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.

New to Tablassert? Start with Installation, work through the Tutorial, or go straight to the CLI reference.

Who this is for¶

Translator ingest authors and knowledge-graph data engineers holding tabular biomedical sources: association tables, assay results, curated gene-disease lists. Tablassert turns those rows into KGX nodes and edges from a declarative YAML mapping, resolving free text to standard CURIEs through an embedded database built from RENCI BABEL exports, so a build needs no hosted resolution service and no per-source Python transform. It also emits the Resource Ingest Guide (RIG) metadata that NCATSTranslator/translator-ingests submissions require.

Questions or bugs? Open an issue at github.com/SkyeAv/Tablassert/issues; see CONTRIBUTING.md to contribute and the Code of Conduct for community expectations.

Documentation Sections¶

Start¶

Installation: install methods, extras, and development setup
Tutorial: build your first knowledge graph from a CSV, step by step
Use Case Gallery: real-world configuration patterns to copy and adapt

How-to guides¶

CLI Reference: every command and flag: build-kg, build-fullmap, validate, validate-kgx, quick-map
Fullmap: obtain and build the entity-resolution database

Reference¶

Configuration: graph-level schema, the required rig: section, and stable edge ids
Table Configuration: sources, statements, entity-resolution rules, provenance, annotations
Advanced Example: a fully-annotated real-world configuration
API Reference: resolve() and quick_map()
Batch Resolution: resolve_many() for scripts and notebooks
Quality Control: the four-stage fullmap_audit() pipeline
Utilities: hashing, store keys, and deterministic edge UUIDs

Contribute¶

Development: dev environment setup, the daily loop, and the docs gate
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¶

Apache License 2.0 (see LICENSE).