We continue to receive submissions of spectral data to ChemSpider and have continued to optimize our processes to submit and display the data. When last I blogged about this we had improved the display. I’m happy to comment that we have incrementally improved it again as shown in the example here.

if you open that example and open the Spectra tab you will see the display shown below. The information available shows the type of spectrum, the associated hyperlink (if submitted by the author), any comments the submitter made (see the IR spectrum at the bottom) as well as whether the data are “Approved”. Approved means that a curator, and ay of you can provide feedback on the quality and appropriateness of the spectra (!), has approved the spectrum as being consistent with the structure.


 If you click on the green image of the spectrum then the JSpecview applet will open to show the spectrum embedded in the page as seen below.

Coincidentally there will be an article about the JSpecView applet showing up shortly in the ChemSpider Journal of Chemistry. The title will be “Color prediction with JSpecView”. Be sure to read how that applet is getting ever more capable.

Stumble it!

7 Responses to “New Display Mode for Spectra and Ongoing Addition of Data”

  1. Cameron Neylon says:

    Tony, an idle thought but is there any way of referencing the actual spectra directly from the outside world, ideally via a URL? I am thinking about the talk I’m giving Thursday to an ELN conference and Chemspider is a great example of what I want to say about data hosting services that understand the data. My question might make more sense in the context of this

  2. Antony Williams says:

    Cameron, Thanks for the feedback.

    The ChemSpiderID will take you directly to the record with the spectrum.

    If you want to know a list of spectra you can go here http://www.chemspider.com/spectra.aspx. Also, we’ve added an open Data column today to show what is open and what is not. You can order on the column by clicking on the column title.

    Are you trying to get a URL that will take you directly to a view of the Spectrum on the page of interest? Something like http://www.chemspider.com/7607/spectrum1 for example?

  3. Cameron Neylon says:

    The latter is close to what I was thinking of – what I have in mind is something like the ability to embed a YouTube video/Slideshare presentation or whatever within a blog/wiki/webpage. The idea of having the lab book point at a data service that knows what to do with an NMR spectra (i.e. Chemspider). Then, if you choose, you cut and paste a little embed code, just like you can grab from youtube, perhaps with some options, that you can cut and paste into the web page. The lab notebook doesn’t need to understand anything about how to handle an NMR spectrum because ChemSpider does the lifting for that – or rather points at JSpecView to do it.

    I guess it is part of the wider question of – if I want to point at a specific spectrum – rather than the a specific structure – can I do that. I wouldn’t suggest it as a high priority. Just that I can see the use of a dedicated data repository services that understand specific data types and ChemSpider is closest in the chemistry space to what I am thinking at the moment.



  4. Antony Williams says:

    Cameron…one more question before I provide you with some information and details that I think will excite you….

    There are two forms of data on ChemSpider…Closed Data or Open Data. I think you likely saw all the discussions on this previously when we set up spectral deposition and were accused of taking copyright?

    It was this discussion:
    PMR> Chemspider also encourages Uploading Spectra Onto ChemSpider. These spectra by default all belong to Chemspider. They are not Open. If you can convince the world at large to donate IPR to you for free, you deserve some form of congratulations for sheer bravado. Note that even if you upload data and metadata you are not allowed to download it (there is a limit of 100 structures).

    AJW>Thanks, again, for the judgments. We have been testing out the system with two of our advisory group and myself. Only JC Bradley’s Lab and Bob Lancashire have deposited and with the understanding, I believe, that the data would be “Open”. Since PMR’s blog posts continue to do damage to our reputation we have no choice but to respond. We do this with coding. Within 24 hours of his comments Open Data was declared, spectra can be downloaded. The intention was always there to do this…just we have higher priorities.

    See here for the continued dialog.: http://www.chemspider.com/blog/who-gets-to-choose-whether-data-is-open-or-not.html

    My question…should we allow embed for Open Data only or Closed Data too? My preference is both but I believe that users have declared their data CLOSED by default means we should exclude CLOSED when allowing EMBEDing

  5. Cameron Neylon says:

    Antony – that’s a really tough one. One can make the argument of course that data is data and therefore not subject to any form of legal protection anyway. Thus if it is exposed it is in the public domain, end of story. However the consequences of that may not be helpful in terms of getting people involved in submitting data. And at bottom may just create more grief.

    There is also the argument over whether an embed is really moving the data off of Chemspider anyway. But again it will _look_ as though it has been. The reality may be otherwise but the impression given is that it has moved.

    So on balance I think the playing nice probably wins over the legalistic or technical position and I agree if the data has been declared closed then it shouldn’t be able to be embedded. In the end this may be positive when people start asking about why they can’t embed some particular piece of data – or why they can’t embed their own data then you have an answer. “Due to the potential of negative perceptions we don’t provide the technical ability to embed data where the uploader has no explicitly declared they want to see the data re-used by third parties i.e. open data declared”. It may well encourage more people to declare their data open.

  6. When molecules go viral : business|bytes|genes|molecules says:

    [...] up on an idea from Cameron Neylon (As per the comments before, Chemspider has had this in the works for a while, but the discussion [...]

  7. ChemSpider Blog » Blog Archive » Why are Spectra Like YouTube Videos? says:

    [...] just showing images but real live spectra in the JSpecView Java Applet so Java must be installed. Thanks to Cameron Neylon for asking the question about whether we could provide the service. Glad to [...]

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