Tablassist

AI-assisted configuration generation for Tablassert — entity resolution, YAML validation, Biolink documentation, and PMC literature discovery.

Tablassert extracts knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON. Tablassist provides the tooling to build those configurations correctly — with CURIE resolution, schema validation, document extraction, data profiling, and PMC integration built in.

Components

Polyglot monorepo with two distributable packages:

Package	Description	Registry
cli/	Python CLI for configuration authoring and validation	PyPI
plugin/	OpenCode plugin exposing CLI tools to AI agents	npm

Quick Start

CLI

pip install tablassist

tablassist validate-config-file config.yaml
tablassist search-curies "breast cancer"
tablassist list-categories

OpenCode Plugin

npm install @skyeav/tablassist

Add to your OpenCode configuration to give AI agents access to CURIE search, schema validation, Biolink docs, PMC discovery, and more.

Features

• Entity Resolution — Search and resolve biological entity identifiers via the Configurator API (search-curies, search-gene-curies, resolve-taxon-id)
• Biolink Schema — Enumerate and fetch documentation for categories, predicates, and qualifiers from the Biolink model
• YAML Validation — Validate configurations against the Tablassert Pydantic schema with detailed per-section error reporting
• Data Profiling — Inspect Excel and CSV files with schema inference, per-column statistics, and sample rows (describe-excel, describe-csv, preview-excel, preview-csv)
• Document Extraction — Fast raw text via Textract (extract-text) or structured Markdown via Docling (extract-text-semantic) with OCR control
• PMC Integration — Search PubMed Central, fetch article metadata, and download archives (search-pmc, get-pmc-summary, download-pmc-tar, download-pmc-oa)
• Discovery Workflow — Ledger-driven multi-paper pipeline with concurrent claim coordination, DATALAKE consolidation, and cross-session state (discovery-ledger, consolidate-datalake)

Development

See cli/README.md and plugin/README.md for package-specific details.

# CLI
cd cli
uv sync
uv run ruff check . && uv run ruff format .
uv run pyright
uv run --group dev python -m pytest

# Plugin
cd plugin
bun install
bun run lint && bun run format
bun x tsc --noEmit
bun test

Pre-commit hooks (via prek.toml) run all checks automatically on git commit.

License

Apache License 2.0

Contributors

Skye Lane Goetz — Institute for Systems Biology, CalPoly SLO