Workshop Biometadata-01 - Data deposition walkthrough1

Select your repository

Check for mandatory criteria or mandatory metadata fields

  • Look for mandatory fields in your selected repository
  • Watch for suggested metadata templates in your selected repository
  • Note whether specific units or value types are expected
  • Check if mandatory criteria include selection of terms from existing ontologies
    • If yes, use the filters of the OLS to refine your search and find relevant terms that apply to your dataset. For instance, for sequencing data, ENA requires terms from ENVO and/or UBERON ontologies for the metadata fields env_broad_scale, env_local_scale, env_medium
    • Use ontology annotators to look-up multiple terms

Assess the quality of ontology and their terms

  • Use the workshop’s criteria to ensure the ontology:
    • has sound terms definitions that you agree with
    • is actively developed and updated to reflect the scientific practices
    • has a community space to exchange with the community (tickets, issues)
    • has an adequate license and appropriate funding (for maintenance)

Fill out your metadata while you research

  • Use the generated metadata template and regularly update the metadata fields regarding your samples and research techniques

Upload your (meta)data before your desired publication date

  • Check if you can create a project in your desired repository in advance
  • Upload your metadata template or pre-fill the fields
  • Create an embargo if you need to delay the access to the data and metadata

Footnotes

  1. This document is available at https://doi.org/10.5281/zenodo.10605803 and is a supplement to the Workshop Biometadata-01 with examples from sequencing data.↩︎