Tablassert¶
Tablassert turns biomedical tables (Excel, CSV, TSV) into NCATS Translator-compliant KGX knowledge graphs, declaratively, with entity resolution built in and optional quality control. Installing? See Installation. First build? Follow the Tutorial. Automating? Use the CLI or the autonomous Agent.
Why Tablassert¶
- Declarative YAML configuration: define data transformations without code
- Entity resolution: map free text to biological entities (genes, diseases, chemicals) with taxonomic filtering and provenance, backed by an embedded redb database
- Optional quality control: four-stage audit (exact → fuzzy → abbreviation → SapBERT embeddings) flags low-confidence mappings
- KGX compliance: emits NCATS Translator-compatible node/edge NDJSON with Biolink categories and predicates
- Performance & reproducibility: lazy Polars pipelines and a UV-based, deterministic development environment
Quick Start¶
pip install "tablassert[cli]" # or: uv tool install "tablassert[cli]"
tablassert build-kg config.yaml
Quality control and runtime-compatible Polars are opt-in extras. See Installation for the full install matrix, extras, and development setup.
Documentation Sections¶
- Installation: install methods, extras, and development setup
- CLI Reference: complete command-line flag reference
- Tutorial: step-by-step example with synthetic data
- Use Case Gallery: real-world configuration patterns
- Fullmap: building and querying the entity-resolution database
- Configuration: graph and table configuration reference
- Agent: the autonomous agent pipeline
- API Reference: core functions documentation
- Development: dev environment setup and contributor workflow
- Changelog: release history
Authors¶
- Skye Lane Goetz: Institute for Systems Biology
- Gwênlyn Glusman: Institute for Systems Biology
- Jared C. Roach: Institute for Systems Biology
License¶
See repository for license information.