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What is a biological database?
A biological database is a collection of data that is structured, searchable, updated periodically, and cross-referenced.
Which of the following is NOT a type of biological database?
What is one of the first databases to emerge in the field of biology?
GenBank
Biological databases are only accessible to specific researchers.
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Primary databases can be further classified as _____ and secondary databases.
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What type of data does a nucleotide database store?
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What is the main purpose of secondary databases?
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Curated databases prioritize the quantity of data over the quality.
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What do composite databases do?
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Study Notes
Biological Databases
- Structured, searchable, updated, and cross-referenced data collections
- Periodically updated by database administrators
- Purpose: Collection and organization of data related to biological systems
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Benefits:
- Computational support for researchers
- User-friendly interface for analyzing data
- Systematization of experiment results
- Storage of all known data, preventing redundancy and repetition
- Data accessibility for global scientists
- Storage of biological data in computer-readable formats for analysis
Kinds of Biological Databases
- Nucleotide Sequence Data Base: Stores DNA/nucleotide sequences
- Protein Sequences Data Base: Stores protein sequence data
- Gene Expression Data Base: Stores and analyzes gene expression data
- Clinical Databases: Stores clinical trial data and patient information
- Metabolic Pathways Database: Provides information on metabolic pathways and reactions
- Structural Databases: Stores 3D structures of proteins, nucleic acids, and other biomolecules
Need for Databases in Biology
- Storage and communication of large datasets
- Dissemination of biological information
- Organized data for analysis and retrieval
- Computer-readable format for data accessibility
Types of Biological Databases
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Primary Databases (Archival Databases)
- Includes original data from researchers
- Publicly available for annotation purposes
- Repository of raw and annotated data
- Accessed freely through the internet
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Sequence database:
- Stores DNA/nucleotide and protein sequences
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DNA/nucleotide databases:
- Stores DNA/nucleotide sequence data
- Share data daily for consistent information across databases
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Protein database:
- Stores information on protein sequences
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Secondary Databases:
- Contains results from analysis of primary database entries
- Manually curated or automatically generated
- Derived from the analysis of primary data
- May utilize data from numerous sources
- Information includes conserved sequences, signature sequences, active site residues of protein families
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Curated Databases:
- Maintained by curators who select only the highest quality data
- Emphasize the high quality of data over quantity
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Composite Databases:
- Combine different primary databases
- Efficiently query and search multiple sources
- Non-redundancy is maintained by filtering data from various primary sources
- Merge diverse primary resources, reducing the need to search multiple databases
Examples of Biological Databases
- NCBI (National Center for Biotechnology Information): A comprehensive resource for biological information, including GenBank, PubMed, and BLAST.
- EMBL (European Molecular Biology Laboratory): A nucleotide sequence database similar to GenBank.
- UniProt (Universal Protein Resource): A database of protein sequences and functional information.
- PDB (Protein Data Bank): A repository of 3D structural data for proteins and nucleic acids.
- PlantPepDB (Plant Protein Database): A database focusing on plant protein sequences and their associated information.
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Description
Explore the various types of biological databases designed to organize and facilitate access to biological data. This quiz highlights the structured collections of nucleotide sequences, protein sequences, gene expression, and clinical data, emphasizing their benefits for researchers. Test your understanding of how these databases support scientific endeavors.
