Indexing Molecules in Second Life

As I've recently commented, there has been media interest in the use of the virtual online world Second Life for chemistry. We also recently demonstrated on Drexel Island that it was possible to visualize molecular docking using the molecular rezzer developed by Andrew Lang.

Nature Island also hosts several common molecules, including buckyballs. As more people start to experiment with representing chemicals and chemistry research in Second Life it would be nice if such examples were discovered by a simple Google search.

All that really needs to be done to accomplish this is to co-locate molecular descriptors with corresponding SLURLs (Second Life URLs) on the same web page. When clicked, the SLURL will automatically start Second Life and teleport the user to the location where the molecule can be found. If the user does not have Second Life, a page pops up explaining how to set up a free account and download the software. This could be a good way to introduce the mainstream chemical community to new modalities of communicating science.

As for descriptors, I am suggesting that we use InChIs and common names at the very least. Google does a fairly good job of finding molecules by InChI.

I created a wiki,
http://secondlifemolecules.wikispaces.com/
and seeded it with a molecule from our malaria research that I've used in several places and with caffeine, which is displayed on Nature Island. I invite anyone to contribute to the wiki and add information that could be useful. (The indexing on Google can take a few days for a new wiki)

There are several other ways of creating this index and I think the more redundancy the better. For example, we could make Second Life a "supplier" on ChemSpider. It might also be possible for Andrew's molecule rezzer to note the location of a molecule when it gets created in Second Life and automatically send off an email to a Blogger account to create a post.



Chemical Blogspace Tags

InChI=1/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
caffeine

InChIMatic, ChemSpider and UsefulChem

Rich Apodaca wrote about using his InChIMatic service to track molecules in UsefulChem.

Because we use InChIs in blog posts and HTML pages generated automatically from the molecules blog, doing an InChI search in Google is a pretty good way to find molecules of interest to UsefulChem. However, Rich makes the valid point that these pages do not always point to the experiments where they are used.

I was aware of the limitations of using a blog to track molecules when I set it up. Because we were limiting ourselves to a few hundred molecules, the blog served its purpose much as I expected it would.

But now, as we move to the manipulation of tens of thousands (and soon to millions) of molecules, we need to transition to a true database.

I've been working with Tony Williams to use ChemSpider for this purpose. UsefulChem has been a supplier in ChemSpider for several weeks and most of our molecules from the molecules blog have been indexed. In the next few days the first 68,000 molecules from the CombiUgi project should be incorporated as well.

This effectively moves the indexing and searching burden to a free hosted service that is designed to handle it. This is the same logic that I used when choosing Wikispaces to act as our group laboratory notebook.

Lets take a look at an example of how this can work.

Click on the Search button of ChemSpider then hit "Advanced". Under "Search by Data Source" select UsefulChem. Scroll to the top of the page and select "Search by Structure" then "Draw". Select "Substructure" then draw a furan ring

You should get about 10 hits.


Click on the 5-methylfurfurylamine to see its record in ChemSpider.


This record can be curated or annotated. I'm hoping we can use this interface to annotate with links to spectra, references, etc. But for now just click on its InChI and you'll get a Google search finding that molecule on UsefulChem blogs, Chemical Blogspace and an experiment page (EXP086) where its was used.

In order for that to work well, we need the InChIs to be generated for every molecule in every experiment. We've been putting the InChIs in the Tags section of each experiment page and it is now on the highest priority of our Experimental Format page to make sure that it gets done quickly.

Note that these InChI's could be scraped fairly easily from every UsefulChem experiment because of the standard format for specifying the experiment page.

The only issue left to really complete the process is an automated way to add new molecules to ChemSpider. Tony says that will be done soon.

Chemical Blogspace Tags

InChI=1/C6H9NO/c1-5-2-3-6(4-7)8-5/h2-3H,4,7H2,1H3
5-methylfurfurylamine