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Five Things I Don’t Like About ChemSpider

26 Jun

So, ChemSpider is still in beta even though we are moving fairly quickly in the “back room”, and the development team has grown. There is a lot of infrastructure work going on despite what you see on the site when you come to crawl with the Spider. You should sense performance improvements when you use it though.

I’m the whiner on the ChemSpider team. That means I use the “whine” function in our bug-tracking system Bugzilla, our Open Source bug-tracking and feature request tracking system. It’s a great system for our needs and if you need a system out-of-the-box which will suffice for moist of your needs go grab it. So, what am I whining about? Here’s my list of Five Things I Don’t Like About ChemSpider.

1) Many of our molecules are simply ugly. The connection table is correct but some of our displays of the molecule are far from perfect – take a look at the two structures below. The one on the left does NOT really have a chlorine attached to the oxygen. The one on the right is simply a mess.
Cleaned Structures - with problems!

This is an issue of Structure Cleaning. It IS difficult. Even the drawing package vendors struggle with this. It needs improving…whine…

2) We really need to do something with the curated data. People have been curating data on our site for a few weeks. We need to do something with it to show that their efforts matter….whine, whine…

3) We need to allow people to deposit data. There are people wanting to flood the system with data…in some cases one structure and in many cases thousands of structures. Right now its a very manual process…data has to come to us. I want a user to be able to submit their own data…sure we’ll validate and review but let people deposit the data at least….whine, whine, whine…

4) I want people to add content and information to structures. Not everything can be done with robots and process…people need to contribute. Wikipedia is all about community participation. Chemists have information about structures, about reactions..about connected data. When they have info they want to associate/link/dump and connect to a structure I want them to be able to do it….whine, whine, whine, whine…

5) ChemSpider was a rushed release. We’ve never hidden it…it was rolled out in time for the ACS in Chicago…and rushed. It went live with a lot of holes. It’s still beta. It’s working, and it’s moving but it’s time for some of the work flows to be improved and the website to be “prettied up”……whine, whine, whine, whine, whine…

Ok…those are my top five whines….and none of them are from a bottle. So, with these in mind it’s what we’re off to work on. Our short to midterm efforts will be in these areas.

What are the things YOU don’t like about ChemSpider? Whine away…we’ll Bugzilla your comments!

 

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 June 26, 2007 in How ChemSpider Runs

 

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