ebel 1.0.37

Installation

The easiest way to install ebel is to use docker-compose. See below instructions to use the docker installation.

ebel can be directly installed from PyPi with pip:

$ pip install ebel

But we want to encourage you to use the latest development version which can be installed with:

$ pip install git+https://github.com/e-bel/ebel

Package Requirements

wget https://repo1.maven.org/maven2/com/orientechnologies/orientdb-community/3.2.2/orientdb-community-3.2.2.tar.gz
tar -xvzf orientdb-community-3.2.2.tar.gz
cd orientdb-community-3.2.2/bin
./server.sh

sudo apt install mysql-server -y

sudo apt install mariadb-server -y

Configuration

Before you start working with e(BE:L), a simple to use wizard helps you to setup all configurations. Make sure OrientDB and MySQL (or MariaDB) are running. Then start the configuration wizard with:

ebel settings

The wizard will create the needed databases and users in OrientDB and MySQL/MariaDB.

Package Components

To test the different components you find here several BEL and already compiled JSON files.

BEL Validation

BEL is a domain-specific language designed to capture biological relationships in a computer- and human-readable format. The rules governing BEL statement generation can be quite complex and often mistakes are made during curation. e(BE:L) includes a grammar and syntax checker that reads through given BEL files and validates whether each statement satisfies the guidelines provided by BEL.bio. Should any BEL statement within the file not adhere to the rules, a report file is created by e(BE:L) explaining the error and offering suggested fixes.

You can use the following command to validate your BEL file:

$ ebel validate /path/to/bel_file.bel

In a single command, you can validate your BEL file as well as generate error reports if there are errors and if there are none, produce an importable JSON file:

$ ebel validate /path/to/bel_file.bel -r error_report.xlsx -j

BEL documents should be properly formatted prior to validation. e(BE:L) contains a repair tool that will check the format and it is highly recommended that this is used prior to validation. The repaired will overwrite the original if a new file path is not specified. Here is an example:

$ ebel repair /path/to/bel_file.bel -n /path/to/repaired_file.bel

Import Process

$ ebel set-mysql --host localhost --user root --password myPassWord --database ebel

$ ebel import-json /path/to/checked_bel.json -u root -p orientdbPassword -d ebel -h localhost -p 2424

$ ebel import-json /path/to/checked_bel.json

$ ebel import-json /path/to/bel_json/dir/

$ ebel import-json /path/to/checked_bel.json -e -g

$ ebel enrich

$ ebel enrich -i uniprot,hgnc

$ ebel enrich -s intact,kegg

Querying the Graph

Once the knowledge graph has been created (and optionally enriched), one can use e(BE:L) to query it directly.

from ebel import Bel
bel = Bel()

relation_query = "SELECT out.bel as subject, @class as relation, in.bel as object FROM bel_relation"
df = bel.query(relation_query)  # Returns results as pandas DataFrame
result_list = bel.query_get_dict(relation_query)  # Returns results as a list of dicts

To specify a different graph database to connect to than the one in your config file, you can pass connection parameters when initializing the Bel class:

from ebel import Bel
config_params = {
    "db": "my_db",
    "user": "superdude",
    "password": "password123",
    "server": "localhost",  # defaults to localhost if none given
    "port": "2424",  # defaults to 2424 if none given
}

bel = Bel(graph_config=config_params)

# To overwrite your default values in the config file
bel = Bel(graph_config=config_params, overwrite_config=True)

Docker installation

Make sure docker and docker-compose are installed.

docker-compose up --build -d
docker exec -it ebel_ebel ebel settings

Several question will follow. You can accept the default values (just press RETURN) except the following questions:

OrientDB server [localhost] ?
ebel_orientdb
OrientDB root password (to create database and users)
ebel
MySQL/MariaDB sever name [localhost]
ebel_mysql
MySQL root password (will be not stored) to create database and user
ebel

It’s strongly recommended, if you are using ebel in the production environment, to change the standard root MySQL and OrientDB passwords in the docker-compose.yml file.

To load example files in container and import.

docker exec -it ebel_ebel git clone https://github.com/e-bel/example_json_bel_files.git
docker exec -it ebel_ebel ebel import-json example_json_bel_files/phago.bel.json -e

To enrich the network:

docker exec -it ebel_ebel ebel enrich

Following services are now available:

1. OrientDB Studio

2. e(BE:L) REST server

3. phpMyAdmin

API

Finally, this package comes equipped with a built-in RESTful API using Flask. Users that have a running and populated set of databases can also create a running API server which contains several queries for retrieving information from both the network itself, as well as the downloaded enrichment information stored in the SQL database.

This server can be activated using:

$ ebel serve

You can also specify certain parameters as options:

$ ebel serve -p 5000 --debug-mode

Disclaimer

e(BE:L) is a scientific software that has been developed in an academic capacity, and thus comes with no warranty or guarantee of maintenance, support, or back-up of data.