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Questions and Answers
What is the primary purpose of biological databases?
To understand and explain biological phenomena, as well as facilitate the fight against diseases and develop medications.
What is a common challenge in managing biological databases?
Ensuring the consistency of information across different databases.
What is the primary function of a database?
To store, search, and retrieve vast amounts of information.
What was one of the first biological sequence databases?
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What is the purpose of accession numbers in biological databases?
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What is the significance of central, shareable resources in biological databases?
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What is the relationship between primary and secondary databases?
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What is the role of bioinformatics tools in biological databases?
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What is a composite database?
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What is the significance of data formatting in biological databases?
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Study Notes
Biological Databases
- Types of biological databases:
- Nucleic acid databases (e.g. GenBank, EMBL, DDBJ)
- Protein databases (primary: PDB, MMDB; secondary: Swiss-Prot, Pfam)
- Whole genome databases (e.g. TIGR)
- Metabolic pathway databases (e.g. EMP, KEGG)
- Organism-specific databases (e.g. Ebola, S. aureus, A. thaliana, mouse genome)
Important Bioinformatics Databases
- GenBank: nucleotide sequences
- Ensembl: human/mouse genome and others
- PubMed: literature references
- SWISS-PROT: protein sequences
- InterPro: protein domains
- OMIM: genetic diseases
- PDB: protein structures
- KEGG: metabolic pathways
Why Biological Databases?
- Need for storing and communicating large datasets
- Make biological data available to scientists in computer-readable form
- Support large-scale analysis efforts
- Make data access easy and updated
- Link knowledge obtained from various fields of biology and medicine
Characteristics of Biological Databases
- Depend on the nature of information stored (sequences, images, etc.)
- Depend on the manner of storage (flat files, relational databases, etc.)
Importance of Biological Databases
- Assist scientists in understanding biological phenomena
- Facilitate the fight against diseases
- Assist in the development of medications
- Help in discovering basic relationships amongst species in the history of life
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Description
Test your knowledge of bioinformatics databases, including nucleic acid databases like GenBank and EMBL, protein databases like PDB, and whole genome databases like TIGR.
