Interactive Bibliographies

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Partly for my dissertation, partly for the sake of our little research community, and partly as a proof of concept, I’ve built an “interactive bibliography” based on SIMILE Timeline. You can play with it here.

Screenshot for interactive bibliography

The rest of the post goes into some of the features and its construction.

A: there are three bands with different time denominations: months, years, and decades.  The details of the bibliography only shows up on the month band.

B: Clicking on the item pops up a little box.  For most items the heading hyperlinks to the article on the publisher’s website.

C: An ACS formatted citation, for the non-bibliographic database users.  I have plans to add a RSC formatted citation option.

D: Links out to a wiki — I’m not sure what to use it for yet, but it’s already in Timeline, so why not? 🙂

E: Filter/Highlight bands.  Snipped this from a Timeline example code, and I’ll try to build a more sophisticated version later on (e.g., one that operates on booleans).  The filter will remove all the papers that do not contain the word; the highlight boxes color them with the particular color.

F: (Most of you won’t care about this.)  The content of the database is the (almost) complete literature of the synthetic ion channel community.  It’s currently missing dissertations.


The way this is constructed is best illustrated with a diagram:

Process for creating the interactive bibliography

I’ll start the description from the upper left.  From a few key reference that would certainly cover the field (and which new papers will certainly cite at least one), I use SciFinder Scholar to slurp the citing and cited articles.  (For this database I used about 8 popular reviews in our field.)  SciFinder has a pretty annoying habit of only letting you export 100 at a time (and no way of selecting only a hundred item), so there’s lots of mind-numbing clicking here.  The references are exported into about a dozen separate RIS.  If you’re a Zotero/Z2B user, you may want to disable the plug-ins; they do really funny things… like opening a hundred windows simultaneously.

I then merge these into a single bibTeX, add in selected papers from my own collection, and manually de-duplicate the items.  Most of the conflicts come from the “selected papers from my own collection”, since I’ve collected those with zotero from the publisher, or from Web of Science, and they often are not perfectly identical (and bibDesk doesn’t pick them out).

A little piece of python code then parse the bibTeX into a JSON string suitable for Timeline.  It’s responsible for constructing the link to the publisher (using the DOI – which is often not supplied in pipelines other than SFS->RIS; I know!) and piecing together the citation/abstract (everything in the pop-up bubble).

Register a free wiki at Wikia; manually make that reference in the JSON file.  The rest of  setting up the HTML/JavaScript/CSS files is straight-forward and can probably be automated.  Timeline has some great documentation going on, and later on I’ll be interested in building a few cool pages with it (musicology, chinese literature, and world history comes to mind – it would be particularly in conjunction with the map APIs out there).

In the future I’ll hope to built a web-app that would take in your bibTeX and give you a nice zipped interactive timeline, but for now, if you’d like one, you can send me your bibTeX and I’ll try to generate the set for you (that said, I am a thesis writing man: so no promise!)


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