Those of you who have been reading the blog will likely recall my views the Open Notebook NMR project. I have been trying to establish whether or not the time-consuming and computationally intensive GIAO calculations associated with Open Notebook NMR provide better performance than standard out-of-the-box PC-based desktop computer calculations taking just a few seconds. We didn’t get to examine that hypothesis out of that work but I have been working on that study with a couple of my ex-colleagues at ACD/Labs and hope to report on it in the future. A paper was released this week by Rzepa and Braddock in J Nat Prod. regarding the “Structural Reassignment of Obtusallenes V, VI, and VII by GIAO-Based Density Functional Prediction” doi:10.1021/np0705918

I want to comment on the new feature of Associating a Publication with a structure, in this case associating the J Nat Prod paper with this structure. In this case the structure of Obtusallene V is in the ChemSpider database.


I added the appropriate identifiers using the usual process and then added the publication. To do this simply select “Add Publication” and the following screen will be displayed.


About 60 seconds of work and I had added the article title, authors, DOI and a short decsription regarding the paper. When I submitted it the publication went to the curator for approval, in this case me. When approved then the article is associated with, and linked via DOI, to the structure.


As articles are associated in this way the literature, both open and closed, becomes structure and substructure searchable extending the reach of ChemSpider even further.

I then deposited the CORRECT structure of Obtusallene V as identified by Rzepa and Braddock. The structure is here and scrolling down shows you the annotation regarding it being the correct structure. I removed the name Obtusallene V from the old structure so that now the search on that name takes you to the new and correct structure. This URL is that query: 

This blog post is a perfect example of what we have been promising since the beginning: structure deposition, curation and cleaning up the quality of data.

Stumble it!

3 Responses to “Adding Publication Details to Chemical Structures on ChemSpider”

  1. David Bradley says:

    That’s a stupendous structure, with those three unconnected oxygens in a ring-arrangement.

    Meanwhile, I guess you have to remember that 60 seconds here, 60 seconds there all mounts up. I suspect there’s no way to automate the process, I guess that’s the whole point that there isn’t…


  2. Antony Williams says:

    David…you are correct that a couple of minutes to every structure would be time-consuming…but that’s the nature of Wikipedia contributions of course.

    Now, is there a way to automate the process. Sure, we could scrape abstracts and titles and even figure out how to link up structures to names in an automated process but the quality would be the issue. How to confirm that the structure-publication association is correct. I think that manual association will certainly offer higher quality. Now, if publishers were allowing InChIs to be embedded then this would be much easier. We could, in theory, deal with RSS feeds with InChIs included and connect those up. What do you think re. copyright? If something is being RSS fed with structures and article titles and partial abstracts is it acceptable to link up to ChemSpider? I think the answer should be yes but….

  3. will says:

    Structures are facts and can’t be copyrighted, regardless of whether the organisation providing the feed thinks that they can be. This, of course, probably does not apply to:
    - images of structures (i.e. creative works)
    - the contents of the file containing the structure e.g. SDF, CIF etc. (i.e. the expression of data)

Leave a Reply