This is just some random notes on an “ideal” taxonomic journal, inspired in part by some recent discussions on “turbo-taxonomy” (e.g., https://doi.org/10.3897/zookeys.1087.76720 and https://doi.org/10.1186/1742-9994-10-15), and also examples such as the Australian Journal of Taxonomy https://doi.org/10.54102/ajt.qxi3r which seems well-intentioned but limited.

I tweeted about this but want to bookmark it for later as well. The paper “A molecular-based identification resource for the arthropods of Finland” doi:10.1111/1755-0998.13510 contains the following: I think this is a very clever way to characterise the project. In an age of machine learning this may be commonest way to share knowledge , namely as expert-labelled training data used to build tools for others.

I've been thinking a bit about how one could use a Markdown wiki-like tool such as Obsidian to work with taxonomic data (see earlier posts Obsidian, markdown, and taxonomic trees and Personal knowledge graphs: Obsidian, Roam, Wikidata, and Xanadu). One "gotcha" would be how to name pages.

Taxonomic treatments have come up in various discussions I'm involved in, and I'm curious as to whether they are actually being used, in particular, whether they are actually being cited. Consider the following quote: "Traditional" academic citation is from article to article.

More arm-waving notes on taxonomic databases. I've started to add data to ChecklistBank and this has got me thinking about the issue of data quality.

Just some thoughts as I work through some datasets linking taxonomic names to the literature. In the diagram above I've tried to capture the different situatios I encounter. Much of the work I've done on this has focussed on case 1 in the diagram: I want to link a taxonomic name to an identifier for the work in which that name was published. In practise this means linking names to DOIs.

Quick notes to self following on from a conversation about linking taxonomic names to the literature. There are different sorts of citation: Paper cites another paper Paper cites a dataset Dataset cites a paper Citation type (1) is largely a solved problem (although there are issues of the ownership and use of this data, see e.g. Zootaxa has no impact factor.

Note to self (basically rewriting last year's Finding citations of specimens). Bibliographic data supports going from identifier to citation string and back again, so we can do a "round trip." 1. Given a DOI we can get structured data with a simple HTTP fetch, then use a tool such as citation.js to convert that data into a human-readable string in a variety of formats.

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.