Blue Brain Search and Graph Examples

How to Use

To use the BBS_BBG_poc notebook, first make sure to have Python version at least 3.7. To be able to install Blue Brain Search package correctly, it is also import to set up MySQL (see link) for instructions to install it depending on your OS). If necessary, create first a virtual environment.

python -m venv venv
source venv/bin/activate

Run the following commands to set everything up:

pip install --upgrade pip wheel setuptools
pip install --requirement requirements.txt

Next follow the instructions on the Blue Brain Search project page to setup the servers. In particular, it is important that the following environment variables are defined:

export DB_URL=<value>
export SEARCH_ENGINE_URL=<value>
export TEXT_MINING_URL=<value>

where <value> has to be replaced by the correct value. For instance, in case of the setup described by the Blue Brain Search - Getting Started, we shall use

export DB_URL=$HOSTNAME:$DATABASE_PORT/$DATABASE_NAME
export SEARCH_ENGINE_URL=http://$HOSTNAME:$SEARCH_PORT
export TEXT_MINING_URL=http://$HOSTNAME:$MINING_PORT

Next, set the paths to the Nexus-forge configuration and the ontology linking data as the following environment variables:

export ONTOLOGY_LINKING_DATA_FILE=<path_to_file>

An example of the ontology linking data can be found by the link (linking data corresponds to the csv table obtained by decompressing the file provided by the link).

Once everything is set up, you can run the notebook server.

jupyter-lab

The jupyter interface will open up in your default browser. Select and open the BBS_BBG_poc notebook and follow the instructions there. If the display of the widgets does not work, one also needs to enable the JupyterLab extension (check this link for the instructions).

For more information about the Search and Graph components, please refer to the corresponding project pages:

• Blue Search: https://github.com/BlueBrain/Search
• Blue Graph: https://github.com/BlueBrain/BlueGraph

Funding & Acknowledgment

This project was supported by funding to the Blue Brain Project, a research center of the Ecole polytechnique fédérale de Lausanne, from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.

COPYRIGHT (c) 2021-2022 Blue Brain Project/EPFL