Does ChemSpider Unashamedly Exploit the PubChem Resource?

05 Jul

As a web subscriber to JCIM (and frequent author to said journal) I was reading the recent articles related to PubChem. If bandwidth allows I’ll post some additional comments shortly but Rich Apodaca has already highlighted them.

In his posting Rich commented “The public is free to download and re-use the entire database of molecules and associated data. <...> witness both eMolecules and ChemSpider, two services that unashamedly exploit the PubChem resource. Expect to see more of this in the months ahead.”

Did we do this? Absolutely. We downloaded the data and used it to test our system since we couldn’t easily source 10 million chemical structures anywhere else. We were very honest in our first press release on March 24th where we said “… the launch of their ChemSpider Service (, an online resource for chemists to search, aggregate and data mine publicly available chemical data. At time of release over 10 million compounds are indexed in the ChemSpider database including the PubChem collection and data provided by a number of other collaborators. ….”

There is no Open Source software that we are aware of that can handle 10 million compounds. So, having constructed our system we needed to performance test it and PubChem was a great resource so we used it. The quality of the database (and I have talked about Zen and Quality already) was irrelevant at that point. We needed to test the system.

The ChemSpider dataset is now over 16 million compounds and the PubChem dataset contributes 10.3 Million of those (10297250 to be precise), just over 60%. We continue to add databases (1,2,3) and have put significant effort into curating the data ourselves and with the assistance of our users (4,5,6). We’ve committed to return curated records back to Pubchem and glad to do it.

We presently have more data to add to the ChemSpider database, unique structures that are not contained in PubChem. Where allowable we will deposit these to PubChem in the future. For right now we have more important things to do, specifically address those Five Things We Don’t Like About ChemSpider.

The work on Quality checking continues and there will be an abundance of data to return to PubChem. See the recent discussions about Taxol and Thimerasol as examples. There’s a lot more where those came from.

Regarding the comment “… eMolecules and ChemSpider, two services that unashamedly exploit the PubChem resource.” I’ll confess that the PubChem database is on ChemSpider. However, eMolecules is a database of 7 million chemicals now and they have received data from many chemical vendors so it appears that they have only utilized a subset of PubChem as appropriate to their business model.

PubChem is a great resource..for those of you interested in how the data are being used/examined I do recommend the papers Rich has pointed out. Also, add Depth-First, Rich’s site, to your BlogRoll…it’s one of the best reads in the blogosphere in my opinion.


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 ( 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 (, 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 ( and the RSC lead for the PharmaSea project ( 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, 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 July 5, 2007 in Uncategorized


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