ChemSpider Blog

ChemSpider has been built primarily around chemical compounds rather than chemical reactions. However, as we move forward we ARE interested in supporting chemical reactions too, not just in figure format as is shown on the recent Open notebook Science description data from the Drexel University lab. We are not there yet..we don’t support reactions as searchable entities.

However, there are many resources out there that do already host reaction data and one of those is “Synthetic Pages“. We are presently doing the manual work necessary to deposit information about appropriate reactions. We are of course connecting it to structures represented in the reactions. An example of this is shown here nd it has the following link out to Synthetic Pages here:Synthetic Pages: Coupling of an imide with an alcohol ; Mitsunobu coupling of maleimides

I’ve blogged previously about ChemSpider users wanting to be able to identify sources of chemicals to purchase in a facile fasion. Joerg provided some excellent feedback regarding his wants. I agree with his intentions and would like to get there. We are making steps to improve the connectivity to information but are taking small steps at present. The easiest step of all was to identify substance vendors easily in the list of data sources. This is done. A substance vendor is indicated now with a Shopping Cart icon. You cannot actually shop on ChemSpider, yet. You still have to contact the vendor directly but at least it reduces the activity barrier to figure out who are the vendors.

Step 1 of many. Done.

For those of you who have been following the discussions of Stevan Harnad, Peter Suber and others regarding institutional repositories and Open Access you will already be up to speed regarding OA mandates and what they could mean in terms of access to data. Rather than go into this area in detail myself I point you specifically to Steven Harnad’s site to review ongoing discussions there (there are mutliple parties exchanging views.

What I am going to so though is point you to this comment on Peter Suber’s blog regarding “ Stanford Opens Access to All Its Education Studies“.

Specifically, the following comments are of interest “Under Stanford’s new policy, only the author’s final, peer-reviewed copy of the article would be posted online —in some cases, potentially months before the printed version becomes available….By early fall, the education school plans to have a Web site in place where the articles will be posted and archived in a searchable database. With approximately 50 scholars on Stanford’s education school faculty, the site could accumulate as many as 100 articles a year, by Mr. Willinsky’s estimate.”

Stanford is not alone in this type of shift. What does this mean for indexing of articles and availability for searching in terms of the work we are doing with ChemSpider right now (1,2,3). Text-indexing of chemistry articles would simply mean turning our spider onto the repository. Using the tools we have available now and the database of 21 million compounds and associated dictionary we could also convert the chemical names to structures and make the articles searchable by both text and structure BEFORE publication, in theory, months before. With the work that is already underway on Open Access articles on ChemSpider and SOON to be unveiled, we could also provide tools for authors to markup their own documents. My preference, as for many others, is that authors of Chemistry articles use semantic authoring tools to allow us to grab the appropriate information from the articles for linking as well as provide a path for semantic connectivity.

The question then is whether or not ChemSpider can index institutional repositories or authors self-archived collections on their university research group websites. The authors self-archived collections will be very valuable but of course most likely to upset the publishers. We’d like to do both.

I envisage a time when articles are indexed and searchable even before they are published and indexed by others. Why not? If there are changes to the article between pre-and post-publication both can be indexed.

We welcome your comments! Anyone want to introduce me to the host of an institutional repository?