Tablassert

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

pip install tablassert
tablassert build-kg config.yaml

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

Installation

pip install tablassert

The base install includes everything needed to build knowledge graphs from CSV/TSV sources. Optional extras are available for CPU compatibility and quality control:

pip install "tablassert[rt]"  # Polars build for CPUs without the required instructions
pip install "tablassert[qc]"  # Enable QC (torch + sentence-transformers BioBERT, scikit-learn)

Excel (.xlsx) inputs are read through Polars' calamine engine and additionally require python-calamine (pip install python-calamine).

QC is opt-in: pass --qc to build-kg to run the three-stage audit (exact → fuzzy → BioBERT). See the CLI Reference for the full flag reference.

Quick Demo

from pathlib import Path
from tablassert.lib import resolve_many

# Resolve gene names to CURIEs against a fullmap database
results = resolve_many(
    col="gene",
    entities=["TP53", "BRCA1", "EGFR"],
    fullmap=Path("/path/to/fullmap"),
    taxon="9606",
)

for row in results:
    print(f"{row['original_gene']} → {row['gene']} ({row['gene_name']})")
# TP53 → HGNC:11998 (TP53)
# BRCA1 → HGNC:1100 (BRCA1)
# EGFR → HGNC:3236 (EGFR)

Point resolve_many() at a fullmap database and resolve any iterable of entity strings to CURIEs — no LazyFrame setup or NLP preprocessing required. For full pipeline builds with YAML configuration, use tablassert build-kg config.yaml.

Key Features

Declarative Configuration — YAML-based, no code required
Entity Resolution — Maps text to biological entities (genes, diseases, chemicals)
Quality Control — Optional three-stage validation (exact → fuzzy → BERT embeddings)
KGX Compliance — NCATS Translator-compatible NDJSON output
Performance — Lazy evaluation pipelines with Polars and an embedded redb-accelerated entity resolution database

Developing

uv sync --group dev --extra qc
uv run maturin develop --manifest-path rust/Cargo.toml
make check

See CONTRIBUTING.md for the full development loop, quality gates, and pull request guidelines.

License

Apache License 2.0

Contributors

Skye Lane Goetz — Institute for Systems Biology

Gwênlyn Glusman — Institute for Systems Biology

Jared C. Roach — Institute for Systems Biology

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Apr 2, 2026

7.2.1

Apr 2, 2026

7.2.0

Apr 2, 2026

7.1.0

Mar 26, 2026

7.0.2

Mar 23, 2026

7.0.1

Mar 17, 2026

7.0.0

Mar 17, 2026

tablassert 8.0.0

Tablassert

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