Ozymandias in Canberra

On Tuesday I was in Canberra to visit the Australian National Insect Collection at CSIRO and give a talk on knowledge graphs. David Yeates, who was a post doc at the AMNH at the same time I was (more years ago than I care to remember), played host and provided lots of stimulating conversation on the state of taxonomy and systematics, the Atlas of Living Australia (ALA), the bias against small organisms (see the wonderful essay A Dream of Invertebrate Utopia), and the joys of code compliance and modern publishing (see "Are taxonomic publications involving nomenclatural acts on Early View Code compliant?" https://doi.org/10.1111/aen.12372).

Ozymandias - from an atlas to a knowledge graph of living Australia from Roderic Page

My talk discussed the Ozymandias knowledge graph, and also show cased the demos Nicole Kearney and I had put together to show the ways we think the ALA could be enhanced using knowledge graphs. One of these (linking names to the literature) has already been discussed here (see Messages from Melbourne: Towards linking all the things). The second demo (Hero images) gives examples of taxa for which ALA has no images, despite such images being available in the published literature via the Biodiversity Literature Repository. For example, the weevil genus Trigonopterus Fauvel, 1862 is richly illustrated in "Revision of the Australian species of the weevil genus Trigonopterus Fauvel" https://doi.org/10.3897/zookeys.556.6126. With a SPARQL query we can link these images to the associated taxa and provide a richer user experience.

The third demo makes use of Wikidata queries to display information on authors of taxonomic work on Australian species. This is very much a work in progress, but could be extended into a directory of Australian taxonomists.

One application of such a directory could be to determine to what extent Australian taxonomy depends on international researchers. Initial results (https://w.wiki/6PX) show that researchers from multiple countries have contribute to knowledge about Australian animal taxonomy and systematics.

There is still a frighteningly large amount of data cleaning and linking to do, but I think we've only scratched the surface of how knowledge graphs can be used to enrich biodiversity databases.

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

I've written up my entry for the 2018 GBIF Challenge ("Ozymandias") and posted a preprint on Biorxiv (https://www.biorxiv.org/content/early/2018/12/04/485854). The DOI is https://doi.org/10.1101/485854 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 https://ozymandias-demo.herokuapp.com.

GBIF Ebbe Nielsen Challenge update

🎉 🎉 CONGRATULATIONS to @UofGlasgow's @rdmpage for winning joint first prize in the 2018 @GBIF Ebbe Nielsen Challenge, the annual innovation competition to advance open science and open data for biodiversity. Well done, Prof Page! @IBAHCM #UofGWorldChangers pic.twitter.com/DjbmP90hTN

— UofG MVLS (@UofGMVLS) October 17, 2018

Quick note to express my delight and surprise that my entry for the 2018 GBIF Ebbe Nielsen Challenge come in joint first! My entry was Ozymandias - a biodiversity knowledge graph which built upon data from sources such as ALA, AFD, BioStor, CrossRef, ORCID), Wikispecies, and BLR.

I'm still tweaking Ozymandias, for example adding data on GBIF specimens (and maybe sequences from GenBank and BOLD) so that I can explore questions such as what is the lag time between specimen collection and description of a species. The bigger question I'm interested in is the extent to which knowledge graphs (aka RDF) can be used to explore biodiversity data.

For details on the other entries visit the list of winners at GBIF. The other first place winners Lien Reyserhove, Damiano Oldoni and Peter Desmet have generously donated half their prize to NumFOCUS which supports open source data science software:

Let’s give back! ❤️We decided to donate half of our @GBIF prize money (5000€) to @NumFOCUS which funds essential #opensource research software like @rOpenSci, #pandas and @ProjectJupyter. https://t.co/R3Bh0Tj8YX

— LifeWatch INBO (@LifeWatchINBO) October 18, 2018

This is a great way of acknowledging the debt many of us owe to developers of open source software that underpins the work of many researchers.

I hope GBIF and the wiser GBIF community found this year's Challenge to be worthwhile, I'm a big fan of anything which increases GBIF's engagement with developers and data analysts, and if the challenge runs again next year I encourage anyone with an interest in biodiversity informatics to consider taking part.