sdrf:contribute

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.

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.

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.

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.

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.

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.