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eMolecules and ChemSpider – A Respectful Comparison of Capabilities

20 Mar

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?

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
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Posted by on March 20, 2008 in Uncategorized

 

0 Responses to eMolecules and ChemSpider – A Respectful Comparison of Capabilities

  1. David Bradley

    March 20, 2008 at 1:01 pm

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

    db

     
  2. Chris Singleton

    March 20, 2008 at 9:18 pm

    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,

    Chris

     
  3. Joerg Kurt Wegner

    March 21, 2008 at 5:28 pm

    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

    March 21, 2008 at 5:49 pm

    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: http://lifechemicals.emolecules.com/) . 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

    March 27, 2008 at 8:53 am

    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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