Professional Documents
Culture Documents
Databases
Databases
Daniela Puiu
Applications Specialist
Center for the Study of Biological Complexity, VCU
dpuiu@vcu.edu
804-827-0952
General Concepts
• Database definition
– Organized collection of logically related data
• Data
– Known facts
– Types: text, graphics, images, sound, videos
• Database management system (DBMS)
– Software package for defining and managing
a database
Database Examples
• Class roster
• Hospital patients
• Literature (published articles in a certain
field)
• Genomic information
• Protein structure
• Taxonomy
• Single nucleotide polymorphism
Example: Microbial Database
Data about the protein coding regions in the microbial
genomes sequenced so far.
Personal 1 Desktop/Laptop/ MB
PDA
Workgroup 5-25 Client/server:2 tier MB-GB
1 m
Organism Gene
Metadata
• Data that describes the properties or
characteristics of other data
• Does not include sample data
• Allows database designers and users to
understand the meaning of the data
Metadata & Data Table
Organism
Name Type Max Length Description
Name Alphanumeric 100 Organism name
Size Integer 10 Genome length (bases)
Gc Float 5 Percent GC
Accession Alphanumeric 10 Accession number
Release Date 8 Release date
Center Alphanumeric 100 Genome center name
Sequence Alphanumeric Variable Sequence
SELECT *
FROM Organism, Gene
WHERE
Organism.Name=“Escherichia coli K12” AND
Organism.Accession=Gene.OAccession AND
Gene.Start>=1,000,000 AND
Gene.End<=2,000,000
DML Example (cont.)
INSERT INTO Gene
(Name, Accession, OAccession, Start, End, Strand, Sequence)
VALUES
(“thrL”, 16127995,”NC_000913”,190,255,’+’,”thr operon leader
peptide”, “MKRI…”)