RO-Crate for Biodiversity Genomics

UNDER CONSTRUCTION

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

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.

View an example RO-Crate which follows the profile here: HTML preview, JSON-LD.

Example crate details

The 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.

For developers – scripts and examples

See Developer Notes.