anatomy-graphdb 1.0.1

Canonical anatomy domain dataset and Neo4j graph builder.

anatomy-graphdb

anatomy-graphdb is a Python package for loading, validating, and exporting a structured human anatomy graph from YAML configuration.

It provides:

• canonical anatomy config data under config/
• typed Python loaders and domain models in anatomy_graphdb/
• a CLI (anatomy-graphdb) for validation, catalog export, and Neo4j ingestion
• packaged overlay SVG assets (anatomy_graphdb/assets/)

What You Can Do With It

• Validate cross-references across anatomy entities (muscles, heads, bones, nerves, arteries, actions)
• Load region-scoped or multi-region anatomy models in Python
• Export canonical catalog JSON for downstream systems
• Export Neo4j CSV artifacts or ingest directly via Bolt
• Run a local Neo4j graph build using Docker Compose + Make

Install

pip install anatomy-graphdb

With Neo4j ingestion support:

pip install "anatomy-graphdb[neo4j]"

For development:

poetry install

Quick Start

Python API

from anatomy_graphdb.databases.anatomy.loader import AnatomyLoader
from anatomy_graphdb.domain import build_anatomy_model

loader = AnatomyLoader()
region = loader.load_region("chest")
model = build_anatomy_model(region)

print(model.region)
print(len(model.muscles))

CLI

List regions:

poetry run anatomy-graphdb --list-regions

Validate all regions:

poetry run anatomy-graphdb --region all --validate-only

Export Neo4j CSV artifacts:

poetry run anatomy-graphdb --region all --output data/neo4j --validate

Export canonical catalog JSON:

poetry run anatomy-graphdb --export-catalog --region all --catalog-output data/catalog/anatomy_catalog.json

Direct Bolt ingestion (requires neo4j extra):

poetry run anatomy-graphdb --region all --mode bolt --validate

Docker Neo4j Workflow

One command end-to-end graph refresh into local Neo4j:

make neo4j-refresh-docker REGION=all

Useful helpers:

make neo4j-up
make neo4j-logs
make neo4j-down

Override defaults if needed:

make neo4j-refresh-docker REGION=chest NEO4J_AUTH=neo4j/password HTTP_PORT=7475 BOLT_PORT=7688

Assets

Packaged assets:

• manifest: anatomy_graphdb/assets/overlay_manifest.json
• SVG files: anatomy_graphdb/assets/anatomy/*.svg

Legacy/reference assets (not packaged):

• svgs/svg_front_muscles
• svgs/svg_rear_muscles
• svgs/muscles
• svgs/manifest.json

Development

Run tests:

poetry run pytest

Docs

• API stability: docs/API_STABILITY.md
• Changelog: CHANGELOG.md
• Releasing: docs/RELEASING.md
• Asset attribution: docs/ASSET_ATTRIBUTION.md

Package Metadata

• Distribution: anatomy-graphdb
• Import namespace: anatomy_graphdb
• Python: 3.12+
• License: MIT