I have reported previously on the possibility to upload and display spectra on ChemSpider. JSpecView is our tool of choice for spectral display and the workflow is described here. I’m happy to announce that people have been uploading spectra and we have over a hundred online at present.

I am happy to announce that we have the first deposition of analytical data onto ChemSpider from a publisher. Bronwen Decker of the Nature Publishing Group (NPG) has facilitated the deposition of data onto the system. A paper entitled”Use of Raman spectroscopy as a tool for in situ monitoring of microwave-promoted reactions” has had two accompanying NMR spectra submitted online (and hooked back to the original article using the DOI number).

The_record here shows the structure, connected data sources, the spectra and supplementary information accompanying the structure (part of the new deposition process). We’re looking forward to working with NPG to facilitate the process of deposition of more analytical data as we move forward.

Stumble it!

6 Responses to “A Growing Collaboration with Publishers – Nature Initiates Deposition of Spectral Data Onto ChemSpider”

  1. Egon Willighagen says:

    Sounds like a breakthrough, assuming the data will be open etc. Does this also mean that you may link the molecules in that paper with the article? I’m really happy to see you make progress.

  2. Antony Williams says:

    Egon…good question…check out http://www.chemspider.com/Chemical-Structure.69959.html and scroll down to Supplementary Information just above the spectra and you will see the paper linked from there.

    Clearly this is just the beginning and we have more design work to do etc but this does send the message of what could be feasible as we move forward.

  3. Joerg Kurt Wegner says:

    Great news, and as said, I think open standards are the key, open access is nice to have, but not a must.

  4. Egon Willighagen says:

    Mmm… a shame that the paper webpage does not list the Chemspider entry as Supp Info or so in the ‘Article Tools’ section… nothing we can’t do with a nice userscript, of course (see the Userscript in Life Sciences paper in BMC Bioinformatics)… Antony, something to think about. Except for the script it only requires a page on ChemSpider that allows checking if CS has extra information on the chemistry behind a DOI. The idea is very like the ‘Comments from Blogspace” for DOIs… Though, ideally, Nature would add that entry to their default ‘Article Tools’ menu….

  5. Egon Willighagen says:

    While browsing the entry in ChemSpider, I felt the urge to look at the other entries related to this DOI, but found this not yet to be possible… please consider this a feature request: a link in the entry page to find all molecules associated with that DOI.

  6. Antony Williams says:

    If I am interpreting your request correctly you are requesting that other structures contained within the paper can be available as nested links inside the ChemSpider record? If so, it’s a good request. What this require though is that the relationship between these is formed through some submission process. If InChIs were scattered across the paper (DOI) then we could form this relationship on the fly. However, this example required the submission of the analytical data associated with a single structure. We would need to have a batch submission for all structures from the paper (already being tested!) and somebody would need to manually perform the batch submission OR we would need to grab the structures through some scraping process (via InChIs again).

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