SBOannotator with refineGEMs

RefineGEMs offers access to the functionalities of SBOannotator[1].

The sboann module is splitted into a lot of small functions which are all annotated, however when using it for SBO-Term annotation it only makes sense to run the function sbo_annotation:

refinegems.sboann.sbo_annotation(model_libsbml: libsbml.Model) → libsbml.Model

Executes all steps to annotate SBO terms to a given model (former main function of original script by Elisabeth Fritze)

Args:

• model_libsbml (libModel): Model loaded with libsbml

Returns:

libModel: Modified model with SBO terms

import refinegems as rg
model_sboann = rg.sboann.sbo_annotation(<path to your model>)
rg.io.write_to_file(model_sboann, <path to modified model>)

If you use it from the refineGEMs toolbox with the config you can get a visualization of the SBO-Term distribution before and after the SBO-Term update.

[1]

Nantia Leonidou, Elisabeth Fritze, Alina Renz, and Andreas Dräger. Sboannotator: a python tool for the automated assignment of systems biology ontology terms. bioRxiv, February 2023. URL: https://doi.org/10.20944/preprints202302.0317.v1, doi:10.20944/preprints202302.0317.v1.