Taxonomy Distribution Report

Overview

• Total Concepts: 480
• Number of Taxonomies: 14
• Average Concepts per Taxonomy: 34.3

Distribution Summary

Category	TaxonomyID	Count	Percentage	Status
Pathways and Disease	PATH	53	11.0%	✅
Graph Theory	GRTH	52	10.8%	✅
Graph Databases	GRDB	45	9.4%	✅
Knowledge Graphs	KNOW	40	8.3%	✅
Sequence Analysis	SEQA	34	7.1%	✅
Phylogenetics	PHYL	34	7.1%	✅
Structural Bioinformatics	STRU	34	7.1%	✅
Tools and Capstone	TOOL	31	6.5%	✅
Foundation Concepts	FOUND	30	6.2%	✅
Protein Interactions	PPIS	29	6.0%	✅
Genomics	GENO	29	6.0%	✅
Transcriptomics	TRNS	29	6.0%	✅
Biological Databases	DBAS	25	5.2%	✅
Data Formats	DFMT	15	3.1%	✅

Visual Distribution

Pathways and Disease      █████  53 ( 11.0%)
Graph Theory              █████  52 ( 10.8%)
Graph Databases           ████  45 (  9.4%)
Knowledge Graphs          ████  40 (  8.3%)
Sequence Analysis         ███  34 (  7.1%)
Phylogenetics             ███  34 (  7.1%)
Structural Bioinformatics ███  34 (  7.1%)
Tools and Capstone        ███  31 (  6.5%)
Foundation Concepts       ███  30 (  6.2%)
Protein Interactions      ███  29 (  6.0%)
Genomics                  ███  29 (  6.0%)
Transcriptomics           ███  29 (  6.0%)
Biological Databases      ██  25 (  5.2%)
Data Formats              █  15 (  3.1%)

Balance Analysis

✅ No Over-Represented Categories

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

Category Details

Pathways and Disease (PATH)

Count: 53 concepts (11.0%)

Concepts:

• 1. Metabolic Network
• 1. Metabolite
• 1. Enzyme
• 1. Enzyme Kinetics
• 1. Metabolic Pathway
• 1. Bipartite Metabolic Graph
• 1. KEGG Pathways
• 1. Reactome Pathways
• 1. BioCyc Pathways
• 1. Flux Balance Analysis
• 1. Constraint-Based Modeling
• 1. Stoichiometric Matrix
• 1. Objective Function
• 1. Metabolic Flux
• 1. Genome-Scale Model
• ...and 38 more

Graph Theory (GRTH)

Count: 52 concepts (10.8%)

Concepts:

• 1. Graph Theory
• 1. Nodes and Edges
• 1. Directed Graphs
• 1. Undirected Graphs
• 1. Weighted Graphs
• 1. Bipartite Graphs
• 1. Labeled Property Graph
• 1. Multigraph
• 1. Hypergraph
• 1. Subgraph
• 1. Graph Properties
• 1. Degree Distribution
• 1. In-Degree
• 1. Out-Degree
• 1. Clustering Coefficient
• ...and 37 more

Graph Databases (GRDB)

Count: 45 concepts (9.4%)

Concepts:

• 1. Graph Database
• 1. Relational Database
• 1. Graph vs Relational Model
• 1. Neo4j
• 1. Memgraph
• 1. Cypher Query Language
• 1. GQL Query Language
• 1. MATCH Clause
• 1. WHERE Clause
• 1. RETURN Clause
• 1. CREATE Clause
• 1. MERGE Clause
• 1. Graph Pattern Matching
• 1. Variable-Length Paths
• 1. Path Queries
• ...and 30 more

Knowledge Graphs (KNOW)

Count: 40 concepts (8.3%)

Concepts:

• 1. Knowledge Graph
• 1. Biomedical Knowledge Graph
• 1. Gene Ontology
• 1. GO Molecular Function
• 1. GO Biological Process
• 1. GO Cellular Component
• 1. GO Term Enrichment
• 1. Disease Ontology
• 1. Human Phenotype Ontology
• 1. Ontology Structure
• 1. Ontology Reasoning
• 1. Semantic Similarity
• 1. Heterogeneous Data
• 1. Data Integration
• 1. Schema Mapping
• ...and 25 more

Sequence Analysis (SEQA)

Count: 34 concepts (7.1%)

Concepts:

• 1. Sequence Alignment
• 1. Pairwise Alignment
• 1. Global Alignment
• 1. Local Alignment
• 1. Smith-Waterman Algorithm
• 1. Needleman-Wunsch Algorithm
• 1. Dynamic Programming
• 1. Scoring Matrices
• 1. BLOSUM Matrix
• 1. PAM Matrix
• 1. Substitution Model
• 1. Gap Penalties
• 1. Affine Gap Penalty
• 1. BLAST
• 1. BLAST E-Value
• ...and 19 more

Phylogenetics (PHYL)

Count: 34 concepts (7.1%)

Concepts:

• 1. Phylogenetic Tree
• 1. Phylogenetics
• 1. Molecular Phylogenetics
• 1. Distance Matrix
• 1. Neighbor-Joining Method
• 1. UPGMA Method
• 1. Maximum Parsimony
• 1. Maximum Likelihood Method
• 1. Bayesian Inference
• 1. Markov Chain Monte Carlo
• 1. Bootstrap Analysis
• 1. Branch Support Values
• 1. Molecular Clock
• 1. Substitution Rate
• 1. Trees as DAGs
• ...and 19 more

Structural Bioinformatics (STRU)

Count: 34 concepts (7.1%)

Concepts:

• 1. Primary Structure
• 1. Secondary Structure
• 1. Alpha Helix
• 1. Beta Sheet
• 1. Tertiary Structure
• 1. Quaternary Structure
• 1. Protein Folding
• 1. Protein Folding Problem
• 1. Homology Modeling
• 1. Threading
• 1. Ab Initio Prediction
• 1. AlphaFold
• 1. AlphaFold Database
• 1. Protein Contact Map
• 1. Contact Map as Graph
• ...and 19 more

Tools and Capstone (TOOL)

Count: 31 concepts (6.5%)

Concepts:

• 1. Python for Bioinformatics
• 1. Biopython
• 1. NetworkX
• 1. Pandas for Bioinformatics
• 1. Scikit-Learn
• 1. Jupyter Notebooks
• 1. Matplotlib
• 1. Seaborn
• 1. Neo4j Python Driver
• 1. Cytoscape API
• 1. Data Wrangling
• 1. Reproducible Analysis
• 1. Version Control for Science
• 1. Workflow Managers
• 1. Conda Environments
• ...and 16 more

Foundation Concepts (FOUND)

Count: 30 concepts (6.2%)

Concepts:

• 1. Bioinformatics
• 1. Computational Biology
• 1. Central Dogma
• 1. DNA Structure
• 1. RNA Structure
• 1. Protein Structure
• 1. Amino Acids
• 1. Nucleotides
• 1. Codons
• 1. Gene
• 1. Genome
• 1. Transcription
• 1. Translation
• 1. Gene Expression
• 1. Sequence Data
• ...and 15 more

Protein Interactions (PPIS)

Count: 29 concepts (6.0%)

Concepts:

• 1. Protein Interaction Network
• 1. Interactome
• 1. Yeast Two-Hybrid
• 1. Co-Immunoprecipitation
• 1. Affinity Purification MS
• 1. Cross-Linking Mass Spec
• 1. PPI Confidence Scoring
• 1. Binary vs Complex PPIs
• 1. Network Hubs
• 1. Network Bottlenecks
• 1. Network Modules
• 1. Hub-and-Spoke Topology
• 1. Date Hubs vs Party Hubs
• 1. Essential Proteins
• 1. Protein Complex Detection
• ...and 14 more

Genomics (GENO)

Count: 29 concepts (6.0%)

Concepts:

• 1. Genome Assembly
• 1. De Bruijn Graph
• 1. K-mer
• 1. K-mer Spectrum
• 1. Contig
• 1. Scaffold
• 1. N50 Metric
• 1. Assembly Quality Metrics
• 1. Reference Genome
• 1. Reference Bias
• 1. Pangenome
• 1. Pangenome Graph
• 1. Variation Graph
• 1. VG Toolkit
• 1. Read Mapping to Graphs
• ...and 14 more

Transcriptomics (TRNS)

Count: 29 concepts (6.0%)

Concepts:

• 1. Transcriptome
• 1. RNA-Seq Pipeline
• 1. Read Quality Trimming
• 1. Read Alignment
• 1. Transcript Quantification
• 1. Differential Expression
• 1. Fold Change
• 1. Statistical Testing for DE
• 1. False Discovery Rate
• 1. Transcription Factor
• 1. Promoter Region
• 1. Enhancer Region
• 1. Cis-Regulatory Element
• 1. Operon
• 1. Gene Regulatory Network
• ...and 14 more

Biological Databases (DBAS)

Count: 25 concepts (5.2%)

Concepts:

• 1. Biological Databases
• 1. NCBI
• 1. GenBank Database
• 1. UniProt
• 1. Swiss-Prot
• 1. TrEMBL
• 1. Protein Data Bank
• 1. Ensembl
• 1. KEGG Database
• 1. Reactome Database
• 1. BioGRID Database
• 1. STRING Database
• 1. IntAct Database
• 1. COSMIC Database
• 1. Gene Ontology Database
• ...and 10 more

Data Formats (DFMT)

Count: 15 concepts (3.1%)

Concepts:

• 1. FASTA Format
• 1. FASTQ Format
• 1. GenBank Format
• 1. GFF3 Format
• 1. OWL Format
• 1. PDB File Format
• 1. VCF Format
• 1. SAM and BAM Format
• 1. BED Format
• 1. SBML Format
• 1. BioPAX Format
• 1. CSV for Bioinformatics
• 1. JSON for Bioinformatics
• 1. Data Format Conversion
• 1. Data Quality Control

Recommendations

• ✅ Excellent balance: Categories are evenly distributed (spread: 7.9%)
• ✅ 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