sdrf:fix

To fix SDRF file formatting errors, this skill identifies and corrects UNIMOD accession mismatches, adds missing ontology prefixes, and resolves case inconsistencies automatically. It then re-runs parse_sdrf validation to ensure your proteomics metadata passes compliance checks.

SDRF validation often fails due to UNIMOD swaps, missing ontology prefixes, or case inconsistencies. This skill detects these common formatting issues, applies automated corrections, and provides a detailed changelog to ensure your file meets the proteomics metadata standard.

Correcting proteomics metadata generates an automated changelog detailing every modification. This report includes the specific row, column, old value, new value, and rationale for each fix applied to your SDRF file, ensuring full transparency for your data submission.

Yes, SDRF error correction supports optional OLS lookup for ontology validation. This feature verifies ontology terms and prefixes while fixing formatting issues, ensuring your proteomics metadata remains accurate and compliant with required standards before downstream analysis.

Common SDRF formatting issues include UNIMOD accession mismatches, missing ontology prefixes, and case inconsistencies. These errors prevent successful validation, but this skill automatically detects and corrects them to prepare your proteomics study data for submission.

Fixing an SDRF file corrects common formatting errors like UNIMOD mismatches and prefix gaps, then re-runs parse_sdrf validation to report any remaining problems. While it resolves standard formatting issues, complex structural errors may require manual review.