Cameron Neylon

It's been an interesting week or so in the Chemistry online world.
Following on from my [musings about data
services](http://blog.openwetware.org/scienceintheopen/2009/01/27/the-integrated-lab-record-or-the-web-native-lab-notebook/)
and the preparation I was doing for a talk the week before last I asked
[Tony Williams](http://www.chemspider.com/blog/) whether it was possible
to embed spectra from [ChemSpider](http://chemspider.com) on a generic
web page in the same way that you would embed a
[YouTube](http://youtube.com) video, [Flickr](http://flickr.com)
picture, or [Slideshare](http://slideshare.net) presentation. The idea
is that if there are services out on the cloud that make it *easier* to
put some rich material in your own online presence by hosting it
somewhere that understands about your data type, then we have a chance
of pulling all of these disparate online presences together.

Tony went on to release two features, one that enables you to [embed a
molecule](http://www.chemspider.com/blog/why-are-chemical-structures-like-youtube-videos.html),
which [Jean-Claude has
demonstrated](http://onschallenge.wikispaces.com/Exp056) over on the
[ONS Challenge Wiki](http://onschallenge.wikispaces.com/). Essentially
by cutting and pasting a little bit of text from ChemSpider into
Wikispaces you get a nicely drawn image of the molecule, and the
machinery is in place to enable good machine readability of the
displayed page (by embedding chemical identifiers within the code) as
well as enabling the aggregation of web based information about the
molecule back at Chemspider.

The second feature was the one I had asked about, [the embedding of
spectra](http://www.chemspider.com/blog/why-are-spectra-like-youtube-videos.html).
Again this is really useful because it means that as an experimentalist
you can host spectra on a service that gets what they are, but you can
*also* incorporate them in a nice way back into your lab book, online
report, or whatever it is you are doing. This has already enabled Andy
Lang and Jean-Claude to build a very cool game, [initially in Second
Life](http://usefulchem.blogspot.com/2009/02/nmr-game-on-second-life.html)
but now also [on the web](http://lxsrv7.oru.edu/~alang/about.php). Using
the spectral and chemical information from Chemspider the player is
presented with the spectrum and three molecules; if they select the
correct molecule they get some points, if they get it wrong they lose
some. As Tony has [pointed
out](http://www.chemspider.com/blog/a-plea-to-the-community-to-help-teach-students-spectroscopy.html),
this is also a way of crowdsourcing the curation process -- if the
majority of people disagree with the "correct" assignment then maybe the
spectrum needs a second look. Chemistry Captchas anyone?

The other even this week has been the [efforts by Mitch over at the
Chemistry
Blog](http://www.chemistry-blog.com/2009/02/10/want-to-author-a-book-with-me/)
to set up an online resource for named reactions by crowdsourcing
contributions and ultimately turning it into a book. Mitch deserves
plaudits for this because he's gone on and *done* something rather than
just talked about it and we need more people like that. Some of us have
[criticised the
details](http://friendfeed.com/e/bf6a718c-08ff-4ad6-ba53-fa9f081a8078/Chemistry-Blog-Blog-Archive-Want-to-author-a-book/)
(also see [comments at the original
post](http://www.chemistry-blog.com/2009/02/10/want-to-author-a-book-with-me/))
of how he is going about it but from my perspective this is definitely
criticism motivated by the hope that he will succeed and that by making
some changes early on, there is the chance to get much more out of the
contributions that he gets.

In particular [Egon](http://chem-bla-ics.blogspot.com/) asked whether it
would be better to use
[Wikipedia](http://en.wikipedia.org/wiki/Main_Page) as the platform for
aggregating the named reaction; a point which I agree with. The problem
that people see with Wikipedia is largely that of image. People are
concerned about inaccurate editing, about the sometimes combative
approach of senior editors that are not necessarily expert in the are.
Part of the answer is to just get in there and do it -- particularly in
chemistry there are a range of people working hard to try and get stuff
cleaned up. Lots of work has gone into the Chemical boxes and named
reactions would be an obvious thing to move on to. Nonetheless it may
not work for some people and to a certain extent as long as the material
that is generated can be aggregated back to Wikipedia I'm not really
fussed.

The bigger concern for us "chemoinformatics jocks" (I can't help but
feel that categorising me as a foo-informatics anything is a little off
beam but never mind (-;) was the [example
pages](http://name.howtochem.com/) Mitch put up where there was very
little linking back of data to other resources. So there was no way, for
instance, to know that this page was even about a specific class of
chemicals. The schemes were shown as plain images, making it very hard
for any information aggregation service to do anything useful.
Essentially the pages didn't make full use of the power of the web to
*connect* information.

Mitch in turn has taken the criticism offered in a positive fashion and
has [thrown down the
gauntlet](http://www.chemistry-blog.com/2009/02/12/open-thread-chemistry-collaborations-round-2/);
effectively asking the question, "well if you want this marked up, where
are the tools to make it easy, and the instructions in plain English to
show how to do it?". He also asks, if named reactions aren't the best
place to start, then what would be a good collaborative project. Fair
questions, and I would hope the Chemspider services start to point in
the right direction. Instead of drawing an image of a molecule and
pasting it on a web page, use the service and connect to the molecule
itself, this connects the data up, and gives you a nice picture for
free. It's not perfect. The ideal situation would be a little chemical
drawing palette. You draw the molecule you want, it goes to the data
service of choice, finds the correct molecule (meaning the user doesn't
need to know what SMILES, InChis or whatever are), and then brings back
whatever you want; image, data, vendors, price. This would be a really
powerful demonstration of the power of linked data and it probably could
be pulled together from existing services.

But what about the second question? What would be a good project? Well
this is where that second Chemspider functionality comes in. What about
flooding Chemspider with high quality, electronic copies, of NMR
spectra. Not the molecules that your supervisor will kill you for
releasing, but all those molecules you've published, all those hiding in
undergraduate chemistry practicals. Grab the electronic files, lets find
a way of converting them all to JCamp online, and get 'em up on
Chemspider as Open Data.


It’s been an interesting week or so in the Chemistry online world. Following on from my musings about data services and the preparation I was doing for a talk the week before last I asked Tony Williams whether it was possible to embed spectra from ChemSpider on a generic web page in the same way that you would embed a YouTube video, Flickr picture, or Slideshare presentation.

Rogue Scholar Posts

The growth of linked up data in chemistry – and good community projects