psimod-validator 0.1.0

PSI-MOD validation and curation tools for quality control and data management

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