2. Major Databases in Bioinformatics
Topic
Presented To: Sir Jehangir Khan
Presented By: Bushra

3. Database
• What is a database?
– A collection of related data elements
• tables
• columns (fields)
• rows (records

4. • Tables (entitites)
– •basic elements of information to
track, e.g., gene, organism, sequence, citation
• Columns (fields)
• attributes of tables, e.g. for citation
table, title, journal, volume, author
• Rows (records)
• actual data
• whereas fields describe what data is stored, the rows of a table are
where the actual data is stored

5. Types of Databases
1. Relational Databases
2. Online Databases
3. Biological Databases

6. Relational Database
• A relational database contains multiple tables and
defines the relationships between them.
invoice_id customer product price quantity total
1 Elmer buckshot $2.00 2 $4.00
2 Wiley Acme snow machine $5.00 1 $5.00
3 Elmer shotgun $25.00 1 $25.00
4 Bugs carrots $0.50 20 $10.00

7. Online Database
• When you query an online database, your query is translated into
SQL, the database is interrogated, and the answer displayed on
your web browser.

8. Biological Database
• Biological databases are libraries of life sciences
information, collected from scientific experiments, published
literature, high-throughput experiment technology, and
computational analyses.
• Over 1000 biological databases
• Vary in size, quality, coverage, level of interest

9. “Some Important Bioinformatics Databases”
• GenBank www.ncbi.nlm.nih.gov nucleotide sequences
• Ensembl www.ensembl.org human/mouse genome
(and others)
• PubMed www.ncbi.nlm.nih.gov literature references
• NR www.ncbi.nlm.nih.gov protein sequences
• SWISS-PROT www.expasy.ch protein sequences
• InterPro www.ebi.ac.uk protein domains
• OMIM www.ncbi.nlm.nih.gov genetic diseases
• Enzymes www.chem.qmul.ac.uk enzymes
• PDB www.rcsb.org/pdb/ protein structures
• KEGG www.genome.ad.jp metabolic pathways