Installation and quick setup guide

Python Module

OntoWeaver is published on the Python Package Index, you may install it from there with pip install ontoweaver.

Users on Debian-derived Linux may have to use sudo apt install python3-ontoweaver.

If thoses does not work on your system, you may still clone the repository and use UV (see the next section).

Using your own repository clone

The project is written in Python and has been tested with the UV environment manager. You can install the necessary dependencies in a virtual environment like this:

git clone https://github.com/oncodash/ontoweaver.git
cd ontoweaver
uv sync

UV will create a virtual environment according to your configuration (either centrally or in the project folder). You can then run any script or command using uv run. For instance, to run the ontoweave command: uv run ontoweave.

Output Database

OntoWeaver can export the created knowledge graph in any format supported by BioCypher (Neo4j, ArangoDB, CSV, RDF, PostgreSQL, SQLite, NetworkX, … see BioCypher’s documentation).

To get access to those formats, you must install the corresponding software and Python modules.

Graph visualization with Neo4j

Neo4j is a popular graph database management system that offers a flexible and efficient way to store, query, and manipulate complex, interconnected data. Cypher is the query language used to interact with Neo4j databases. In order to visualize graphs extracted from databases using OntoWeaver and BioCypher, you can download the Neo4j Graph Database Self-Managed for your operating system. It has been extensively tested with the Community edition.

To create a global variable to Neo4j, add the path to neo4j-admin to your PATH and PYTHONPATH. In order to use the Neo4j browser, you will need to install the correct Java version, depending on the Neo4j version you are using, and add the path to JAVA_HOME. OntoWeaver and BioCypher support versions 4 and 5 of Neo4j.

To run Neo4j (version 5+), use the command neo4j-admin server start after importing your results via the neo4j import sequence provided in the ./biocypher-out/ directory. Use neo4j-admin server stop to disconnect the local server.

By default, Neo4j Community Edition (CE) and Neo4j Enterprise Edition (EE) report a small amount of usage data. If necessary, reporting can be turned off with the configuration setting dbms.usage_report.enabled=false.

Tests

Tests are located in the tests/ subdirectory and may be a good starting point to see OntoWeaver in practice. You may start with tests/test_simplest.py which shows the simplest example of mapping tabular data through BioCypher.

To run tests, use pytest:

uv run pytest