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References: Biological Databases

  1. National Center for Biotechnology Information - Wikipedia - Overview of NCBI's history, mission, and suite of databases including GenBank, PubMed, and Entrez, which form the backbone of public bioinformatics data access.

  2. UniProt - Wikipedia - Describes the Universal Protein Resource, its component databases Swiss-Prot and TrEMBL, curation processes, and role as the primary protein sequence and annotation repository.

  3. Protein Data Bank - Wikipedia - History and organization of the PDB archive of macromolecular structures, covering deposition, validation, and access to experimentally determined three-dimensional protein structures.

  4. Bioinformatics: Sequence and Genome Analysis (2nd Edition) - David Mount - Cold Spring Harbor Laboratory Press - Thorough introduction to biological databases, sequence retrieval methods, and programmatic access tools with practical examples for each major database.

  5. Bioinformatics and Functional Genomics (4th Edition) - Jonathan Pevsner - Wiley-Blackwell - Covers NCBI, UniProt, PDB, and KEGG databases with hands-on tutorials showing how to search, retrieve, and analyze biological data programmatically.

  6. NCBI Entrez Help - NCBI - Official documentation for the Entrez search and retrieval system, explaining cross-database linking, query syntax, and E-utilities for programmatic access.

  7. UniProt Help - UniProt Consortium - Comprehensive help pages for searching, downloading, and using the UniProt REST API, including batch retrieval and ID mapping between biological databases.

  8. KEGG: Kyoto Encyclopedia of Genes and Genomes - KEGG - Documentation for the KEGG pathway, compound, and disease databases, explaining how metabolic and signaling pathway data is organized and accessed.

  9. Reactome Pathway Database User Guide - Reactome - Guide to browsing, searching, and analyzing biological pathways in Reactome, including pathway hierarchy navigation, species comparison, and data export options.

  10. RCSB PDB Education Portal - RCSB PDB - Educational resources for understanding protein structures in the PDB, including Molecule of the Month articles and guides to structure visualization and interpretation.