Obsidian Ontology Manager

Obsidian Ontology Manager is a Python automation tool for any who maintain strict, axiomatic knowledge bases.

It treats Markdown notes as objects in a compiled graph. Instead of manually naming files, this script generates filenames based on their metadata and relationship to other nodes (Owners, Superclasses, Parts). When a file's "Recursive Title" changes, the script renames the file and automatically refactors every Wikilink in the vault to maintain integrity.

🚀 Key Features

• Logic-Based Naming: Filenames are not static; they are compiled from NamingTags that traverse the relationship graph.
• Recursive Pathing: A file can name itself by fetching data from its Owner, its Owner's Super, or any arbitrary depth in the graph (e.g., OS1N).
• Referential Integrity: Renames are propagated globally. If Note A is renamed to Note B, all instances of [[Note A]] in your vault are updated to [[Note B]].
• Inheritance: Nodes without explicit Owners can inherit ownership from their Supers or PartOf parents.
• Orphan Detection: Generates a dashboard (Owner.md) listing nodes disconnected from the graph.

📄 Metadata Schema

The script relies on YAML frontmatter. If no NamingTags are present, the file simply uses its Title attribute (Default Behavior).

---
attributes:
  Title: "Absciss"
  Owner: "[[Ordered Pair(Set)]]" 
  Supers:
    - "[[Relation (Set)]]"
  NamingTags:                # Logic to construct the full filename
    - "-1ON" 
---

This is how i like to distinguish them

1. Title: what ever word you want to be as the ground or base for the note final title
2. Owner: a link to another note O, Hypothetcly if the current note would dissappear from existence Note O would not get effected. Ex: (Owner - Owned) (Human - Human Body) (Ordered Pair - Absciss) (Light - Ligth Reflection Phenomenon)
3. PartOf: a link to another note P, Hypothetcly if the current note would dissappear from existence Note P would have no meaning. Ex: (Emerging - Part) (Human Body - Hand) (Proper Class - Set) (Atom - Electron)
4. Supers: a list of links, that the current note is inhiriting. (Child - Parent) (Flat Bone - Rib) (Relation - Set) (Elementry Boson - Photon)

🧠 The Naming Logic (NamingTags)

The core engine of this script is the NamingTags parser. It constructs a title by placing segments before (-) or after (+) the file's intrinsic Title.

Syntax

[Sign][Position][Path...][Terminator]

1. Sign: * -: Prefix (placed before the Title).
   • +: Suffix (placed after the Title).
2. Position: An integer (1, 2, 3...) determining distance from the center.
   • Note: Position 0 is reserved for the file's own Title.
   • -1 is immediately before the title; -2 is before -1.
3. Path (Recursive): A chain of steps to find the target node.
   • O : Go to Owner.
   • S + Index: Go to Superclass at specific index (e.g., S0 is first super, S1 is second).
   • P + Index: Go to PartOf at specific index.
   • Chaining: You can chain these. OS1 means "Go to my Owner, then go to their 2nd Super."
4. Terminator: What data to extract from the target node.
   • N: Name (The target's raw Title attribute).
   • T: RTitle (The target's fully compiled Recursive Title).

Visualizing the Order

If the File Title is [TITLE], the positions fill as follows: ... [-2] [-1] [TITLE] [+1] [+2] ...

---

🧪 Examples

Example 1: Simple Prefix

• Title: Tissue
• Owner: [[Pathophysiology. Body]] (Title: "Body")
• NamingTag:
  1. -1ON: -1: Prefix, immediate left, O: Go to Owner (Pathophysiology. Body), N: Get Name ("Body").
• Result: Body Tissue.md

Example: Composition with a title

• Title: Carpal
• PartOf: [[Human Wrist(Joint)]] (RTitle: "Human Wrist")
• Supers: [[Body. Tunnel]] (RTitle: "Body")
• NamingTags:
  1. -1OT: Prefix (-1), Owner (O), Recursive Title (T) -> "Human"
  2. +1S0T: Suffix (+1), First Super (S0), Recursive Title (T) -> "Body"
• Result: Human Carpal Tunnel.md Note: Since their is no owner the owner is taken from the first PartOf

Example: Composition without a title

• Owner: [[Taxonomy. Human]] (RTitle: "Human")
• Supers: [[Pathophysiology. Body]] (RTitle: "Body")
• NamingTags:
  1. -1OT: Prefix (-1), Owner (O), Recursive Title (T) -> "Human"
  2. +1S0T: Suffix (+1), First Super (S0), Recursive Title (T) -> "Body"
• Result: Human Body.md

🛠️ Installation & Usage

1. Dependencies:

   pip install python-frontmatter

2. Setup: Place .py in the root of your Obsidian vault.
3. Run:

   python .py

⚠️ Warning: This script performs destructive actions (renaming files and rewriting content). Always backup your vault before running.