In his ongoing comments regarding our efforts here at ChemSpider Peter Murray-Rust has provided “interesting feedback”. This is one of MANY commentaries (1,2,3,….). Despite repeated requests to direct his comments directly to us/me, and suggestions to use the feedback form or participate on our blogs he prefers to comment on his blog.

For those of you who read our blogs and watch our service I hope that you see we are responsive to requests and feedback. I have chosen to take all comments, however directed, as opportunities for improvement so, in less than 24 hours, and because of the commitment of our development team to help preserve our reputation, here’s what we have done…

We looked at the CrystalEye system as a model of Open Data. CrystalEye is hosted by Peter’s Lab. We took this as an appropriate model and now when a user submits spectral data to ChemSpider they have a CHOICE to make the data Open or not. Their choice, not ours. This is a simple checkbox as shown below.

Open Data Spectra
The Open Data policies are those listed here. When a user allows us to host their data as Open Data then we allow others to download it and use it. When a spectrum is submitted as Open Data then those data can be downloadable. Simply click on the DOWNLOAD SPECTRUM button as shown in the image below (an example spectrum here) and you can download the JCAMP spectrum to your desktop.

Download Spectrum

Welcome to the world of Open Data on ChemSpider.

Stumble it!

13 Responses to “Spectral Data Can Now Be Declared Open Data”

  1. baoilleach says:

    Why is the default Closed? Why even offer the option of Closed?

  2. Antony Williams says:

    Why not offer the option of Closed? That is the submitters decision. When a user logs on to ChemSpider they end up with “My ChemSpider”. They can deposit data onto the system including structures, text and analytical data. We are presently working on data tags allowing people to keep their data private, have it within a group environment but not publicly viewable, have it public and not open and have it public and open. These are all valid. it’s not our role to force Openness of data onto users. We are working to create an environment that provides value to ChemSpider users rather than one that forces them into a policy regarding openness. Personally, I would prefer to have access to data to help answer a question, even if they are NOT Open Data, than to not have access to those data.

  3. Antony Williams says:

    I have asked all of the people who have submitted data or had me submit data to ChemSpider whether they would like to have their data moved to open. 2 said yes (Bob Lancashire and JC Bradley) and two said no (Gary Martin and Scott van Bramer). I do NOT intend to force people to adhere to making their data Open. That is their choice, not mine. We are creating a community for collaboration. There is value in having access to data whether it is Open or not. if you look at the recent conversations about RSC and their Free Access versus Open Access we must agree that there IS value to Free Access to there articles despite the fact that they are not Open Access.

  4. Gary Martin says:

    Regarding the open/closed question on deposited data. Interesting question. For 1D spectra the question is less of an issue than when you start thinking about 2D NMR spectra and what can be done with them. Consider the following. With the advent of unsymmetrical indirect covariance processing methods, one can take 2D NMR spectra and calculate other 2D spectra from them. In principle, someone could download an assortment of spectra for a given molecule, calculate some other spectra, and then write a paper without ever recording a single NMR spectrum of their own. Would they then include the individual who deposited the spectra as a co-author or even acknowledge the source of the spectra that they used? Who knows. The possibility of this happening, however, is real, and from my perspective I would chose not to make any 2D spectra that I ever deposit as open and feely downloadable. There to be compared by scientists interested in dereplication, sure. Free to use in the manner that I’ve suggested that is now possible, sorry, not with my data. If someone wants a spectrum in digital form, they can always request the data by e-mail from whoever deposited the data.

  5. baoilleach says:

    There will always be people who don’t acknowledge the source of their data; but I don’t understand what science or you gain by restricting the data in this way. Sometimes, if you love your data, you have to set it free. That way more people will be able to use it, and on average, the more citations you will get.

    By the way, I didn’t know that about unsymmetrical indirect covariance processing methods. It seems that this would be a very useful service to provide calculated 2D NMR spectra for a variety of compounds. Maybe something ChemSpider could do…

  6. Antony Williams says:

    In regards to your comment “I don’t understand what science or you gain by restricting the data” I am assuming that the “you” means us, ChemSpider. Again, it is NOT my choice to make other people’s data Open. We are providing a service to people and I will not take on the role of telling people that they can only deposit data that will be Open. I encourage you or others to take on this role and I judge that Peter Murray Rust is about to do that with the SPECTRa project based on discussions on his blog. I support the project and, if all of the data on that project is Open then there is no reason that the Open Data on ChemSpider and the data on his site cannot be mashed up, merged, exchanged or whatever for the good of the community. But, I have no rights to give away Free Access data

  7. baoilleach says:

    (Sorry, to clarify, by “you” I was referring to Gary)

  8. Gary Martin says:

    After generating data for 250+ publications, chapters, reviews, etc., I guess you could say I have little sympathy for those who tend to borrow other’s data without bothering to acknowledge the source. IMO, that ranks right down there with plagiarism. But then again, I also take a rather dim view of those who don’t bother to cite lead or seminal references or those from a competing lab in a given field, I suppose to make their own contribution appear to be somewhat more prestigious? Irrespective of that, as it’s my choice on open/closed WRT MY data (the operative word here!) someone can e-mail me and request it if they want it in digital form assuming that Tony and the ChemSpider crew provide a mechanism for the eventual deposition of 2D spectra.

    As far as unsymmetrical indirect covariance processing, the capabilities are still being explored by us and have been the subject of a string of papers this year in Magn. Reson. Chem. You can, for example, take an HSQC and COSY spectrum and coprocess them together to derive an HSQC-COSY spectrum analogous to the low sensitivity HSQC-TOCSY spectrum in much less time and with much higher overall sensitivity (see for exmaple, J. Het. Chem., 44, 163-166 (2006) or J. Nat. Prod, 70, 1393-1396 (2007)).

  9. Egon Willighagen says:

    Gary, I strongly disagree with your argument of people not citing the data source to support keeping your data closed. There always be unethical scientists; that quite orthogonal to the concept of Open or Proprietary data. This basically is plagiarism, and if you detect that, bring it up with the journal editor and get justice.

    Also, Open data *is* Copyrighted, and there are many licenses which allow you to *require* to be cited, such as the CC-BY license [1]. If the ‘forget’ to cite you then, the are breeching license and copyright, and you have every right to take it to court if you like.

    I understand your concern, but it is absolutely *no* reason to not make your data Open.


  10. Gary Martin says:

    Egon, you’re more than welcome to disagree with me…. vehemently even, if you wish.

    You said,

    “This bascally is plagiarism, and if you detect that, bring it up with the journal editor and get justice.”

    You also said,

    “If they ‘forget’ to cite you then they are breeching license and copyright and you have every right to take it to court if you like.”

    First, I have neither the time nor the inclination to ‘police’ the literature monitoring the behavior of the unethical types who would be inclined to “borrow” data without bothering to cite the source. Second, why in the world would I want to take on the burden of having to seek justice with editors when I can pre-empt the use my data illicitly by clicking the closed box. As I said, if someone wants it, THEY can go to the trouble of e-mailing me to get it. That might even spawn a collaborative interaction! If that’s too much work, I guess they really didn’t need it or want the data all that badly. Third, why should I go to the trouble and expense to try to take someone to court when they may well and probably would be in some other country and could thumb their nose at the illegality of their behavior.

    There are three reasons why I’m not going to change my position on the open/closed posting of my data, Egon. As I said, feel completely free to disagree with me but I’m not about to change my position. In my not so spare time I’m also a professional photographer and I’ve had to deal several times with imbeciles who think they can download and use someone else’s work without permission or credit. Photographs are a whole lot easier to recognize than data files. In one instance, a friend in Australia spotted the illicit use of one of my images and brought it to my attention. In that case the guilty party complained that I was being unduly harsh when I sent a letter to her webhosting service demanding that she remove my copyrighted material from her commercial website. Personally, I’m going to preclude the problem of inappropriate usage insofar as my data is concerned by opting for the closed check box. If that means that I have a closed mind on the open data issue, so be it.

  11. baoilleach says:

    Just to mention a point which hasn’t already been stated…not to be morbid, but my data remains closed after I die, leaving my life’s work in the hands of my estate. I think that most scientists would not attempt to get permission to use it after this.

    On the flip side, at least uploading the data to a third-party means that (while I’m alive at least) I won’t be able to mislay the data. I’ve asked for data from papers from several years ago, and while the authors were, in principle, happy to give it to me, they weren’t able to find it. I wonder though whether this should be the role of the journal and supporting information, rather than a third-party site.

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