semantic-markdown-converter 0.5.5

Converts different typed link formats in Markdown into each other and to external formats. Supports Obsidian Neo4j plugin.

Neo4j Graph View

Adds a new and much more functional graph view to Obsidian. It does so by connecting to a Neo4j database. Features:

• Selectively style nodes and edges by tags, folders and link types
• Selective expansion and hiding of nodes
• View images within the graph
• Cypher querying
• Typed links using - linkType [[note 1]], [[note 2|alias]]
• Hierarchical layout

Installation

1. Make sure you have Python 3.6+ installed
2. Make sure you have Neo4j desktop installed
3. Create a new database in Neo4j desktop and start it. Record the password you use!
4. In the settings of the plugin, enter the password. Then run the restart command.

Use

On an open note, use the command "Neo4j Graph View: Open local graph of note". You can run commands using ctrl/cmd+p. Alternatively, you can bind this command to a hotkey in the settings.

Graph functionality

• Click on a node to open it in the Markdown view
• Double-click on a node to expand its neighbors
• Shift-drag in the graph view to select nodes
  • Use E to expand the neighbors of all selected nodes
  • Use H or Backspace to hide all selected nodes from the view
  • Use I (invert) to select all nodes that are not currently selected
  • Use A to select all nodes
• All notes visited are added to the graph

The settings contains several options, such as coloring based on folders and a hierarchical layout.

Cypher Querying

Create code blocks with language cypher. In this code block, create your Cypher query. Then, when the cursor is on this code block, use the Obsidian command 'Neo4j Graph View: Execute Cypher query'. Example:

Possible problems

All changes made in obsidian should be automatically reflected in Neo4j, but this is still very buggy. There also seem to be problems with duplicate nodes in the graph.

If you are running into issues, enable Debug in the settings and check out the developer console (View -> Toggle Developer Tools). On Windows, this can be opened using Ctrl+Shift+I. Here are some issues found so far:

• xcrun: error: invalid active developer path... missing xcrun at...: Install xcrun) in terminal using xcode-select --install

Semantics

This collects all notes with extension .md in the input directory (default: markdown/). Each note is interpreted as follows:

• Interprets tags as entity types
• Interprets YAML frontmatter as entity properties
• Interprets wikilinks as links with type inline, and adds content
• Lines of the format "- linkType [[note 1]], [[note 2|alias]]" creates links with type linkType from the current note to note 1 and note 2.
• The name of the note is stored in the property name
• The content of the note (everything except YAML frontmatter and typed links) is stored in the property content
• Links to notes that do not exist yet are created without any types.

This uses a very simple syntax for typed links. There is no agreed-upon Markdown syntax for this as of yet. If you are interested in using a different syntax than the list format "- linkType [[note 1]], [[note 2|alias]]", please submit an issue.

Other visualization and querying options

Another use case for this plugin is to use your Obsidian vault in one of the many apps in the Neo4j desktop Graph Apps Store. Using with this plugin active will automatically connect it to your vault. Here are some suggestions:

Neo4j Bloom

Neo4j bloom is very powerful graph visualization software. Compared to the embedded graph view in Obsidian, it offers much more freedom in customization.

GraphXR

GraphXR is a 3D graph view, which looks quite gorgeous!

Neo4j Browser

A query browser that uses the Cypher language to query your vault. Can be used for advanced queries or data anlysis of your vault.

Python code: Semantic Markdown to Neo4j

This Obsidian plugin uses the Python package semantic-markdown-converter, which is also in this repo. It creates an active data stream from a folder of Markdown notes to a Neo4j database.

Getting started

Note: The obsidian plugin automatically installs this package!

Requires python 3.5+ and Neo4j desktop

• Install with pip install --upgrade semantic-markdown-converter
• Create a new database in Neo4j desktop and start it
• Run smds --input "folder with notes" --password "neo4j database password"

WARNING: This clears all current data in the active neo4j database!

Supported input formats

There is currently only one input format supported. An issue or use a pull request for different formats are appreciated! In particular for different markdown syntax for interpreting semantic links.

Semantic Markdown to Neo4j server

The command smds first uploads the complete folder of notes into the active Neo4j database. Then, it listens to changes in the notes to update the Neo4j database.

Options

• --password: Provide the password of the Neo4j database
• --input: Provide the folder where to look for notes
• --index_content: Set to true if you want Neo4j Bloom to search through the content of your notes when using the search bar. Can impact performance.

Conversion mode

The command smdc only converts

Neo4j

Streams the input into the currently active Neo4j database. WARNING: This clears all the data in your database by default! Run with --retaindb if this is not desired.

1. Start the database in Neo4j you want to use
2. Run using smdc --input "folder with notes" --password "neo4j database password". This can take a couple of minutes for large vaults.