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Physical Property Predictions – Filtering Out Potential Problematic Data on ChemSpider…or is it NOT a problem?

15 May

During the past couple of weeks there have been a number of comments regarding the association of Physicochemical Properties with chemical structures inside the ChemSpider database. Specifically the comments have been directed at inorganic and organometallic compounds.

Based on this feedback we are considering a series of actions regarding physicochemical predictions and these are outlined below.

1) Filter the ChemSpider database and remove the following PhysChem predictions (ACD/LogP, ACD/LogD (pH 5.5), ACD/LogD (pH 7.4), Number of Rule of 5 Violations, Number of H bond acceptors, Number of H bond donors, Number of Freely Rotating Bonds, Polar Surface Area) for substances with the following properties:

• Exclude multi-component substances
• Exclude substances represented as a single atom
• Exclude radicals
• Exclude structures with a delocalized charge
• Exclude structures containing isotopes
• Exclude substances containing elements other than As,B,Br,C,Cl,F,Ge,H,I,N,O,P,Pb, S,Se,Si,Sn, the elements supported by ACD/PhysChem predictors

A question for readers..do you believe that structures with isotopes should be excluded from PhysChem prediction of the properties listed? I have my own opinions but would like community feedback as to whether this is necessary and is all inclusive for all isotopes. Also, should all multicomponent systems be excluded? For example, if there is one water of solvation present should the parameters NOT be calculated for the primary component?

2) For any future updates to the database pre-filter using the criteria listed above

3) Apply the criteria above prior to performing PhysChem predictions on the Services Page

Our predicted properties for certain structures have created a response suggesting that we should alter our application of such algorithms. The suggested path forward is listed above. We welcome feedback from the community! These questions have also been posted to PMR’s blog supporting the suggestions. Please provide your feedback at either site. It will be important in helping to make the decision. It is possible that there will not be sufficient feedback but a decision does need to be made and we will determine a path forward regardless.

 

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 15, 2007 in ChemSpider Services

 

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