claude

sdrf-skills

SDRF annotation skills - expert-level proteomics metadata workflows for AI assistants

19 on GitHubby Yasset Perez-Riverolv0.2.0MITupdated 18 days agodomain-specific
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Plugin sdrf-skills from marketplace sdrf-skills in bigbio/sdrf-skills. Commands read from the repo's manifest — 18 days ago.

This plugin runs code on your machine — its hooks fire automatically on events like tool use and it starts local MCP servers. The exact commands are listed below; read them before installing.

What it installs

Skills (4)

  • sdrf-adversarial-review

    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 when

  • sdrf-annotate

    Use for anything about one SDRF file - create it from a PXD accession (always followed by an independent review), review, validate, check, score or fix an existing .sdrf.tsv, look up a cell line or an ontology term, verify technical metadata from raw files, plan what to capture before there is a fil

  • sdrf-campaign

    Use when the user wants to run an SDRF annotation campaign over a class of studies rather than one dataset — screen or shortlist proteomics studies from PRIDE, MassIVE or ProteomeXchange against user-defined inclusion criteria and write an evidence-backed resumable TSV, then annotate the included da

  • sdrf-contribute

    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.

MCP servers (1)

  • sdrf-pride-pmc

    runs: ${CLAUDE_PLUGIN_ROOT:-.}/.venv/bin/python ${CLAUDE_PLUGIN_ROOT:-.}/mcp/server.py

Hooks (2)

  • SessionStart

    bash "${CLAUDE_PLUGIN_ROOT}/hooks/check-deps.sh"

  • Stop

    python3 "${CLAUDE_PLUGIN_ROOT}/tools/review_gate.py" stop-hook

View source on GitHub sdrf.quantms.org

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