From 4aee4e3530772d619afdb9c3965f151f2a56c02b Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 12 Oct 2023 12:16:25 +0200 Subject: [PATCH] Assume all CURIEs are valid Follow-up to https://github.com/biopragmatics/biomappings/pull/123 --- src/semra/sources/biopragmatics.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/src/semra/sources/biopragmatics.py b/src/semra/sources/biopragmatics.py index 3f98cb5..aae22ab 100644 --- a/src/semra/sources/biopragmatics.py +++ b/src/semra/sources/biopragmatics.py @@ -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"]) @@ -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"]),