This post describes an issue I’ve had with writing correct types when using PEP-696 defaults in typing.TypeVar. I posted the exploration in a companion repository on GitHub. The motivation behind this comes from my work in biomedical data integration and the semantic web.

ChEMBL periodically curates clinical trial information into its DRUG_INDICATION table. However, there’s some weird inconsistencies in the way it references disease concepts in external vocabularies. This blog post is an exploration of that table.

I’ve recently worked with clinical studies from ClinicalTrials.gov and other international registries.

Here’s the books I read in 2024. If I were Dudley Dursley, I’d be very upset that I read one fewer new book than in 2023. But then, I’d remember that I re-read a lot of Cosmere in 2024 to prepare for Wind and Truth , which was great.

I was working on making data about scholarly conferences more FAIR and a big question crossed my mind: what are all the conference venues? This post is about some queries I wrote for Wikidata, data issues I found, and a few drive-by curations that I did while looking for an answer, and my ideas for the future.

This stub post contains my notes about funding for open source software. It doesn’t follow a story like a lot of my posts, and is more like an ever-evolving notes sheet.

Brandon Sanderson has been releasing a few chapters a week of his upcoming novel, Wind and Truth, on his publisher’s website leading up to its December 6 ^th release. This includes the audiobook chapters, but they’re posted to Soundcloud and there’s no good way to listen at 1.6x speed. This post is a note sheet on how to download audio from Soundcloud and prepare it for my audiobook reader.

PEP 735 introduced dependency groups in packaging metadata, which are complementary to optional dependencies in that they might not correspond to features in the package, but rather be something like development or release dependencies. I am slowly working towards updating my cookiecutter template cookiecutter-snekpack to use PEP 735. So far, uv and tox have released support - all that’s left is ReadTheDocs.

Graphviz is software for graph visualization written in C. PyGraphviz provides a nice Python wrapper for it. The issue is that getting Python to know about the C headers changes every few months. I’ll try and keep this blog post updated every time there are some changes.

I’m working through making a contribution to pandoc that adds first-class support for author role annotations using the Contribution Role Taxonomy (CRediT) and also outputs compliant Journal Publishing Tag Set (JATS) XML. This has lead me down a (losing) journey with learning the Haskell programming language, so I thought I would post a short note on a function I tried to understand.

The International Society of Biocuration (ISB) partners with the journal Database to get discounts for its members when they publish there. This means the ISB’s executive committee needs to send a member list to the journal’s editor.