bridgedb / data

Repository to mimic the old data/gene_database/ API

data

Repository to mimic the old data/gene_database/ API, available at https://bridgedb.org/data/gene_database/.

The input is a JSON file from which the gene_database/readme.md is autogenerated with the scripts in this folder:

groovy update.groovy > docs/gene_database/readme.md

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

groovy makeGDBconfig.groovy

This conversion is automatically done by GitHub Actions. The same workflow also triggers the build and push workflow for the BridgeDB docker image.

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.

HTML page

The HTML page hosted by GitHub Pages is in this repository stored as a Markdown file, which is created from the JSON files. The Markdown contains Bioschemas annotation for the datasets. This annotation looks like this (created with the information in the JSON files):

{
  "@context": "https://schema.org/",
  "@type": "Dataset",
  "http://purl.org/dc/terms/conformsTo": {
    "@type": "CreativeWork",
    "@id": "https://bioschemas.org/profiles/Dataset/0.4-DRAFT/"
  },
  "name": "Ag_Derby_Ensembl_Metazoa_39.bridge",
  "description": "BridgeDb identifier mapping file for Anopheles gambiae for genes and proteins",
  "identifier": "10.5281/zenodo.3667670/Ag_Derby_Ensembl_Metazoa_39.bridge",
  "license": "https://zenodo.org/record/3667670/files/LICENSE?download=1",
  "keywords": "BridgeDb, mapping file, identifier, ELIXIR RIR, Anopheles gambiae, gene, protein",
  "url": "https://doi.org/10.5281/zenodo.3667670",
  "distribution": [
    {
      "@type": "DataDownload",
      "name": "Ag_Derby_Ensembl_Metazoa_39.bridge",
      "contentURL": "https://zenodo.org/record/3667670/files/Ag_Derby_Ensembl_Metazoa_39.bridge?download=1"
    }
  ],
  "isAccessibleForFree": true
}