weird-science

Repository dedicated to organizing and versioning study topics in systems theory, formal ontologies, and related areas. These materials serve as stepping-stones for future paper development.

📚 Study Topics

General Systems Theory

Collection of documents exploring systems theory, complexity, and emergent phenomena.

Foundations of General Systems Theory: A Survey of Formal Definitions

A systematic compilation of foundational definitions of systems and major theoretical insights drawn from the mathematical literature on General Systems Theory.

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Non-well-founded Hierarchies of Nested Systems

A systematic investigation of the definitional foundations of complex systems, articulating a formalism grounded in the recursive nesting of subsystems and examining emergence as a structural phenomenon arising from inter-level functional dependencies.

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Formal Ontologies

Collection of documents on formal ontologies and knowledge representation.

Definitional Architectures: From Conceptualization to Ontology

A philosophical excavation of formal system concepts, tracing the conceptual trajectory from extensional mathematical structures through intensional conceptualizations to formal ontologies, situated within the broader discourse of General Systems Theory.

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📁 Repository Structure

weird-science/
├── general-systems-theory/
│   ├── gst-overview/
│   │   ├── README.md
│   │   ├── main.tex
│   │   ├── sections/
│   │   │   ├── foundational-definitions.tex
│   │   │   └── theoretical-insights.tex
│   │   └── references/
│   │       └── bibliography.bib
│   └── nested-systems/
│       ├── README.md
│       ├── main.tex
│       ├── sections/
│       │   ├── introduction.tex
│       │   ├── preliminaries.tex
│       │   ├── systems.tex
│       │   ├── subsystems.tex
│       │   └── hierarchies.tex
│       └── references/
│           └── bibliography.bib
└── formal-ontologies/
    ├── README.md
    ├── main.tex
    ├── sections/
    │   ├── introduction.tex
    │   ├── extensional-foundations.tex
    │   ├── intensional-turn.tex
    │   ├── ontological-commitment.tex
    │   ├── intended-models.tex
    │   ├── ontology-specification.tex
    │   └── conclusion.tex
    └── references/
        └── bibliography.bib

Each document folder contains:

• main.tex - Main LaTeX document
• sections/ - LaTeX source files organized by section
• references/ - Bibliography files and reference materials
• README.md - Document-specific information

🔨 Building PDFs

PDFs are automatically built via GitHub Actions on every push to dev and for pull requests. You can:

• Download the latest PDFs from the Releases page
• Build locally by running pdflatex in each document directory
• View PR-specific builds as artifacts on pull request pages

📚 Zotero Integration

This repository is integrated with a Zotero group library to maintain literature references and generate knowledge artifacts:

• Project Summaries - Each project folder contains a project-summary.md with references matched to the Zotero library
• Knowledge Database - The knowledge-database/ directory contains atomic concept articles organized hierarchically
• Automated Generation - GitHub Actions workflow generates knowledge base from LaTeX sources and Zotero data
• Semantic Analysis - Extracts concepts (Γ) from LaTeX and expands to related Zotero items (Γ⁺)
• Interactive Exploration - Local Docker setup provides a web UI for querying the Zotero library

For details, see:

• Knowledge Base Workflow - Automated generation process
• Zotero Integration - Complete integration guide

Quick Start

# Generate knowledge base from LaTeX and Zotero
python scripts/zotero-integration/zotero_sync.py
python scripts/zotero-integration/knowledge_base_generator.py

# Or use the automated workflow (in GitHub Actions)
# Triggers on: manual dispatch or merges to dev with .tex changes

# Run local exploration UI
cd tools/zotero-mcp
docker-compose up -d
# Access at http://localhost:5000

🤝 Contributing

This repository uses comprehensive LaTeX .gitignore rules to keep auxiliary files out of version control while preserving source files and important assets.