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Reviewing Data Quality in the NCGC Pharmaceutical Collection Browser

28 Apr

I wasn’t aware of the NCGC Pharmaceutical Collection Browser until today. The work behind the development of the database and the browser is discussed in the publication here:

R. Huang, N. Southall, Y. Wang, A. Yasgar, P. Shinn, A. Jadhav, D.-T. Nguyen, C. P. Austin. The NCGC Pharmaceutical Collection: A Comprehensive Resource of Clinically Approved Drugs Enabling Repurposing and Chemical Genomics. Science Translational Medicine, 2011; 3 (80): 80ps16 DOI: 10.1126/scitranslmed.3001862

As is usual with new databases that come online I always concern myself with data quality. In order to take a look at the data quality I looked at the HTS amenable compounds subset of data. It’s a dataset of >7600 compounds. I ran a couple of very simple filters to try and identify potential issues with the data. In particular I was looking for presence/absence/confusions in stereochemistry. The filters also checked for valency issues and charge imbalance. Based on these checks my estimates are, for the HTS amenable compounds at least, the errors in the data amount to a minimum of 5% and probably over 10%. This is an estimate of course and it would be a lot of work to clean it all up. I’ll try and take a look at the entire database shortly.

Some examples of the errors I saw are below…Unfortunately there are many hundreds of errors in just this subset of the database. We keep creating databases, and in this case a 90 Mbyte desktop browser solution, but WHO is curating and checking the data? What is the cost to develop software that keeps getting invested relative to building quality datasets to use in the various systems? And so it continues….

Charge Balance Issues

NCGC Browser Charge Balance Issues - Screenshots from Browser

 

Imperfect, Absent and Incorrect Stereochemistry

Stereo Issues: Left Hand Side NCGC Structures, Right Hand Side "Correct Structures"

Incorrect Valence Issues

Valence Issues for "Tannic Acid Glycerite" - Screenshot from NCGC Browser

And, just to clarify…I am not saying that our own database, ChemSpider, is perfect. It’s not. But the crowds can help us improve it and curate the data online and immediately. One thing I DO like is that the developers thought ahead about getting immediate feedback as shown below. Unfortunately when I tried to use it it threw a message that there was an error so I don’t know whether the message got through. I hope to get a response at my email address.

Feedback Screen in the NPC Browser

 

 

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 April 28, 2011 in Data Quality, Quality and Content

 
 
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