BioDownload

BioDownload is a small utility library used at the Robinson lab to download HPO, MONDO, UBERON, GO ontologies.

How to use

Once the library is added to a project, it can be used the following way:

First, create BioDownloaderBuilder and provide path to the folder where the files will be downloaded:

Path destination = Paths.get("destination");
BioDownloaderBuilder builder = BioDownloader.builder(destination);

Then, add resources for download by calling methods of the builder. For instance, download HPO JSON file and HP disease annotations:

builder.hpoJson()
  .hpDiseaseAnnotations();

Finally, get the downloader and download the files:

BioDownloader downloader = builder.build();
List<File> files = downloader.download();

The files are downloaded into the destination folder and paths to the downloaded files are returned in a List.