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.
Connect polish.get_set_of_curies() to the dictionaries mapping database names to database prefixes in the module cvterms to retrieve valid database prefixes -> Impossible as not all possible combinations of a database prefix can be mapped to the correct database prefix version!
Or correct with bioregistry API? 🤔 -> Correction with bioregistry API not possible BUT bioregistry API can be used in polish to ensure MIRIAM compliance of the annotation strings
=> I will adjust polish to use the bioregistry API.
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
polish.get_set_of_curies()
to the dictionaries mapping database names to database prefixes in the modulecvterms
to retrieve valid database prefixes -> Impossible as not all possible combinations of a database prefix can be mapped to the correct database prefix version!polish
to ensure MIRIAM compliance of the annotation strings=> I will adjust
polish
to use the bioregistry API.