ChemSpider Blog

From the early days of the acquisition of ChemSpider by the RSC we have been focused on accessing the rich content that the RSC has contained in its databases and in its rich archive. We have been working hard for a number of months now to integrate systems, projects and processes into ChemSpider so that RSC chemistry is more discoverable. What we will be unveiling in the next few days we believe is big. We’ll roll it out one piece at a time. The last blog post discussed the deposition of new compounds from RSC prospected articles into ChemSpider. The email below results from the deposition of compounds from one article. One set of 10 structures from one article that are directly deposited into ChemSpider when the article goes live. These are compounds that are deposited and live immediately, not abstracted later. Imagine when we are doing this for all RSC articles, database and books….

ALL of the compounds below are NEW to the ChemSpider database…everyone of them. While not all RSC articles are only about novel compounds clearly there are new compounds moving into the database from the RSC publications.

Dear RSC Prospect,

This email is to notify that your deposition (#3427) has been published. Below please find a list of links to the structures that belong to your deposition:

http://www.chemspider.com/Chemical-Structure.23558982.html

http://www.chemspider.com/Chemical-Structure.23558983.html

http://www.chemspider.com/Chemical-Structure.23558984.html

http://www.chemspider.com/Chemical-Structure.23558985.html

http://www.chemspider.com/Chemical-Structure.23558986.html

http://www.chemspider.com/Chemical-Structure.23558987.html

http://www.chemspider.com/Chemical-Structure.23558988.html

http://www.chemspider.com/Chemical-Structure.23558989.html

http://www.chemspider.com/Chemical-Structure.23558990.html

http://www.chemspider.com/Chemical-Structure.23558991.html

Cheers,

ChemSpider

The structures link back directly to the RSC article via DOI as shown below.

We’ve taken the first step towards user being able to seamlessly bounce back and forth between finding compounds of interest using the ChemSpider search and selection tools and finding more information about them in RSC journals…

I’m pleased to announce that we’ve just switched on a deposition system which will take compounds from the prospected version of RSC articles as they are published and automatically deposit them into ChemSpider, making a link back to the original article from the new compound page. An example of a new compound is here which was generated when this article was prospected. The same deposition process is used to make links from existing ChemSpider compounds to new RSC articles, for example here was generated when this article was published.

This is basically a way to stick our toe in the water to investigate how much intervention and cleaning is necessary to deposit compounds when all the information that we have been storing for them is the InChI without any 2D layout information (which is an issue that other potential data sources may also face too).  To do this we’ve been making use of the ChemSpider webservices http://www.chemspider.com/InChI.asmx to download the mol files of InChIs already in ChemSpider, or using the InChItoMol webservice to generate new mol files where they don’t exist already.  Tracking and fixing problems as they crop up at this manageable rate will help us when we face the larger task of importing all of the compounds that have been prospected in the past into ChemSpider.