Hypabase

Hypabase is a Python library for storing and querying relationships between entities. A single edge connects two or more nodes, every edge tracks where it came from (source and confidence), and the whole graph lives in a local SQLite file with no server or configuration.

Use it to build knowledge graphs, retrieval-augmented generation pipelines, and structured agent memory. Recent research explores hypergraph representations for these tasks:

HyperGraphRAG — n-ary knowledge retrieval across medicine, agriculture, CS, and law
Cog-RAG — dual-hypergraph retrieval with theme-level and entity-level recall
Hypergraph Memory for Multi-step RAG — hypergraph-based memory for long-context relational modeling

Install

uv add hypabase

Quick example

from hypabase import Hypabase

hb = Hypabase("my.db")  # local SQLite, zero config

# One edge connecting five entities
hb.edge(
    ["dr_smith", "patient_123", "aspirin", "headache", "mercy_hospital"],
    type="treatment",
    source="clinical_records",
    confidence=0.95,
)

# Query edges involving a node
hb.edges(containing=["patient_123"])

# Find paths between entities
hb.paths("dr_smith", "mercy_hospital")

Provenance

Every edge carries source and confidence:

hb.edge(
    ["patient_123", "aspirin", "ibuprofen"],
    type="drug_interaction",
    source="clinical_decision_support_v3",
    confidence=0.92,
)

# Bulk provenance
with hb.context(source="schema_analysis", confidence=0.9):
    hb.edge(["a", "b"], type="fk")
    hb.edge(["b", "c"], type="fk")

# Query by provenance
hb.edges(source="clinical_decision_support_v3")
hb.edges(min_confidence=0.9)

# Overview of all sources
hb.sources()

Namespace isolation

Isolate data into separate namespaces within a single database file:

hb = Hypabase("knowledge.db")

drugs = hb.database("drugs")
sessions = hb.database("sessions")

drugs.node("aspirin", type="drug")
sessions.node("s1", type="session")

drugs.nodes()     # → [aspirin]
sessions.nodes()  # → [s1]

Features

N-ary hyperedges — an edge connects 2+ nodes in a single relationship
O(1) vertex-set lookup — find edges by their exact node set
Provenance — every edge carries source and confidence
Provenance queries — filter by source and min_confidence, summarize with sources()
SQLite persistence — local-first, zero-config
Namespace isolation — .database("name") for scoped views in a single file
MCP server — 14 tools + 2 resources for AI agent integration
CLI — hypabase init, hypabase node, hypabase edge, hypabase query

Documentation

docs.hypabase.app

License

Apache 2.0

hypabase