Thursday, April 07, 2022

Obsidian, markdown, and taxonomic trees

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Returning to the subject of personal knowledge graphs Kyle Scheer has an interesting repository of Markdown files that describe academic di...
Tuesday, February 08, 2022

Duplicate DOIs (again)

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This blog post provides some background to a recent tweet where I expressed my frustration about the duplication of DOIs for the same artic...
Thursday, February 03, 2022

Deduplicating bibliographic data

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There are several instances where I have a collection of references that I want to deduplicate and merge. For example, in Zootaxa has no imp...
Sunday, January 02, 2022

Large graph viewer experiments

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I keep returning to the problem of viewing large graphs and trees, which means my hard drive has accumulated lots of failed prototypes. Insp...
Monday, December 20, 2021

GraphQL for WikiData (WikiCite)

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I've released a very crude GraphQL endpoint for WikiData. More precisely, the endpoint is for a subset of the entities that are of inter...
Saturday, December 11, 2021

The Business of Extracting Knowledge from Academic Publications

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Markus Strasser ( @mkstra write a fascinating article entitled "The Business of Extracting Knowledge from Academic Publications" ...
Tuesday, November 23, 2021

Revisiting RSS to monitor the latest taxonomic research

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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 v...
Monday, October 25, 2021

Problems with Plazi parsing: how reliable are automated methods for extracting specimens from the literature?

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The Plazi project has become one of the major contributors to GBIF with some 36,000 datasets yielding some 500,000 occurrences (see Plazi...
Thursday, October 07, 2021

Reflections on "The Macroscope" - a tool for the 21st Century?

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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 ...
Friday, August 27, 2021

JSON-LD in the wild: examples of how structured data is represented on the web

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I've created a GitHub repository so that I can keep track of the examples of JSON-LD that I've seen being actively used, for example...
Friday, July 23, 2021

Species Cite: linking scientific names to publications and taxonomists

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I've made Species Cite live. This is a web site I've been working on with the GBIF Challenge as a notional deadline so I'll act...
Thursday, July 22, 2021

Towards a WikiCite search engine

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I've released a simple search engine for publications in Wikidata. Wikicite Search takes its name from the WikiCite project, which was...

Citation parsing tool released

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Quick note on a tool I've been working on to parse citations, that is to take a series of strings such as: Möllendorff O (1894) On a ...
Tuesday, June 15, 2021

Compiling a C++ application to run on Heroku

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TL;DR Use a buildpack and set "LDFLAGS=--static" --disable-shared I use Heroku to host most of my websites, and since I mostly ...
Friday, June 04, 2021

Thoughts on BHL, ALA, GBIF, and Plazi

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If you compare the impact that BHL and Plazi have on GBIF, then it's clear that BHL is almost invisible. Plazi has successfully in carve...
Friday, May 28, 2021

Finding citations of specimens

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Note to self. The challenge of finding specimen citations in papers keeps coming around. It seems that this is basically the same problem ...

Maximum entropy summary trees to display higher classifications

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How to cite: Page, R. (2021). Maximum entropy summary trees to display higher classifications https://doi.org/10.59350/af01t-6sw74 A chall...
Tuesday, May 18, 2021

Preprint on Wikidata and the bibliography of life

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Last week I submitted a manuscript entitled "Wikidata and the bibliography of life". I've been thinking about the "biblio...