Repository to mimic the old data/gene_database/ API.
The input is a JSON file from which the gene_database/readme.md is autogenerated
with the scripts in this folder:
groovy update.groovy > gene_database/readme.mdA second script generated gdb.config content for BridgeDb servers:
groovy makeGDBconfig.groovyThe data model for each identifier mapping file looks like this:
{
"species": "Human Coronaviruses",
"file": "humancorona-2021-11-27.bridge",
"downloadURL": "https://zenodo.org/record/5734440/files/humancorona-2021-11-27.bridge?download=1",
"doi": "10.5281/zenodo.5734440",
"license": "http://creativecommons.org/publicdomain/zero/1.0/",
"date": "2021-11-27",
"size": "2.1 MB"
}The species field is not always a species, like in the above example or for metabolites. The file and size fields
are the filename and exact size of the mapping file, and the downloadURL the exact URL to directly download
the Derby file ready for use. The doi and license field is the DOI and (open) license associated with the
data release.
For the date field, this is the data when the data was released. This could be the date when the archive was
released (so, the release date of the DOI record) or the data when the original data from which the Derby file
was created was released. For example, it could be the Ensembl release date for gene/protein mapping data.