draeger-lab / refinegems

refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).
https://refinegems.readthedocs.io/en/latest/
MIT License
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Connect the `polish` module to the bioregistry API #91

Closed GwennyGit closed 11 months ago

GwennyGit commented 1 year ago

Describe the bug If a model contains an annotation containing the string seed.reactions the corresponding URI is incorrect. Currently, polish only takes the database prefix from the URI and changes the separator between the database prefix and the local unique identifier. However, this should be changed as otherwise incorrect database prefixes are kept.

Expected behaviour Change incorrect database prefixes.

Considered solutions

=> I will adjust polish to use the bioregistry API.

GwennyGit commented 11 months ago

Successfully connected the polish module to the bioregistry API. Closing this issue now.