Tablassert

Version 6.0.0 (Beta)

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

# Enter development shell
nix develop -L .

# Run CLI
tablassert-cli --help

Usage (With Nix)

Method 1: Development Shell (Recommended)

Best for exploring Tablassert or active development.

# Clone and enter development shell
git clone https://github.com/SkyeAv/Tablassert.git
cd Tablassert
nix develop -L .

# CLI is now available
tablassert-cli -i /path/to/graph-config.yaml

Method 2: Direct Run from Flake

Run without cloning or installing.

nix run github:SkyeAv/Tablassert#default -- -i /path/to/config.yaml

Method 3: User Profile Installation

Install persistently to your user environment.

# Install
nix profile install github:SkyeAv/Tablassert#default

# Use anywhere
tablassert-cli -i /path/to/config.yaml

Method 4: Use as Overlay

Integrate into your own Nix flake or NixOS configuration.

{
  inputs = {
    nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable";
    tablassert.url = "github:SkyeAv/Tablassert";
  };

  outputs = { self, nixpkgs, tablassert }: {
    # Add overlay to nixpkgs
    pkgs = import nixpkgs {
      system = "x86_64-linux";
      overlays = [ tablassert.overlays.default ];
    };

    # Tablassert available as pkgs.python313Packages.tablassert
    devShells.default = pkgs.mkShell {
      packages = [ pkgs.python313Packages.tablassert ];
    };
  };
}

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