Earlier this week at the sixth NFDI4Chem consortium meeting, Torsten Schrade from the NFDI4Culture consortium gave a lovely and whimsical talk entitled A Data Alchemist’s Journey through NFDI which explored ways that we might federate and jointly query both consortia’s knowledge via their respective SPARQL endpoints.

Using standard CURIE prefixes and URI prefixes in semantic web artifacts such as Resource Description Framework (RDF) promotes interoperability, enables reuse in downstream data integration, and makes data more FAIR. The Bioregistry defines a set of standard CURIE prefixes and URI prefixes against which RDF files can be validated/standardized.

I’ve recently submitted an article to the Journal of Open Source Software (JOSS) describing chembl-downloader, a Python package for automating downloading and using ChEMBL data in a reproducible way. In this post, I use chembl-downloader to show how the number of compounds, assays, activities, and other entities in ChEMBL have changed over time.

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.

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.

I’ve spent the better part of this weekend putting OpenAI’s latest offerings through their paces - both the newly released open-weight models and GPT-5 itself. Armed with a selection of coding challenges, mathematical problems, and the sort of esoteric research queries that usually separate the wheat from the chaff, I’ve been conducting what amounts to a weekend-long torture test of these systems.

The Ontology Lookup Service (OLS) is now indexing dense embeddings for ontology terms constructed from term labels, synonyms, and descriptions using LLMs. I maintain a Python client library for the OLS (ols-client) and was recently asked to implement a wrapper to the OLS’s API endpoint that exposes these embeddings.

I have finally opened a Posts section on my website! Every post should now automatically get a DOI.

Introduction In scientific blogging, references and citations are essential. Unfortunately, Hugo’s support for citations is limited, see e.g. this discourse . So here’s a workflow for spacemacs that works for me. Editing Export to org with org-ref-export Export to hugo compatible markdown Workflow Editing I write my posts in spacemacs org-mode.

The Greeks loved oracles. The average temple of Apollo, who among others was in charge of soothsaying and predictery, was adorned to the gills with gifts from grateful worshippers whose inscrutable questions got equally inscrutable answers from Apollo’s oracles. None of these were more famous than the Pythia, the young ladies high as a kite on volcanic fumes at Apollo’s temple in Delphi.

There’s a curious terminological schism that nobody talks about at what passes for dinner parties for the AI crowd.