CLiDE and more complexity. ChemSpider has Agents and EyeBalls

03 Oct

Yesterday I wrote about the potential advantages of using Dictionary Look-Up and Optical Structure Recognition over the “copying of molecules” from a manuscript or webpage. I noted that the copying of structures might be prone to loss of “fragments” and suggested that might have happened with discodermolide. Liquidcarbon has confirmed that was the case…the original structure came from Org. Proc. Res & Dev.

I’ve continued to look at other examples. Here’s one very complex structure…the whole structure is not visible. the images on the right are SCANNED images and those on the left are the converted connection tables. Very damned impressive I would say. If the structures are examined in detail a couple of hydroxyl groups ARE dropped as well as a couple of wedge bonds being dropped. They can be edited in easily.


The conversion process is not perfect and manual checking is necessary. But it took a few seconds to open the image and convert to a connection table. Try drawing the structure at the bottom in a few structures.

In regards to my previous post on drawing, versus look-up versus software conversion my comments have stirred a response.


My post was written with the intent that there are better ways to reproduce structures from articles that redrawing. Redrawing can introduce, as acknowledged by liquidcarbon, errors. Look-up is less prone to errors provided that work has been done ahead of time to provide a highly curated data source. I wanted to expose the scan-and convert approach because I believe it could be the process by which we convert structures from patents into connection tables for the ChemSpider database. It’s an interesting technology. The error happened to be on discodermolide…it could have been on Penicillin G or THC…the fact is that look-up or scanning are likely more efficient than redrawing and less prone to errors. BUT, both have their problems…there is no holy grail. I’ve already blogged many times on Taxol and, going with “Taxol is important” have shown that there is confusion out there (1,2,3). As I commented there…Wikipedia was linked to the incorrect structure on PubChem (but it’s edited now). The community, of which i am a member, has to have a fine eye for detail and work collaboratively to help clean up the historical records.

By the way, hexacyclinol only has five hits in Pubmed but is fairly well known in the blogosphere and is being used as the foundation for grant writing …


Now, the Agents and Eyeballs approach is very interesting to me.I like it! It’s the community approach to cleaning up the data. We’ve already provided a path to curate data online at ChemSpider. We HAVE agents running. We HAVE eyeballs reviewing. All we ask to do so is be a registered user. We would prefer non-anonymity for people when they are curating the data. It allows curators to be aware of who’s doing what. Is  the process optimal yet? No, I don’t think so. But it’s underway already.

This week I gave a presentation to the PubChem Working group. I published this tonight here. In this presentation I discussed the need for curation of data (slides 15-20). Slide 15 shows somebody actively curating data on ChemSpider – scroll to the bottom of this record. Slide 16 shows the results of curating taxol on wikipedia (left hand side before; right hand side after). Slide 17 is the list of synonyms for 1-butanol on an online database and originating at PubChem. Slide 19 is curation on ChemSpider…see the list of identifiers here.

I happen to think the efforts to clean up date are important. People curating data are some of my heroes. Some people talk about highly curated data. Some people help create highly curated data. Vision is great..execution is better.

I’ll recognize some of these heroes in a later 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 October 3, 2007 in Uncategorized


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