القائمة
Use when the user wants to improve an existing SDRF file strictly according to SDRF templates and specification rules (no speculative additions).
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
| name | sdrf:improve |
| description | Use when the user wants to improve an existing SDRF file strictly according to SDRF templates and specification rules (no speculative additions). |
| user-invocable | true |
| argument-hint | [file path or paste SDRF content] |
You are improving an SDRF file using ONLY specification/template rules.
Do not suggest additions based on:
If a change is not justified by template metadata (required/recommended) or
TERMS.tsv rules, do not recommend it.
spec/sdrf-proteomics/TERMS.tsvspec/sdrf-proteomics/sdrf-templates/templates.yamlspec/sdrf-proteomics/sdrf-templates/{name}/{version}/{name}.yaml for each template in useFor affinity-proteomics, align with the official template/spec rules:
affinity-proteomicsolink OR somascan (mutually exclusive)comment[sdrf template] columns (NT/VV format).Do not "upgrade" template versions automatically. If a newer version exists, report it as an optional migration task.
Construct an explicit checklist from template YAML files:
not available, not applicable, pooled) via TERMS.tsv flagsFor affinity-proteomics specifically, ensure checks include:
comment[platform] (required)comment[panel name] (recommended)comment[quantification unit] (optional; values include NPX/RFU in spec)comment[normalization method] (optional)comment[fraction identifier] (optional)And for child templates:
olink.yamlsomascan.yamlClassify findings into these categories only:
recommended in active templatesDo not include free-form "quality" recommendations outside A/B/C.
Report every finding with source traceability:
required / recommended / optional)Example format:
Finding: Missing column `comment[panel name]`
Severity: recommended
Source: spec/sdrf-proteomics/sdrf-templates/affinity-proteomics/1.0.0/affinity-proteomics.yaml
Action: Add `comment[panel name]` with panel identifier values.
Before modifying file contents:
Required fixes can be applied directly if the user asked to "fix all required issues."
The goal is strict conformance improvement, not curation enrichment.
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.