# -*- coding: utf-8 -*-
"""Align EDAM with the Bioregistry."""
from typing import Mapping
from bioregistry.align.utils import Aligner
from bioregistry.external.edam import get_edam
__all__ = [
"EDAMAligner",
]
[docs]class EDAMAligner(Aligner):
"""Aligner for the EDAM ontology."""
key = "edam"
getter = get_edam
alt_key_match = "name"
curation_header = ("name", "description")
[docs] def get_skip(self) -> Mapping[str, str]:
"""Get entries that should be skipped and their reasons."""
return {
"1164": "MIRIAM URI not relevant",
"1175": "BioPAX ontologies aren't globally unique",
"2582": "GO sub-hierarchy",
"2583": "GO sub-hierarchy",
}
if __name__ == "__main__":
EDAMAligner.cli()