Bioinformatics

1. Biological Databases
   1. Genomic Databases
      1. Nucleotide Sequence Databases
         1. GenBank
            1. Features and offerings
            2. Data submission and retrieval
            3. Tools for sequence comparison
         2. European Nucleotide Archive (ENA)
            1. Scope and coverage
            2. Data submission protocols
            3. Access and search functionalities
         3. DNA Data Bank of Japan (DDBJ)
            1. Collaborative initiatives with GenBank and ENA
            2. Data exchange and synchronization
            3. Tools for data analysis and interpretation
      2. Genome Browsers
         1. UCSC Genome Browser
            1. Visualizing genomic data
            2. Custom tracks and annotations
            3. Integration with external datasets
         2. Ensembl
            1. Comparative genomics tools
            2. Gene annotation features
            3. Tools for evolutionary analysis
   2. Protein Databases
      1. UniProt
         1. Comprehensive protein sequence and functional information
         2. Sub-databases: UniProtKB, UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc)
         3. Protein annotation standards and tools
      2. Protein Data Bank (PDB)
         1. Structural data of biomolecules
         2. Methods for structure submission
         3. Visualization and analysis tools
      3. Swiss-Prot
         1. Manually annotated records
         2. Protein function prediction models
         3. Integration with other databases
   3. Specialized Databases
      1. Metabolic Pathways (KEGG)
         1. Mapping and visualization of biochemical pathways
         2. Integration with gene and protein information
         3. Applications in drug discovery and metabolic engineering
      2. Disease-specific Databases
         1. Cancer genomics
            1. TCGA (The Cancer Genome Atlas)
            2. International cancer genome consortium
         2. Genetic disorders
            1. OMIM (Online Mendelian Inheritance in Man)
            2. ClinVar
      3. Gene Expression Databases (GEO)
         1. Storage and access to high-throughput gene expression data
         2. Tools for data normalization and comparison
         3. Analysis of gene expression patterns across conditions
   4. Data Integration and Interoperability
      1. Challenges in data standardization
         1. Data format heterogeneity
         2. Ontologies and controlled vocabularies
      2. Technologies for data sharing
         1. Web services and APIs
         2. Linked data and semantic web technologies
      3. Cross-referencing and linking databases
         1. Data citation and provenance
         2. Harmonization of database entries for robust analysis
      4. Collaborative platforms and initiatives
         1. Open-source data integration tools
         2. International partnerships and consortia for data sharing