Rabbits, Potatoes and other Vegetables in the NCGC Database

19 Jul

No wonder I’m so healthy…I like rabbits, eat lots of potatoes, drink “green sludge in a bottle” to get my vegetables and also have lots of other “ingredients” in my diet. According to the NCGC data collection that I have been browsing through the NPC Browser on my desktop these are all parts of the NCGC data collection. While chatting with a number of pharmaceutical scientists last week regarding data quality in public domain databases the NPC Browser was used as an example of data content “to review”. If you’d like to review the contents yourself you will find many issues regarding stereochemistry, valency, charge balance, incorrect associations between structures and identifiers but you can also review the data in table format and look at the content that doesn’t have structures associated and scratch your head at some of the content. To see the errors go to tabular mode as shown below and scroll down past record 8000.

How to display the tabular format for the NCGC Data in the NPC Browser

Notice that the drugs “water Lily”, “Water Cress” and “Water Hemlock” are listed. I wonder what water cress is used for? It all becomes much more fun when you see some of the others listed below. Rabbit…now that’s a good…take two in the morning, without food, and repeat dosage for 7 days. Cures “big sharp pointy teeth”. Vegetables…ah yes, nothing specific. Just “vegetables”. Kind of a cure all really. Take 5 portions per day, with food, obviously. And potatoes…good for a stiff neck (starch collar syndrome). If you browse through you’ll also find “ingredients” listed as a compound. Glad about that really…most drugs have ingredients. I am sure there is a reason that these are listed, though I cannot imagine what the reason would be. If there is no good reason it is time to decommission this dataset until it is cleaned up in a major way. Clearly the contents are suspect at best.

A Rabbit in the NCGC Collection - I pity the rabbit during high-throughput screening

Potatoes - the drug of choice for many McDonald's visitors. Fry-style


Momma was right - eat your vegetables and you'll be healthy. They are drugs?


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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