![\"\"](\"/assets/images/bridgedbDownloadsImage.png\")
The BridgeDb project (doi:10.1186/1471-2105-11-5)\n(and ELIXIR recommended interoperability resource) has several\naims, all around identifier mapping:
\n\nThe last one is more recent and two aspects are under development here: secondary identifiers and dead identifiers. More\nabout that in some future post. About the first and the third I am also not going to tell much in this post. Just follow the\nabove links.
\n\nI do want to say something in this post about the actually identifier mapping databases, in particular those we distribute as\nApache Derby files, the storage format used by the Java libraries. These are the files you download if you want mapping databases\nfor PathVisio (doi:10.1371/journal.pcbi.1004085).\nBridgeDb has mapping files for various things and some example databases the data it maps between:
\n\nThe BridgeDb API is agnostic to the things it can map identifiers for.
\n\nDownloading mapping files:\nBridgeDb has an BioSchemas-powered\nweb page with an overview of the latest released mapping files.\nIt looks like this:
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This webpage is the result from the cyber attack in late 2019, disrupting a good bit of the infrastructure. This is why we\nrenewed the website, including the download page. The new page actually is hosted on GitHub as a Markdown file,\nbut this is where things get interesting. The Markdown file is actually autogenerated from a JSON file with all the info. Everything,\nincluding the BioSchemas annotation is created from that. Basically, JSON gets converted into Markdown (with a custom script), which\ngets converted into HTML by a GitHub Action/Pages. So, when someone releases a new mapping file on Zenodo or Figshare, they only have\nto send me a pull request with updated JSON file.
\n\nNow, previously, downloading all released mapping files, for example for the BridgeDb webservice, was a bit complicated. The\ninformation was a HTML file generated by the webserver for a folder. No metadata. Nuno wrote code to extract the relevant info\nand download all the files. However, since the information is now available in a public JSON file, it is a lot easier. The\nfollowing code uses wget and jq, two tools readily available on the popular operating systems. Have fun!
\n\n!/bin/bash\n\nwget -nc https://bridgedb.github.io/data/gene.json\nwget -nc https://bridgedb.github.io/data/corona.json\nwget -nc https://bridgedb.github.io/data/other.json\n\njq -r '.mappingFiles | .[] | \"\\(.file)=\\(.downloadURL)\"' gene.json > files.txt\njq -r '.mappingFiles | .[] | \"\\(.file)=\\(.downloadURL)\"' corona.json >> files.txt\njq -r '.mappingFiles | .[] | \"\\(.file)=\\(.downloadURL)\"' other.json >> files.txt\n\nfor FILE in $(cat files.txt)\ndo\n readarray -d = -t splitFILE<<< \"$FILE\"\n echo ${splitFILE[0]}\n wget -nc -O ${splitFILE[0]} ${splitFILE[1]}\ndone\nActually, while writing this blog post, I notice the code can be further simplified.
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