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Bioinformatics Databases

A deep, hands-on tour of the public databases that bioinformatics runs on — NCBI, Ensembl, UniProt, PDB, KEGG and more — tracing one real gene, BRCA1, from accession to structure to pathway. You will learn to read any accession, cross-link records, and turn point-and-click lookups into reproducible, scripted pipelines.

Bioinformatics Databases

Syllabus

The database landscape4 lessons
  1. Why Bioinformatics Runs on Databases9 min
  2. Primary vs Derived Databases11 min
  3. The Two Hubs: NCBI Entrez and EMBL-EBI10 min
  4. A Field Map of the Major Databases10 min
Accessions & identifiers5 lessons
  1. What an Accession Number Is9 min
  2. Reading a Prefix: Provenance and Molecule Type11 min
  3. Versioning: accession.version and Why Records Change10 min
  4. GI Numbers, UIDs, and Ensembl Stable IDs10 min
  5. Project and Sample Accessions Across INSDC9 min
The NCBI ecosystem6 lessons
  1. The NCBI Entrez Ecosystem8 min
    1. GenBank and the Nucleotide Archive10 min
    2. RefSeq: Curated Reference Sequences11 min
    3. NCBI Gene: the Gene-Centric Hub9 min
    4. dbSNP and ClinVar: Variation and Clinical Significance11 min
    5. SRA: the Raw Sequencing Read Archive9 min
EMBL-EBI, UniProt & structures6 lessons
  1. EMBL-EBI, UniProt and Structures8 min
    1. ENA: the European Nucleotide Archive9 min
    2. Ensembl and the Genome Browser12 min
    3. UniProt: Swiss-Prot vs TrEMBL12 min
    4. PDB: 3D Structures at RCSB and PDBe11 min
    5. InterPro and Pfam: Domains and Families10 min
Pathways, interactions & specialized databases4 lessons
  1. Pathways: KEGG and Reactome11 min
  2. STRING: Protein Interaction Networks9 min
  3. GEO and Functional-Genomics Archives10 min
  4. Literature: PubMed and Europe PMC8 min
Cross-references & interoperability4 lessons
  1. db_xref: How Records Point at Each Other10 min
  2. ID Mapping in Practice12 min
  3. MANE: One Gene, One Agreed Transcript10 min
  4. Genome Assemblies and Builds11 min
Programmatic access & reproducibility8 lessons
  1. From Clicking to Scripting8 min
    1. Searching Web UIs Well (No Code)10 min
    2. Batch Retrieval Without Code10 min
    3. NCBI E-utilities with Biopython13 min
    4. The Ensembl REST API12 min
    5. UniProt, KEGG and RCSB PDB APIs12 min
    6. The Formats Databases Emit11 min
    7. Reproducibility and the BRCA1 Dossier (Capstone)13 min