Earlier this week, a question was asked on OBO Foundry Slack on where to find semantic mappings to terms in the Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT). While some are available in the SeMRA Disease Mappings Database, there are many more available within BioPortal, which has access to the entire SNOMED-CT source data and has produced semantic mapping predictions using LOOM.
Hype, slop, craft: the evolutionary ecology of AI There’s a patch of ground near Chernobyl that botanists call Рудий ліс, the Red Forest. In the immediate aftermath of the 1986 disaster, 1 the radiation killed mostly everything, turning the pine trees a rust-red colour before they died. That’s poetic, but hardly unexpected – not even Polesian pines can withstand a firehose of low enriched uranium decay products.
A much cited essay by Bret Victor, "Explorable Explanations", argues for supporting and encouraging active reading in communicating ideas. Explanatory text should thus be complemented by interactive visualizations and computational demonstrations, allowing the reader to actively engage with the ideas. If you haven't read Victor's essay yet, please do so now, and then come back here. It's not very long.
The Latin verb agere means “to do, to act, to drive forward”. From it we get not only “agent” but also “action”, “actor”, and curiously enough, “agile”. The Romans understood what we seem to have forgotten: that agency is fundamentally about motion, about transformation, about the capacity to change the world.
This is about the time of year when I get the sudden and irresistible urge to make kimchi.
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.