Odessit007

Readability and best practices | Type hinting for add_features in module 3 code

1

It seems to be a better practice to use generic type hints in such cases (it looks nicer and doesn't get notifications from some IDEs like PyCharm)

Random state doesn't work with metric='precomputed'

2

Hi. I'm facing an unexpected reproducibility issue with my dataset. I have quite a large matrix and doing some hyperparameter tuning that includes UMAP. To optimize run time, I cached...

Potential bug | ValueError: identifier already in use when loading MONDO ontology

1

Hi. Thank for the great package. Unfortunately, I encountered an issue while trying to load [MONDO](https://mondo.monarchinitiative.org/) ontology in RDF/XML format using ``` import pronto o = pronto.Ontology.from_obo_library('mondo.owl') ``` I'm getting...

Possible issue | non-MONDO term in is_a clause

5

I see in the latest mondo.obo PATO:0000001 being is_a term for MONDO:0021125. Is this intended or a bug because several tools that I use t parse OBO files fail on...