RO-Crate for Biodiversity Genomics

Developer Notes

These notes are relevant to the GitHub repository for the profile: https://github.com/eScienceLab/bge-ro-crate-profile.

Code

The make_crate_genome.py and make_crate_barcode.py scripts create example crates that represent the profile.

Currently the scripts are more defined than the profile text.

To run the scripts you must install the requirements listed in requirements.txt.

The scripts automatically run validation against the RO-Crate 1.1 specification when generating the RO-Crate. This should tell you if you did anything wrong according to the base spec (but does not mean that all entities are linked correctly).

The scripts generate RO-Crates in the bge-crate-genome and bge-crate-barcode folders respectively. To generate a HTML preview of the crate (useful for checking things are linked as intended):

npm install ro-crate-html
rochtml bge-crate-genome/ro-crate-metadata.json

Where to find useful metadata and identifiers

• People: https://orcid.org/
• Organizations: https://ror.org/
• Places: https://www.geonames.org/v3/
• Taxonomy: https://www.ncbi.nlm.nih.gov/taxonomy
• BioProjects: https://www.ncbi.nlm.nih.gov/search/ (though at time of writing, search results may give 500 errors)
• Protocols: https://protocols.io/
• Samples (example accession SAMEA114402090):
  • https://www.ebi.ac.uk/ena/browser/ (preferred)
  • https://www.ebi.ac.uk/biosamples/
• Sequencing experiments (example accession ERX12519568):
  • https://www.ebi.ac.uk/ena/browser/ (preferred)
  • https://www.ncbi.nlm.nih.gov/sra
• Assembled genome (example accession GCA_964187845.1):
  • https://www.ebi.ac.uk/ena/browser/ (preferred)
  • https://www.ncbi.nlm.nih.gov/datasets/genome/