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A Quality Alert and Call for Improved Curation of Public Chemistry Databases

09 Aug

Our article regarding a quality alert and call for curation of public chemistry databases has been published as an Article in Press in Drug Discovery Today here.

Abstract for our DDT Article

 

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.
2 Comments

Posted by on August 9, 2011 in Publications and Presentations

 

2 Responses to A Quality Alert and Call for Improved Curation of Public Chemistry Databases

  1. Egon Willighagen

    August 11, 2011 at 5:49 am

    It must be stressed that the cause of these errors are not always found in the database structure, maintainers, or curators… in most cases, it is the input that was faulty. I am enjoying my $36/yr Nature subscription, and already noted problems with structure representation there.

    What is the database supposed to do here: make an accurate (faulty) structure-paper relation, or make assumptions, overall introducing error of another kind. Another common problem is exchange formats. Imprecise formats are still the standard, causing lots of trouble here. If only all would support the NG cheminformatics formats will explicit semantics, like CML… that would greatly improve things. I have been making this point for more than a decade now (I actually started using CML in 1997, before it got fully rebased on the first XML recommendation in Feb 1998), and have been trying to show how things can be done in a better way since. To some success, looking at my Google Scholar Citation profile 🙂 But there is still very much wrong, and this post just shows that.

    The more important question is, what is our next step to improve things. For example, maybe ChemSpider could promote the use of the better file formats a bit more. For example, encourage people to download in, e.g., CML, rather than MDL molfiles (V3000 seems better then V2000). And at least have explicit hydrogens, mind the 999 atom limitation 🙂

    Summarizing, database quality does not merely reflect itself in database content, but also in how database do things.

     
  2. tony

    August 11, 2011 at 12:08 pm

    I can only agree with some of your points I’m afraid. In terms of the content of the database, and let’s isolate to organic molecules that can adequately be represented by even old molfile formats and with no need to try out new semantic file formats. In that case the quality of the data is simply the responsibility of the host. I FULLY agree that where the data comes from is a direct influence on the quality of what end up in our databases – whether publishers, vendors, aggregators etc. For sure we have, unfortunately, contaminated other databases. We have inherited junk and it has been passed on to other systems. In the early days our deposition to PubChem carried in a lot of erroneous data that we had inherited from many of our depositors. We are presently trying to deprecate the entire set and redeposit much cleaner data. It’s not as easy as you might think.

    AS a part of the OpenPHACTS project we will be working on new approaches for structure handling and standardization, data exchange etc and I believe these will all provide major contributions to some of the issues you list.

    But data quality…primarily depends on people.

    I just tweeted your Google Scholar Citation profile. VERY nice!!!

     

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