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Generating Databases from Name to Structure Conversion Software

03 May

In continuing to expand the ChemSpider index we have chosen to trawl through the web and download databases of chemical names and associated information (allowed by consent). We have converted these to chemical structures using the Name to Structure conversion software provided to us as part of our collaboration with ACD/Labs. In order to produce the chemical structures for posting in ChemSpider and, where appropriate, linking back to the appropriate structural record on a website, we used a combination of software products. The process will be reported in a technical note to be posted elsewhere and I will point to that when posted. The database will also be made available via PubChem when we submit it.

In a related vein I have reported previously on the issue of quality of nomenclature in patents. It is shockingly distressing how bad the nomenclature is in many of our peer-reviewed publications. Gernot Eller has commented on how software can help improve the quality of nomenclature in publications (check it out…its on Molecules…an Open Access Journal!) I have to agree…I’ve been involved with the development of nomenclature software for 10 years. Nomenclature is NOT easy..but there are an abundance of resources available to assist if you know where to look…IUPAC Rules online, inside freeware drawing packages, an online naming service and even the ability to integrate FREE NAMING into your own webpages (These are all-provided by members of the dark side…one of those commercial chemistry software providers that many frown on…sure, it is NOT open source but it’s damn good for free!)

With people using these types of free tools, even though restricted in capability, the quality of nomenclature in publications and databases will improve dramatically. It will make the conversion of chemical names in publications to chemical structures much more successful.

We are presently in the process of applying Name to Structure technologies to the conversion of names in Open Access publications and will demonstrate the results of this technology in the near future. Watch this space!!!!

 

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 3, 2007 in ChemSpider Chemistry

 

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