3C Workshop on Semantic Web for Life Sciences Cambridge MA 27 th -28 th October 2004. The babel fish – universal language. Data Type. Data format(s). Data Domain. Supplier. Supported Databases. Protein Structure. PDB, mmCIF.

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Babel-fish in Cheminformatics

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  1. Babel-fish in Cheminformatics W3C Workshop on Semantic Web for Life Sciences Cambridge MA 27th-28th October 2004

  2. The babel fish – universal language

  3. Data Type Data format(s) Data Domain Supplier Supported Databases Protein Structure PDB, mmCIF Target Validation and Lead Identification RCSB PDB Sequence FASTA, Swiss-Prot, PIR, EMBL, GenBank, GCGdata, GCG, ClustalW, MSF Target Identification and Target Validation GENBANK, EMBL, NBRF, Stanford, SIB, EBI SWISS-PROT, PIR, EMBL, TrEMBL, GenBank, Wisconsin, SeqStore, GenoMax, PROSITE, Merops, SRS Small Molecule Mol, mol2, SMILES, SD, .msi, .skc, .chm, .cpd, sdf, Lead Identification and Lead Optimisation MDL, CambridgeSoft, Accelrys, Tripos, Daylight, IDBS ISISBase, DayCartUnity, Catalyst, Chemfinder Image Jpeg, gif, tiff, eps, ps, pict Any Northplains systems, SciMagix SIMS, Telescope HTS/Assay .xls, txt, delimited ASCII Lead Identification and Lead Optimisation IDBS, MDL ActivityBase, AssayExplorer Text Doc, txt, pdf Any Multiple Documentum, Lotus, Verity, RetreivalWare, Muscat Xray CSSR, .csd, .fdat, .dat, cif, mif Target Validation and Lead Identification CCDC, SERC IsoStar, CSD Cheminformatics – infinite data formats

  4. 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.

  5. Impact of heterogeneity • TIME and MONEY • A very small initiative • …compound collections

  6. Use Case – Compound Collections

  7. Thinking about the bigger picture…

  8. Return on investment • Save FTE time • Real-time updates • Accurate availabilities and amounts • Automated ordering • Compound brokerage • Save money • Less delays • You know what you’re getting!

  9. So why is no one interested?

  10. 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

  11. And they’re all at it…so more formats!

  12. 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

  13. So where’s my Babel-fish? • Data first, fish second • Standardisation groups and initiatives • W3C • I3C • OMG LSR • CSAR • LSID • Compound Collections?

  14. WORKING GROUP CHAIRS at LSR • Contacts: • juan.esteva@intellsolutions.com (Juan Esteva) • steve_chervitz@affymetrix.com (Steve Chervitz) • richard.scott@denovopharma.com (Richard Scott) • charles_troup@agilent.com (Charles Troup) • senger@ebi.ac.uk (Martin Senger) • t_kano@ot.olympus.co.jp (Tokio Kano)

  15. LSR WANTS

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