--- type: CKG Bundle title: Bioinformatics tags: [Healthcare & Life Sci] timestamp: 2026-06-18T00:00:00Z ckg: id: bioinformatics nodes: 480 license: CC BY 4.0 --- # Bioinformatics — Compressed Knowledge Graph ```csv ConceptID,ConceptLabel,TaxonomyID 1,Bioinformatics,FOUND 2,Computational Biology,FOUND 3,Central Dogma,FOUND 4,DNA Structure,FOUND 5,RNA Structure,FOUND 6,Protein Structure,FOUND 7,Amino Acids,FOUND 8,Nucleotides,FOUND 9,Codons,FOUND 10,Gene,FOUND 11,Genome,FOUND 12,Transcription,FOUND 13,Translation,FOUND 14,Gene Expression,FOUND 15,Sequence Data,FOUND 16,Molecular Biology,FOUND 17,Cell Biology Basics,FOUND 18,Genetic Code,FOUND 19,Open Reading Frame,FOUND 20,Complementary Base Pairing,FOUND 21,Chromosomes,FOUND 22,Mutations,FOUND 23,Single Nucleotide Polymorphism,FOUND 24,Insertion and Deletion,FOUND 25,Structural Variant,FOUND 26,Copy Number Variation,FOUND 27,Epigenetics,FOUND 28,DNA Methylation,FOUND 29,Histone Modification,FOUND 30,Central Dogma Exceptions,FOUND 31,Biological Databases,DBAS 32,NCBI,DBAS 33,GenBank Database,DBAS 34,UniProt,DBAS 35,Swiss-Prot,DBAS 36,TrEMBL,DBAS 37,Protein Data Bank,DBAS 38,Ensembl,DBAS 39,KEGG Database,DBAS 40,Reactome Database,DBAS 41,BioGRID Database,DBAS 42,STRING Database,DBAS 43,IntAct Database,DBAS 44,COSMIC Database,DBAS 45,Gene Ontology Database,DBAS 46,Disease Ontology Database,DBAS 47,Human Phenotype Ontology DB,DBAS 48,BioCyc Database,DBAS 49,OMIM Database,DBAS 50,Hetionet Database,DBAS 51,Database Cross-References,DBAS 52,Programmatic Database Access,DBAS 53,REST APIs for Biology,DBAS 54,Batch Data Download,DBAS 55,Data Provenance,DBAS 56,FASTA Format,DFMT 57,FASTQ Format,DFMT 58,GenBank Format,DFMT 59,GFF3 Format,DFMT 60,OWL Format,DFMT 61,PDB File Format,DFMT 62,VCF Format,DFMT 63,SAM and BAM Format,DFMT 64,BED Format,DFMT 65,SBML Format,DFMT 66,BioPAX Format,DFMT 67,CSV for Bioinformatics,DFMT 68,JSON for Bioinformatics,DFMT 69,Data Format Conversion,DFMT 70,Data Quality Control,DFMT 71,Graph Theory,GRTH 72,Nodes and Edges,GRTH 73,Directed Graphs,GRTH 74,Undirected Graphs,GRTH 75,Weighted Graphs,GRTH 76,Bipartite Graphs,GRTH 77,Labeled Property Graph,GRTH 78,Multigraph,GRTH 79,Hypergraph,GRTH 80,Subgraph,GRTH 81,Graph Properties,GRTH 82,Degree Distribution,GRTH 83,In-Degree,GRTH 84,Out-Degree,GRTH 85,Clustering Coefficient,GRTH 86,Centrality Measures,GRTH 87,Degree Centrality,GRTH 88,Betweenness Centrality,GRTH 89,Closeness Centrality,GRTH 90,Eigenvector Centrality,GRTH 91,PageRank,GRTH 92,Connected Components,GRTH 93,Strongly Connected Comp,GRTH 94,Graph Traversal,GRTH 95,Breadth-First Search,GRTH 96,Depth-First Search,GRTH 97,Shortest Path Algorithms,GRTH 98,Dijkstra Algorithm,GRTH 99,Graph Density,GRTH 100,Graph Diameter,GRTH 101,Scale-Free Networks,GRTH 102,Small-World Networks,GRTH 103,Power-Law Distribution,GRTH 104,Random Graph Models,GRTH 105,Erdos-Renyi Model,GRTH 106,Barabasi-Albert Model,GRTH 107,Network Motifs,GRTH 108,Graph Isomorphism,GRTH 109,Adjacency Matrix,GRTH 110,Edge List Representation,GRTH 111,Graph Database,GRDB 112,Relational Database,GRDB 113,Graph vs Relational Model,GRDB 114,Neo4j,GRDB 115,Memgraph,GRDB 116,Cypher Query Language,GRDB 117,GQL Query Language,GRDB 118,MATCH Clause,GRDB 119,WHERE Clause,GRDB 120,RETURN Clause,GRDB 121,CREATE Clause,GRDB 122,MERGE Clause,GRDB 123,Graph Pattern Matching,GRDB 124,Variable-Length Paths,GRDB 125,Path Queries,GRDB 126,Aggregation in Cypher,GRDB 127,Graph Schema Design,GRDB 128,Node Labels,GRDB 129,Relationship Types,GRDB 130,Property Keys,GRDB 131,Index and Constraints,GRDB 132,RDF Triple Model,GRDB 133,Subject-Predicate-Object,GRDB 134,SPARQL Query Language,GRDB 135,LPG vs RDF Comparison,GRDB 136,Graph Data Loading,GRDB 137,CSV Import to Graph DB,GRDB 138,ETL for Graph Databases,GRDB 139,Graph Query Optimization,GRDB 140,Query Profiling,GRDB 141,Distributed Graph Databases,GRDB 142,Graph Partitioning,GRDB 143,Graph Scalability,GRDB 144,Graph Transactions,GRDB 145,Graph Access Control,GRDB 146,Sequence Alignment,SEQA 147,Pairwise Alignment,SEQA 148,Global Alignment,SEQA 149,Local Alignment,SEQA 150,Smith-Waterman Algorithm,SEQA 151,Needleman-Wunsch Algorithm,SEQA 152,Dynamic Programming,SEQA 153,Scoring Matrices,SEQA 154,BLOSUM Matrix,SEQA 155,PAM Matrix,SEQA 156,Substitution Model,SEQA 157,Gap Penalties,SEQA 158,Affine Gap Penalty,SEQA 159,BLAST,SEQA 160,BLAST E-Value,SEQA 161,BLAST Heuristics,SEQA 162,PSI-BLAST,SEQA 163,Sequence Homology,SEQA 164,Orthologs,SEQA 165,Paralogs,SEQA 166,Sequence Identity,SEQA 167,Sequence Similarity,SEQA 168,Sequence Similarity Network,SEQA 169,Graph Model for Similarity,GRDB 170,Multiple Sequence Alignment,SEQA 171,Clustal,SEQA 172,MUSCLE Aligner,SEQA 173,Progressive Alignment,SEQA 174,Consensus Sequence,SEQA 175,Sequence Profile,SEQA 176,Hidden Markov Model,SEQA 177,Profile HMM,SEQA 178,Sequence Motif,SEQA 179,Regular Expressions,SEQA 180,Motif Discovery,SEQA 181,Phylogenetic Tree,PHYL 182,Phylogenetics,PHYL 183,Molecular Phylogenetics,PHYL 184,Distance Matrix,PHYL 185,Neighbor-Joining Method,PHYL 186,UPGMA Method,PHYL 187,Maximum Parsimony,PHYL 188,Maximum Likelihood Method,PHYL 189,Bayesian Inference,PHYL 190,Markov Chain Monte Carlo,PHYL 191,Bootstrap Analysis,PHYL 192,Branch Support Values,PHYL 193,Molecular Clock,PHYL 194,Substitution Rate,PHYL 195,Trees as DAGs,PHYL 196,Phylogenetic Networks,PHYL 197,Reticulate Evolution,PHYL 198,Horizontal Gene Transfer,PHYL 199,Recombination,PHYL 200,Incomplete Lineage Sorting,PHYL 201,Graph Model for Evolution,GRDB 202,Cladogram,PHYL 203,Phylogram,PHYL 204,Monophyletic Group,PHYL 205,Paraphyletic Group,PHYL 206,Outgroup,PHYL 207,Rooted vs Unrooted Trees,PHYL 208,Tree Topology Comparison,PHYL 209,Robinson-Foulds Distance,PHYL 210,Ancestral Reconstruction,PHYL 211,Divergence Time Estimation,PHYL 212,Gene Tree vs Species Tree,PHYL 213,Coalescent Theory,PHYL 214,Phylogenomics,PHYL 215,Comparative Genomics,PHYL 216,Primary Structure,STRU 217,Secondary Structure,STRU 218,Alpha Helix,STRU 219,Beta Sheet,STRU 220,Tertiary Structure,STRU 221,Quaternary Structure,STRU 222,Protein Folding,STRU 223,Protein Folding Problem,STRU 224,Homology Modeling,STRU 225,Threading,STRU 226,Ab Initio Prediction,STRU 227,AlphaFold,STRU 228,AlphaFold Database,STRU 229,Protein Contact Map,STRU 230,Contact Map as Graph,STRU 231,Residue Interaction Network,STRU 232,Graph Model for Contacts,GRDB 233,Structural Alignment,STRU 234,RMSD,STRU 235,Protein Domain,STRU 236,Domain Classification,STRU 237,SCOP Database,STRU 238,Pfam Database,STRU 239,Protein Surface Analysis,STRU 240,Binding Site Prediction,STRU 241,Molecular Docking,STRU 242,Ligand-Protein Interaction,STRU 243,Drug-Likeness,STRU 244,ADMET Properties,STRU 245,Protein-Ligand Graph,STRU 246,Molecular Fingerprints,STRU 247,Chemical Similarity,STRU 248,Structure-Activity Relation,STRU 249,Protein Function Inference,STRU 250,Structural Genomics,STRU 251,Protein Interaction Network,PPIS 252,Interactome,PPIS 253,Yeast Two-Hybrid,PPIS 254,Co-Immunoprecipitation,PPIS 255,Affinity Purification MS,PPIS 256,Cross-Linking Mass Spec,PPIS 257,PPI Confidence Scoring,PPIS 258,Binary vs Complex PPIs,PPIS 259,Network Hubs,PPIS 260,Network Bottlenecks,PPIS 261,Network Modules,PPIS 262,Graph Model for PPIs,GRDB 263,Hub-and-Spoke Topology,PPIS 264,Date Hubs vs Party Hubs,PPIS 265,Essential Proteins,PPIS 266,Protein Complex Detection,PPIS 267,Clique Detection,PPIS 268,Dense Subgraph Mining,PPIS 269,Network Rewiring,PPIS 270,Dynamic PPI Networks,PPIS 271,Tissue-Specific PPIs,PPIS 272,Host-Pathogen PPIs,PPIS 273,Viral Interactome,PPIS 274,PPI Prediction Methods,PPIS 275,Interaction Domain Pairs,PPIS 276,Co-Evolution Analysis,PPIS 277,Network Alignment,PPIS 278,Network Comparison,PPIS 279,Graphlet Analysis,PPIS 280,Network Centrality in PPIs,PPIS 281,Genome Assembly,GENO 282,De Bruijn Graph,GENO 283,K-mer,GENO 284,K-mer Spectrum,GENO 285,Contig,GENO 286,Scaffold,GENO 287,N50 Metric,GENO 288,Assembly Quality Metrics,GENO 289,Reference Genome,GENO 290,Reference Bias,GENO 291,Pangenome,GENO 292,Pangenome Graph,GENO 293,Variation Graph,GENO 294,VG Toolkit,GENO 295,Graph Model for Variants,GRDB 296,Read Mapping to Graphs,GENO 297,Genome Annotation,GENO 298,Gene Prediction,GENO 299,Next-Gen Sequencing,GENO 300,Short Reads,GENO 301,Long Reads,GENO 302,Sequencing Depth,GENO 303,Coverage,GENO 304,Variant Calling,GENO 305,SNP Calling,GENO 306,Structural Variant Calling,GENO 307,Genotyping,GENO 308,Haplotype,GENO 309,Phasing,GENO 310,Population Reference Graph,GENO 311,Transcriptome,TRNS 312,RNA-Seq Pipeline,TRNS 313,Read Quality Trimming,TRNS 314,Read Alignment,TRNS 315,Transcript Quantification,TRNS 316,Differential Expression,TRNS 317,Fold Change,TRNS 318,Statistical Testing for DE,TRNS 319,False Discovery Rate,TRNS 320,Transcription Factor,TRNS 321,Promoter Region,TRNS 322,Enhancer Region,TRNS 323,Cis-Regulatory Element,TRNS 324,Operon,TRNS 325,Gene Regulatory Network,TRNS 326,Co-Expression Network,TRNS 327,WGCNA,TRNS 328,ARACNE,TRNS 329,GENIE3,TRNS 330,Mutual Information,TRNS 331,Network Inference Methods,TRNS 332,Boolean Network Model,TRNS 333,Bayesian Network Model,TRNS 334,Graph Model for Regulation,GRDB 335,Single-Cell RNA-Seq,TRNS 336,Cell Type Clustering,TRNS 337,Trajectory Analysis,TRNS 338,Spatial Transcriptomics,TRNS 339,Alternative Splicing,TRNS 340,Non-Coding RNA,TRNS 341,Metabolic Network,PATH 342,Metabolite,PATH 343,Enzyme,PATH 344,Enzyme Kinetics,PATH 345,Metabolic Pathway,PATH 346,Bipartite Metabolic Graph,PATH 347,KEGG Pathways,PATH 348,Reactome Pathways,PATH 349,BioCyc Pathways,PATH 350,Flux Balance Analysis,PATH 351,Constraint-Based Modeling,PATH 352,Stoichiometric Matrix,PATH 353,Objective Function,PATH 354,Metabolic Flux,PATH 355,Graph Model for Metabolism,GRDB 356,Genome-Scale Model,PATH 357,Essential Reaction,PATH 358,Minimal Growth Medium,PATH 359,Metabolic Engineering,PATH 360,Synthetic Biology,PATH 361,Pathway Enrichment,PATH 362,Metabolomics,PATH 363,Mass Spec for Metabolomics,PATH 364,Metabolic Network Compare,PATH 365,Metabolic Graph Alignment,PATH 366,Cell Signaling Cascade,PATH 367,Signal Transduction,PATH 368,Receptor,PATH 369,Kinase Cascade,PATH 370,Second Messenger,PATH 371,Directed Signaling Graph,PATH 372,Feedback Loop,PATH 373,Feed-Forward Loop,PATH 374,Network Medicine,PATH 375,Disease Module,PATH 376,Network Proximity,PATH 377,Guilt by Association,PATH 378,Drug Target,PATH 379,Drug Target Validation,PATH 380,Drug Repurposing,PATH 381,Drug-Target-Disease Graph,PATH 382,Graph Model for Repurposing,GRDB 383,Pharmacogenomics,PATH 384,Cancer Driver Genes,PATH 385,Tumor Suppressor Gene,PATH 386,Oncogene,PATH 387,Cancer Network Analysis,PATH 388,Precision Medicine,PATH 389,Biomarker Discovery,PATH 390,Clinical Network Analysis,PATH 391,Side Effect Prediction,PATH 392,Drug-Drug Interaction Graph,PATH 393,Adverse Event Network,PATH 394,Comorbidity Network,PATH 395,Disease Gene Prioritization,PATH 396,Knowledge Graph,KNOW 397,Biomedical Knowledge Graph,KNOW 398,Gene Ontology,KNOW 399,GO Molecular Function,KNOW 400,GO Biological Process,KNOW 401,GO Cellular Component,KNOW 402,GO Term Enrichment,KNOW 403,Disease Ontology,KNOW 404,Human Phenotype Ontology,KNOW 405,Ontology Structure,KNOW 406,Ontology Reasoning,KNOW 407,Semantic Similarity,KNOW 408,Heterogeneous Data,KNOW 409,Data Integration,KNOW 410,Schema Mapping,KNOW 411,Entity Resolution,KNOW 412,Graph Embeddings,KNOW 413,Node2Vec,KNOW 414,TransE,KNOW 415,Knowledge Graph Embedding,KNOW 416,Link Prediction,KNOW 417,Triple Classification,KNOW 418,Relation Extraction,KNOW 419,Named Entity Recognition,KNOW 420,Text Mining for Biology,KNOW 421,Graph Neural Networks,KNOW 422,Message Passing,KNOW 423,GNN for Molecules,KNOW 424,Graph Model for Knowledge,GRDB 425,Hetionet,KNOW 426,Multi-Omics Integration,KNOW 427,Genomics Layer,KNOW 428,Transcriptomics Layer,KNOW 429,Proteomics Layer,KNOW 430,Metabolomics Layer,KNOW 431,Unified Omics Graph,KNOW 432,Graph Model for Multi-Omics,GRDB 433,Community Detection,GRTH 434,Louvain Algorithm,GRTH 435,Leiden Algorithm,GRTH 436,Modularity Score,GRTH 437,Graph Clustering,GRTH 438,Spectral Clustering,GRTH 439,Graph Visualization,GRTH 440,Vis-Network Library,GRTH 441,Cytoscape Tool,GRTH 442,Force-Directed Layout,GRTH 443,Hierarchical Layout,GRTH 444,Network Layout Algorithms,GRTH 445,Patient Similarity Network,KNOW 446,Clinical Data Graph,KNOW 447,Survival Analysis,KNOW 448,Patient Stratification,KNOW 449,Network-Based Biomarkers,KNOW 450,Python for Bioinformatics,TOOL 451,Biopython,TOOL 452,NetworkX,TOOL 453,Pandas for Bioinformatics,TOOL 454,Scikit-Learn,TOOL 455,Jupyter Notebooks,TOOL 456,Matplotlib,TOOL 457,Seaborn,TOOL 458,Neo4j Python Driver,TOOL 459,Cytoscape API,TOOL 460,Data Wrangling,TOOL 461,Reproducible Analysis,TOOL 462,Version Control for Science,TOOL 463,Workflow Managers,TOOL 464,Conda Environments,TOOL 465,Capstone Project Design,TOOL 466,Graph Data Model Design,TOOL 467,Antibiotic Resistance Graph,TOOL 468,Resistance Gene Network,TOOL 469,Mobile Genetic Elements,TOOL 470,Rare Disease Knowledge Graph,TOOL 471,Phenotype-Gene Mapping,TOOL 472,Metabolic Model Comparison,TOOL 473,Cross-Species Graph Align,TOOL 474,Protein Function Predict,TOOL 475,GO Annotation Prediction,TOOL 476,Multi-Omics Stratification,TOOL 477,Patient Subgroup Discovery,TOOL 478,Graph-Based Discovery,TOOL 479,Bench to Bedside Pipeline,TOOL 480,Future of Graph Bioinform,TOOL ``` ## Edges (prerequisite -> concept) 1 -> 2 1 -> 3 3 -> 4 3 -> 5 3 -> 6 6 -> 7 4 -> 8 5 -> 8 8 -> 9 18 -> 9 4 -> 10 10 -> 11 4 -> 12 5 -> 12 5 -> 13 6 -> 13 9 -> 13 12 -> 14 13 -> 14 4 -> 15 5 -> 15 6 -> 15 3 -> 16 1 -> 17 3 -> 18 10 -> 19 18 -> 19 4 -> 20 8 -> 20 4 -> 21 11 -> 21 4 -> 22 10 -> 22 22 -> 23 22 -> 24 22 -> 25 21 -> 25 25 -> 26 14 -> 27 27 -> 28 4 -> 28 27 -> 29 21 -> 29 3 -> 30 12 -> 30 13 -> 30 15 -> 31 31 -> 32 32 -> 33 31 -> 34 6 -> 34 34 -> 35 34 -> 36 31 -> 37 6 -> 37 31 -> 38 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455 450 -> 456 456 -> 457 450 -> 458 114 -> 458 441 -> 459 450 -> 459 453 -> 460 455 -> 461 462 -> 461 461 -> 463 450 -> 464 466 -> 465 127 -> 466 397 -> 467 198 -> 467 467 -> 468 198 -> 469 467 -> 469 397 -> 470 404 -> 470 470 -> 471 356 -> 472 364 -> 472 472 -> 473 365 -> 473 412 -> 474 249 -> 474 474 -> 475 398 -> 475 448 -> 476 426 -> 476 476 -> 477 433 -> 477 416 -> 478 396 -> 478 388 -> 479 478 -> 479 478 -> 480 *Free CKG · Graphify.md · `pip install ckg-mcp` for all · own the knowledge layer, rent the model*