Referring to a one-degree square in RDF using c-squares

I'm in the midst of rebuilding iSpecies (my mash-up of Wikipedia, NCBI, GBIF, Yahoo, and Google search results) with the aim of outputting the results in RDF. The goal is to convert iSpecies from a pretty crude "on-the-fly" mash-up to a triple store where results are cached and can be queried in interesting ways. Why? Partly because I think such a triple store is an obvious way to underpin a "biodiversity hub" of the kind envisaged by PLoS (see my earlier post).

As ever, once one embarks down the RDF route (and I've been here before), one hits all the classic stumbling blocks, such as "what URI do I use for a thing?", and "what vocabulary do I use to express relationships between things?". For example, I'd like to represent the geographic distribution of a taxon as depicted on a GBIF map. How do I describe this in a RDF document?

To make this concrete, take one of my favourite animals, the New Zealand mud crab Helice crassa. Here's the GBIF map for this taxon:


This map has the URL (I kid you not):

http://ogc.gbif.org/wms?request=GetMap
&bgcolor=0x666698
&styles=,,,
&layers=gbif:country_fill,gbif:tabDensityLayer,gbif:country_borders,gbif:country_names
&srs=EPSG:4326
&filter=()(
%3CFilter%3E
%3CPropertyIsEqualTo%3E
%3CPropertyName%3Eurl
%3C/PropertyName%3E
%3CLiteral%3E
%3C![CDATA[http%3A%2F%2Fdata.gbif.org%2Fmaplayer%2Ftaxon%2F17462693%2FtenDeg%2F-45%2F160%2F]]%3E
%3C/Literal%3E
%3C/PropertyIsEqualTo%3E
%3C/Filter%3E)()()
&width=721
&height=362
&Format=image/png
&bbox=160,-45,180,-35

(or http://bit.ly/cuTFW9, if you prefer). Now, there's no way I'm using this URL! Plus, the URL identifies an image, not the distribution.

But, if we look at the map we see that it is made of 1° × 1° squares. If each of those had a URI then I could simply list those squares as the distribution of the crab. This seems straightforward as GBIF has a service that provides these squares. For example, the URL http://data.gbif.org/species/17462693 (where 17462693 corresponds to Helice crassa) returns:

MINX	MINY	MAXX	MAXY	DENSITY
167.0	-45.0	168.0	-44.0	5
174.0	-42.0	175.0	-41.0	20
174.0	-38.0	175.0	-37.0	17
174.0	-37.0	175.0	-36.0	4

These are the 1° × 1° squares for which there are records of Helice crassa. Now, what I'd like to do is have a URI for each square, and I'd like to do this without reinventing the wheel. I've come across a URI space for points of the globe (the WGS 84 Geographic Point URI Space"), but not one for polygons. Then it dawned on me that perhaps c-squares, developed by Tony Rees at the CSIRO in Australia, would do the trick¹. To quote Tony:

C-squares is a system for storage, querying, display, and exchange of "spatial data" locations and extents in a simple, text-based, human- and machine- readable format. It uses numbered (coded) squares on the earth's surface measured in degrees (or fractions of degrees) of latitude and longitude as fundamental units of spatial information, which can then be quoted as single squares (similar to a "global postcode") in which one or more data points are located, or be built up into strings of codes to represent a wide variety of shapes and sizes of spatial data "footprints".

C-squares appeal partly (and this says nothing good about me) because they have a slightly Byzantine syntax. However, they are short, and quite easy to calculate. I'll let the reader find out the gory details. To give an example, my home town, Auckland, has latitude -36.84, longitude 174.74, which corresponds to the 1° × 1° c-square with the code 3317:364.

Now, all I need to do is convert c-squares into URIs. If you append the c-square to http://bioguid.info/csquare:, like this, http://bioguid.info/csquare:3317:364, you get a linked data-friendly URI for the c-square. In a web browser you get a simple web page like this:


A linked data client will get RDF, like this:

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF 
   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
   xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" 
   xmlns:dcterms="http://purl.org/dc/terms/" 
   xmlns:dwc="http://rs.tdwg.org/dwc/terms/" 
   xmlns:geom="http://fabl.net/vocabularies/geometry/1.1/">
   <dcterms:Location rdf:about="http://bioguid.info/csquare:3307:364">
      <rdfs:label>3307:364</rdfs:label>
      <geom:xmin>74</geom:xmin>
      <geom:ymin>-37</geom:ymin>
      <geom:xmax>75</geom:xmax>
      <geom:ymax>-36</geom:ymax>
      <dwc:footprintWKT>POLYGON((-37 75,-37 74,-36 74,-36 75,-37 75))</dwc:footprintWKT>
   </dcterms:Location>
</rdf:RDF>

Now, I can refer to each square by it's own URI. This will also enable me to query a triple store by c-square (e.g., what other taxa occur within this 1° × 1° square?).

1. Tony Rees had emailed me about this in response to a tweet about URIs for co-ordinates, but it took me a while to realise how useful c-square notation could be.

To wiki or not to wiki?

What follows are some random thoughts as I try and sort out what things I want to focus on in the coming days/weeks. If you don't want to see some wallowing and general procrastination, look away now.

I see four main strands in what I've been up to in the last year or so:

1. services
2. mashups
3. wikis
4. phyloinformatics

Let's take these in turns.

Services
Not glamourous, but necessary. This is basically bioGUID (see also hdl:10101/npre.2009.3079.1). bioGUID provides OpenURL services for resolving articles (it has nearly 84,000 articles in it's cache), looking up journal names, resolving LSIDs, and RSS feeds.

Mashups
iSpecies is my now aging tool for mashing up data from diverse sources, such as Wikipedia, NCBI, GBIF, Yahoo, and Google Scholar. I tweak it every so often (mainly to deal with Google Scholar forever mucking around with their HTML). The big limitation of iSpecies is that it doesn't make it's results reusable (i.e., you can't write a script to call iSpecies and return data). However, it's still the place I go to to quickly find out about a taxon.

The other mashups I've been playing with focus on taking standardised RSS feeds (provided by bioGUID, see above) and mashing them up, sometimes with a nice front end (e.g., my e-Biosphere 09 challenge entry).

Wiki
I've invested a huge amount of effort in learning how wikis (especially Mediawiki and its semantic extensions) work, documented in earlier posts. I created a wiki of taxonomic names as a sandbox to explore some of these ideas.

I've come to the conclusion that for basic taxonomic and biological information, the only sensible strategy for our community is to use (and contribute to) Wikipedia. I'm struggling to see any justification for continuing with a proliferation of taxonomic databases. After e-Biosphere 09 the game's up, people have started to notice that we've an excess of databases (see Claire Thomas in Science, "Biodiversity Databases Spread, Prompting Unification Call", doi:10.1126/science.324_1632).

Phyloinformatics
In truth I've not been doing much on this, apart from releasing tvwidget (code available from Google Code), and playing with a mapping of TreeBASE studies to bibliographic identifiers (available as a featured download from here). I've played with tvwidget in Mediawiki, and it seems to work quite well.

Where now?
So, where now? Here are some thoughts:

1. I will continue to hack bioGUID (it's now consuming RSS feeds from journals, as well as Zotero). Everything I do pretty much depends on the services bioGUID provides


2. iSpecies really needs a big overhaul to serve data in a form that can be built upon. But this requires decisions on what that format should be, so this isn't likely to happen soon. But I think the future of mashup work is to use RDF and triple stores (providing that some degree of editing is possible). I think a tool linking together different data sources (along the lines of my ill-fated Elsevier Challenge entry) has enormous potential.


3. I'm exploring Wikipedia and Wikispecies. I'm tempted to do a quantitative analysis of Wikipedia's classification. I think there needs to be some serious analysis of Wikipedia if people are going to use it as a major taxonomic resource.


4. If I focus on Wikipedia (i.e., using an existing wiki rather than try to create my own), then that leaves me wondering what all the playing with iTaxon was for. Well, actually I think the original goal of this blog (way back in December 2005) is ideally suited to a wiki. Pretty much all the elements are in place to dump a copy of TreeBASE into a wiki and open up the editing of links to literature and taxonomic names. I think this is going to handily beat my previous efforts (TbMap, doi:10.1186/1471-2105-8-158), especially as errors will be easy to fix.

So, food for thought. Now, I just need to focus a little and get down to actually doing the work.