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Zen and the Art of Chemical Structure Databases. What is the definition of “Quality”?

16 May

Zen and the Art of Motorcycle Maintenance…for those of you interested in a discussion about Quality this is a great read (or listen on a long ride with an audio book. Persig discusses the Metaphysics of Quality as a philosophy, a theory about reality and asks questions such as what is real, what is good and what is moral. The narrator of the book, Phaedrus, named after the character from the Plato dialogue of the same name, criticizes his instructors for poorly educating the students.

Now, poorly educating the students is an issue and certainly this concern has been raised recently in regards to the ChemSpider system. The question this leads to is about Quality. The Quality of LARGE public domain databases. ChemSpider is an example and not without challenges…to be expected with over 10 million compounds. However, as shown in a couple of specific posts about sodium chloride and recently prussian blue issues regarding the judgment of quality of both our system and other databases abound.

Rich Apodaca has recently posted a request for information about new free access/free speech/free beer databases to follow on from his very popular posting regarding 32 free chemistry databases. For those of you who do not frequent Depth-First I HIGHLY recommend a browse…one of my top sites for commentary on our domain. There will be a number of databases submitted for inclusion in Rich’s next list. However, the question I will have then will be about Quality. It is a concern as we choose to post certain content or not…there actually should be a quality flag depending on data sources in our opinion. Some are simply better than others.

We are already in the process of curating the ChemSpider content ourselves as well as with the assistance of some dedicated individuals. Clearly there are issues with some of the content within the index. With 10 million structures what is one to expect? The database is set to double in size over the next couple of months we believe and, in parallel, the number of potential errors will grow also.

So, the questions I have tumbling around my rather non-Zen brain this time of night are:

1) Assuming perfection is not feasible and errors will occur in a large free database of millions of structures, what level of error/misinformation is acceptable? This is after all an issue of cost versus quality in many cases. If you were paying $50 per search the expectations of quality would be much higher I would assume.

2) There are different criteria for quality for different data – it may be acceptable to have a poor predicted property for a compound since it IS a prediction but what if the structure itself is wrong, one stereocenter is mislabeled, one trade name is misspelled. Can you identify the highest quality data and for which is it acceptable to have errors?

3) What are peoples experiences of other large free databases…there are many out there as posted in Richard Apodaca’s list? What is the quality like?

4) Which public domain free online database is the gold standard by which others should be measured? How good is the database? What level of error content? What type of errors?

Any other commentary is welcomed. The question I posit is “How is Quality measured in terms of public domain free online databases?”

 

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 May 16, 2007 in Quality and Content

 

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