Skip to content

Filter out TrEMBL protein nodes from EC ontology transform #479

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Filter out TrEMBL protein nodes from EC ontology transform #479

Changes from 1 commit
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 4 additions & 3 deletions kg_microbe/transform_utils/ontologies/ontologies_transform.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -472,9 +472,10 @@ 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:"]
Copy link

Copilot AI Dec 23, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The "TrEMBL:" prefix is hardcoded as a string literal, which is inconsistent with the codebase pattern. The UNIPROT_PREFIX constant is imported from constants.py (line 47), but no corresponding TREMBL_PREFIX constant exists. Consider defining a TREMBL_PREFIX constant in kg_microbe/transform_utils/constants.py (similar to UNIPROT_PREFIX at line 452) and importing it here for consistency and maintainability.

Copilot uses AI. Check for mistakes.
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
Expand Down