An interactive and extensible web application for comparative analysis of pathway databases. ComPath is available at https://compath.scai.fraunhofer.de/.
This package exposes the Bio2BEL pathway packages into a web application containing multiple built-in visualization and analytics tools allowing for their analysis and comparison. By default, this packages wraps the following default packages:
New pathway/gene signatures resources can be added by forking the ComPath Template Repository.
How to Use¶
Install and load the required packages
If you just cloned the repo, you can run the sh script “load_compath.sh” by typing
sh load_compath.shin your terminal. This script will first install all packages and later populate the database.
If you have already installed the packages, but not loaded the data. First, load Bio2BEL HGNC (see next section). Next, load all individual pathway database packages KEGG, Reactome, WikiPathways, and MSigDB with
python3 -m compath populate. This command assumes that these packages are already installed in your Python environment. You can check the packages installed by running
python3 -m compath lsin your terminal. Alternatively, you can populate each package independently by running:
python3 -m bio2bel_kegg populate,
python3 -m bio2bel_reactome populate,
python3 -m bio2bel_wikipathways populate, or
python3 -m bio2bel_msig populate.
The final step is to start the web application locally (runs by default on port 5000 -> http://localhost:5000) by running
python3 -m compath web
Mapping across gene/protein identifiers¶
In order to load the gene sets from default packages, ComPath assumes that Bio2BEL HGNC has been already installed and populated. This package is required to perform the mapping from multiple Protein/Gene identifiers to HGNC symbols. The following steps are needed to install Bio2BEL HGNC:
python3 -m pip install bio2bel_hgnc
python3 -m bio2bel_hgnc populate