Wednesday, December 05, 2018

Biodiversity data v2Glasgow University's Institute of Biodiversity, Animal Health & Comparative Medicine, where I'm based, hosts Naturally Speaking featuring "cutting edge research and ecology banter". Apparently, what I do falls into that category, so Episode 65 features my work, specifically my entry for the 2018 GBIF Challenge (Ozymandias). The episode page has a wonderful illustration by Eleni Christoforou which captures the idea of linking things together very nicely. Making the podcast was great fun, thanks to the hosts Kirsty McWhinnie and Taya Forde. Let's face it, what academic doesn't love to talk about their own work, given half a chance? I confess I'm happy to talk about my work, but I haven't had the courage yet to listen to the podcast.

Ozymandias: A biodiversity knowledge graph available as a preprint on Biorxiv

LwyH1HFe 400x400I've written up my entry for the 2018 GBIF Challenge ("Ozymandias") and posted a preprint on Biorxiv ( The DOI is which, last time I checked, still needs to be registered.

The abstract appears below. I'll let the preprint sit there for a little while before I summon the enthusiasm to revisit it, tidy it up, and submit it for publication.

Enormous quantities of biodiversity data are being made available online, but much of this data remains isolated in their own silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to con-struct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space. Motivated by the 2018 GBIF Ebbe Nielsen Challenge I explore the feasibility of constructing a "biodiversity knowledge graph" for the Australian fauna. These steps involved in constructing the graph are described, and examples its application are discussed. A web interface to the knowledge graph (called "Ozymandias") is available at