The Bioregistry is a database and toolchain for standardization of prefixes, CURIEs, and URIs that appear in linked (open) data. While I created it in 2019 as a component of PyOBO in order to support parsing database cross-references appearing in biomedical ontologies, it has since become an independent project with a community-driven governance model and much broader applications. This post is a first attempt to quantify its usage and impact.

Best AI for R, the weight of a cell, R+MCP, AI is a mass delusion event, AI hiring freezes, Quarto+Positron, biology moonshots, Julia for R users, AI hallucination, nf-core advisories...

The Bioregistry is a community-driven registry of semantic spaces and their metadata. When I learned about BiomarkerKB at the International Society for Biocuration’s 18th Annual International Biocuration Conference, I was excited to curate new records (and prefixes) in the Bioregistry to cover BiomarkerKB’s semantic spaces on biomarkers.

Kürzlich ist eine von Jens Eder (Filmuniversität Babelsberg KONRAD WOLF, Potsdam) verfasste Publikation im Open Access erschienen, die durch den Publikationsfonds des Landes Brandenburg gefördert wurde.

That's a wrap for the next decade with Aarhus 2025, where I presented our paper on "Steps towards an Ecology for the Internet". I was a little unsure about how to approach the presentation, largely because the ideas seem a little crazy if they'd been proposed even a year ago! Luckily my co-authors strengthened my spine with encouragement and gin, and the event was tremendous fun packed with useful insights.

I am pleased to share that our research group is a partner of the “Berlin – City of Open Knowledge for Academia, Administration, Civil Society & Culture” conference. The conference will take place on October 23, 2025, from 9:30 AM to 4:30 PM, as part of the international Open Access Week 2025. This event will bring together experts, practitioners, and engaged citizens to explore the future of open knowledge-sharing in Berlin.

Rodrigo Mop, DR © Oleo pastel en papel Ciudad de México, 2025 Sitio del autor Esta es una reproducción digital, con fines de divulgación, de una obra original proporcionada por su autor o propietario. Todos los derechos están reservados por el artista.

Genome annotation, viral genome clustering, metagenomic diagnostics, SV analysis on ONT reads, functional prediction, gene loss, DNA damage/repair, CRISPR metagenomics, LLM lit review, ...

We are so happy to announce the release of a new package, dcmdata. The goal of dcmdata is to provide easy access to data sets that can be used for demonstrating and testing diagnostic classification models (DCM; also called cognitive diagnostic models [CDMs]). You can install dcmdata from CRAN with: install.packages("dcmdata") This blog post will highlight the major features and plans for future development.

Note This is a version of the AI course policy I’m introducing this semester. 🚫 When in doubt: No. There is no aspect of this course for which it is recommended, appropriate, or acceptable to turn to a Large Language Model (more commonly called an AI) such as ChatGPT. This includes: Working on graded assignments, quizzes, or discussion prompts. As a supplement to the readings or course notes.

There are a number of galaxies that have been reported to lack dark matter. This is weird in a universe made of dark matter. It is also weird in MOND, which (if true) is what causes the inference of dark matter. So how can this happen?