As part of BHL's "Celebrating 10 years of inspiring discovery through free access to biodiversity knowledge" at the NHM and Kew Gardens in London, I was interviewed by Martin Kalfatovic (@UDCMRK). We chatted about BHL, the work I've been doing on BioStor, and the future of BHL.
The follow is a guest post by Bob Mesibov, who has contributed to iPhylo before. Like many iPhylo readers, I deal with large, pre-existing compilations of biodiversity data. The compilations come from museums, herbaria, aggregation projects and government agencies.
After experimenting with a dynamic, online version of my notes "Towards a biodiversity knowledge graph" I've published a static version in RIO: doi:10.3897/rio.2.e8767.
TL;DR; The Plant List is now in GBIF http://doi.org/10.15468/btkum2. Readers of this blog may recall that I've had a somewhat jaundiced view of The Plant List.
I’ve thrown together some notes on building a biodiversity knowledge graph, and in the interests of making it interactive it's in the form of a web page: http://bionames.org/~rpage/towards-knowledge-graph/. There are buttons to click that display live data, and I hope to dd more examples as I flesh out the ideas.
Last week (25-26 February) I was in London for CISCO Pit Stop event. Thursday evening was at the Natural History Museum where I gave a talk extolling the virtues of linking stuff together: My slides are here: Cisco Digital Catapult from Roderic Page Friday we assembled at the Digital Catapult Centre, which as Sandy Knapp notes, has some amazing views from it's 9th floor.
I'm continuing to play with the new version of iSpecies, seeing just how far one can get by simply grabbing JSON from various sources and mashing them up. Since the Open Tree of Life is pretty unresolved ("OMG it's full of stars") I've started to grab trees from TreeBASE and add those.
In a recent Twitter conversation including David Shorthous and myself (and other poor souls who got dragged in) we discussed how to demonstrate that adopting JSON-LD as a simple linked-data friendly format might help bootstrap the long awaited "biodiversity knowledge graph" (see below for some suggestions for keeping JSON-LD simple). David suggests partnering with "Three small, early adopting projects". I disagree.
A decade ago (OMG, that can't be right, an actual decade ago) I created "iSpecies", a simple little tool to mashup a variety of data from GBIF, NCBI, Yahoo, Wikipedia, and Google Scholar to create a search engine for species.
My paper "Surfacing the deep data of taxonomy" (based on a presentation I gave in 2011) has appeared in print as part to a special issue of Zookeys : The manuscript was written shortly after the talk, but as is the nature of edited volumes it's taken a while to appear. My tweet about the paper sparked some interesting comments from David Shorthouse.
OK, so the title is pure click bait, but here's the thing. It seems to me that the Semantic Web as classically conceived (RDF/XML, SPARQL, triple stores) has had relatively little impact outside academia, whereas other technologies such as JSON, NoSQL (e.g., MongoDB, CouchDB) and graph databases (e.g., Neo4J) have got a lot of developer mindshare. In biodiversity informatics the Semantic Web has been a round for a while.