Installation

To use the current version of BENT it is required:

• OS: Debian>=11/Ubuntu>=20.04

• • Python >=3.7, <=3.10.13

• Required space between 5.5 GB - 10 GB * Dependencies: 2.5 GB * Data: between 3.0 GB (base) or 7.5 GB (if you use all available knowlegde bases for Named Entity Linking)

pip installation

Install the BENT package using pip:

pip install bent

The following knowledge bases can be configured:

• ‘medic’ (MEDIC)

• ‘do’ (Disease ontology)

• ‘chebi’ (ChEBI ontology)

• ‘ctd_chem’ (CTD-Chemicals)

• ‘ncbi_gene’ (NCBI Gene)

• ‘ctd_gene’ (CTD-GENES)

• ‘ncbi_taxon’ (NCBI Taxonomy)

• ‘go_bp’ (Gene Ontology-Biological Process)

• ‘ctd_anat’ (CTD-Anatomy)

• ‘fma’ (Foundation model of Anatomy)

• ‘uberon’ (UBERON ontology)

• ‘go_cc’ (Gene Ontology-Cellular Component)

• ‘cell_ontology’ (Cell Ontology)

• ‘cellosaurus’ (Cellosaurus)

After the pip installation, it is required a further step to install non-Python dependencies and to download the necessary data. Run in the command line:

bent_setup

Only the default knowledge bases ‘medic’ and ‘chebi’ will be available at this point.

To disable annoyng messages in the terminal run:

export TF_CPP_MIN_LOG_LEVEL='3'

Docker image

If you have Docker installed in your system, you can pull the BENT Docker image (~15 GB) from Docker Hub and run a container on Debian Gnu/Linux 12 with Python 3.10.13

Pull the Docker image:

::

docker pull pedroruas18/bent

Then start a container using the built image.

Get additional knowlegde bases

You can download more knowledge bases later by specifying the desired knowledge bases among the ones that are available:

python -c "from bent.get_kbs import get_additional_kbs;get_additional_kbs([<kb1>, <kb2>])"

Example: to download the NCBI Taxonomy and the NCBI Gene run:

python -c "from bent.get_kbs import get_additional_kbs;get_additional_kbs(['ncbi_taxon', 'ncbi_gene'])"

Alternatively, you can add your own knowledge base from text files (see ‘Upload custom knowledge base/graph/ontology’ in Usage)