This package orchestrate cMD metadata curation processes, including initiation, status check, and deploy. To contribute a new data to cMD, (Note: For cMD curation team, ODM should handle steps 3 and 4.)
- Look at the template and already curated studies to see what curated files should look like.
- To add a new study, open an issue using the template 'curatedMetagenomicData study curation by DOI'.
This will create two curation template files in a directory under
inst/curated.
- the name of the dedicated directory for your study is
{last name of the first author}{initial of the first author’s first name}_{year published}(e.g., 'AsnicarF_2017') - two files in this directories are
{dir_name}_study.tsvand{dir_name}_sample.tsv(e.g., 'AsnicarF_2017_study.tsv' and 'AsnicarF_2017_sample.tsv')
-
Starting from these templates, please curate your metadata. Commit and create a pull request. Or if you don't like git, use Github.com's "Upload Files" button to upload to create a pull request without the need to use git.
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Add a 'ready to review' label if your metadata is ready for the team's final review. cMD curation team will review/validate your metadata. If it passes, it will be added into cMD package. Any validation fails will be reported back to you for your revision/update.
Starting from the upcoming cMD4 release (expected Fall 2025), we are implementing new metadata schema. To help you understand this change, here are the metadata tables for 93 cMD3 studies following the current and new metadata schema.
The complete reference for curators is provided at this page's wiki.