Poneglyph

Poneglyph is a research-first Obsidian plugin that transforms your knowledge graph into a living, cited research artifact — powered by a local deep research agent.

Disclaimer

Poneglyph is an AI-assisted research tool, not a replacement for actual research or a literature survey.

The deep research agent accelerates your ability to explore and map a research space, but it is not infallible. Generated nodes may contain hallucinated citations, outdated information, or shallow treatment of complex topics. Human verification is a first-class citizen of this plugin's design — the verified status tag exists precisely because no AI output should be trusted without review.

Use Poneglyph to accelerate your research mapping, not to replace the rigour of reading primary sources.

Overview

Poneglyph turns every markdown node in your Obsidian graph into a deeply researched, cited artifact — generated by a local research agent. The graph itself becomes a navigable, living map of your research understanding.

Each node is a markdown file. Nodes are connected relationally, tagged by lifecycle status and topic, and anchored to a vault-wide citation ledger (SOURCES.md). You drive the research; the agent does the heavy lifting.

Prerequisites

Poneglyph's indexing runs entirely locally and requires the following services to be running before use:

One-command setup scripts are available in the setup/ folder:

Run the appropriate script once to install and configure both dependencies before enabling the plugin.

You would also need a LLM Provider; this can be either Cloud (OpenAI/Anthropic/Mistral etc.) or Local (Ollama).

Features

Deep Research Node Creation

In the IDEA.md markdown, write your thesis/idea. The agent uses it to perform research and generate a fully cited markdown file. Generated nodes begin as draft and get's shifted to researched once the markdown is written.

Thesis Generation

Tag nodes which you want to research about as extract-idea. The plugin traverses the graph from that node back through its ancestry, identifies what is missing — topics referenced but unexplored, contradictions unresolved, threads not yet followed — and generates a focused research suggestion grounded in that gap. You decide whether to pursue it by creating a new node. You can trigger Generate Thesis to surface research gaps.

Paste the thesis which you want to research about in the IDEA.md file to trigger back the deep research.

Semantic Backlinking

When a new node is created, Poneglyph uses ChromaDB to compare it semantically against every existing node in the vault. If sufficiently similar nodes are found, bidirectional links are automatically inserted — surfacing conceptual connections that a manual graph would miss. This keeps your graph dense and meaningful as it grows.

Graph Visualization

Poneglyph maps node metadata to visual properties via CSS snippets or the Style Settings plugin:

Your graph becomes a semantic map — colour and connection carry meaning at a glance.

Citation Ledger — SOURCES.md

Every node creation automatically updates SOURCES.md, a single deduplicated citation table sorted by h-index:

Sources are keyed (e.g. smith2021) and referenced directly from node frontmatter. SOURCES.md is never used as agent context.

Vault Structure

A Poneglyph vault revolves around three special files alongside your research nodes:

vault/
├── SOURCES.md            ← Central citation ledger, 
├── IDEA.md               ← Your thesis or research idea 
├── TEMP.md               ← Scratch file created and deleted by the agent during runs
├── Root Topic.md         ← Foundational seed node
├── Sub-topic A.md        ← Researched child node
├── Sub-topic B.md        ← Draft child node (awaiting ratification)
└── ...

IDEA.md is the one file you author directly. It defines the research question or thesis that gives your graph its direction. TEMP.md is managed entirely by the agent and should not be edited manually.

Node Metadata

Every node carries the following frontmatter, automatically managed by the plugin:

---
title: "The title of the note"
tags:
  - draft
  - <topic-tag>
created: YYYY-MM-DD
updated: YYYY-MM-DD
---

Lifecycle Status

Nodes move through three stages. Only the final promotion is a human action.

Topic Tags

In addition to lifecycle status, each node is tagged with one or more topic labels derived automatically from its content. These drive the semantic backlinking system and help you filter and navigate large graphs by research area.

Configuration

Navigate to Settings → Poneglyph after enabling the plugin. See the settings panel for the full list of options, including:

• LLM provider, API key, and model ID (supports OpenAI, Anthropic, Gemini, Groq, Mistral, and local Ollama models)
• Unpaywall email for open-access paper discovery
• Draft ratification toggle — require human approval before draft nodes can expand

Installation

Community Plugins

1. Open Settings → Community Plugins
2. Search for Poneglyph
3. Click Install, then Enable

Manual Installation

1. Download the latest release from GitHub Releases
2. Extract and copy the folder to your vault's .obsidian/plugins/ directory
3. Reload Obsidian
4. Enable the plugin under Settings → Community Plugins

Run the setup script for your platform before first use — see Prerequisites.

Roadmap

• Community Plugin store release
• Zotero integration for citation and source management
• LaTeX export of the research graph as a structured literature review
• Automatic contradiction identification across the graph, surfaced alongside thesis generation
• Multi-agent support — different models per node type
• Node diff view — track how understanding of a topic evolves over time

License

MIT License — see LICENSE for details.