PSI-MOD Curator
Validation and curation tools for the PSI-MOD protein modification ontology. Focuses on structure validation using RDKit, cross-reference checking, and mass/formula consistency.
Installation
uvx psimod-validator
or
pipx run psimod-validator
Usage
Command Line
# Validate entire ontology
psimod-validator validate PSI-MOD.obo
# Validate and auto-fix issues (writes PSI-MOD.fixed.obo)
psimod-validator validate PSI-MOD.obo --fix
# Strict mode (warnings become errors)
psimod-validator validate PSI-MOD.obo --strict
# JSON or Markdown output
psimod-validator validate PSI-MOD.obo --format json -o report.json
# Check specific terms
psimod-validator check --ontology PSI-MOD.obo MOD:00046 MOD:00047
# Verify cross-references online (slow)
psimod-validator validate PSI-MOD.obo --check-online
Python API
from psimod_validator import PsiModValidator
validator = PsiModValidator("PSI-MOD.obo")
report = validator.validate_all()
print(f"Errors: {report.error_count}")
print(f"Warnings: {report.warning_count}")
print(f"Fixable: {len(report.fixable_issues)}")
for issue in report.errors:
print(f"{issue.mod_id}: [{issue.category}] {issue.message}")
Validation Rules
| Category | What it checks | Severity |
|---|---|---|
| SMILES | Parseable by RDKit, canonical form, valence errors, undefined stereocenters | ERROR / WARNING |
| Backbone | Dummy atom patterns via SMARTS, term_spec consistency | WARNING / ERROR |
| Mass | SMILES-computed mass/formula vs MassMono/Formula annotations | ERROR (fixable) |
| Charge | RDKit formal charge vs FormalCharge annotation | ERROR (fixable) |
| Xref | Unimod/UniProt PTM/Origin format, optional online verification | ERROR / WARNING |
| Structure | Term name, definition, parent relationships | ERROR / WARNING / INFO |
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