Charles Tapley HoytOct 15

in my first double blog post ever, I wrote about encoding databases as ontologies, the PyOBO software package, and the design choices and philosophy behind the HGNC (@genenames) to ontology converter.

1️⃣ background and software - https://cthoyt.com/2025/10/14/databases-as-ontologies-1-background.html

2️⃣ case study with HGNC https://cthoyt.com/2025/10/14/databases-as-ontologies-2-hgnc.html

#foss #floss #reproducibility #owl #obo #ontologies #ontology #biopragmatics #fair

Databases as Ontologies Part 1 - Background and Software

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. See also the second part which describes how I applied these tools to encode the HGNC (HUGO Gene Nomenclature Committee) database as an ontology.

Biopragmatics
BioregistryMay 22, 2023

The Bioregistry resource pages now show project logos! Thanks for the suggestion @Cmungall and the implementation @cthoyt

Here's how it looks for @wikipathways (see yourself at https://bioregistry.io/wikipathways)

#python #semanticweb #foss #bioregistry #biopragmatics #biocuration

Bioregistry - WikiPathways

An open source, community curated registry, meta-registry, and compact identifier (CURIE) resolver.