tablassert 7.3.4

Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in.

Tablassert

Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in.

pip install tablassert
tablassert build-knowledge-graph config.yaml

Full Documentation — installation guides, tutorials, configuration reference, and API docs.

Installation

pip install tablassert

All dependencies (ML, web, Excel support) are included in the base install. An optional extra is available for CPU compatibility:

pip install "tablassert[rtcompat]"  # Polars build for CPUs without required instructions

Docker

docker pull ghcr.io/skyeav/tablassert:latest

docker run --rm \
  -v /path/to/config:/data \
  -v /path/to/datassert:/datassert \
  ghcr.io/skyeav/tablassert:latest \
  build-knowledge-graph /data/graph-config.yaml

Quick Demo

# Build a knowledge graph from a YAML configuration
$ tablassert build-knowledge-graph graph-config.yaml
⠋ Loading table configurations...
⠋ Resolving entities across 10 DuckDB shards...
⠋ Compiling subgraphs...
⠋ Deduplicating nodes and edges...
✓ Finished — wrote MY_GRAPH_1.0.0.nodes.ndjson and MY_GRAPH_1.0.0.edges.ndjson

Define your entities and relationships in YAML, point tablassert at your data, and get NCATS Translator-compliant KGX NDJSON out the other side — no code required. Intermediate section artifacts are staged in .storassert/ during the build.

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 — Lazy evaluation pipelines with Polars and DuckDB-accelerated entity resolution

Contributing

See CONTRIBUTING.md for development setup, code style, and pull request guidelines.

License

Apache License 2.0

Contributors

Skye Lane Goetz — Institute for Systems Biology, CalPoly SLO

Gwênlyn Glusman — Institute for Systems Biology

Jared C. Roach — Institute for Systems Biology