sdrf-skills

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.

Use when the user wants to create or annotate an SDRF file for a proteomics dataset. Triggers on PXD accessions, requests to create SDRF, or annotation tasks.

Use when the user wants to set up SDRF skills dependencies, install parse_sdrf and techsdrf, or configure the environment for the first time.

Use when the user wants to validate an SDRF file, check for errors, or verify ontology terms. Triggers on requests to check, validate, or review SDRF content.

Use when the user needs to look up cell line metadata or enrich an SDRF with cell-line-derived characteristics (organism, disease, sex, sampling site, ancestry, age). Triggers on cell line names (HeLa, MCF-7, A549, …), Cellosaurus accessions (CVCL_XXXX), or "annotate cell line" requests.

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.

Use when the user wants to improve an existing SDRF file strictly according to SDRF templates and specification rules (no speculative additions).

Use when the user asks about SDRF templates, wants to select templates for an experiment, or needs to understand template layers, inheritance, mutual exclusivity, and selection rules.

Use when the user wants to plan what metadata to capture for a new experiment, or discuss experimental design and SDRF strategy before creating the file.

Use when the user wants to refine or verify SDRF technical metadata (instrument, tolerances, modifications, DDA/DIA) using raw MS file analysis via techsdrf.

Use when the user wants to choose an analysis pipeline, check SDRF compatibility with a pipeline, or understand how to go from SDRF to analysis.

Use when the user wants to analyze the experimental design encoded in an SDRF file, check for batch effects, confounders, or replication issues.

Use when the user asks about SDRF concepts, columns, errors, format rules, or wants to understand why something is done a certain way.

Use when the user asks about the SDRF format, column naming rules, ontology mappings, modification format, reserved words, label types, or any SDRF specification question. Also serves as background knowledge for all other SDRF skills.

Use when the user needs to find, verify, or compare ontology terms for SDRF columns. Triggers on questions about ontology terms, accessions, or which term to use.