So it looks like TreeBASE is in trouble, it's legacy Java code a victim of security issues. Perhaps this is a chance to rethink TreeBASE, assuming that a repository of published phylogenies is still considered a worthwhile thing to have (and I think that question is open). Here's what I think could be done.

Returning to the subject of personal knowledge graphs Kyle Scheer has an interesting repository of Markdown files that describe academic disciplines at https://github.com/kyletscheer/academic-disciplines (see his blog post for more background). If you add these files to Obsidian you get a nice visualisation of a taxonomy of academic disciplines.

This blog post provides some background to a recent tweet where I expressed my frustration about the duplication of DOIs for the same article. I'm going to document the details here.

There are several instances where I have a collection of references that I want to deduplicate and merge.

I keep returning to the problem of viewing large graphs and trees, which means my hard drive has accumulated lots of failed prototypes. Inspired by some recent discussions on comparing taxonomic classifications I decided to package one of these (wildly incomplete) prototypes up so that I can document the idea and put the code somewhere safe.

I've released a very crude GraphQL endpoint for WikiData. More precisely, the endpoint is for a subset of the entities that are of interest to WikiCite, such as scholarly articles, people, and journals. There is a crude demo at https://wikicite-graphql.herokuapp.com. The endpoint itself is at https://wikicite-graphql.herokuapp.com/gql.php.

Markus Strasser (@mkstra write a fascinating article entitled "The Business of Extracting Knowledge from Academic Publications". His TL;DR: After recounting the many problems of knowledge extraction - including a swipe at nanopubs which "are ... dead in my view (without admitting it)" - he concludes: Well worth a read, and much food for thought.

Over a decade ago RSS (RDF Site Summary or Really Simple Syndication) was attracting a lot of interest as a way to integrate data across various websites. Many science publishers would provide a list of their latest articles in XML in one of three flavours of RSS (RDF, RSS, Atom). This led to tools such as uBioRSS [1] and my own e-Biosphere Challenge: visualising biodiversity digitisation in real time.

The Plazi project has become one of the major contributors to GBIF with some 36,000 datasets yielding some 500,000 occurrences (see Plazi's GBIF page for details). These occurrences are extracted from taxonomic publication using automated methods.

This is a guest post by Tony Rees. It would be difficult to encounter a scientist, or anyone interested in science, who is not familiar with the microscope, a tool for making objects visible that are otherwise too small to be properly seen by the unaided eye, or to reveal otherwise invisible fine detail in larger objects.