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Filter out TrEMBL protein nodes from EC ontology transform #479

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Merged
realmarcin merged 3 commits into from
Dec 23, 2025
Merged

Filter out TrEMBL protein nodes from EC ontology transform #479

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16321e8
Filter out TrEMBL protein nodes from EC ontology transform
realmarcin Dec 23, 2025
4fe320e
Correct misleading comment in Rhea mappings transform
realmarcin Dec 23, 2025
201cb9e
Replace hardcoded TrEMBL prefix with TREMBL_PREFIX constant
realmarcin Dec 23, 2025
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1 change: 1 addition & 0 deletions kg_microbe/transform_utils/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -450,6 +450,7 @@
UNIPROT_DISEASE_COLUMN_NAME = "Involvement in disease"
UNIPROT_GENE_PRIMARY_COLUMN_NAME = "Gene Names (primary)"
UNIPROT_PREFIX = "UniprotKB:"
TREMBL_PREFIX = "TrEMBL:"
CHEMICAL_TO_PROTEIN_EDGE = "biolink:binds"
# PROTEIN_TO_GO_EDGE = "biolink:enables"
PROTEIN_TO_ORGANISM_EDGE = "biolink:derives_from"
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8 changes: 5 additions & 3 deletions kg_microbe/transform_utils/ontologies/ontologies_transform.py
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Expand Up @@ -45,6 +45,7 @@
UNIPATHWAYS_REACTION_PREFIX,
UNIPATHWAYS_XREFS_FILEPATH,
UNIPROT_PREFIX,
TREMBL_PREFIX,
XREF_COLUMN,
)
from kg_microbe.utils.ontology_utils import replace_category_ontology
Expand Down Expand Up @@ -472,9 +473,10 @@ def _fix_ec_iri(line, iri_index):
line = _replace_special_prefixes(line)
new_ef_lines.append(line)
if name == "ec":
# Remove Uniprot nodes since accounted for elsewhere
new_nf_lines = [line for line in new_nf_lines if UNIPROT_PREFIX not in line]
new_ef_lines = [line for line in new_ef_lines if UNIPROT_PREFIX not in line]
# Remove UniProt and TrEMBL nodes since accounted for elsewhere
protein_prefixes = [UNIPROT_PREFIX, TREMBL_PREFIX]
new_nf_lines = [line for line in new_nf_lines if not any(prefix in line for prefix in protein_prefixes)]
new_ef_lines = [line for line in new_ef_lines if not any(prefix in line for prefix in protein_prefixes)]
# elif name == "rhea":
# # Remove debio nodes that account for direction, since already there in inverse triples
# # Note that CHEBI and EC predicates do not match Rhea pyobo, so removing them
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2 changes: 1 addition & 1 deletion kg_microbe/transform_utils/rhea_mappings/rhea_mappings.py
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Expand Up @@ -319,7 +319,7 @@ def run(self, data_file: Union[Optional[Path], Optional[str]] = None, show_statu
all_terms_writer.writerow(
[*subject_info, *predicate_info, *object_info]
)
# Filter out TrEMBL/UniProt entries - they should not be added
# Only include CHEBI, EC, and GO entries (filter out UniProt entries)
if any(
object_info[0].startswith(prefix)
for prefix in [
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