OntoGene Bio Term Hub

The Bio Term Hub (BTH) is an aggregator of biomedical terminologies sourced from manually curated databases.

Setup/Installation

To initiate a running instance with a web interface and an automatic updater, a few steps are necessary:

• Paths and other configuration parameters must be adapted in bth/core/settings.py.
• Change into the directory containing this file and run make. This will create empty directories and log files according to the configuration in settings.py.
• The run executable provides a command-line interface to the BTH. Call it as ./run CMD [OPTIONS], where CMD can be "server" or "aggregate", among others.
• To start a web server, call eg. ./run server -i localhost -p 1234, then point your browser to http://localhost:1234. Before starting the server for the first time, you should initialise the resource cache with ./run fetch-remote all.
• Optional: In order to include UMLS identifiers (CUIs), run make umls-cuis. This will download a Bash script to bth/update/curl-uts-download.sh. Edit this file to include your personal UTS credentials at the top. Then execute ./run extract-umls-cuis -f to download all of UMLS and extract the relevant CUI entries (this will take a while).

Python Package Structure

Subpackages:

• bth.core: global settings, central resource compiler
• bth.inputfilters: separate modules for each input resource
• bth.lib: helpers
• bth.server: run the BTH as a web server
• bth.stats: counting and plotting
• bth.update: fetch up-to-date original-resource dumps

License

Licensed under the AGPL-3.0 License, see LICENSE.