Annotations in the SBML-qual files

[lunaticstarr]

I found that all SBMl-qual models in the models folder contains no annotation strings, e.g., gene/protein identifiers or resources of the interactions. However, from the source files of certain models, i can see some of them do contain annotations.
Is there a way to get annotations in the SBML-qual files?

[daemontus]

Hi! Great question!

Since this collection was originally intended to serve as a benchmark database, we did not really consider how to properly preserve all model metadata throughout the validation/normalization steps... Alas, they are useful for some applications, so we are working on incorporating this in the future.

Unfortunately, I can't promise how close that future is yet :/ We should be able to get it done in the following year, but probably not in the next month or two.

Until then, I guess the best course of action is to use the .sbml files from the source directory (at least for models that have them, for the other models, we don't really have any metadata anyway). If the model had some issues, those should generally be fixed in the source files too (for models where we fixed issues, there should be the original .raw.sbml version, and then the fixed .sbml file). Would that work for you for now?

[lunaticstarr]

Thanks for the reply. Yes, and I think the annotation would be really useful in many applications when people want to reproduce or reuse previous published models.
The reason I am asking this is because I am working on annotating SBML models and would like to extend it to SBML-qual models. I am looking for some testing data for building an automatic tool, and this looks like a really comprehensive dataset - I appreciate your effort in putting together them, and look forward to the new feature!