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Markush Misrepresentations in ChemSpider

29 Apr

Following on from the many comments made about the recent post about the NPC Browser Markus Sitzmann highlighted a “fun molecule” that he found on ChemSpider. It was here as ChemSpiderID 19053748 shown below but it has now been deprecated…I logged in and deprecated it .

A "fun structure" on ChemSpider

Markus also commented on Sean Ekin’s blog here:

“Well, particularly ChemSpider belongs to the group of “polluters” in PubChem. Count the number of Aspirin, Benzene or Ethanol structures submitted by ChemSpider to PubChem (only linking to a “deprecated” ChemSpider record). Or make an advanced search for ChemSpider records containing also Argon, here is an example:

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=20187034&loc=ec_rcs

There are many other examples.”

Markus is CORRECT. I have commented on this publicly myself on a number of occasions and many people have noticed that there are data in PubChem that are in error and originally came from ChemSpider. There’s no point denying it as it’s there for all to see ! We have had the intention for a LONG time to deprecate this data from PubChem and replace it with an updated deposition of cleaner data. The intention remains but the challenge is finding the time to do it. We will do it.

Where did the data came from? These “argon” issues are really NOT argon issues…they are the results of molfiles finding their way into ChemSpider from “patent molecules” where the -Ar is expected to represent a Markush structure where Ar means “Aryl”. This is like  -Alk meaning alkyl. Similar issues arise when molecules are drawn as -X, -Y and -Z and lists of X,Y,Z substitutions are give. For example X=CH3, C2H5, Y=F, Br and Z= Br, Cl. Unfortunately Y is not only a substitution it’s an element, Yttrium. So when a molecule is drawn with a supposed Markush bond to -Y then we have a REAL molecule with Yttrium attached. Agh.

A list of the examples of “interesting Ar molecules” are shown below.

At this point these have all been deprecated…takes about 30 seconds per molecule..but if they were in our original deposition to PubChem they are still there until we deprecate. Ahh…the ongoing joys of data curation.

 

 

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.

4 Responses to Markush Misrepresentations in ChemSpider

  1. Markus Sitzmann

    April 29, 2011 at 10:38 pm

    Well, from my analysis with our local copy of ChemSpider here (taken from PubChem) I estimate the number of problematic/fishy structures in ChemSpider between 1 and 2 million CSIDs (in this regard 30 sec/molecule is a long time 😉 ). I spot-checked maybe a few hundreds of them with the ChemSpider web page – most of them are marked as “deprecated”. Since doing things like this with a web page is cumbersome, it would be great if the information “deprecated CSID” is available in an easier manner (e.g. as URL API or something like this).

     
  2. tony

    April 29, 2011 at 10:43 pm

    Yup…many of those marked as deprecated on our site, and therefore necessary to deprecate from PubChem, are from a historic definition of patent data. These will all get removed when we deprecate and when we redeposit will be gone from the set. NONE of the Argon related compounds that I deprecated tonight came from that dataset. If you look at my post on Mercury Argon for example that originated with PubChem as did some of the others. But now they are gone….from our site at least.
    Watch for the news shortly about the work we are doing to share deprecation information out with appropriate feeds. You should be able to use these directly when we expose!

     
  3. Egon Willighagen

    April 30, 2011 at 2:44 am

    Antony, the CDK project has a fairly decent atom typing framework, which would catch many issues like this. Now, if the ChemSpider data would have been Open, then you would have seen alerts on structures like these at least two years ago.

     
    • tony

      April 30, 2011 at 9:52 pm

      Egon….despite the fact that PubChem is not “open” per se, as we have discussed before, the PubChem data is avaialable for download so it would be good to see how the atom typing framework would perform on PubChem. Is it feasible to take on their 30 million structures and check them?

       

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