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Assume all CURIEs are valid
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cthoyt committed Oct 12, 2023
1 parent 74d154d commit 4aee4e3
Showing 1 changed file with 1 addition and 5 deletions.
6 changes: 1 addition & 5 deletions src/semra/sources/biopragmatics.py
Original file line number Diff line number Diff line change
Expand Up @@ -67,10 +67,6 @@ def _process(mapping_dicts, confidence: float = 0.999) -> list[Mapping]:
mapping_set = MappingSet(name="biomappings", confidence=confidence, license="CC0", version=biomappings_version)
rv = []
for mapping_dict in tqdm(mapping_dicts, unit_scale=True, unit="mapping", desc="Loading biomappings", leave=False):
try:
p = Reference.from_curie(mapping_dict["relation"])
except ValueError:
continue # TODO fix speciesSpecific
source_prefix = mapping_dict["source prefix"]
target_prefix = mapping_dict["target prefix"]
author = Reference.from_curie(mapping_dict["source"])
Expand All @@ -79,7 +75,7 @@ def _process(mapping_dicts, confidence: float = 0.999) -> list[Mapping]:
prefix=source_prefix,
identifier=bioregistry.standardize_identifier(source_prefix, mapping_dict["source identifier"]),
),
p=p,
p=Reference.from_curie(mapping_dict["relation"]),
o=Reference(
prefix=target_prefix,
identifier=bioregistry.standardize_identifier(target_prefix, mapping_dict["target identifier"]),
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