The RSC eScience Team has always been keen to get more links to literature references and we are currently engaged in work to extract much more information from the wealth of articles that are published in our journals (keep your eyes peeled for more information on this in the future).

The RSC now encourages authors for several of our journals to supply extra information, structures and spectra in their original file formats – which are attached to the article as supplementary information. Already we’ve seen several submissions of data that we have incorporated into ChemSpider records, both enriching the ChemSpider database and also showcasing the research of these authors through their publications. In this way, the RSC hopes to encourage the addition of reusable data files to the research paper as the start of its efforts to promote increased data sharing within chemical science research.

In a few short weeks we’ve received a number of submissions from authors that include key chemical structures as mol files and in some cases extra data including 1H and 13C NMR spectra as well as UV and IR spectra.

We’ve selected a few examples that show how this data not only enriches ChemSpider but, we hope, has benefits to researchers as authors and as consumers of chemical data.

Below are 4 articles for which we received additional supplementary files – the first 2 entries are from submissions where mol files were provided, which allowed us to deposit the structures and associate the article references with the ChemSpider records. The 3rd and 4th entries are examples of submissions where spectra were also provided

10.1039/c3ob40642c  - 26 structures – 4  new to ChemSpider (eg. CSID 28945604)

10.1039/C3OB40745D  – 26 structures – 24 new to ChemSpider (eg. CSID 28941464)

10.1039/C3CC43488E - 9 structures – 7 new to ChemSpider (eg. CSID 16462787CSID 28605621 - both of which have 1H and 13C NMR spectra)

10.1039/C3CC42396D  – 5 new ChemSpider records (eg. CSID 28945607 - Has 1H 13C  NMR and also IR and Raman spectra)

 

A closer look at the data

Taking this last example, let us investigate some of the benefits of supplying these files along with the submission:

1. With the mol file that was supplied we were able to create a new ChemSpider record (CSID 28945607) and then use the DOI of the article to insert the literature reference of the source article.

Feringa-Browne_reference

2. With the spectra files that were supplied we were able to add them to the ChemSpider record as interactve components; we hope that making the spectra interactive makes them easier to use. Lets compare the PDF version of the 1H NMR spectrum with the ChemSpider version – the screenshots below are taken as they appeared on my screen (then scaled to 80% to fit in the blog post). At first glance, they seem similar but. . .

1H NMR Spectrum

1H NMR Spectrum from Supplementary Information PDF

 

Feringa-Browne spectrum in ChemSpider record

1H NMR Spectrum from CSID 28945607


In the ChemSpider record you can use your cursor to easily select an area of interest and instantly see the peaks’ fine structure.

Feringa-Browne_CS_zoom_spectrum

The authors have supplied a very high quality PDF  - so you can zoom in on the PDF to get a better view of the splitting of the peaks, but there are always limitations. In the final image (below) we can see a comparison of the peak centred at 4.23 ppm. In embedded spectrum on ChemSpider you can clearly distinguish the splitting – but looking at the same peak from the PDF we reach the limit of the resolution (this shot was taken when the pdf was scaled to 1200% in the viewer)

Feringa-Browne_Zoom_comp_spectrum

Comparison of the peak centred at 4.23 ppm in ChemSpider and the PDF

 

So by supplying their NMR data as supplementary information it has become easier to discover and use.

3. We can provide links to relevant sources and a comment that can contain extra information above any spectra or CIF files that are displayed in ChemSpider. In this way, rather than your article pointing others to useful data within it, you are using your data to showcase and point back to your article.

 

How can you get involved?

If you are already publishing in the RSC  journals ChemComm, OBC, MedChemComm and Toxicology Research - when you receive the Author Revision email it will contain details about how you can supply extra Supplementary Information. If you have already had your article published (either with the RSC or another publisher) you can email us at chemspider-at-rsc.org and we can add data for you, or alternatively you can register for a ChemSpider account and add your own data at your leisure.

If you have any questions please do leave a comment (or email us directly). We look forwards to hearing from you!

Stumble it!

8 Responses to “More research data and publications flowing into ChemSpider”

  1. Egon Willighagen says:

    Excellent initiative!

    I looked at this entry: http://www.chemspider.com/Chemical-Structure.28605621.html

    I do not see an Open Data logo, so I am wondering under what conditions the authors provide the additional experimental data. Does the “Author Revision” email explain licensing and copyright? If this applies to the manuscript itself, do author reassign copyright for this data to the RSC? Or do they provide the data under a CCZero waiver?

  2. Richard says:

    And an excellent question Egon

    For any supplementary data, the author grants the RSC a right to publish the data. There’s no copyright transfer, if copyright actually applied to the data, which in our view it doesn’t.

  3. Egon Willighagen says:

    Will you consider asking the authors to provide the data under an Open license, preferably Open Data, which people can do already in ChemSpider, and thus increasing the amount of Open Data in ChemSpider?

  4. Matt Swain says:

    I think there might be a bug in the javascript used to display the spectra on ChemSpider, which means the spectra will not display in Chrome or Safari.

    The relevant code is the function SpectrumHTML on line 108 of http://www.chemspider.com/scripts.js. It runs a browser check to supply different HTML to embed the Java applet for Internet Explorer and Firefox – for all other browsers it just prints an incorrect error message saying Java is not installed.

    A simple fix would be to change the line “if ($.browser.mozilla)” to “if ($.browser.mozilla || $.browser.webkit)” or just “else”. For reference, here is what $.browser returns in each browser for me:

    Safari: {safari: true, version: “536.30.1″, webkit: true}
    Chrome: {chrome: true, version: “27.0.1453.116″, webkit: true}
    Firefox: {mozilla:true, version:”15.0″}

    However I believe $.browser has been removed in jQuery 1.9 so long-term it might be worth finding another method to supply the IE-specific HTML.

    It also looks like there is a similar bug for CIFs.

  5. Chris says:

    In what format are the spectra stored?

  6. David says:

    Hi Chris,

    In this case the spectra are uploaded in the JCAMP format. For more details, see our help materials for users who want to upload spectra: http://www.chemspider.com/help_uploadspectra.aspx

  7. Alex Clark says:

    Following the links for all 4 articles, only the second one provides downloadable molfiles as part of the supplementary information. What happened to the rest of them?

  8. Chris says:

    As a temporary fix you can change the user agent in Safari on a Mac to enable you to view the spectra.

    http://www.macinchem.org/blog/files/17c8f865b8d3b75618e1be029dfcb858-1267.php

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