Tag: Biological

A Guide to Biological Databases - Interactive View Technical Architecture Guide Biological Database Ecosystem An exhaustive analysis of bioinformatics infrastructure, from metadata standards to AI-driven structural predictions. 1. Institutions 2. Data Flow 3. Metadata 4. Catalog 5. Case Study Part One The Institutional Pillars Comparison of the architectural philosophies of NCBI and EMBL-EBI. NCBI (USA) Literature-Centric Entrez & "Neighboring" Pre-computes similarity between records across 20+ databases, allowing seamless traversal from sequence to literature. Visit NCBI EMBL-EBI (Europe) Service-Oriented Job Dispatcher Framework Middleware for piping database records directly into analytical tools like BLAST and Clustal Omega. Visit EMBL-EBI Part Two Stratified Information Pipeline The flow from raw archival data to processed structural models. Primary Archive 1 Raw Nucleotide Data GenBank / ENA / SRA Curated Tier 2 Secondary Knowledge UniProtKB (Swiss-Prot) / RefSeq Contextual Tier 3 Integrated Genomes Ensembl Browser Predictive Tier 4 Protein Structure PDB / AlphaFold DB Part Three The Metadata Hierarchy How raw sequencing data is categorized for discovery. SRA Data Model 1. BioProject Study goals and funding. 2. BioSample Physical source (tissue, strain). 3. Experiment Library prep details. 4. Run The actual SRR data file. GEO Data Types GPL Platform e.g., Affymetrix Array GSM Sample Individual expression data. GSE Series Group of related samples. Part Four Technical Catalog Industry-standard repositories with direct access links. Archival GenBank Global archive for all publicly available DNA sequences. Syncs daily via INSDC. Visit GenBank Integrative Ensembl Genome browser for vertebrates with high-quality automated annotation. Visit Ensembl Knowledge UniProtKB Protein function hub. Swiss-Prot (Reviewed) is the curation gold standard. Visit UniProt Structural PDB Global archive for atomic coordinates from experimental 3D structures. Visit PDB AI-Driven AlphaFold DB AI-predicted models for 200M+ proteins. Covers the entire UniProt space. Visit AlphaFold DB Clinical ClinVar Database of relationships between variants and human health phenotypes. Visit ClinVar Part Five Detailed Case Study Tracing KCNQ1 Arg450Leu from Variant to Mechanism. Conclusion: Scientific Synergy By chaining metadata, sequence, and structure, a "Variant of Uncertain Significance" is upgraded to "Likely Pathogenic," informing critical clinical decisions.

Tag: Biological

A Guide to Biological Databases

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