babel-fish in cheminformatics w3c workshop on semantic web for life sciences cambridge ma 27 th -28...
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Babel-fish in Cheminformatics
W3C Workshop on
Semantic Web for Life SciencesCambridge MA 27th-28th October 2004
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The babel fish – universal language
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Cheminformatics – infinite data formats
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, DayCartUnity, 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
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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 you’re 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 they’re all at it…so 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 where’s 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: [email protected] (Juan Esteva)
[email protected] (Steve Chervitz)
[email protected] (Richard Scott)
[email protected] (Charles Troup)
[email protected] (Martin Senger)
[email protected] (Tokio Kano)
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LSR WANTS