This is a first draft currently in active development. Everything is subject to change.

See BGE Profile, currently under construction.

The make_crate.py script creates an example crate that represents the profile.

Currently the script is more defined than the profile text.

To run the make_crate.py script you must install the requirements listed in requirements.txt.

The script automatically runs 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 script generates an RO-Crate in the bge-crate folder. To generate a HTML preview of the crate (useful for checking things are linked as intended):

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

The example is built using information about the following mosquito genomes:

1. Culex laticinctus
   SAMEA114402090, SAMEA114402091, SAMEA114402094, SAMEA114402071
   ERX12519568, ERX12433627, ERX12405204, ERX12405205
   GCA_964187845.1, GCA_964187835.1
   https://github.com/ERGA-consortium/EARs/blob/main/Assembly_Reports/Culex_laticinctus/idCulLati1/idCulLati1_EAR.pdf

2. Culex theileri
   SAMEA114402095, SAMEA114402096, SAMEA114402099, SAMEA114402076
   ERX13020690, ERX12671962, ERX12671963
   GCA_964340515.1, GCA_964340705.1
   https://github.com/ERGA-consortium/EARs/blob/main/Assembly_Reports/Culex_theileri/idCulThei1/idCulThei1_EAR.pdf

3. Culex perexiguus
   SAMEA114402089, SAMEA114402085, SAMEA114402086, SAMEA114402066
   ERX12317846, ERX12326304, ERX12519566
   GCA_964243045.1, GCA_964248615.1
   https://github.com/ERGA-consortium/EARs/blob/main/Assembly_Reports/Culex_perexiguus/idCulPerx1/idCulPerx1_EAR.pdf

4. Culex modestus
   SAMEA114402100, SAMEA114402102, SAMEA114402103, SAMEA114402081
   ERX12326303, ERX12317845, ERX12519565
   GCA_964213205.1, GCA_964213185.1
   https://github.com/ERGA-consortium/EARs/blob/main/Assembly_Reports/Culex_modestus/idCulMode1/idCulMode1_EAR.pdf

Project Coordination: Maria Jose Ruiz Lopez Sample Collection: Maria Jose Ruiz Lopez, Sonia Cebrián-Camisón, Sergio Magallanes, Josué Martínez-de la Puente, Jordi Figuerola Species Identification: Jordi Figuerola, Sonia Cebrián-Camisón Sample Preservation: Sonia Cebrián-Camisón Metadata Provision: Maria Jose Ruiz Lopez DNA Extraction & Sequencing: Caroline Howard, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team Genome Assembly: Shane McCarthy, Kerstin Howe, Mark Blaxter, Wellcome Sanger Institute Tree of Life Core Informatics team

(Genome Assembly Review: Jèssica Gómez-Garrido (perexiguus & laticinctus), Fernando Cruz (modestus) & Tom Brown (theileri)

When substantial changes are made to the code, the example-bge-crate/ folder should also be updated with the generated example crate and the HTML preview.

• 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/