I've been playing with the graph database Neo4J to investigate aspects of the classification of taxa in GBIF's backbone classification. Neo4J is a graph database, and a number of people in biodiversity informatics have been playing with it. Nicky Nicolson at Kew has a nice presentation using graph databases to handle names Building a names backbone, and the Open Tree of Life project use it in their tree machine.

Note to self about a possible project. This PLoS ONE paper: describes a method for inferring a hierarchy from a set of tags (and cites related work that is of interest). I've grabbed the code and data from http://hiertags-beta.elte.hu/home/ and put it on GitHub. Possible project Use Tibély et al. method (or others) on taxonomic names extracted from BHL text (or other) and see if we can reconstruct taxonomic classifications.

One of my pet projects is BioStor, which has been running since 2009 (gulp). BioStor extracts articles from the Biodiversity Heritage Library (details here: http://dx.doi.org/10.1186/1471-2105-12-187), and currently has over 110,000 articles, all open access. The site itself is showing its age, both in terms of performance and design, so I've wanted to update it for a while now.

Quick notes on modelling taxonomic names in databases, as part of an ongoing discussion elsewhere about this topic. Simple model One model that is widely used (e.g., ITIS, WoRMS) and which is explicit in Darwin Core Archive is something like this: We have a table for taxa and we don't distinguish between taxa and their names. the taxonomic hierarchy is represented by the parentID field, which points to your parent.

In my (previous post ) I discussed the potential for the Biodiversity Data Journal (BDJ) to be a venue for nano (or near-nano publications). In this post I want to draw attention to what I think is a serious stumbling block, which is the lack of machine readable statements in the journal.

I stumbled across this intriguing paper: The authors are arguing that there is scope for a unit of publication between a full-blown journal article (often not machine readable, but readable) and the nanopublication (a single, machine readable statement, not intended for people to read), namely the Single Figure Publications (SFP): It seems to me that this is something that the Biodiversity Data Journal is potentially heading towards.

These are some quick thoughts on the games on the BHL site, part of the Purposeful Gaming and BHL Project. As mentioned on Twitter, I had a quick play of the Beanstalk game and got bored pretty quickly.

Browsing JSTOR's Global Plants database I was struck by the number of comments people have made on individual plant specimens. For example, for the Holotype of Scorodoxylum hartwegianum Nees (K000534285) there is a comment from Håkan Wittzell that the "Collection number should read 1269 according to Plantae Hartwegianae". In JSTOR the collection number is 1209. Now, many (if not all) of these specimens will also be in GBIF.

Steve Baskauf has concluded a thoughtful series of blog posts on RDF and biodiversity informatics with http://baskauf.blogspot.co.uk/2015/07/confessions-of-rdf-agnostic-part-7.html. In this post he discussed the "Rod Page Challenge", which was a series of grumpy posts I wrote (starting with this one) where I claimed RDF basically sucked, and to illustrate this I issued a challenge for people to do something interesting with some RDF I provided.

Two ongoing challenges in biodiversity informatics are getting data into a form that is usable, and linking that data across different projects platforms. A recent and interesting approach to this problem are "data journals" as exemplified by the Biodiversity Data Journal. I've been exploring some data from this journal that has been aggregated by GBIf and EOL, and have come across a few issues.