Comments on: Will the Correct Structure of Taxol Please Stand Up. Part 3.

By: Noel

Noel — Sat, 06 Oct 2007 16:03:28 +0000

Fascinating post. Pubchem has to take at face value the structures and names deposited by others. But the savvy user should be looking at the SIDs, not the CIDs, to see what reputable sources deposited the information. There are 36 taxol CIDs in pubchem. Would you rather use ChemIDPlus’s (CID:36314, the correct structure, also the most ‘linked’ structure), or Cambridgesoft’s (CID:5321715 incorrect stereo), or ChemBlock’s (that is the one you cite above; also incorrect)? I personally find that ‘known drugs’ are best annotated by ChemIDPlus – which makes sense given how much money and effort went in to curating that particular data.

By: ChemSpider Blog » Blog Archive » Curators Perform Heroic Duties. They Should be Celebrated!

Thu, 04 Oct 2007 16:41:45 +0000

[...] a result of reading that post you saw me go off and check on Taxol, post a few comments and come out the other end of the work with a “more highly curated record” on [...]

By: Antony Williams

Antony Williams — Mon, 01 Oct 2007 13:45:09 +0000

The systematic name and the link to PubChem have been updated in Wikipedia now so all is now appropriate and accurate. This is the outcome of the Open Data nature of Wikipedia plus a major concern about the quality of what’s in there. Thanks to all who contributed to me resolving this issue.

http://en.wikipedia.org/wiki/Paclitaxel

By: Antony Williams

Antony Williams — Sat, 29 Sep 2007 02:18:10 +0000

We have checked the chemical name in C&E News relative to expectations. The name generated by software we have tested is correct. AS far as we are concerned the name in C&E News is incorrect but the structure itself is correct.

By: Antony Williams

Antony Williams — Sat, 29 Sep 2007 02:15:43 +0000

Ivan..your comments are accurate. I could have gone directly to the literature.. certainly I could have used ChemRefer on ChemSpider to easily find papers. See http://www.chemspider.com/ChemRefer.aspx?zoom_query=taxol&zoom_and=0 for the results set where there are SO many papers.

What I was out to discuss though was the proliferation of Taxol structures in databases, both Open Access and for fee databases. I think I achieved the goal…”take care of Open Access databases AND double check and curate!”

By: Ivan

Ivan — Fri, 28 Sep 2007 08:38:55 +0000

I see you have found an answer already, but here is what I would have suggested. If you want to find the correct structure for Taxol, forget about the databases and news stories. They can always introduce accidental errors. Look instead at the books and papers of some of the people who have actually worked on synthesizing Taxol or determining its structure (e.g., K.C. Nicolaou). That should give you a more authoritative answer.

By: David Bradley

David Bradley — Fri, 28 Sep 2007 07:37:47 +0000

Phew….