sdrf-skills
01Plugin Claude Code
SDRF annotation skills — expert-level proteomics metadata workflows for AI assistants.
15 yesterday A
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original MIT
sdrf-skills
02Cursor rule Cursor
Structured skills for expert-level SDRF (Sample and Data Relationship Format) annotation in proteomics.
15 yesterday A 0 tokens
original MIT
MCP server Claude CodeCodexCursor +2
MCP server "sdrf-pride-pmc" as configured in bigbio/sdrf-skills. Runs mcp/server.py with ./.venv/bin/python.
15 yesterday A
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original MIT
Instructions file
Instructions for bigbio/sdrf-skills, covering claude.md, what this repo is, commands, tools cli (no consolescripts; requires cwd == repo root) and architecture.
15 yesterday A 5,429 tokens
original MIT
Instructions file Gemini CLI
Instructions for bigbio/sdrf-skills, covering sdrf-skills — sdrf annotation skills, available workflows, specification data and key rules.
15 yesterday A 987 tokens
original MIT
SessionStart
06Hook
Runs when a session starts on startup, resume, clear and compact, running an inline shell check. From bigbio/sdrf-skills.
15 yesterday A
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original MIT
Stop
07Hook
Runs when the agent finishes a response, executing review_gate.py via python3. From bigbio/sdrf-skills.
15 yesterday A
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original MIT
Skill Claude CodeCodex
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…
15 yesterday A 83 tokens
original MIT
Skill Claude CodeCodex
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…
15 yesterday A 75 tokens
original MIT
Skill Claude CodeCodex
Use when the user wants to create or annotate an SDRF file for a proteomics dataset. Also use to plan what metadata to capture and discuss experimental design/strategy before creating the file. Triggers on PXD accessions, requests to create SDRF, planning/strategy questions, or annotation tasks.
15 yesterday A 68 tokens
original MIT
Skill Claude CodeCodex
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.
15 yesterday A 48 tokens
original MIT
Skill Claude CodeCodex
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 (CVCLXXXX), or "annotate cell line" requests.
15 yesterday A 83 tokens
original MIT
Skill Claude CodeCodex
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.
15 yesterday A 46 tokens
original MIT
sdrf:convert
14Skill Claude CodeCodex
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.
15 yesterday A 36 tokens
original MIT
sdrf:design
15Skill Claude CodeCodex
Use when the user wants to analyze the experimental design encoded in an SDRF file, check for batch effects, confounders, or replication issues.
15 yesterday A 36 tokens
original MIT
sdrf:fix
16Skill Claude CodeCodex
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.
15 yesterday A 39 tokens
original MIT
Skill Claude CodeCodex
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, wants a plain-language explanation of a column/error/concept, or needs to find/verify/compare ontology terms and accessions for a column. Also…
15 yesterday A 81 tokens
original MIT
Skill Claude CodeCodex
Use when the user needs to screen or shortlist proteomics studies from PRIDE, MassIVE, or ProteomeXchange accessions, or from a manifest, using detailed user-defined inclusion/exclusion criteria — run this before sdrf:autoresearch; extract study-level metadata from repository records and publications; and write an…
15 yesterday A 88 tokens
original MIT
sdrf:review
19Skill Claude CodeCodex
Use when the user wants a comprehensive quality review of an SDRF file, a PR review of an SDRF submission, a quality score assessment, or to improve/score an existing SDRF strictly against templates and specification rules (specificity, completeness, consistency; no speculative additions).
15 yesterday A 62 tokens
original MIT
sdrf:setup
20Skill Claude CodeCodex
Use when the user wants to set up SDRF skills dependencies, install parsesdrf and techsdrf, or configure the environment for the first time.
15 yesterday A 39 tokens
original MIT
Skill Claude CodeCodex
Use when the user wants to refine or verify SDRF technical metadata (instrument, tolerances, modifications, DDA/DIA) using raw MS file analysis via techsdrf.
15 yesterday A 45 tokens
original MIT
Skill Claude CodeCodex
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.
15 yesterday A 41 tokens
original MIT
Skill Claude CodeCodex
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.
15 yesterday A 42 tokens
original MIT