sdrf:contribute

Submit validated SDRF annotations as pull requests to the bigbio/proteomics-sample-metadata GitHub repository.

11|9|Updated Mar 18, 2026

Search Tags:#pull request #community #github #validation #annotation #proteomics #sdrf

Ready to run

npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-contribute

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: sdrf:contribute
Source: https://github.com/bigbio/sdrf-skills/tree/main/skills/sdrf-contribute
Command: npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-contribute

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This skill streamlines the final step of sharing a completed SDRF annotation for a ProteomeXchange dataset, ensuring the contribution is correctly validated, formatted, and submitted as a pull request to the community repository.

Core Features & Use Cases

Validation: Checks SDRF file integrity and runs optional validation before submission.
Automated PR creation: Generates fork, branch, commit, and PR using the GitHub CLI when available.
Guided contribution: Provides copy‑paste commands for environments without the CLI.
Supports new and update submissions: Handles both fresh annotations and updates to existing entries.

Quick Start

Ask the assistant to submit your annotated SDRF for a specific PXD accession to the community repository.

Frequently Asked Questions about sdrf:contribute

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I submit a proteomics SDRF annotation to a GitHub community repository?▼

To submit an SDRF annotation, you create a pull request on the bigbio/proteomics-sample-metadata GitHub repository using the GitHub CLI or manual git commands. The process requires a validated SDRF file and a specific ProteomeXchange PXD accession number.

What is the process for creating a pull request for a validated SDRF file?▼

Creating a pull request for a validated SDRF file involves generating a fork, creating a branch, committing the file, and pushing it to the community repository. This skill automates these steps using the GitHub CLI or provides copy-paste commands for manual execution.

Do I need the GitHub CLI installed to contribute an SDRF annotation?▼

No, you do not need the GitHub CLI installed to contribute an SDRF annotation. If the CLI is unavailable, the skill provides guided copy-paste git commands so you can manually execute the fork, branch, commit, and pull request steps.

Can I update an existing SDRF annotation for a ProteomeXchange dataset?▼

Yes, you can update an existing SDRF annotation for a ProteomeXchange dataset. The submission process handles both fresh annotations and updates to existing entries by adhering to the repository's file naming and directory conventions.

How does SDRF validation work before submitting a proteomics dataset?▼

SDRF validation works by checking file integrity and running optional validation checks before submission. This ensures your completed SDRF annotation for a ProteomeXchange dataset is correctly formatted before creating a pull request to the community repository.

Why is my SDRF annotation pull request failing repository conventions?▼

Your SDRF annotation pull request may be failing due to incorrect file naming or directory placement. You must strictly adhere to the bigbio/proteomics-sample-metadata repository conventions and ensure your SDRF file is validated for the specific PXD accession.