菜单
Use when the user has an SDRF file with known errors and wants them fixed automatically. Triggers on requests to fix, correct, or repair SDRF errors.
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
Independently falsify and review a created, modified, or proposed SDRF against its specification, ontology terms, source evidence, repository files, and experimental design. Use after SDRF annotation or repair, before contribution or completion, when a review gate reports a pending artifact, or whenever an isolated reviewer must distrust the producer's self-assessment and issue a hash-bound verdict.
Create or improve an SDRF through a producer-reviewer workflow with deterministic validation, an evidence manifest, fresh-context adversarial review, repair, and mandatory re-review. Use when an SDRF must be independently verified before completion or contribution, when the user requests adversarial review, or when automated review hooks require a passing hash-bound receipt.
Use when the user wants SDRF annotation to run as an autonomous retained-improvement loop over one dataset, a manifest, or a dataset class such as all PRIDE cell line or crosslinking datasets.
Use when the user has a completed SDRF annotation for a ProteomeXchange dataset and wants to contribute it back to the community via a PR to sdrf-annotated-datasets.
Use when the user wants a comprehensive quality review of an SDRF file, a PR review of an SDRF submission, or a quality score assessment.
Use before sdrf:autoresearch when the user needs to screen or shortlist proteomics studies from PRIDE, MassIVE, ProteomeXchange accessions, or a manifest using detailed user-defined inclusion/exclusion criteria; extract study-level metadata from repository records and publications; and write an evidence-backed TSV for downstream annotation, review, or meta-analysis.
| name | sdrf:fix |
| description | Use when the user has an SDRF file with known errors and wants them fixed automatically. Triggers on requests to fix, correct, or repair SDRF errors. |
| user-invocable | true |
| argument-hint | [file path or paste SDRF content] |
You are fixing known common errors in an SDRF file. Apply fixes systematically.
Verify that parse_sdrf is available (run parse_sdrf --version or which parse_sdrf). If it is not installed:
/sdrf:setup or conda env create -f environment.yml && conda activate sdrf-skills (or pip install -r requirements.txt)| 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.
| Wrong | Correct |
|---|---|
0000305 | EFO:0000305 |
9606 | NCBITaxon:9606 |
0002107 | UBERON:0002107 |
Fix: Detect bare numbers, infer ontology from column type, add prefix.
| 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).
| 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.
| 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.
| 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.
| 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.
| 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.
Fix: Trim all cell values and column names.
| 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="<instrument>", ontologyId="ms")
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)
After applying all fixes, always run programmatic validation before presenting results to the user.
git submodule update --remote --recursive
Save the fixed SDRF to a file and validate with the detected templates:
parse_sdrf validate-sdrf \
--sdrf_file fixed.sdrf.tsv \
--template <template1> \
--template <template2>
Detect templates from comment[sdrf template] columns in the SDRF.
If parse_sdrf is not installed, tell the user: pip install sdrf-pipelines
spec/sdrf-proteomics/TERMS.tsv and check allow_not_available/allow_not_applicable fieldsPresent 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.