# 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.

- **Type:** Skill
- **Install:** `agentstack add skill-bigbio-sdrf-skills-sdrf-contribute`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [bigbio](https://agentstack.voostack.com/s/bigbio)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [bigbio](https://github.com/bigbio)
- **Source:** https://github.com/bigbio/sdrf-skills/tree/main/skills/sdrf-contribute
- **Website:** https://sdrf.quantms.org

## Install

```sh
agentstack add skill-bigbio-sdrf-skills-sdrf-contribute
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# SDRF Contribution Workflow

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: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`):
```text
Look for: datasets/{PXD}/{PXD}.sdrf.tsv
```

You can check via the GitHub API without cloning:
```bash
gh api repos/bigbio/sdrf-annotated-datasets/contents/datasets/{PXD} \
  --silent && echo "exists" || echo "new"
```

- **New annotation**: The PXD folder does not exist → this is a new contribution
- **Update**: The PXD folder already exists → this updates an existing annotation
- Report which case it is to the user

## Step 2: Validate Before Contributing

Before contributing, the SDRF must pass validation:

1. **Suggest programmatic validation**:
   ```bash
   pip install sdrf-pipelines
   parse_sdrf validate-sdrf --sdrf_file {PXD}.sdrf.tsv
   ```

2. **Optionally run `/sdrf:validate`** for a thorough check including ontology verification

3. **Check file structure**:
   - All rows have the same number of columns (no ragged rows)
   - No trailing whitespace in column names or values
   - File is valid TSV (tab-delimited)
   - File extension is `.sdrf.tsv`

Do NOT proceed to contribution if there are validation errors.
Warnings are acceptable — mention them but allow the user to proceed.

## Step 3: Prepare the File

### 3.1 File naming convention
The community repository (`bigbio/sdrf-annotated-datasets`) uses this structure:
```text
datasets/
└── {PXD}/
    └── {PXD}.sdrf.tsv
```

For datasets with multiple sub-experiments:
```text
datasets/
└── {PXD}/
    ├── {PXD}-celllines.sdrf.tsv
    └── {PXD}-tissues.sdrf.tsv
```

### 3.2 Save the file
Save the SDRF content to the correct path:
```text
{PXD}/{PXD}.sdrf.tsv
```

Ensure the file:
- Uses tab delimiters (not spaces or commas)
- Has a single trailing newline at the end
- Has no BOM (byte order mark)
- Uses Unix line endings (LF, not CRLF)

## Step 4: Contribute

Ask the user which mode they prefer:

### Mode A — Automated (recommended if `gh` CLI is available)

Execute the full contribution flow:

```bash
# 1. Fork the repository (if not already forked)
gh repo fork bigbio/sdrf-annotated-datasets --clone=false

# 2. Clone the user's fork
gh repo clone {username}/sdrf-annotated-datasets /tmp/sdrf-annotated-datasets
cd /tmp/sdrf-annotated-datasets

# 3. Create a branch
git checkout -b annotation/{PXD}

# 4. Create the directory and copy the file
mkdir -p datasets/{PXD}
cp {source_path}/{PXD}.sdrf.tsv datasets/{PXD}/

# 5. Commit
git add datasets/{PXD}/
git commit -m "Add SDRF annotation for {PXD}"

# 6. Push
git push -u origin annotation/{PXD}

# 7. Create the PR
gh pr create \
  --repo bigbio/sdrf-annotated-datasets \
  --title "Add SDRF annotation for {PXD}" \
  --body "$(cat <<'EOF'
## Add SDRF annotation for {PXD}

**Dataset**: [{PXD}](https://www.ebi.ac.uk/pride/archive/projects/{PXD})
**Organism**: {organism}
**Templates**: {template_list}
**Rows**: {row_count} | **Columns**: {col_count}
**Factor values**: {factor_description}

### Validation
- [x] Validated with `sdrf-pipelines validate-sdrf`
- [x] Ontology terms verified via OLS

### Annotation source
Annotated using [sdrf-skills](https://github.com/bigbio/sdrf-skills).
EOF
)"
```

Before executing, present the full plan to the user and ask for confirmation.
Fill in the template variables from the SDRF content:
- `{organism}`: from `characteristics[organism]` unique values
- `{template_list}`: from `comment[sdrf template]` columns
- `{row_count}`: number of data rows (excluding header)
- `{col_count}`: number of columns
- `{factor_description}`: from `factor value[...]` column names and unique values

### Mode B — Guided (show commands for the user to run)

Present the same sequence of commands as Mode A, but as a copyable code block
with all variables already filled in. The user copies and executes them.

Preface with:
```text
Here are the commands to contribute your SDRF annotation to the community repository.
Copy and run them in your terminal:
```

### For updates to existing annotations

If the PXD already exists, adjust:
- PR title: `Update SDRF annotation for {PXD}`
- Commit message: `Update SDRF annotation for {PXD}`
- PR body: add a "Changes" section explaining what was updated
- Branch name: `annotation/{PXD}-update`

## Step 5: Post-Contribution

After the PR is created:

1. **Show the PR URL** so the user can track it
2. **Explain the review process**:
   - Community reviewers will check the annotation for correctness
   - Automated CI will run `sdrf-pipelines validate-sdrf` on the PR
   - Reviewers may request changes (more specific ontology terms, missing columns, etc.)
   - Once approved, the annotation is merged and available to the community
3. **Thank the user** for contributing to the community annotation effort
4. **Mention impact**: The annotation will be available in PRIDE's SDRF Explorer and
   usable by analysis pipelines (quantms, sdrf-pipelines) for automated reprocessing

## Important Rules

- NEVER create a PR without user confirmation
- NEVER skip validation before contributing
- NEVER modify the SDRF content during the contribution step (that's what `/sdrf:fix` and `/sdrf:improve` are for)
- If the user doesn't have `gh` CLI installed, always fall back to Mode B (guided commands)
- If the user doesn't have a GitHub account, explain that one is needed and point to https://github.com/signup
- For non-PXD accessions (MSV, PMID), the same workflow applies — just use the accession as the folder name

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [bigbio](https://github.com/bigbio)
- **Source:** [bigbio/sdrf-skills](https://github.com/bigbio/sdrf-skills)
- **License:** MIT
- **Homepage:** https://sdrf.quantms.org

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-bigbio-sdrf-skills-sdrf-contribute
- Seller: https://agentstack.voostack.com/s/bigbio
- Browse the marketplace: https://agentstack.voostack.com/browse

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