BAZOO

So much to do, so little time

Trying to squeeze sense out of chemical data

Ubiquity and chemical information

with 4 comments

Ubiqiuity is a new command interface to Firefox that is quite similar to QuickSilver or Launchy.

Essentially, it presents something akin to a natural language interface using a wide variety of “commands”. The magic is in these commands. As shown in the video on the Mozilla Labs homepage, it allows you select text on a web page and search various websites, query Google Maps, translate, perform a calculation and so on.

The key to all this functionality is the use of a variety of web accessible services such as the API’s provided by Google and Amazon. As a result, the interface makes all these distributed services ubiquitious in the sense that they are always available where ever you maybe on the web – no need to open another window or visit another site. In a sense one could replicate the functionality of Greasemonkey using this. Indeed, many things that might have required a full blown plugin can be done at a much lower cost using this interface.

Of course there are caveats – it’s a prototype, so whether it’ll last is not clear. Also, since commands are basically Javascript functions, it’s pretty much wide open to malicious code.

OK, enough of background (for more details take a look at the Wiki). How does it help chemists and cheminformatics? At this point I’m not going to go into details about how one implements Ubiquity commands. Rather I’ll describe some that I quickly whipped up. These are available here

If you’re browsing a web page and come across a SMILES, it’s easy to get a quick depiction using the “depict” command. So, bring up Ubiquity and then type something like “c1ccccc1″ (or select a SMILES on a webpage). You’ll see image in the preview panel. But it goes one step further. If you’re in an online Rich Text box (such as when you compose a mail in GMail), the image gets inserted.

Alternatively, lets say you’re browsing and come across a compound called “phenobarbitol”. What’s the SMILES for this? What does the molecule look like in 2D? Bring up Ubiquity and simply type the compound name and look at the results. Alternatively just select the text and then bring up Ubiquity – no need to type anything.

Another useful command is one that converts a SMILES string to an InChI or InChI key or SDF formatted string. It’s a little restricted because most people don’t always directly write a SMILES string, but with a little work it could be useful when writing blog posts and very easily include an InChI at the end to allow easy indexing, extraction and so on.

The final example, is the “toxic” command – select a piece of text (or type it at the prompt) and bring up Ubiquity and get an estimation of whether it’s going to be toxic or not.

Granted these are very simplistic commands (and the “toxic” command is not too accurate either). But they were very quick to write, since I didn’t have to bother about interfaces, packaging and so on. Another reason why presenting these features was so easy was that they make use of cheminformatics web services hosted at Indiana University. So we get depictions by calling a web service and perform name to structure conversion using a web service interface to a local mirror of PubChem.

For me at least, Ubiquity presents a really low barrier to entry for writing mashups.

Written by Rajarshi Guha

August 30th, 2008 at 3:05 am

Posted in software

4 Responses to 'Ubiquity and chemical information'

Subscribe to comments with RSS or TrackBack to 'Ubiquity and chemical information'.

  1. Egon is currently showing me how it works – very nice :)

  2. Great – it looks like an excellent way to insert chemical information into online pages and documents

    Rajarshi Guha

    31 Aug 08 at 9:48 pm

  3. Great work. It’s really awesome to see how Ubiquity is being used in education. :)

    abi

    13 Sep 08 at 12:45 pm

  4. Thanks

    Rajarshi Guha

    13 Sep 08 at 1:19 pm

Leave a Reply