biokb-chebi 0.1.0

A Python package to import ChEBI data in MySQL and Neo4J

-ChEBI

• allows to import ChEBI into relational database (like MySQL, sqlite, POSTGres), create RDF triples (turtles) and import the triples into graph database (Neo4J).
• Provides REST API and CLI to run the steps.
• is part of the biokb python package family which allow to combine knowledge graphs from different domain in the context of biology and medicine.

Installation

If uv is installed:

uv venv
source .venv/bin/activate
uv pip install biokb_chebi

Otherwise:

python3 -m venv .venv
source .venv/bin/activate
pip install biokb_chebi

Quick Start

biokb_chebi run-api

http://localhost:8000/docs#/

1. Import data
2. Export ttls
3. Import Neo4J

Create turtles and import into Neo4J

For docker just replace podman with docker in the commands below.

biokb_chebi create-ttls
podman run -d --rm --name biokb-neo4j -p7474:7474 -p7687:7687 -e NEO4J_AUTH=neo4j/neo4j_password neo4j:latest
# Remove `--rm` if you want to keep the container after stopping it.
# wait a bit until Neo4J is started
biokb_chebi import-neo4j -p neo4j_password

http://localhost:7474 (user/password: neo4j/neo4j_password)

podman stop biokb-neo4j

Run as Podman/ Docker container

For docker just replace podman with docker in the commands below.

Build & run with Podman:

git clone https://github.com/biokb/biokb_chebi.git
cd biokb_chebi
podman build -t biokb_chebi .
podman run -d --rm --name biokb_chebi -p 8000:8000 biokb_chebi

• Login: admin
• Password: admin

With environment variable for user and password for more security:

podman run -d --rm --name biokb_chebi -p 8000:8000 -e API_PASSWORD=your_secure_password -e API_USER=your_secure_user biokb_chebi

http://localhost:8000/docs

On the website:

1. Import data
2. http://localhost:8000/docs#/Database%20Management/get_report_export_ttls__get

Neo4j import in this context is not possible because Neo4J is not running as service.

Run as Podman/Docker networked containers with Neo4J and MySQL

Build & run with Docker:

git clone https://github.com/biokb/biokb_chebi.git
cd biokb_chebi
podman-compose -f docker-compose.db_neo.yml --env-file .env_template up -d

http://localhost:8000/docs

stop with:

docker stop biokb_chebi

rerun with:

docker start biokb_chebi

Run with MySQL and Neo4J as podman-compose services

git clone https://github.com/biokb/biokb_chebi.git
cd biokb_chebi 
podman-compose -f docker-compose.db_neo.yml --env-file .env_template up -d
podman-compose --env-file .env_template up -d

In production copy .env_template to .env and use secure passwords (and skip --env-file .env_template in the last command)!

podman-compose -f docker-compose.db_neo.yml --env-file .env_template up -d
podman-compose --env-file .env_template up -d

http://localhost:8001/docs

On the website:

1. Import data
2. Export ttls
3. Import Neo4J

CLI

Install with

pip install biokb_chebi

Import data into relational database

Usage: biokb_chebi import-data [OPTIONS]

biokb_chebi import-data

-> SQLite database in ~/.biokb/biokb.db. Open with e.g. DB Browser for SQLite

Option	long	Description	default
-f	--force-download	Force re-download of the source file	False
-k	--keep-files	Keep downloaded source files after import	False
-c	--connection-string TEXT	SQLAlchemy engine URL	sqlite:///chebi.db

If you want to use different relational database (MySQL, PostgreSQL, etc.), provide the connection string with -c option. Examples:

• MySQL: mysql+pymysql://user:password@localhost/biokb
• PostgreSQL: postgresql+psycopg2://user:password@localhost/biokb

For more examples please check how to create database URLs

Create RDF turtles

Usage: biokb_chebi create-ttls [OPTIONS]

biokb_chebi create-ttls

-> RDF turtles will be created in ~/.biokb/chebi/data/ttls.zip

Option	long	Description	default
-c	--connection-string TEXT	SQLAlchemy engine URL	sqlite:///chebi.db

Import into Neo4J

Start Neo4J ...

podman run --rm --name biokb-neo4j-test -p7474:7474 -p7687:7687 -e NEO4J_AUTH=neo4j/neo4j_password neo4j:latest

Note: Remove --rm if you want to keep the container after stopping it. Replace podman with docker if you use Docker.

... and import into Neo4J:

biokb_chebi import-neo4j -p neo4j_password

Option	long	Description	default
-i	--uri	Neo4j database URI	bolt://localhost:7687
-u	--user	Neo4j username	neo4j
-p	--password	Neo4j password

http://localhost:7474 (user/password: neo4j/neo4j_password)

For testing you can install from TestPyPI:

uv venv
source venv/bin/activate
uv pip install --no-cache-dir -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ biokb-chebi==0.1.0