RO-Crate for Biodiversity Genomics

Note: This is a first draft currently in active development.

RO-Crate Profile for Biodiversity Genomics Europe

A RO-Crate profile for biodiversity genomics is being developed as part of the BGE project.

Read the profile here: BGE Profile.

There are two example RO-Crates which follow the profile:

• Genome example: HTML preview, JSON-LD.
• Barcode example: HTML preview, JSON-LD.

Example crate details

Genome example

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

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

Future examples may describe the following genomes:

1. 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

2. 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

3. 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-genome/ folder should also be updated with the generated example crate and the HTML preview.

Barcode example

The barcode example is built using metadata retrieved from BOLD for the Process ID MHMXN361-07. The script make_crate_barcode.py is used to generate the example.

Examples can also be made using BGE-related process IDs such as BHNHM001-24 - the process ID can simply be swapped in the make_crate_barcode.py script. The reason for not using a BGE record is that these do not yet have GenBank Accessions, as these barcodes are not yet submitted to ENA, therefore related metadata cannot yet be fetched using the accession.

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

For developers – scripts and examples

See Developer Notes.

Licensing

Profile Crates and JSON-LD examples within this specification are distributed under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.

Other files, including the specification text and helper scripts, are licensed under the Apache License, Version 2.0.