In 1790, the French Academy of Sciences commissioned a rather ambitious survey. The goal was to measure the distance from the North Pole to the Equator along the meridian passing through Paris, then use that measurement to define a new universal unit of length: the metre.

This is the second of a two-part post about encoding databases as ontologies. In the first part, I gave a background on how I started working on this problem and the software stack I developed along the way. In this post, I explain the philosophy and design about how I encoded the HGNC (HUGO Gene Nomenclature Committee) database as an ontology using PyOBO.

This is the first of a two-part post about encoding databases as ontologies. In this post, I give a background on the problems in biocuration that led me to start encoding databases as ontologies, the software I have written to do it, and the repository I have created to store the resulting artifacts in a FAIR, open, and sustainable way.

Roughly 541 million years ago, something extraordinary happened in Earth’s oceans. Over a geologically brief period of perhaps 20 million years, the fossil record explodes with an almost obscene diversity of body plans.

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. He proposed a toy example in which he linked paintings depicting alchemists trying to make gold to compounds containing gold.

Around two years ago, almost to the day, I spent an absolutely frantic evening in Berkeley, going through enough coffee to power a mid-sized city, hammering away at my laptop on trying to figure out what comes after LLMs. What to most people was still barely on the horizon at the time has been a subject I have been working on in various capacities for the best part of the past decade, on and off.

There’s a cave in Ethiopia, in an area called Dikika. At some point, around 3.4 million years ago, an early hominin made some incisions on an animal carcass, leaving some notches on a bone as the makeshift knife cut past the muscle and sinew into the bone, tell-tale kerf marks that speak of the first time one of our ancestors used a tool. ¹ What happened in that cave changed everything for our species. ¹ McPherron, S.

I was looking at the different NFDI consortia in the Research Organization Registry (ROR), and found that the only two that have a parent relations to the NFDI (ror:05qj6w324) are NFDI4DS (ror:00bb4nn95) and MaRDI (ror:04ncnzm65). This felt strange to me, so I started looking around Wikidata to see if I could automatically make a curation sheet to send along to them.

I became aware of just while watching Hynek’s second video on uv a few months ago. I immediately fell in love with its elegance and simplicity, so I have begun replacing task running in my repositories that relied on tox with just. This post gives a bit of background, context, and walks through making the switch on one of my repositories that has some annoying dependencies.

When Pygmalion carved Galatea from ivory, he fell so deeply in love with his creation that he begged Aphrodite to bring her to life. The goddess, moved by his devotion, granted his wish. ¹ It’s a beautiful myth about art, obsession and the blurring lines between creation and creator. What the myth doesn’t tell us is whether Galatea charged a monthly subscription fee. ¹ Ovid, Metamorphoses , Book 10, 243-297.

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.