Download curated SBML models from BioModels

The Systems Biology Markup Language (SBML) is the de facto standard to encode biological and biomedical models. As it turns out, I worked quite a bit with models encoded in SBML. For example, part of the experiments I ran for my PhD thesis consists in converting reaction-based models (encoded in SBML) into Boolean networks (encoded in the bnet format).

My dataset is made of SBML models stored in the curated branch of the repository BioModels. At the time of the experiments, I used the latest archive available at that time on the ftp of ebi (release r31 from 2017-06-26).

Since then, a new archive has been released (from 2023-09-13) but it seems empty (??? oO).

I wanted a method to update my dataset whenever I am pleased, as well as to retrieve a bunch of info available on BioModels website (such as the figures used for the model curation). I decided to go with a custom python script that scraps the website of BioModels.

---updated on 20240116---
You can **dl my script** along with **the resulting archive** containing all the 1059 sbml files it downloads, from the curated branch of BioModels. Note that in BioModels, the filenames are not standardised and that I renamed all the models with the same pattern : BIOMD_ID.sbml. Also, my script relies on a tons of hacks to manage a bunch of exceptions inherent to web scrapping. Feel free to reach out and propose changes.
Anyway. Enjoy !

Alternative programming methods to dive into BioModels (which I did not used, for various reasons):