graph-db

name	graph-db
description	Use when building or querying a lightweight CogDB graph layer for agentic research, planning, provenance, citations, blockers, or markdown-derived relationship indexes.
version	1.1.0
author	Hermes Agent
license	MIT
metadata	{"hermes":{"tags":["cogdb","graph","research","planning","provenance"],"related_skills":["database-operations","obsidian"]}}

Graph DB

Overview

Use CogDB as a derived graph index over durable notes/data. It is useful for agent planning and research because it makes relationships queryable without replacing the canonical archive.

Best stack:

Markdown / JSONL / SQLite = canonical archive
CogDB = relationship traversal layer

When to Use

Use for:

• claim/source/provenance graphs
• task blockers and plan dependencies
• citation/literature maps
• entity/topic/source relationships
• markdown-derived wikilink/tag indexes
• lightweight local graph prototypes for agents

Do not use for:

• the only source of truth
• production transactional storage
• concurrent multi-writer agent memory
• full-text search or vector ANN search
• data that needs mature backups, replication, ACLs, or operations tooling

Setup

python3 -m pip install cogdb==3.8.2

Always configure a durable path. CogDB defaults under /tmp; these scripts default to ./.agent-state, so pass --state-dir for project-specific state.

from cog.torque import Graph
from cog.config import CogConfig

cfg = CogConfig(COG_HOME="cogdb", COG_PATH_PREFIX="/path/to/project/.agent-state")
g = Graph("research", config=cfg)

Good Edge Shapes

claim_x --supported_by--> source_y
task_a --blocked_by--> task_b
goal_g --requires--> task_t
paper_a --cites--> paper_b
note_n --mentions--> entity_e
answer_a --derived_from--> source_s

Query Patterns

# blockers
g.v("task:write-report").out("blocked_by").all()

# provenance
g.v("claim:graph-useful").out("supported_by").all()

# context expansion
g.v("goal:evaluate-cog").bfs(direction="out", max_depth=2).all()

# reverse lookup
g.v("source:README").inc("supported_by").all()

Rules

• Keep source text/data canonical elsewhere; write graph edges as an index.
• Use stable IDs: note:path-slug, source:url-sha, claim:slug, task:slug.
• Prefer JSON/JSONL script output so agents can parse it reliably.
• Use one-shot traversal chains starting with v(); Graph keeps mutable traversal state.
• Do not share one mutable Graph object across concurrent writers.
• Avoid exposing g.serve() to untrusted users; remote query execution uses restricted eval().
• Prefer SQLite/Postgres/NoSQL for transactions, concurrent writes, full-text search, backups, and production durability.

Example Scripts

Linked scripts:

• scripts/research_graph_demo.py — seed/query a claim-task-source graph; emits JSON.
• scripts/markdown_link_index.py — index markdown wikilinks and tags into CogDB; supports --dry-run and emits JSON.

Run:

python scripts/research_graph_demo.py --state-dir /tmp/cogdb-demo-state

mkdir -p /tmp/cogdb-vault
printf '# A\n\nLinks to [[B]] and #research.\n' > /tmp/cogdb-vault/A.md
printf '# B\n' > /tmp/cogdb-vault/B.md
python scripts/markdown_link_index.py /tmp/cogdb-vault --state-dir /tmp/cogdb-demo-state --dry-run
python scripts/markdown_link_index.py /tmp/cogdb-vault --state-dir /tmp/cogdb-demo-state

Expected output shape:

{"graph": "notes", "notes_indexed": 2, "edges": 3}

Verification Checklist

• python3 -m pip install cogdb==3.8.2 succeeds in the active environment.
• research_graph_demo.py emits valid JSON with requirements/blockers/provenance keys.
• markdown_link_index.py --dry-run emits valid JSON triples without writing.
• Persistent uses pass a non-/tmp --state-dir.