Command Line Interface (CLI)

BioKb-ChEBI provides a command line interface (CLI) to import ChEBI data into a relational database, create RDF turtles from it, and import the turtles into a Neo4J graph database.

CLI Options

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)