Missing omim_to_mondo_dict.pkl file in data - how to generate/retrieve?

[poddarharsh15]

Hi @EmilyAlsentzer

Issue: preprocess_mygene2.py fails due to missing omim_to_mondo_dict.pkl

The data preparation script expects:

with open(str(project_config.PROJECT_DIR / 'omim_to_mondo_dict.pkl'), 'rb') as handle:
    omim_to_mondo_map = pickle.load(handle)

omim_to_mondo_dict.pkl is NOT provided in the data download links, and these issues

https://github.com/mims-harvard/SHEPHERD/issues/11
https://github.com/mims-harvard/SHEPHERD/issues/8

You DO provide orphanet_to_mondo_dict.pkl - what's the difference?

Where can we download omim_to_mondo_dict.pkl?

Thanks!