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ChemGate, eMolecules and Discussions About Copyright

09 Sep

Peter Murray-Rust has initiated a very LIVELY conversation about Wiley’s Chemgate rollout in collaboration with eMolecules. He has expressed his views of receiving spam about ChemGate (link) and I won’t comment about that…some of the commenters about the post did that.

In that blog Peter posed an interesting question – “Now, Wiley publish a lot of chemistry. And they accompany this with supplemental info – data which they copyright. Do you think if I ask them nicely they will let me aggregate this non-copyrightable data in the same way as we have done for CrystalEye? Please, Wiley, let me know. And if you say yes, I’ll forget about the spamming as an oversight.”

This is a very interesting opening for a discussion that has concerned me for a while. Specifically, many companies are aggregators of published data which is then commercialized. Most groups who build databases extract from the literature – whether these are databases of PhysChem properties, assigned NMR shifts, toxicology data etc these are commonly extracted from the literature. This has been going on for decades. if the data are copyrighted within the article then is this permissible? The data on NMRShiftDB may exist within articles and be online…permissible? The data on QSAR World are from the literature..permissible? If there are copyright issues with extracting single measured data points (e.g solubility, pKa, logP values) from the literature or even NMR assignments then the number of potential lawsuits is enormous. I don’t believe it’s possible.

What would happen now if someone chose to post a structure and a “value” extracted from a paper to the submission system on ChemSpider? Illegal?

Peter then posted a little more asking a direct question about copyrighting. He commented:

“This is an offer to Wiley (or eMolecules) to explain why they feel they are legally and morally allowed to copyright data and resell it. This blog is developing a tradition of offering publishers a chance to put their view in a highly public forum, so I would be grateful of a reply. ”

also “I realise that not all entries in ChemGate come from Wiley journals – some are private contributions, and presumably some are abstracted from competitor journals. But I would be amazed if there were not entries corresponding to Wiley journals.”

I am not aware of the details regarding the spectral collections on ChemGate in terms of copyright so I did a search online and found that the original ChemGate was probably served up by Specinfo technologies and listed the databases on there under their own branding. I believe this is a revenue sharing model with the generators of the data – there is lots of detail online regarding the providers of the data so I won’t bore you with it – however, I don’t believe any of it is extracted from Wiley publications which is what I believe Peter is pointing to. Is there any evidence that any of the data are extracted from Wiley publications? MORE comments below after the list..

NMR Collection
Wiley H NMR Organic Compounds Volume 1
Wiley H NMR Organic Compounds Volume 2
Wiley H NMR Organic Compounds Volume 3
Wiley C13 NMR Organics Volume 1
Wiley C13 NMR Organics Volume 2
Wiley C13 NMR Organics Volume 3
Wiley C13 NMR Flavors and Fragrances
Wiley C13 NMR Natural Products
Wiley 19F NMR
Wiley 31P NMR
Wiley 29Si NMR

MS Collection
Wiley MS Organic Compounds 1st Edition
Wiley MS Chemical Concepts Collection
Wiley MS Volatile Organic Compounds in Food
Wiley MS Geochemicals, Petrochemicals
Wiley MS Drugs, Pharmaceuticals, and their Metabolites
Wiley MS Steroids, 2nd Edition

IR Collection
Wiley IR Industrial Chemicals
Wiley Near Infrared
Wiley IR Hummel Industrial Polymers Volume 1
Wiley IR Hummel Industrial Polymers Volume 2
Wiley IR Hummel Industrial Polymers Volume 3
Wiley IR Hummel Surfactants

I believe that Wolfgang Robien’s spectral collection has likely been added to the list above (but it might actually already be a subset of the Wiley collection and licensed from Robien directly. Peter has already commented recently about NMR data and predictions directly in relation to NMRShiftDB discussions. This discussion is different since I believe this is about a spectral curve collection OR spectra reconstructed from assigned data.

My best judgment is that the data on ChemGate are likely all appropriately copyrighted. Why do I say this? If you visit ChemGate online at http://chemgate.emolecules.com/ you will see the list of NMR nuclei is : 1H, 13C, 11B, 15N, 17O, 19F , 29Si, 31P. if you visit the Modgraph site then you will see the following statement:

“The main NMRPredict program is supplied with 131,569 C13 records abstracted from the literature by Professor Robien and co-workers at the University of Vienna over the past 25 years. Three optional additional database available are:

* 131,414 C13 records from the SpecInfo collection licenced from Wiley
* 82,325 C13 records from Professor Robien and Wiley
* 79,324 X-nuclei data including (combined Robien-Wiley collection):
o 31,082 – 19F records
o 23,820 – 31P records
o 9,882 – 11B records
o 6,407 – 15N records
o 5,002 – 17O records
o 3,131 – 29Si records”

If you compare the nuclei in the list above, and the list on ChemGate, as well as look at the bolded statements, then I judge that ChemGate is serving up the Wiley copyrighted collections (licensed or purchased from their collaborators) rather than serving up any copyrighted data from their articles. So, I think Peter can relax about that.

However, based on the comments made on ModGraph’s site and bolded above there may be an issue about copyrights. “In the next few years a dramatic expansion of the databases behind NMRPredict can be expected. The journals selected will cover mainly heterocyclic and medicial chemistry in order to give reliable predictions for candidates for drug discovery (Lipinski’s “Rule of Five”). ” It is unlikely that assigned spectra will be extracted only from Wiley publications despite their special relationship 🙂 .

I DO NOT believe that there is an issue with extracting assigned spectral data and associated structures from any publications. If there is an issue with this I am very interested in having a publisher declaring that here since I know there are parties reading this blog that do exactly that for their business!

I will be contacting Wiley this week with the request to index the structures and links back to ChemGate here on ChemSpider. Having been involved with creating spectral databases over the years I believe that the pricing for access to over 700,000 spectra is actually very good. Academic prices are likely lower than those listed online.

Question for all… we are presently accepting both spectra and, shortly, structures and associated data onto ChemSpider. Question for the readers – what is the preferred Creative Commons license you would like to see attributed to the user uploaded data?

Peter commented on his post “I had offered eMolecules 250 000 MOPAC calculations as Open Data.” Peter, we’d welcome the opportunity to host your data for everyone.

 

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 September 9, 2007 in Uncategorized

 

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