ChemSpider Blog

There are a number of groups in the “free access to chemistry information” domain at present and all are working hard to provide access to data, knowledge and connectivities to serve the chemistry community. Two of the most common questions I get asked are in regards to the difference between ChemSpider and PubChem and between ChemSpider and eMolecules. Yesterday I was asked the question about the difference in regards to eMolecules three times. So, overnight I put together what I hope is an objective comparison of capabilities. I welcome any feedbac or additional questions. It’s a living document as both of our sites are changing (and I know ChemSpider better than I know eMolecules of course).

I know members of the eMolecules team from my previous role when I facilitated the connection between eMolecules (or Chmoogle as it was then) and ChemSketch.  I then had the pleasure of meeting with their VP of Sales at the Chicago ACS meeting one day after ChemSpider went live and we discussed our opinions about our mutual intentions to deliver value to the community. I like the eMolecules offering. There are some nice visual elements on the site. ChemSpider IS different and has a different focus based on what I see eMolecules delivering. We are out to build a structure centric community for chemists. I believe eMolecules is focused on delivering a centralized resource for sourcing chemicals for purchase and has a business model based on advertising and delivering websites for chemical vendors. We will shortly complete our first “depositor skin” that will provide to one of our collaborators a way to display their content only from ChemSpider and “branded” with their logo etc. so will offer a similar service to depositors.

A number of people now visit ChemSpider asking us where they can source a particular chemical. If we cannot find it on ChemSpider then I do visit eMolecules and point people to the link if I find it. At present that’s only about 10% of the time. Despite the fact that ChemSpider is about 2.5 times bigger as a database than eMolecules their focus is commercial vendors and at present they do have more commercial vendors than us. Our collection is growing at about 2-3 new depositors per week, mostly chemical vendors requesting that we ad them to our database. Some people think that ChemSpider is simply a rewrapping of the PubChem database. On day 1 we went live with only the PubChem collection but the data sources collection is much more diverse now and we actually deposited back to PubChem (which I don’t believe eMolecules has yet?). Our structures are unique..but you MUST be careful with that consideration. For example, there ARE multiple flavors of taxol on ChemSpider but the same is true of Taxol on eMolecules. Actually, the reality is that there are multiple flavors of the “Taxol Skeleton” on ChemSpider (42 to be precise! http://www.chemspider.com/q/RCINICONZNJXQF) but NOW, after our curation and redicretion efforts, there is only one compound, the CORRECT one, that will be retrieved based on a search on the name Taxol (http://www.chemspider.com/q/taxol) relative to the seven on eMolecules where you have to determine for yourself which one is Taxol. The 42 Taxol skeletons include multiple stereochemisties and isotopically labeled compounds - C-13, C-11, Tritium, Deuterium etc). So, be careful when people talk about unique structures!

It would be great to have the eMolecules collection in ChemSpider and direct traffic to their site and to their commercial vendors and extend the community. What do you think?