InChI, ChemSketch Freeware, ChemSpider and Wikipedia Integration

30 Apr

I recently became engaged in a Wikipedia discussion after being approached by a member of the structure template group during my “day job”. Their request was whether we would support PNG and SVG format in ACD/ChemSketch.  

What’s the result? The beta version supporting PNG is already coded and is about to be delivered for testing to the Wikipedia group. I initiated a discussion about how Wikipedia could be made structure searchable with InChI likely being the solution of choice…to facilitate searching of Wikipedia by those ¾ million ChemSketch downloaders and the commercial users if they need it.  Within the Wikipedia team it was decided that embedding InChI as a tag into the image file would be of value. It’s also finished. Shortly ACD/Labs will release an updated version of ChemSketch FREEWARE including PNG support with InChI tag embedding…and everyone can take it. SVG will come later…it’s a lot more work and ACD/Labs has commercial priorities to deliver on for our formal release cycle for our commercial users. There is a UNIX program already available with this capability..

I join the Wikipedia team in encouraging all the other vendors to consider adoption of PNG/SVG export and now with InChI tagging..we will have to see whether the search engines will index or whether Wikipedia would be willing to expose InChI searching through their API…thoughts for another day. 

The reason I pushed on Wikipedia searching is simple. ChemSpider offers an index of chemical structures, millions of them. The ultimate goal is to offer a chemical community for chemists to submit their own structures into the system, to submit their reactions, to submit their spectra. The hope is to create a community around a structure centric database. With the support of chemists willing to curate each others data the potential value to the community is immense. HOWEVER, why re-create what’s on Wikipedia as information about chemistry and chemical compounds. If it’s on Wikipedia then let ChemSpider index it. We’re NOT there yet but this past week ChemSpider and Wikipedia were integrated via synonyms, trade names and systematic IDs. Following a structure search on ChemSpider  the Details View will display all synonyms and are automatically linked to those Synonyms on Wikipedia. Our experience to date is that the synonyms extracted by the supplier are DIRTY…very dirty. I am presently working with Martin Walker to get the list of all chemical compounds from Wikipedia so that we can do direct links. Peter Murray-Rust has spent some time discussing the issue of “name-structure pair” quality  in a recent blog.


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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Posted by on April 30, 2007 in ChemSpider Chemistry


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