Obsidian links your notes.Graphify maps your code.
Connect a repository in Graphify and your coding agent gets the code graph over MCP, with nothing to install. Obsidian is a notes app, and its graph view shows the links you write, so it is the right pick for a research vault, a journal or a personal wiki. The two also work together. Graphify can write that code graph into an Obsidian vault and a canvas.
Checked against Obsidian's help and pricing on 9 November 2026.
Four things Graphify does with code.
- 01
The graph is built from the code
Connect a repository and Graphify builds a node for each function, class and file and an edge for each call, import and inheritance. You type no links. Open-source Graphify can do the same parse on your machine, with tree-sitter and no model.
How Obsidian compares. Its graph view draws notes as circles and internal links as lines. A line is there because someone wrote a wikilink or a Markdown link.
- 02
It answers questions about code
Who calls this function, and what a change reaches, come back by walking real edges, with the file and line. The hosted app re-indexes the default branch on every push, so the next question sees the new code.
How Obsidian compares. Its accepted formats are Markdown, bases, canvas, images, audio, video and PDF. Source code is not on that list.
- 03
A coding agent can query it
Claude Code, Cursor, Codex and other MCP clients ask the graph questions while they write. Graphify serves a hosted MCP server at
api.graphify.com/mcp, with nothing to install. Open-source Graphify ships ten MCP tools as well.How Obsidian compares. Its command line, from installer 1.12.7, searches and reads the vault. The first command launches the app if it is closed. It does not read calls or imports out of a repository.
- 04
Every link says how it was found
Each edge is EXTRACTED when it is written in the source, INFERRED when Graphify worked it out, and AMBIGUOUS when the model pass could not settle it. An agent can trust the first and check the last.
How Obsidian compares. A link in Obsidian is one you wrote. Its help describes no confidence labels.
Graphify and Obsidian, row by row.
Obsidian does the notes job well. The rows say where.
When Obsidian is the right pick.
Choose Graphify if
- A coding agent needs to know how the code connects: who calls what, and what a change reaches
- You want that map built from the repository, not written by hand
- You want Claude Code, Cursor or Codex to query it over MCP
- You want to know which links were found in the source and which were inferred
Choose Obsidian if
- You are writing notes, a journal, research or a personal wiki
- You want to choose every link yourself, and see those links as a graph
- You want the notes as plain Markdown on your own device
- You want filters, color groups, a local graph and a time-lapse of the notes you wrote
Use both if
- You keep project notes in a vault and want the code map beside them
- You want to read a repository as linked notes in a tool you already use
Graph a repository, then open it in Obsidian.
Start free at app.graphify.com. The free plan covers 3 repositories and needs no card. Connect a repository and add the MCP server. Your coding agent gets the graph with nothing to install.
To keep the graph on your machine, install Graphify CLI with uv tool install graphifyy, run graphify install, then type /graphify . in your assistant. The code maps locally, with no API key. To read that graph in Obsidian, run graphify export obsidian --dir /path/to/your/vault. Graphify CLI writes one note per node, plus a community overview. Each connection is a wikilink with the relation and an EXTRACTED, INFERRED or AMBIGUOUS tag, and graph.canvas lays the communities out as groups. The canvas keeps the 200 highest weight edges so a large graph stays openable. The notes still list every connection. Your own notes and your .obsidian settings stay in place. Review the folder before you sync a shared vault. The export docs show one code only graph of the httpx repository, built with graphify 0.9.97, writing 2,530 notes and a graph.canvas. Your repository will differ.
Graphify vs Obsidian: questions
What people ask when they are choosing between a code graph and a notes graph.
No. They do different jobs. Obsidian is where you write and link your own notes, and its graph view draws those links. Graphify builds a graph of a codebase for coding agents and the people who work on it. Use Obsidian for the notes. Use Graphify for the code. Many people use both, because Graphify can write that code graph into an Obsidian vault.
It shows notes, not a parsed repository. Obsidian's help says circles are notes and lines are internal links, and that a note gets bigger as more notes link to it. The accepted formats are Markdown, bases, canvas, images, audio, video and PDF. Source code is not on that list, and the graph holds only links someone wrote. It does not read calls or imports.
It is the graph view of a vault: the notes you wrote, joined by the links you typed. Filters, color groups, a local graph with adjustable depth and a time-lapse of creation time are all in Obsidian's own graph view help. That is a knowledge graph of your notes. It is not a knowledge graph of function calls. Graphify is the one that builds the code graph.
Start free on the hosted app, connect a repository, and add the MCP server. The free plan covers 3 repositories and needs no card. To open that graph in Obsidian, run graphify export obsidian with --dir pointing at a vault folder. That command writes one Markdown note per node, a community overview, and a graph.canvas. Each connection is a wikilink with the relation and an EXTRACTED, INFERRED or AMBIGUOUS tag. The canvas groups notes by community and draws the 200 highest weight edges, so a large graph stays openable. The notes still list every connection. The export docs say this keeps your own notes and .obsidian settings. Review the output before you sync a shared vault.
For how the code connects, Graphify. The agent queries the graph over MCP and gets file and line back. For your own notes, plans and research, Obsidian, whose command line can search and read the vault. An agent can use both, as long as a question about code goes to the code graph and a question about notes goes to the vault.
The hosted app has a free plan with no card for 3 repositories. Paid plans are on the pricing page. Open-source Graphify is free under Apache 2.0 and needs no account. Obsidian is free with no sign up. On 9 November 2026 its pricing page listed Sync at $4 a user a month and Publish at $8 a site a month, both billed yearly, and an optional commercial licence of $50 a user a year that is not required for work. Check that page before you buy. Those prices can change.
The hosted app builds the graph for the repositories you connect. Open-source Graphify parses code on your machine and collects no usage data. Docs, PDFs and images go to the model you choose, which can be a local one. Obsidian keeps notes on your device, and its pricing page says its apps collect no telemetry. Sync is optional. If you turn it on, Obsidian says that copy is end to end encrypted.
Obsidian rows come from its own pages, read on 9 November 2026: graph view, internal links, accepted file formats, command line and pricing. Sync and Publish prices are that day's listing. Check the pricing page again before you buy. Graphify rows come from the export docs, export.py on the v8 branch and pricing. Obsidian belongs to its makers. Graphify Labs is not affiliated with it. Spotted something out of date? Tell us on GitHub.
More comparisons: Graphify vs RAG, Graphify and Claude Code, Graphify and Cursor, all comparisons.