University of Glasgow

Roderic Page

![Unknown](http://lh6.ggpht.com/-hoG9F68aBoA/UvjtfuhfddI/AAAAAAAADQk/QmMlAV8U39E/Unknown.png?imgmax=800 "Unknown.png"){border="0"
width="135" height="135" style="float:right;"}I gave a remote
presentation at a
[proiBioSphere](http://wiki.pro-ibiosphere.eu/wiki/MS12_-_Workshop_on_mark-up_of_biodiversity_literature)
workshop this morning. The slides are below (to try and make it a bit
more engaging than a desk of Powerpoints I played around with Prezi).  
  

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There is a version on Vimeo that has audio as well.  
  

  
I sketched out the biodiversity \"knowledge graph\", then talked about
how mark-up relates to this, finishing with a few questions. The
question that seems to have gotten people a little agitated is the
relative importance of markup versus, say, indexing. As Terry Catapano
pointed out, in a sense this is really a continuum. If we index content
(e.g., locate a string that is a taxonomic name) and flag that content
in the text, then we are adding mark-up (if we don\'t, we are simply
indexing, but even then we have mark-up at some level, e.g. \"this term
occurs some where on this page\"). So my question is really what level
of markup do we need to do useful work? Much of the discussion so far
has centered around very detailed mark-up (e.g., the kind of thing
*ZooKeys* does to each article). My concern has always been how scalable
this is, given the size of the taxonomic literature (in which *ZooKeys*
is barely a blip). It\'s the usual trade off, do we go for breadth (all
content indexed, but little or no mark-up), or do we go for depth
(extensive mark-up for a subset of articles)? Where you stand on that
trade off will determine to what extent you want detailed mark up,
versus whether indexing is \"good enough\".  


I gave a remote presentation at a proiBioSphere workshop this morning. The slides are below (to try and make it a bit more engaging than a desk of Powerpoints I played around with Prezi).  There is a version on Vimeo that has audio as well. I sketched out the biodiversity "knowledge graph", then talked about how mark-up relates to this, finishing with a few questions.

Mark-up of biodiversity literature

Quick post on a little tool I came across,
[moz-hocr-edit](http://jimgarrison.org/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](http://iphylo.blogspot.com/2010/12/bhl-and-ocr.html) I decided
to take it for a spin.  
  
**moz-hocr-edit** uses the [hOCR](http://en.wikipedia.org/wiki/HOCR),
which is a format for representing the output of OCR software, and is
used by tools such as [OCRopus](http://en.wikipedia.org/wiki/OCRopus)
(you can see the public specification for hOCR
[here](http://docs.google.com/View?docid=dfxcv4vc_67g844kf)). 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](http://biostor.org/reference/80780). For the demo to work
you will need to use the Firefox web browser with the
[moz-hocr-edit](https://addons.mozilla.org/en-US/firefox/addon/11067)
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](http://en.wikipedia.org/wiki/ABBYY) 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\":  
    ![Statusbar](http://lh6.ggpht.com/-UvG_XpBDCgw/Th2LnwmpZtI/AAAAAAAAA6g/VMW6guACy5U/statusbar.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
    border="0" width="397" height="130"}
4.  Firefox will open a new tab that will look something like this:  
    ![Screenshot](http://lh5.ggpht.com/-W1g4z7-IiDY/Th2Lo2GMvJI/AAAAAAAAA6k/_P49tsGwSUU/screenshot.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
    border="0" width="400" height="289"}
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.  


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.

Messaggi di Rogue Scholar

Mark-up of biodiversity literature

Correcting OCR using hOCR in Firefox