Attention publishers: the data in your tables want to be free! Free!

The Neurosynth database is getting an upgrade over the next couple of weeks; it’s going to go from 4,393 neuroimaging studies to around 5,800. Unfortunately, updating the database is kind of a pain, because academic publishers like to change the format of their full-text HTML articles, which has a nasty habit of breaking the publisher-specific HTML parsers I’ve written. When you expect ScienceDirect to give you <table cellspacing=10>, but you get <table> with no cellspacing attribute (the horror!), bad things happen in XPath land. And then those bad things need to be repaired. And I hate repairing stuff! So I don’t do it very often. Like, once every 6 to 9 months.

In an ideal world, there would be no need to write (and fix) custom filters for different publishers, because the publishers would all simultaneously make XML representations of their articles available (in addition to HTML, PDF, etc.), and then people who have legitimate data mining reasons for regularly downloading hundreds of articles at a time wouldn’t have to cry themselves to sleep every night. But as it stands, only one major publisher of neuroimaging articles (PLoS) provides XML versions of all articles. A minority of articles from other publishers are available in XML from BioMed Central, but that’s still just a fraction of the existing literature.

Anyway, the HTML thing is annoying, but it’s possible to work around it. What’s much more problematic is that some publishers lock up the data in the tables of their articles. To make Neurosynth work, I have to be able to identify rows in tables that look like brain activations. That is, things that look roughly like this:

Most publishers are nice enough to format article tables as HTML tables; which is to say, I can look for tags like <table> and then work down the XPath tree to identify all the the rows, and then scan each rows for values that look activation-like. Then those values go into the database, and poof, next thing you know, you have meta-analytic brain activation maps from hundreds of studies. But some publishers–most notably, Frontiers–throw a wrench in the works by failing to format tables in HTML; instead, they present the tables as images (see for instance this JPEG table, pulled from this article). Which means I can’t really extract any data from them, and as a result, you’re not going to see activations from articles published in Frontiers journals in Neurosynth any time soon. So if you publish fMRI articles in Frontiers in Human Neuroscience regularly, and are wondering why I’ve been ignoring you (I like you! I promise!), now you know.

Anyway, on the remote chance that anyone reading this has any sway with people high up at Frontiers, could you please ask them to release their data? Pretty please? Lack of access to data in tables seems to be a pretty common complaint in the data mining community; I’ve talked to other people in the neuroinformatics world who’ve also expressed frustration about it, and I imagine the same is true of people in other disciplines. It’s particularly surprising given that Frontiers is, in theory, an open access publisher. I can see the data in your tables, Frontiers; why won’t you also let me read it?

Okay, I know this kind of stuff doesn’t really interest anyone; I’m just venting. The main point is, Neurosynth is going to be bigger and (very slightly) better in the near future.

2 thoughts on “Attention publishers: the data in your tables want to be free! Free!”

  1. This bug shows up in other unexpected places as well. One that frustrates me is the polling reports from the Pew Center for People and the Press (which also chooses to use a horrid font to make their table images and has a number of other formatting issues).

  2. Annoying. I wonder if you could crowdsource the problem away? Collect all of the offending jpegs, split them into lines (should be quite easy to do that automatically), then you could make people who want to use Neurosynth have to convert a line of a random table into text.

    …that probably annoy your users though… maybe make it voluntary.

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