Taxonomy Distribution Report

Overview

• Total Concepts: 379
• Number of Taxonomies: 17
• Average Concepts per Taxonomy: 22.3

Distribution Summary

Category	TaxonomyID	Count	Percentage	Status
Agents and Tool Use	AGENT	35	9.2%	✅
Agent Teams and Orchestration	ORCH	35	9.2%	✅
How Language Models Work	LLM	30	7.9%	✅
Prompting and Context Engineering	PROMPT	30	7.9%	✅
Markdown and Project Knowledge	MDKB	30	7.9%	✅
Data Analysis and Scientific Coding	DATA	30	7.9%	✅
Agent Skills	SKILL	25	6.6%	✅
Responsible and Ethical Use	ETHIC	24	6.3%	✅
Foundations of AI-Assisted Research	FOUND	20	5.3%	✅
Literature Search and Synthesis	LIT	20	5.3%	✅
Manuscript Preparation	MANU	19	5.0%	✅
Always-On Personal Agents	PERS	19	5.0%	✅
Verification and Reproducibility	VERIF	16	4.2%	✅
Case Studies and Capstone	CASE	14	3.7%	✅
MicroSims and Research Communication	COMM	12	3.2%	✅
Brainstorming and Problem Framing	BRAIN	10	2.6%	ℹ️ Under
Personal Knowledge Graphs	PKG	10	2.6%	ℹ️ Under

Visual Distribution

Agents and Tool Use       ████  35 (  9.2%)
Agent Teams and Orchestra ████  35 (  9.2%)
How Language Models Work  ███  30 (  7.9%)
Prompting and Context Eng ███  30 (  7.9%)
Markdown and Project Know ███  30 (  7.9%)
Data Analysis and Scienti ███  30 (  7.9%)
Agent Skills              ███  25 (  6.6%)
Responsible and Ethical U ███  24 (  6.3%)
Foundations of AI-Assiste ██  20 (  5.3%)
Literature Search and Syn ██  20 (  5.3%)
Manuscript Preparation    ██  19 (  5.0%)
Always-On Personal Agents ██  19 (  5.0%)
Verification and Reproduc ██  16 (  4.2%)
Case Studies and Capstone █  14 (  3.7%)
MicroSims and Research Co █  12 (  3.2%)
Brainstorming and Problem █  10 (  2.6%)
Personal Knowledge Graphs █  10 (  2.6%)

Balance Analysis

✅ No Over-Represented Categories

All categories are under the 30% threshold. Good balance!

ℹ️ Under-Represented Categories (<3%)

• Brainstorming and Problem Framing (BRAIN): 10 concepts (2.6%)
• Note: Small categories are acceptable for specialized topics
• Personal Knowledge Graphs (PKG): 10 concepts (2.6%)
• Note: Small categories are acceptable for specialized topics

Category Details

Agents and Tool Use (AGENT)

Count: 35 concepts (9.2%)

Concepts:

• 1. Agent Loop
• 1. Tool Use
• 1. Tool Call
• 1. Tool Definition
• 1. File Access
• 1. Shell Commands
• 1. Web Search
• 1. Web Fetch
• 1. Code Execution
• 1. Sandboxing
• 1. Permissions
• 1. Permission Modes
• 1. Subagent
• 1. Parallel Agents
• 1. Agent Memory
• ...and 20 more

Agent Teams and Orchestration (ORCH)

Count: 35 concepts (9.2%)

Concepts:

• 1. Planning Agent
• 1. Execution Agent
• 1. Planner Executor Pattern
• 1. Reviewer Agent
• 1. Research Agent
• 1. Coding Agent
• 1. Writing Agent
• 1. Analysis Agent
• 1. Literature Agent
• 1. Agent Roles
• 1. Agent Team
• 1. Orchestration
• 1. Orchestrator
• 1. Planning Agent Team
• 1. Execution Agent Team
• ...and 20 more

How Language Models Work (LLM)

Count: 30 concepts (7.9%)

Concepts:

• 1. Token
• 1. Tokenization
• 1. Context Window
• 1. Context Limit
• 1. Prompt
• 1. Completion
• 1. System Prompt
• 1. Temperature
• 1. Training Data
• 1. Knowledge Cutoff
• 1. Hallucination
• 1. Fabricated Citation
• 1. Model Selection
• 1. Model Size
• 1. Reasoning Model
• ...and 15 more

Prompting and Context Engineering (PROMPT)

Count: 30 concepts (7.9%)

Concepts:

• 1. Prompt Engineering
• 1. Context Engineering
• 1. Clear Instructions
• 1. Role Prompting
• 1. Few-Shot Examples
• 1. Chain of Thought
• 1. Structured Output
• 1. Output Format
• 1. Constraints
• 1. Acceptance Criteria
• 1. Iterative Refinement
• 1. Prompt Template
• 1. Prompt Library
• 1. Negative Instructions
• 1. Source Grounding
• ...and 15 more

Markdown and Project Knowledge (MDKB)

Count: 30 concepts (7.9%)

Concepts:

• 1. Markdown
• 1. Plain Text
• 1. Markdown Syntax
• 1. Headings
• 1. Lists and Tables
• 1. Code Blocks
• 1. YAML Frontmatter
• 1. Project Instruction File
• 1. AGENTS.md File
• 1. CLAUDE.md File
• 1. Project Goals
• 1. Project Conventions
• 1. Project Constraints
• 1. Glossary File
• 1. Research Notes
• ...and 15 more

Data Analysis and Scientific Coding (DATA)

Count: 30 concepts (7.9%)

Concepts:

• 1. Data Cleaning
• 1. Measurement Data
• 1. Exploratory Analysis
• 1. Statistical Analysis
• 1. Data Visualization
• 1. Plotting
• 1. Python
• 1. Analysis Script
• 1. Unit Tests
• 1. Code Review
• 1. Debugging
• 1. Error Messages
• 1. Silent Errors
• 1. Numerical Sanity Check
• 1. Simulation Script
• ...and 15 more

Agent Skills (SKILL)

Count: 25 concepts (6.6%)

Concepts:

• 1. Agent Skill
• 1. SKILL.md File
• 1. Skill Name
• 1. Skill Description
• 1. Skill Instructions
• 1. Skill Triggering
• 1. Supporting Files
• 1. Scripts in Skills
• 1. Reference Documents
• 1. Progressive Disclosure
• 1. Skill Scope
• 1. Single Purpose Skill
• 1. Skill Testing
• 1. Skill Evaluation
• 1. Skill Versioning
• ...and 10 more

Responsible and Ethical Use (ETHIC)

Count: 24 concepts (6.3%)

Concepts:

• 1. Responsible AI Use
• 1. Academic Integrity
• 1. Citation of AI Use
• 1. AI Disclosure
• 1. Authorship Policy
• 1. Privacy
• 1. Confidential Data
• 1. Unpublished Results
• 1. Intellectual Property
• 1. Copyright
• 1. Licensing
• 1. Data Governance
• 1. Bias and Fairness
• 1. Environmental Cost
• 1. Dual Use Risk
• ...and 9 more

Foundations of AI-Assisted Research (FOUND)

Count: 20 concepts (5.3%)

Concepts:

• 1. Research Workflow
• 1. Literature Search
• 1. Data Analysis
• 1. Brainstorming
• 1. Scientific Coding
• 1. Manuscript Preparation
• 1. Research Question
• 1. Research Productivity
• 1. Generative AI
• 1. Large Language Model
• 1. AI Assistant
• 1. AI Agent
• 1. Agentic Research
• 1. Researcher as Orchestrator
• 1. Human in the Loop
• ...and 5 more

Literature Search and Synthesis (LIT)

Count: 20 concepts (5.3%)

Concepts:

• 1. Literature Review
• 1. Search Strategy
• 1. Keyword Generation
• 1. Citation Chaining
• 1. Paper Summarization
• 1. Annotated Bibliography
• 1. Reading List
• 1. Research Gap
• 1. Related Work
• 1. Citation Verification
• 1. DOI Lookup
• 1. Reference Manager
• 1. BibTeX
• 1. Paper Triage
• 1. Claim Extraction
• ...and 5 more

Manuscript Preparation (MANU)

Count: 19 concepts (5.0%)

Concepts:

• 1. Paper Structure
• 1. Abstract Writing
• 1. Outline Generation
• 1. Drafting
• 1. Revision
• 1. Author Voice
• 1. LaTeX
• 1. Figure Preparation
• 1. Figure Captions
• 1. Reference Formatting
• 1. arXiv Submission
• 1. Peer Review Response
• 1. Technical Editing
• 1. Style Consistency
• 1. Grammar and Clarity
• ...and 4 more

Always-On Personal Agents (PERS)

Count: 19 concepts (5.0%)

Concepts:

• 1. Personal Agent
• 1. Always-On Agent
• 1. Cloud Agent Computer
• 1. Self-Hosted Agent
• 1. Teachable Routine
• 1. Delegated Sign-In
• 1. Grok Bot
• 1. Dots
• 1. Muse
• 1. Claude Cowork
• 1. OpenClaw
• 1. Hermes Agent
• 1. Agent Blast Radius
• 1. Usage Metering
• 1. Agent Comparison Criteria
• ...and 4 more

Verification and Reproducibility (VERIF)

Count: 16 concepts (4.2%)

Concepts:

• 1. Verification
• 1. Validation
• 1. Independent Check
• 1. Primary Source Check
• 1. Cross Model Check
• 1. Test Driven Research
• 1. Result Replication
• 1. Uncertainty Awareness
• 1. Overconfidence
• 1. Sycophancy
• 1. Output Bias
• 1. Audit Trail
• 1. Reproducibility Package
• 1. Peer Verification
• 1. Acceptance Review
• ...and 1 more

Case Studies and Capstone (CASE)

Count: 14 concepts (3.7%)

Concepts:

• 1. Case Study
• 1. MicroSims Paper
• 1. Intelligent Textbook Project
• 1. Textbook Workflow
• 1. Skill Pipeline
• 1. Lessons Learned
• 1. Failure Case
• 1. Workflow Documentation
• 1. Capstone Project
• 1. Agent Team Design
• 1. Personal Skill Library
• 1. Group Workflow
• 1. Presentation of Results
• 1. Adoption Plan

MicroSims and Research Communication (COMM)

Count: 12 concepts (3.2%)

Concepts:

• 1. Slide Deck
• 1. MicroSim
• 1. Interactive Simulation
• 1. Intelligent Textbook
• 1. Learning Graph
• 1. p5.js
• 1. Embedding Simulations
• 1. Research Communication
• 1. Teaching From Research
• 1. Open Educational Resources
• 1. MicroSim Generation
• 1. Concept Dependency

Brainstorming and Problem Framing (BRAIN)

Count: 10 concepts (2.6%)

Concepts:

• 1. Problem Framing
• 1. Idea Generation
• 1. Hypothesis Development
• 1. Devils Advocate Prompt
• 1. Analogical Thinking
• 1. Experiment Design
• 1. Feasibility Assessment
• 1. Research Roadmap
• 1. Idea Ranking
• 1. Novelty Check

Personal Knowledge Graphs (PKG)

Count: 10 concepts (2.6%)

Concepts:

• 1. Knowledge Graph
• 1. Entity and Relationship
• 1. Personal Knowledge Graph
• 1. Graph Schema
• 1. Backlinks
• 1. Entity Extraction
• 1. Graph Querying
• 1. Graph Retrieval Augmented Generation
• 1. Knowledge Graph Memory
• 1. Personal Knowledge Privacy

Recommendations

• ✅ Excellent balance: Categories are evenly distributed (spread: 6.6%)
• ✅ MISC category minimal: Good categorization specificity

Educational Use Recommendations

• Use taxonomy categories for color-coding in graph visualizations
• Design curriculum modules based on taxonomy groupings
• Create filtered views for focused learning paths
• Use categories for assessment organization
• Enable navigation by topic area in interactive tools

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Report generated by learning-graph-reports/taxonomy_distribution.py