Cameron Neylon is one of my favorite scientists advocating Open Science. He is actively contributing to the domain by not only discussing what Open Notebook Science can deliver but actually getting down to the work and showing what it can deliver. He is actively at work supporting the UsefulChem Solubility project too. In a recent exchange about spectral data Cameron suggested that we provide the ability to “embed” data in a similar way to the manner in which YouTube videos can be embedded.

So, it’s time to rollout a capability that we set up a few weeks ago as new functionality. We have had a few beta-testers work with our “embedding” capability. So, why are chemical structures on ChemSpider like YouTube videos?

Well, it’s easy to test. You need to be a registered user of ChemSpider and login to get access to this capability. It’s free to register of course. Then, search/find the compound of interest and click on Embed, situated adjacent to the structure as shown below.

An embed window will be displayed allowing the dimensions to be rescaled, an associated “link title” to be entered and the Javascript provided for embedding. The window looks like this:

If you are embedding the structure into a blog post or online document that ChemSpider can link to then enter the title of that link and we will link from the structure record on ChemSpider and back to your blogpost/article.

If you copy the Javascript code shown here:

“<script type=”text/javascript” src=”″></script>

then you will see the result shown here, a structure grabbed from ChemSpider and inserted into the page. For those of who who embed YouTube videos then you’ll see the similarity.

Stumble it!

7 Responses to “Why Are Chemical Structures Like YouTube Videos?”

  1. Cameron Neylon says:

    Cool, I’m impressed with the responsiveness of these webservices to requests. And aggregating the links with some additional metadata is a good way of adding value.

  2. When molecules go viral : business|bytes|genes|molecules says:

    [...] What happens when a compound goes viral? I am sure you’ve thought about this many times. For the 2 of you not on FriendFeed, I point you to a post by Antony Williams on the Chemspider blog where he announces embeddable chemical structures. [...]

  3. Joerg Kurt Wegner says:

    The idea is nice, two potential extensions could be to

    First, add more sematics, e.g. via an valid InChiKey HTML element, e.g. used by the chemical blogspace

    Second, this could be also used to backlink to ChemSpider, e.g. which blogs, documents, etc. link to this chemical structure? The creation button could trigger a tracing element added to a database and to link away from a structure entry. Link-out spam could be a major concern and this will require some careful control mechanism.

  4. Antony Williams says:

    Point 1 – good comment. Will add it to the list of things to do. Should the InChIKey be buried data in the image file or actually displayed?

    Point 2 – it already works that way . We are debugging that aspect at present because when other people pick up a blog post from an original blog post it just proliferates….

  5. Joerg Kurt Wegner says:

    Point 1. – Embedding in the image is an option, too, but I was more thinking about HTML microformats which could be found by getting the HTML text. Details embedded in the image alone are not helping, because who could read them and how much effort is this?

    Point 2: Interesting, looking forward to hear more ;-)

  6. Joerg Kurt Wegner says:

    One more thing, if there would be some API release allowing people to modify the widget with a pre-, main-, and post-HTML element, then people could adapt and release customized widgets and mashups on ChemSpider.

    Just look at iGoogle or Facebook, it is all about customizable widgets ;-)

  7. Science in the open » The growth of linked up data in chemistry - and good community projects says:

    [...] 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 [...]

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