sdrf-contribute

SDRF Contribution Workflow

Bundle paths. spec/, tools/ and data/ ship with this skill, not with your working directory. Resolve every such path below against the bundle root (SDRF_SKILLS_ROOT, else CLAUDE_PLUGIN_ROOT, else your sdrf-skills checkout): ${SDRF_SKILLS_ROOT:-${CLAUDE_PLUGIN_ROOT}}/spec/sdrf-proteomics/TERMS.tsv. The helpers are the sdrf-tools command (install notes: sdrf-annotate/references/setup.md; check with sdrf-tools doctor); no PYTHONPATH or bundle-root variable is needed to run them. Files the user is annotating stay relative to the working directory.

You are helping the user contribute an annotated SDRF file back to the community repository (bigbio/sdrf-annotated-datasets). This is the final step after annotation, validation, and review — closing the loop from "I annotated a dataset" to "the community can reuse it."

Step 1: Check Prerequisites

1.1 Verify the PXD accession

• A ProteomeXchange accession (PXD######) must be provided
• If not provided, ask the user for it

1.2 Verify the SDRF content

• The SDRF must be available as a file on disk or from a previous annotation step
• If the user just finished /sdrf-skills:sdrf-annotate, the content is in the conversation
• Ask the user to confirm the file path or provide the content

1.3 Check if this is a new annotation or an update

Check if the PXD already exists in the community repository (bigbio/sdrf-annotated-datasets):

Look for: datasets/{PXD}/{PXD}.sdrf.tsv

You can check via the GitHub API without cloning:

gh api repos/bigbio/sdrf-annotated-datasets/contents/datasets/{PXD} \
  --silent && echo "exists" || echo "new"

Classify at the level of the file you are about to write, not the directory. A PXD folder may legitimately hold several SDRFs with descriptive suffixes (PXD006430-tmt.sdrf.tsv + PXD006430-silac.sdrf.tsv), so an existing folder does not mean you are replacing anything:

gh api repos/bigbio/sdrf-annotated-datasets/contents/datasets/{PXD} \
  --jq '.[] | select(.name | endswith(".sdrf.tsv")) | .name' 2>/dev/null