Tablassert

By Skye Lane Goetz, Gwênlyn Glusman, and Jared C. Roach

Tablassert is a highly performant declarative knowledge graph backend designed to extract knowledge assertions from tabular data while exporting NCATS Translator-compliant Knowledge Graph Exchange (KGX) NDJSON.

Documentation

Full Documentation

Complete guides covering installation, configuration, tutorials, and API reference.

Quick Start

# Clone repository
git clone https://github.com/SkyeAv/Tablassert.git
cd Tablassert

# Install with UV (requires Python 3.13+)
uv sync

# Run CLI
uv run tablassert --help

Or install the CLI directly from PyPI:

# Option A: UV tool install
uv tool install tablassert

# Option B: pip install
pip install tablassert

# Option C: runtime-compatible Polars build
# (for CPUs without the required Polars instructions)
uv tool install "tablassert[rtcompat]"
# or
pip install "tablassert[rtcompat]"

tablassert --help

Usage (With UV)

Prerequisites

• Python 3.13 or higher
• UV package manager

Method 1: Development Installation (Recommended)

Best for exploring Tablassert or active development.

# Clone and install dependencies
git clone https://github.com/SkyeAv/Tablassert.git
cd Tablassert
uv sync

# Run CLI through UV
uv run tablassert build-knowledge-graph /path/to/graph-config.yaml

Method 2: Install from PyPI

Recommended for most users.

# Option A: standard install (UV)
uv tool install tablassert

# Option B: standard install (pip)
pip install tablassert

# Option C: runtime-compatible Polars build
# (for CPUs without the required Polars instructions)
uv tool install "tablassert[rtcompat]"
# or
pip install "tablassert[rtcompat]"

tablassert build-knowledge-graph /path/to/graph-config.yaml

Method 3: Install from GitHub main

Use this when you want the latest main-branch build before a tagged release.

uv tool install git+https://github.com/SkyeAv/Tablassert.git@main
tablassert build-knowledge-graph /path/to/graph-config.yaml

If your CPU does not support the instructions required by default Polars builds, use Method 2 with tablassert[rtcompat].

Method 4: Local source install

For contributors testing local changes.

# Clone repository
git clone https://github.com/SkyeAv/Tablassert.git
cd Tablassert

# Install CLI tool from local source
uv tool install .

# CLI is now available
tablassert build-knowledge-graph /path/to/graph-config.yaml

Key Features

• Declarative Configuration: YAML-based, no code required
• Entity Resolution: Maps text to biological entities (genes, diseases, chemicals)
• Quality Control: Three-stage validation (exact → fuzzy → BERT embeddings)
• KGX Compliance: NCATS Translator-compatible NDJSON output
• Performance: Parallel processing with disk caching

Contributors

Skye Lane Goetz - Institute for Systems Biology, CalPoly SLO

Gwênlyn Glusman - Institute for Systems Biology

Jared C. Roach - Institute for Systems Biology