compath 0.1.2

A web application for exploring and comparing the overlaps across pathway resources

An integrative and extensible web application for exploring, analyzing, and curating pathway databases. ComPath is publicly 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:

• Bio2BEL KEGG

• Bio2BEL Reactome

• Bio2BEL WikiPathways

• Bio2BEL MSig

New pathway/gene signatures resources can be added by forking the ComPath Template Repository.

Citation

If you use ComPath in your work, please cite [1]:

[1]

Domingo-Fernández, D., et al. (2019). ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases. npj Syst Biol Appl., 5(1):3.

Installation

compath can be installed easily from PyPI with the following code in your favorite terminal:

python3 -m pip install compath

or from the latest code on GitHub with:

python3 -m pip install git+https://github.com/bio2bel/compath.git@master

Setup

Easiest

After installing compath, run from the command line:

python3 -m compath populate

This command populates all of the relevant Bio2BEL repositories for the default list, and if any optional ComPath repositories have been registered with entry points, will also populated.

For Developers

If you just cloned the repo and installed it from the source code, you can run the sh script load_compath.sh by typing sh load_compath.sh in 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 ‘Mapping across gene/protein identifiers’ 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 ls in 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.

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:

1. python3 -m pip install bio2bel_hgnc

2. python3 -m bio2bel_hgnc populate

Running the Web Application

The application can be run simply with

python3 -m compath web

This command the Flask development server locally, by default on port 5000 (http://localhost:5000).

Curation Interface

Load mappings between pathways directly from the ComPath Curation package.

python3 -m compath load_mappings --connection="sqlite:////data/bio2bel.db"

Load hierarchical mappings from a pathway database already containing that information (e.g., Reactome).

python3 -m compath load_hierarchies --connection="sqlite:////data/bio2bel.db"

Create a user.

python3 -m compath manage --connection="sqlite:////data/bio2bel.db" users make_user  'email' 'password'

Make user admin.

python3 -m compath manage --connection="sqlite:////data/bio2bel.db" users make_admin 'email'

Docker Instructions

Deployment of ComPath with Docker

1. Build the container with compath as a name.

docker build -t compath:0.0.1 .

2. Create the data container in which the data will be located.

docker create -v /data --name compath-data compath:0.0.1

3. Run docker container and connect it with the data container

docker run --name=compath --volumes-from compath-data --restart=always -d compath:0.0.1

For admin purposes and deploying ComPath inside Fraunhofer you can also run the following command

sh create_and_build_container.sh

Load Data

Loads the KEGG, Reactome, and WikiPathways modules into ComPath.

docker exec -t -it compath /opt/compath/src/bin/load_data.sh

Restart Container

Restarts the compath container

docker restart compath