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The Entire ChemSpider Database is On Its Way to PubChem!

28 Nov

I have blogged previously about the fact that we are willing to share the entire ChemSpider structure collection with anyone who wants it. Specifically PubChem are willing to accept it..and YES, I have pointed out that they will be receiving back their own structure collection too since we deposited it on ChemSpider.

What’s the value of redepositing the same structures to PubChem? There are actually many – structures on PubChem connected out to ChemSpider will now be connected to Patents, those structures will be connected to analytical data, they will be connected to additional identifiers not available on PubChem, they will be connected to curated identifiers (compare the list of names for methane on PubChem versus ChemSpider), they will be connected to Supplementary Data, and they will be connected to additional predicted properties. So, there is actually a LOT of value in having the links back to ChemSpider from PubChem.

Our best estimate is that there will be about 8 million new structures finding their way to PubChem from ChemSpider.

Now, I was close to thinking that we could declare that the ChemSpider structure collection was Open Data. I’ve posted about Open Data and it’s definitions and challenges previously (1,2). PMR , one of the primary evangelists of Open Data and its definitions is continuing to refine the definitions of Open Data. Extracting from Peter’s post

“I reiterate some guidelines. I’m still working these out and would welcome comment. (I don’t feel we should stray too far from the The Open Knowledge Foundation guidelines. ) As a start I would suggest the following:

  • There must be some mechanism whereby the community could, if it wished, capture the resource for public archival without permission. This could be as simple as spidering the site, or a relational dump, or a massive file, or an iterator.
  • There must be no permission barriers to re-use including commercial re-use.
  • The data must either be the whole work (at a given point in time) or be clearly bounded (i.e. there should be no hidden data that the world cannot get access to in the same way).
  • There should be no time limits on access and re-use.”

For right now I am giving up on trying to track where Open Data might end up. Based on my previous discussions with Peter Suber regarding navigating the complexities of Open Access definitions, I understand there is a need to define our own policies. I’m not going to do that here but what I will be clear with is that once the ChemSpider structure set is deposited in PubChem then we are at the mercies of THEIR data sharing policies. I believe Peter holds up PubChem as the primary example of Open Data (but maybe not). So, I believe it should be true to say that the ChemSpider structure set IS Open Data when accessed/downloaded/shared from PubChem. But I understand that will then be the PubChem data set and all association with us will likely be lost. But that is fully acceptable!

 

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 November 28, 2007 in Uncategorized

 

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