Overview of Key Biological Databases

Biological databases are repositories where data from various biological studies are stored, curated, and maintained, allowing researchers worldwide to access, compare, and analyze the information.

  1. Nucleotide Sequence Databases:
    • GenBank: Hosted by the National Center for Biotechnology Information (NCBI), it’s a comprehensive database of publicly available nucleotide sequences and their annotations.
    • ENA (European Nucleotide Archive): Europe’s primary nucleotide sequence database, equivalent to GenBank.
    • DDBJ (DNA Data Bank of Japan): Asia’s counterpart to GenBank and ENA.
  2. Protein Sequence and Structure Databases:
    • UniProt: A comprehensive, high-quality database of protein sequence and functional information.
    • PDB (Protein Data Bank): Stores 3D structures of proteins, nucleic acids, and complex assemblies.
  3. Genomic Databases:
    • Ensembl: Provides genome resources for chordate genomes with a particular focus on human genome data.
    • UCSC Genome Browser: Allows visualization and exploration of genomes.
  4. Pathway and Network Databases:
    • KEGG (Kyoto Encyclopedia of Genes and Genomes): Provides information on systems, genomes, diseases, drugs, and pathways.
    • Reactome: Focuses on pathways and processes in human biology.
  5. Expression Databases:
    • GEO (Gene Expression Omnibus): A public functional genomics data repository supporting MIAME-compliant data submissions.
  6. Variation and Disease Databases:
    • dbSNP: Provides a collection of single nucleotide polymorphisms and multiple small-scale variations.
    • ClinVar: A freely accessible archive that aggregates information about genomic variation and its relationship to human health.
  7. Organism-Specific Databases: Such as FlyBase (for Drosophila), TAIR (for Arabidopsis), and WormBase (for Caenorhabditis elegans).

Data Retrieval and Curation

1. Data Retrieval:

  • Many databases provide user-friendly interfaces to search and download data.
  • Programmatic access is often available via APIs (Application Programming Interfaces) or specialized tools, e.g., Entrez for NCBI databases or BioMart for Ensembl.
  • Some databases offer specialized tools for data visualization and analysis, such as genome browsers.

2. Data Curation:

  • Data curation involves organizing, integrating, and maintaining the biological data to ensure its quality and reliability.
  • Manual curation involves experts reviewing and annotating data entries, ensuring the accuracy and relevance of information. For instance, UniProt heavily relies on expert curation.
  • Automated curation involves algorithms and pipelines to process and annotate large datasets, but it’s often complemented by manual curation for validation.

Biological databases and resources play an indispensable role in modern biology. They not only store and provide access to vast amounts of biological data but also organize and annotate the data, enabling meaningful analyses and discoveries. Proper data retrieval and curation ensure that these databases remain updated, relevant, and reliable for researchers globally.