Linking biodiversity data

Time for a Friday folly. I've made a clunky screencast showing an example of linking biodiversity data together, using bioGUID as the universal wrapper around various data sources. I started with GenBank sequence EF013683, added another, EF013555, then explored some links (specimen, publication, taxon, journal), using the OpenLink RDF Browser:

Linking biodiversity data from Roderic Page on Vimeo.

You can try the URIs I used in the linked data browser of your choice:

• http://bioguid.info/genbank:EF013683
• http://bioguid.info/genbank:EF013555
• http://bioguid.info/occurrence:antweb:casent0106008
• http://bioguid.info/taxonomy:411739
• http://bioguid.info/doi:10.1073/pnas.0605858103
• http://bioguid.info/issn:0027-8424

The demo is a bit clunky, partly because the linked data browser is generic. What we really need is a browser that is tailored to displaying the kind of data we're interested, and hides the gory details under the hood. But the goal is to show that, once everything we care about has a resolvable URI that provides data in a consistent form, and we re-use identifiers, then we can glue stuff together with relative ease. In principle we can simply crawl this web of data (you can append other DOIs, ISSNs, and Genbank accession numbers to http://bioguid.info and get RDF to your heart's content).

None of this is particularly new, we've had RDF in biodiversity informatics for at least five years, there are various linked data-style projects, such as GeoSpecies and the first iteration of bioGUID, and some people (such as Roger Hyam) have been pushing HTTP URIs + RDF for a while, but we seem remarkably unable to get traction on this. Notably, no major biodiversity provider provides RDF (by major I mean GenBank or GBIF size). We make diagrams like the one I drew for GBIF last year, we make the case that linking is a Good Thing™, and yet nothing much happens. This suggests that the idea is still not be presented in a compelling enough fashion. Certainly, clunky demos like the one above probably won't help much. Linked Data clients are generally pretty awful things to use. I think we're going to need some compelling applications that really grab people's attention.

Drawing a phylogeny in a web browser using the canvas element

Some serious displacement activity. I'm toying with adding phylogenies to iSpecies, probably sourced from the PhyLoTA browser. This raises the issue of how to display trees on a web page. PhyLoTA itself uses bitmap images, such as this one:

but I'd like to avoid bitmaps. I toyed with using SVG, but that has it's own series of issues (it basically has to be served as a separate file). So, I've spent a couple of hours playing with the <canvas> element. This enables some quite nice drawing to be down in a browser window, without plugins, SVG, or Flash. I wrote a quick PHP script to parse a Newick tree and draw it using <canvas>. It's really pretty simple, and the results are quite nice:

One minor gotcha is interacting with the diagram (this is one advantage of SVG). Turns out we need a hack, so I've used the trick of a blank, transparent GIF and a usemap (see Greg Houston's Canvas Pie Chart with Tooltips). The picture above is a screen shot, you can see a live example here.

Why we need wikis

I've just spent a frustrating few minutes trying to find a reference in BioStor. The reference in question is

Heller, Edmund 1901. Papers from the Hopkins Stanford Galapagos Expedition, 1898-1899. WIV. Reptiles. Proc. Biol. Soc. Washington 14: 39-98

and comes from the Reptile Database page for the gecko Phyllodactylus gilberti HELLER, 1903. This is primary database for reptile taxonomy, and supplies the Catalogue of Life, which repeats this reference verbatim.
Thing is, this reference doesn't exist! Page 39 of Proc. Biol. Soc. Washington volume 14 is the start of Gerrit S Miller (1901) A new dormouse from Italy. Proc Biol Soc Washington 14: 39-40.
After much fussing with trying diferent volumes and dates for Proc. Biol. Soc. Washington, I searched BHL for Phyllodactylus gilberti, and discovered that this name was published in Proceedings of the Washington Academy of Sciences:

Edmund Heller (1903) Papers from the Hopkins Stanford Galapagos Expedition, 1898-1899. XIV. Reptiles. Proceedings of the Washington Academy of Sciences 5: 39-98

(see http://biostor.org/reference/20322). Three errors (wrong journal, wrong date, minor typo in title), but enough to break the link between a name and the primary source for that name.

Anybody who demands authoritative, expert-vetted resources, and thinks the Catalgoue of Life is a shining example of this needs to think again. Our databases are riddled with errors, which are repackaged over and over again, yet these would be so easy to fix if they were opened up and made easy to edit. It's time to get serious about wikis.