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

13 February 2009 6 views 10 Comments

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. 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, which Jean-Claude has demonstrated over on the ONS Challenge Wiki. 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. 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 but now also on the web. 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, 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 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 (also see comments at the original post) 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 asked whether it would be better to use Wikipedia 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 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; 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.

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  • http://www.thesynapticleap.org/schisto/community Mat Todd

    It HAS been an interesting week. I was supposed to be writing a grant.

    Asked the question about whether we should upload to one site, or post our own and expect bots to find them, here: http://tinyurl.com/bryw7u.

    I found uploading a synthetic procedure and a spectrum to Chemspider very easy. It’s also easy to publish it myself somewhere random.

  • http://www.thesynapticleap.org/schisto/community Mat Todd

    It HAS been an interesting week. I was supposed to be writing a grant.

    Asked the question about whether we should upload to one site, or post our own and expect bots to find them, here: http://tinyurl.com/bryw7u.

    I found uploading a synthetic procedure and a spectrum to Chemspider very easy. It’s also easy to publish it myself somewhere random.

  • http://openwetware.org/wiki/User:Cameron_Neylon Cameron Neylon

    I don’t think it hurts to put it anywhere that you trust as long as the aggregation works. Is it more convenient to you to host locally on some other service? It’s all early days anyway – none of this works as well as it might so exploring the options is the way forward in my view. Ideally Chemspider/ChemBlogSpace/Others would aggregate all mentions via whatever identifiers and everything gets nicely indexed at multiple services – we’re some way away from that yet.

  • http://openwetware.org/wiki/User:Cameron_Neylon Cameron Neylon

    I don’t think it hurts to put it anywhere that you trust as long as the aggregation works. Is it more convenient to you to host locally on some other service? It’s all early days anyway – none of this works as well as it might so exploring the options is the way forward in my view. Ideally Chemspider/ChemBlogSpace/Others would aggregate all mentions via whatever identifiers and everything gets nicely indexed at multiple services – we’re some way away from that yet.

  • http://www.chemspider.com/ ChemSpiderMan

    Yes, yes, yes…we need those spectra! See: http://www.chemspider.com/blog/a-plea-to-the-community-to-help-teach-students-spectroscopy.html

    We also need help with this one…a little more of a “How well can the community come together to solve a problem? ” http://www.chemspider.com/blog/where-in-the-world-is-katie-crow-and-what-type-of-spectrum-is-she.html

  • http://www.chemspider.com ChemSpiderMan

    Yes, yes, yes…we need those spectra! See: http://www.chemspider.com/blog/a-plea-to-the-community-to-help-teach-students-spectroscopy.html

    We also need help with this one…a little more of a “How well can the community come together to solve a problem? ” http://www.chemspider.com/blog/where-in-the-world-is-katie-crow-and-what-type-of-spectrum-is-she.html

  • http://miningdrugs.blogspot.com/ Joerg Kurt Wegner

    Agreed, this was a fantastic community week.

    Great summary, thanks !

  • http://miningdrugs.blogspot.com/ Joerg Kurt Wegner

    Agreed, this was a fantastic community week.

    Great summary, thanks !

  • http://coroflot.com/jeffandries JeffJAndries

    Hi Cameron,
    Interesting blog. You might find this interesting: http://www.wikiprofessional.org. Currently the focus is life sciences but the goal is to broaden its spectrum to chemistry and other disciplines. It seeks to synthesize data-mining and community collaboration in a semantic/contextual Wiki environment. (i was involved as designer/developer)

    Jeff

  • http://coroflot.com/jeffandries JeffJAndries

    Hi Cameron,
    Interesting blog. You might find this interesting: http://www.wikiprofessional.org. Currently the focus is life sciences but the goal is to broaden its spectrum to chemistry and other disciplines. It seeks to synthesize data-mining and community collaboration in a semantic/contextual Wiki environment. (i was involved as designer/developer)

    Jeff