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Annotation of ChEMBL with compound availability data

By jpo

We are starting to plan a few things, and one of these is to provide links through to the sources of physically available compounds for ChEMBL. To help us, here's a few questions - I tried to set up an online poll, but lost the will to live with all the spam on polls that is out there.

Here are the questions:

  • Is integration of available compounds in ChEMBL a good idea?
  • Should we integrate available compounds via current informatics resources (e.g. ZINC, ChemSpider)?
  • Should we set up a small set of available compounds from actual suppliers (e.g. NCGC, MolPort, Prestwick, ChemDiv, Tocris, etc. etc.). If so what suppliers should we use?

If you want to contribute,  free to mail if you have any specific ideas, or can help us out on this.
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Comments

eMolecules said…
You might consider eMolecules, which lists only in-stock compounds. Most other data collections list historic and virtual compounds, leading to success rates of actually getting the compounds below 50%. Maintaining your own collection of supplier catalogs is very time consuming and it is hard to keep them up to date.
Our data content is publicly available.

klaus@emolecules.com
22 June 2011 at 16:13
Bio to Chem said…
One way or the other most suppliers are already connected via the PubChem and ChemSpider outlinks. I would not have thought it worth your efforts (vs other good stuff) to add these directly. JFTR its easy to make the intersects in PubChem (e.g. a ChEMBL AID > CIDs > history > AND source MolPort OR ZINC OR... etc)
24 June 2011 at 13:15
Imants said…
As Chris mentions, you already have a link to Molport and other databases via PubChem. A more direct integration with an ordering platform has some additional benefits, however. For example, at Molport we are thinking of ways how to give partner applications a quick way to check which compounds are available today, at the moment the user views the compound. Here is my blog post about it: http://blog.molport.com/2011/06/quick-way-to-programmatically-check.html

I agree with Dr. Gubernator - it is huge task to keep supplier catalogs updated.
29 June 2011 at 21:53
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