Correcting OCR using hOCR in Firefox

Quick post on a little tool I came across, moz-hocr-edit. This Firefox add-on lets you proofread Optical Character Recognition (OCR) output. Given my interest in OCR and the Biodiversity Heritage Library I decided to take it for a spin.

moz-hocr-edit uses the hOCR, which is a format for representing the output of OCR software, and is used by tools such as OCRopus (you can see the public specification for hOCR here). Basically it's a microformat, that is, it's HTML with some additional tags. Given some hOCR, moz-hocr-edit enables you to edit the OCR output line-by-line.

Demo
I've created a simple demo based upon Case 3368 Eatoniella Dall, 1876 and EATONIELLIDAE Ponder, 1965 (Mollusca, Gastropoda): proposed conservation. For the demo to work you will need to use the Firefox web browser with the moz-hocr-edit installed.

1. Go to http://dl.dropbox.com/u/639486/hocr/80780.html
2. You will see a simple HTML representation of the OCR text from "Case 3368 Eatoniella Dall, 1876 and EATONIELLIDAE Ponder, 1965 (Mollusca, Gastropoda): proposed conservation". I created this HTML from the original ABBYY FineReader XML from the Internet Archive.
3. On the bottom right-hand of the Firefox browser window you should see hOCR. Click on it and select "Edit this hOCR document":
   
4. Firefox will open a new tab that will look something like this:
   
5. You can now edit individual lines of text, and see your edits applied to the HTML below.

moz-hocr-edit is a neat little tool. With appropriate web server settings (and, as the tool's author Jim Garrison suggests, autoversioning) it could the basis of a great tool for correcting OCR errors in BHL.

Talk @vizbi on phylogeny visualisation

The talks from the 2001 workshop on Visualizing Biological Data (VizBi 2011) are now available on Vimeo. There were some great talks at VizBi, especially the keynotes (the "featured videos" on the Vimeo page for VizBi).

My own (slightly breathless) talk was on phylogeny visualisation, which you can watch below.

Visualization of phylogenetics & phylogeography from Roderic Page on Vimeo.

In the talk I mention that the slides are also on SlideShare, and that is where you'll find URLs for the projects I mention. The URls aren't all that easy to get that way, so here they are:

• http://evolution.genetics.washington.edu/phylip/software.html#Plotting
• http://loco.biosci.arizona.edu/paloverde/paloverde.html
• http://www.wellcometreeoflife.org/
• http://dx.doi.org/10.1186/1471-2105-5-48
• http://dx.doi.org/10.1093/sysbio/46.3.523
• http://dx.doi.org/10.1186/1471-2105-8-213
• http://iphylo.blogspot.com/2007/06/earth-not-flat-official.html
• http://systbio.org/?q=node/184
• http://dx.doi.org/10.1080/10635150701266848
• http://www.ncbi.nlm.nih.gov/pubmed/17968069
• http://innovis.cpsc.ucalgary.ca/Research/CollaborativeTreeComparison
• http://www.perceptivepixel.com/
• http://iphylo.blogspot.com/2008/08/perceptive-pixel-taxonomy-demo.html
• http://www-ab.informatik.uni-tuebingen.de/software/dendroscope
• http://dx.doi.org/10.1126/science.300.5626.1692
• http://loco.biosci.arizona.edu/
• http://iphylo.blogspot.com/2007/08/visualising-very-big-trees-part-iv.html
• http://iphylo.blogspot.com/2011/02/live-demo-of-zooming-large-tree.html

Mendeley Hack4Knowledge: towards an "ego wall"

I'm taking a virtual part in Mendeley's Hack4Knowledge event. I'm using this a chance to explore some ideas about building novel interfaces to bibliographic data in Mendeley. One idea is to display a user's entire library in one screen. I think the user interfaces employed by most bibliographic software are too conservative and there some cool things that could be done. For example, see A fluid treemap interface for personal digital libraries (doi:10.1145/1065385.1065512, PDF available from CiteSeer).

One idea I'm playing with is to display all a Mendeley user's papers as a quantum treemap, with thumbnails of the papers and "badges" indicating, for example, how many readers each paper has. The idea is that at a glance you can see all your publications, and which ones are being read the most. You can think of it as an "ego wall" — a quick way to see what others think about your work. Below is part of my library. You can see the full treemap here as an SVG file. Imagine this as an iPad interface to a user's Mendeley library.



Eventually I'll make this live. I'm doing this yet as the script to create the visualisation is slow due to the multiple requests I need to make to get the necessary information. I have to get the list of a user's papers from Mendeley, then I call the API for each paper to get basic bibliographic details. I have to screen scrape the corresponding paper's web page to get the thumbnail and the paper's UUID, which I can then use to get the readership stats via Mendeley's API via yet another API call. Sigh.

Anyway, this is enough hacking for one day. Hope to spend some more time on this project tomorrow.