data

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.md

A second script generated gdb.config content for BridgeDb servers:

groovy makeGDBconfig.groovy

data model

The 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.