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! 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 ( 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?

Stumble it!

5 Responses to “eMolecules and ChemSpider – A Respectful Comparison of Capabilities”

  1. David Bradley says:

    Thumbs up to your last paragraph! The mutual benefits to ChemSpider eMolecules and the wider chemistry community surely far outweigh any individual interests.


  2. Chris Singleton says:

    Definitely a good idea, their collection will enhance chemspider and I’m sure they would like the chance to gain a wider audience with little effort on their part. Plus it would save you the time of trying to find vendors/suppliers for people. I’m all for it,


  3. Joerg Kurt Wegner says:

    What would be the bonus for eMolecules, if they share their data? I would guess that it was some work compiling the vendor data they have on their list.

    Assuming that recognition would not be sufficient here, what else could be an attractive option for them?

    In other words, as simple minded user I am pro for sharing, but I would guess that they are working on their business model, are’nt they? And I would like to know what they would need in exchange for making it attractive for them? As said before, is there a kind of token system, or recognition system for users, vendors providing data? E.g. something like curator of the month, or data provider of the year? What could be potential mechanisms for paying back efforts from users? Might e.g. some sponsors be willingly providing some gifts, tools, or whatever? … of course all those things would require some technical solutions first.

  4. Antony Williams says:

    What’s the benefit for eMolecules? I’ll position the same question for ChemSpider to deposit our entire database in PubChem. What’s the benefit to ChemSpider to have done all of that work? And what would be the benefit to eMolecules to deposit their data in PubChem?

    The only expectation of data depositors depositing into ChemSpider, eMolecules or PubChem is to deposit their structures and “database IDs”, with these preferably linking back to the URL for further review. So, when the structures are deposited at PubChem for example users can find a compound of interest and then navigate back to the original data source. This works for ChemSpider and I have about 10 requests per week at present for people sourcing compounds. I point people to the data sources of chemical vendors and suggest they contact the vendor directly. ChemSpider doesn’t make money from this and, I hope, doesn’t have to look at this way to provide income to support ChemSpider. However, I believe that eMolecules has a focus on helping users to buy compounds from vendors and have special agreements in place hosting websites for vendors (for example: . This is ALL supposition by the way.

    My belief is that if eMolecules deposit their structure collection with eMolecules IDs to ChemSpider, and give us the URL structure to direct people to their site then eMolecules will direct users to purchase chemicals and, I think, will derive direct revenue from that. For ChemSpider we’re simply building community and reducing the work to help people source chemicals. For eMolecules we help direct traffic to their site to help fulfil their role of sourcing chemicals for the community.

    Regarding compiling the vendor data it should be a simple export from the DB and burning to DVD.

  5. Joerg Kurt Wegner says:

    Sorry for my late reply, I was busy with moving stuff around 600 km ;-)
    As said, I am pro, but it comes down to the question what the eMolecule people are after? As mentioned earlier and on several occasions would I prefer some feedback from them. This would lower hurdles (if they exist?) and help in getting the maximum out of any potential collaboration.

    My last discussion with them was years ago and I had some contacts in-between about OpenSmiles, but no eMolecules-related discussions recently.

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