Sdrf:fix

SDRF Auto-Fix Workflow

You are fixing known common errors in an SDRF file. Apply fixes systematically.

Step 0: Check parse_sdrf availability

Verify that parse_sdrf is available (run parse_sdrf --version or which parse_sdrf). If it is not installed:

• Inform the user that re-validation after fixes will need to be done manually
• Suggest /sdrf:setup or conda env create -f environment.yml && conda activate sdrf-skills (or pip install -r requirements.txt)
• Continue with the fixes; the user can validate later once dependencies are installed

Common Error Patterns and Their Fixes

1. UNIMOD Accession Swaps (45% of all errors)

| Wrong | Correct | Modification | |-------|---------|-------------| | UNIMOD:21 for Acetyl | UNIMOD:1 | Acetyl | | UNIMOD:1 for Phospho | UNIMOD:21 | Phospho | | UNIMOD:34 for Oxidation | UNIMOD:35 | Oxidation | | UNIMOD:35 for Methyl | UNIMOD:34 | Methyl |

Fix: Parse NT= field, look up correct UNIMOD accession, replace AC= field.

2. Missing Ontology Prefix (30%)

| Wrong | Correct | |-------|---------| | 0000305 | EFO:0000305 | | 9606 | NCBITaxon:9606 | | 0002107 | UBERON:0002107 |

Fix: Detect bare numbers, infer ontology from column type, add prefix.

3. Case Normalization (25%)

| Wrong | Correct | |-------|---------| | Male | male | | Female | female | | Homo Sapiens | Homo sapiens | | Not Available | not available |

Fix: Lowercase sex values and reserved words. Organism names follow binomial rules (capital genus, lowercase species).

4. Python/Programming Artifacts (15%)

| Wrong | Correct | |-------|---------| | ['breast cancer'] | breast cancer | | nan | not available | | None | not available | | "" | (empty or not available) |

Fix: Strip brackets, quotes; replace nan/None with reserved words.

5. Reserved Word Standardization

| Wrong | Correct | |-------|---------| | N/A | not applicable | | NA | not available | | n/a | not applicable | | unknown | not available | | null | not available | | - | not available |

Fix: Replace with correct SDRF reserved words.

6. DIA/DDA Terminology

| Wrong | Correct | |-------|---------| | data-dependent acquisition | Data-Dependent Acquisition | | data-independent | Data-Independent Acquisition | | DDA | Data-Dependent Acquisition | | DIA | Data-Independent Acquisition |

Fix: Use the ontology-standard full name.

7. Age Format

| Wrong | Correct | |-------|---------| | 58 years | 58Y | | 58 | 58Y | | 6 months | 6M | | 14 days | 14D | | 58yo | 58Y |

Fix: Extract number, map unit to Y/M/D suffix.

8. Modification Parameter Format

| Wrong | Correct | |-------|---------| | Carbamidomethyl (C) | NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed | | Oxidation (M) | NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable | | NT=Acetyl;AC=UNIMOD:1;TA=Protein N-term | NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable |

Fix: Parse free-text mods, construct proper NT/AC/TA/MT format.

9. Trailing Whitespace

Fix: Trim all cell values and column names.

10. Instrument Format

| Wrong | Correct | |-------|---------| | Q Exactive | AC=MS:1001911;NT=Q Exactive | | Orbitrap Fusion Lumos | AC=MS:1002732;NT=Orbitrap Fusion Lumos |

Fix: If missing AC= format, search OLS MS ontology and construct proper format.

mcp OLS → searchClasses(query="", ontologyId="ms")

Fix Procedure

1. Parse the SDRF into a structured table
2. Scan every cell for each error pattern above
3. Apply fixes — for ontology-dependent fixes, verify via OLS before changing
4. Log changes — track every change made (row, column, old value, new value, reason)
5. Present changelog to user before outputting the fixed SDRF
6. Output the corrected SDRF as a TSV code block

Changelog Format

Changes Applied:
  Row 3, comment[modification parameters]:
    OLD: NT=Acetyl;AC=UNIMOD:21;TA=Protein N-term;MT=Variable
    NEW: NT=Acetyl;AC=UNIMOD:1;PP=Protein N-term;MT=Variable
    FIX: UNIMOD:21 is Phospho, not Acetyl. Correct accession is UNIMOD:1. Also TA→PP for position.

  Row 5, characteristics[sex]:
    OLD: Male
    NEW: male
    FIX: Sex values must be lowercase per SDRF specification.

  All rows, comment[data file]:
    FIX: Trimmed trailing whitespace from 12 values.

Summary: 15 fixes applied (3 UNIMOD corrections, 5 case fixes, 7 whitespace trims)

Step After Fixes: Re-Validate with sdrf-pipelines

After applying all fixes, always run programmatic validation before presenting results to the user.

1. Update spec to latest version

git submodule update --remote --recursive

2. Run sdrf-pipelines validation

Save the fixed SDRF to a file and validate with the detected templates:

parse_sdrf validate-sdrf \
  --sdrf_file fixed.sdrf.tsv \
  --template  \
  --template 

Detect templates from comment[sdrf template] columns in the SDRF. If parse_sdrf is not installed, tell the user: pip install sdrf-pipelines

3. Interpret results

1. If validation passes → present the changelog + fixed SDRF to the user
2. If validation finds new errors → fix them and re-run until clean
3. Verify fixed UNIMOD accessions match the NT= modification names
4. Read spec/sdrf-proteomics/TERMS.tsv and check allow_not_available/allow_not_applicable fields
5. Count: total fixes applied, remaining issues not auto-fixable

Present the re-validation summary alongside the changelog.

If all errors are fixed and the SDRF is for a ProteomeXchange dataset (PXD accession), suggest contributing the corrected annotation via /sdrf:contribute {PXD} to the sdrf-annotated-datasets community repository.

When NOT to Auto-Fix

• Values that might be intentionally different (ask the user)
• Ontology terms where the "correct" version is ambiguous
• Missing columns (suggest but don't add without user approval)
• Factor values (design decisions — always ask)
• Cell line names (need Cellosaurus verification)
• Organism names that might be intentional (e.g., hybrid organisms)

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: bigbio
• Source: bigbio/sdrf-skills
• License: MIT
• Homepage: https://sdrf.quantms.org

Install and usage instructions live in the source repository linked above.