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 “main” function:

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

1import refinegems as rg
2model_sboann = rg.sboann.sbo_annotation(<path to your model>)
3rg.io.write_to_file(model_sboann, <path to modified model>)

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