GeoCouch

@mikeal a little tedious. you can take OSM and then convert it to SHP and then http://github.com/maxogden/shp2geocouchless than a minute ago via webmax ogden
maxogden

The tweet above inspired me to take a quick look at GeoCouch, a version of CouchDB that supports spatial queries. This is something I need if I'm going to start playing seriously with CouchDB. So, it was off to Installing and working with GeoCouch, grabbing a copy of HomeBrew (yet another package manager for Mac OS X), in the hope of installing GeoCouch. Things went fairly smoothly, although it took what seemed like an age to build everything. But I now have GeoCouch running. Previously I'd been running CouchDB using http://janl.github.com/couchdbx/, which launches vanilla CouchDB. However, if you launch CouchDBX after starting GeoCouch from the command line, CouchDBX is talking to GeoCouch.

I then grabbed shp2geocouch to try some shape files (I grabbed some shape files from the IUCN to play with). If you're on a Mac grab GISLook to get Quick Look previews of these files. Since I'm new to ruby there were a couple of gotchas, such as lacking some prerequisites (httparty and couchrest, both installed by typing gem install <name of package>), and there was the small matter of needing to add ~/.gem/ruby/1.8/bin to my path so I could find shp2geocouch (spot the ruby neophyte). The shape file didn't get processed completely, but at least I managed to get some data into GeoCouch.


So far I've been playing with the examples at http://github.com/vmx/couchdb, and things seem to work. At least, the basic bounding box queries work. I'm tempted to play with this some more (and get my head arounbd GeoJSON), perhaps trying to recreate the functionality of my Elsevier Challenge entry, for which I wrote a custom key-value database that was awfully clunky.

Finding scientific articles in a large digital archive: BioStor and the Biodiversity Heritage Library

Yesterday I uploaded a manuscript to Nature Precedings that describes the inner workings of BioStor. The title is "Finding scientific articles in a large digital archive: BioStor and the Biodiversity Heritage Library", and you can grab it here: hdl:10101/npre.2010.4928.1.

Manuscripts describing databases are usually pretty turgid affairs, and this isn't an exception, despite my attempts to spice it up with the tale of Leviathan, oops, Livyatan (see doi:10.1038/nature09381 and Wikipedia). Plus, I can't escape the thought that BioStor would have been a lot more fun to write if I'd used a key-value database like CouchDB. I fear this is often the way of things. By the time it comes to writing something up, you realise that if you could start over you'd do it rather differently.

BHL and the iPad

@elyw I'd leave bookmarking to 3rd party, e.g. Mendeley. #bhlib specific issues incl. displaying DjVu files, and highlighting taxon namesless than a minute ago via Tweetie for MacRoderic Page
rdmpage

Quick mock-up of a possible BHL iPad app (made using OmniGraffle), showing a paper from BioStor(http://biostor.org/reference/50335). Idea is to display a scanned page at a time, with taxonomic names on page being clickable (for example, user might get a list of other BHL content for this name). To enable quick navigation all the pages in the document being viewed are displayed in a scrollable gallery below main page.



Key to making this happen is being able to display DjVu files in a sensible way, maybe building on DjVu XML to HTML. Because BHL content is scanned, it makes sense to treat content as pages. We could extract OCR text and display that as a continuous block of text, but the OCR is sometimes pretty poor, and we'd also have to parse the text and interpret its structure (e.g., this is the title, these are section headings, etc.), and that's going to be hard work.