Biological Databases

Biological Databases Functions and Data Types

• Biological databases primarily store biological data in a digitalized, systematically accessible format
• They facilitate the storage, management, access, and exchange of biological data, mainly to make it accessible to researchers
• They contain a wide range of data types, including DNA, RNA, protein sequence data, structural information, and gene expression data

Databases vs Databanks

• A database is searchable by SQL
• A databank consists of unrelated text files (flat files)

RDBMS

• A relational database management system (RDBMS) organizes information into tables that are linked
• This allows for efficient storage and cross-referencing

DBMS

• A Database Management System (DBMS) handles information storage, entity management, and data display
• Conducting wet-lab experiments is not a primary function of a DBMS

Key Objectives of Biological Databases

• The chief objective is to organize data in a set of structured records
• This enables easy retrieval of information

FASTA File

• The FASTA format includes a carat, a unique SeqID, and no spaces, but does not contain the nucleotide sequence itself
• It is straightforward: it includes a line describing the sequence, followed by the actual sequence
• The definition line provides a simple, unique identifier and description for the sequence

FASTQ File

• Quality scores in a FASTQ file show how reliable each base call is, helping with data quality control
• FASTQ format is specifically designed for storing raw sequencing reads from Next-Generation Sequencing (NGS) technologies, including quality scores
• FASTQ files store quality scores for each nucleotide base uniquely, which is essential for assessing the reliability of sequence data

VCF File

• VCF (Variant Call Format) is specifically designed to store variations (e.g., SNPs, insertions, deletions) identified in genomic data

EMBL

• The European Molecular Biology Laboratory (EMBL) is maintained by the European Bioinformatics Institute (EBI)

Genomic Databases

• GOLD (Genomes Online Database) keeps track of complete and ongoing genome projects worldwide
• The Gene Expression Omnibus (GEO) is designed to contain transcriptome data used to identify differentially expressed genes.

Protein Analysis Databases

• TrEMBL is the computer-annotated supplement to Swiss-Port, offering translations of nucleotide sequences from EMBL
• The Protein Data Bank (PDB) is the main primary database for 3D structures of biological macromolecules
• ProDom is automatically generated from Swiss-Port and TrEMBL to identify protein domains
• SMART database is particularly noted for its reliability and sensitivity in identifying protein domains
• PIR is aimed at supporting genomic and proteomic investigations, offering resources that promote consistency in protein annotations

Metabolic Pathway Analysis Databases

• The KEGG PATHWAY Database is focused on providing graphical pathway maps for metabolic pathways across different organisms
• EcoCyc is dedicated to E. coli, offering detailed information on its genomic and biochemical aspects
• The LIGAND database contains chemical information about enzyme reactions

Model Organism Databases

• TAIR is specifically designed for information related to Arabidopsis thaliana, a model plant organism

Swiss-Port

• Swiss-Port is known for being a curated database
• This ensures a high level of data integration, reduced redundancy, and detailed annotation

INSDC

• The International Sequence Database Collaboration (INSDC) aims to coordinate and harmonize sequence data resources worldwide
• INSDC stands for International Sequence Database Collaboration, which coordinates major public sequence databases

Database Types

• Primary databases directly store raw sequence data from researchers
• Secondary databases contain curated or analyzed information derived from that raw data

Text Files

• Simple text files cannot accommodate essential annotations, such as chromosomal location and data quality

SAM and BAM Files

• SAM files are human-readable text files
• BAM files are their binary equivalent

Genome Annotation

• GFF/BED formats are used for storing genome annotations
• GFF/BED formats provide details about gene locations, regulatory elements, and other genomic features

Curation in Biological Database

• Curation involves expert review and annotation to improve the quality, accuracy, and consistency of database entries

Genome Analysis

• Primary databases are essential references for genome analysis
• These databases contain raw sequence data that can be compared and analyzed

Specialized File Formats

• Specialized file formats address the need to include essential annotations and metadata alongside the sequence data, which simple text files cannot fulfill

Collaborative Swiss-Port Maintenance

• Collaborative maintenance ensures a high degree of reliability via direct human input
• This minimizes the chance that entries have inaccuracies in their annotation, a key feature for reliable research conclusions