Posted by: woodforthetrees | March 16, 2010

Taming biology databases using widgets

Interrogating a biological database can be a bewildering and frustrating experience. There are so many of them, all using different search terms, interfaces and serving up different data types. If you want to correlate a protein’s structure with its interaction profile and with its cellular location, for example, you’re going to need to open a lot of windows on your computer.

Google Chrome might be able to deal with this browser window nightmare, but is it really the ideal solution? A team from the RCSB Protein Data Bank (PDB) has an alternative – and I think better – solution. They advocate the use of widgets.

What is a widget? The PDB guys describe it as a piece of computer code that can be embedded into a webpage to provide some of the function of the originating site. They are a bit like applets, but simpler. I’m pleased to say that the first example that the paper gives is from the Structural Genomics Knowledgebase and the widget code is here.

Structural Genomics Knowledgebase widget

We really developed it as a way of advertising and linking to the site from the other protein structure initiative (PSI) websites but it can be embedded in any site. The nice thing is that it automatically detects new articles, new structures and new features and takes you straight to them.

The PDB widget is more useful. Using it, you can compare two protein structures or two protein sequences from the PDB without going to the website.

So why do I like these widgets so much? I can see lots of advantages:

  • It ensures that the current version is always used (so no out of date software to deal with)
  • Makes the website’s content accessible to a wider range of users
  • As a user there is no need to maintain your own applications or databases – let someone else do all the work!
  • Simple to use (no need to navigate a complicated website)
  • Eventually you’ll be able to develop your own desktop of widgets you routinely use, creating order out of chaos

There are some downsides, but they aren’t insurmountable:

  • Remote users might not count as visitors to the site – a disadvantage if you’re applying for grants or trying to attract advertising/sponsorship
  • I’m demonstrating one here – if you can’t edit your webpage either because you haven’t got access to the code or because you don’t know how then you can’t embed the widget (I think I can’t edit code for this wordpress-hosted site, but may well be demonstrating the latter point)
  • Missing out on new features from the originating website that might have been helpful. By not exploring the original website, serendipity is lost

This isn’t “new” technology – we’re used to using apps, widgets or gadgets all over the place, but this looks to be the first examples of their use for biology. I think this offers great potential for developing our own personal workbench or desktop, bringing together all the applications and databases your routinely use in one place. Now, what I need is a very simple way to drag and drop them into one place…

Reference: Bourne PE, Beran B, Bi C, Bluhm W, Dunbrack R, et al. (2010) Will Widgets and Semantic Tagging Change Computational Biology? PLoS Comput Biol 6(2): e1000673. doi:10.1371/journal.pcbi.1000673

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