ChemSpider Blog

Previously we introduced the ability to submit chemical structures to the database using the Single Structure Deposition process. This allows users to submit single structures to the database and associate with publications, URLs, Pubmed IDs and so on. An example of the result can be seen here for Quesnoin…the structure and associated supplementary info was deposited online using the outlined process.

We have previously unveiled the ability to add publication details to existing structures on the database as outlined here. What we’ve heard is that it would be just as useful, and in the time of Web 2.0, even better to allow allow connections to other web pages by allowing URLs to be connected to existing structures on the database. The process is easy.

You need to be logged in to Add URLs, Publications etc. The only action that can be done without logging in is the Posting of Comments. The reason we do this is to help us protect from vandalism, if possible. When logged in then click on Add URL. The example below is for me wanting to form a link between the structure record of Xanax and the article on Wikipedia.

A dialog box will be displayed. Input the Title that you want displayed in the supplementary info and the URL of the associated link. See below:

Filling the information will show as follows:

Then Click OK. The submission will be sent to a curator for approval and should be approved very quickly. The reason for this process is to ensure that we don’t get adorned with “inappropriate links”. The information will show as “Supplementary info” at the bottom of the structure record as shown here.

Two particular Open Access resources providing enormous value to Life Sciences nowadays are PubMed and PubChem. I’m sure everyone reading this blog has heard of them and used them both. We previously announced our deeper collaboration with ChemRefer. We have been busily working in the background to integrate ChemRefer into ChemSpider and the very “alpha” version of the integration is now available online. It can be accessed from the Search menu as shown below. Simply click on ChemRefer

When selected it will open the ChemRefer search window and a list of Publishers who have allowed us to index them as shown below. All can be searched or the search can be limited by using the Check Boxes.

The search results for searching on taxol are shown here.The figure below, while too small to see detail, shows that the word searched is highlighted in the text.

Notice that the RSC is no longer indexed at their request. We were sad to lose them from our searches.

We have also integrated to Entrez, for searching health sciences databases at the National Center for Biotechnology Information (NCBI) website. This can be searched by choosing NCBI Entrez from the Search drop down menu. It is available here. An example of the results is shown here. For this first integration we limit the results to 100 hits.

Clicking on any of the titles is a direct hyperlink to the article in PubMed Central.

These integrations to these text searching engines are only the first part of our work. We have already been extracting chemical names and linking them up to structures in the ChemSpider database.Our first efforts in this area will be unveiled shortly. In this case it will be possible to simultaneously perform structure/substructure and text-based searches. This is a very significant undertaking but we are well underway to bringing our vision of structure and text based indexing of the Open Access literature to fruition.

Adam Azman is building an Open Data Chemical Dictionary as discussed by David Bradley over on ChemSpy. With due respect to the work done by Adam and David Bradley to date I point you to ChemSpy to review the details.

Adam is local to me and attends UNC-Chapel Hill. Recently I had the opportunity to spend some time with Adam and talk about how the ChemSpider list of identifiers could be used by Adam to expand his dictionary. We have millions of identifiers and it is likely a rich resource for Adam to build his dictionary. Our contribution has already been made to Adam and he is presently working through extracting from the file. We’re looking forward to seeing the results!

The dictionary as it presently exists can be downloaded from the ChemSpy site here.

I have written previously about the joys and frustrations of participating in the blogging community. One of my greatest joys is what I learn from others in the domain. In regards to the discussions about CAS Numbers I was very interested to read this comment from PhysChim62, a member of the Wikipedia:Chem team, regarding the European Union Database Directive.

I have extracted certain statements from that comment: “The restrictions it purports to impose of the reuse of its product would appear to breach anti-trust legislation on both sides of the Atlantic. Users of CAS databases in the European Union can take heart from Art. 8.1 of the Database Directive (96/6/EC): The maker of a database which is made available to the public in whatever manner may not prevent a lawful user of the database from extracting and/or re-utilising insubstantial parts of its contents, evaluated qualitatively and/or quantitatively, for any purposes whatsoever.”

Now I get to go off and read up on the Database Directive…while ChemSpider is trying to build a structure centric community for chemists I have to acknowledge the benefits to myself personally in terms of what I am learning from the participants in this community and specifically the people commenting on the blog. Thank you to those of you who comment!