Download (Relational) Databases

Relational Databases:
Basic Concepts
BCHB524
2015
Lecture 21
By Edwards & Li
Slides: https://goo.gl/rl1wFL
Outline
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What is a (relational) database?
When are relational databases used?
Commonly used database management
systems
Using existing databases
Creating and populating new databases
Python and relational databases
Exercises
(Relational) Databases
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Databases store information
Bioinformatics has lots of file-based information:
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FASTA sequence databases
Genbank format sequences
Store sequence, annotation, references, annotation
Good as archive or comprehensive reference
Poor for a few items
Relational databases also store information
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Good for a few items at a time
Flexible on which items
Relational Databases
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Store information in a table
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Rows represent items
Columns represent items' properties or attributes
Name
Continent
Region
Surface Area
Population
GNP
Brazil
South America
South America
8547403
170115000
776739
Indonesia
Asia
Southeast Asia
1904569
212107000
84982
India
Asia
Southern and Central Asia
3287263
1013662000
447114
China
Asia
Eastern Asia
9572900
1277558000
982268
Pakistan
Asia
Southern and Central Asia
796095
156483000
61289
United States
North America
North America
9363520
278357000
8510700
Relational Databases
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Tables can be millions of rows
Can access a few rows fast
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Countries more than 100,000,000 in population?
Countries on the “Asia” continent?
Countries that start with “U”?
Countries with GNP = 776739
Name
Continent
Region
Surface Area
Population
GNP
Brazil
South America
South America
8547403
170115000
776739
Indonesia
Asia
Southeast Asia
1904569
212107000
84982
India
Asia
Southern and Central Asia
3287263
1013662000
447114
China
Asia
Eastern Asia
9572900
1277558000
982268
Pakistan
Asia
Southern and Central Asia
796095
156483000
61289
When are Relational
Databases Used?
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LARGE datasets
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Store data first ...
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For single key, simple data structures often work
Store results of expensive compute or data-cleanup
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... ask questions later
Lookup or sort by many keys
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Does data fit in memory?
Compute once and return results many times
"Random" or unknown access patterns
Specialized data-structures not appropriate
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Use string/sequence indexes for sequence data
What is RDBMS?
• RDBMS stands for Relational Database
Management System.
• RDBMS is the basis for SQL, and for all modern
database
• The data in RDBMS is stored in database objects called
tables.
• A table is a collection of related data entries and it
consists of columns and rows.
Common DBMS
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Oracle
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MySQL
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Commercial, market leader, widely used in
businesses
Free, open-source, widely used in bioinformatics,
suitable for large scale deployment
Sqlite
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Free, open-source, minimal installation
requirements, no users, suitable for small scale
deployment
http://db-engines.com/en/ranking
What is SQL?
• SQL stands for Structured Query Language
• SQL lets you access and manipulate
databases
• SQL is an ANSI (American National
Standards Institute) standard
• Although SQL is an ANSI (American National
Standards Institute) standard, there are
different versions of the SQL language.
http://www.w3schools.com/sql/sql_intro.asp
What Can SQL do?
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SQL can execute queries against a database
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SQL can retrieve data from a database
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SQL can insert records in a database
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SQL can update records in a database
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SQL can delete records from a database
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SQL can create new databases
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SQL can create new tables in a database
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SQL can create stored procedures in a database
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SQL can create views in a database
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SQL can set permissions on tables, procedures, and views
http://www.w3schools.com/sql/sql_intro.asp
Lets look at some examples
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We'll use a third-party program to "look at"
Sqlite databases:
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Download examples:
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SqliteStudio (Linux), SqliteSpy (Windows), …
World.db3, taxa.db3 from Course data folder
Use SqliteStudio to look at examples
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World.db3, taxa.db3
Using existing databases
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Use the "select" SQL command to find
relevant rows
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select * from Country where Population > 100000000;
select * from Country where Continent = 'Asia';
select * from Country where Name like 'U%';
select * from Country where GNP = 776739;
Each command ends in semicolon ";".
"where" specifies the condition/constraint/rule.
"*" asks for all attributes from the relevant rows.
Lets experiment with world and taxa databases.
Using existing databases
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Select can combine (“join”) multiple tables
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Use the where condition to match rows from each
table and “link” corresponding rows…
select * from taxonomy, name
where
taxonomy.rank = 'species'
and
name.name_class = 'misspelling'
and
name.tax_id = taxonomy.tax_id
Using existing databases
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Select can sort and/or return top 10
select * from taxonomy
limit 10;
select * from taxonomy
order by scientific_name;
select * from taxonomy
order by tax_id desc
limit 10;
Using existing databases
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Select can count and do string matching.
select count(*) from taxonomy
where scientific_name like 'D%';
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"like" uses special symbols:
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% matches zero or more symbols
_ match exactly one symbol
Some RDBMS support regular expressions
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MySQL, for example.
Creating databases
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Use the "create" SQL command to create
tables
CREATE TABLE taxonomy (
tax_id INTEGER PRIMARY KEY,
scientific_name TEXT,
rank TEXT,
parent_id INT
);
CREATE TABLE name (
id INTEGER PRIMARY KEY,
tax_id INT,
name TEXT,
name_class TEXT
);
Populating databases
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Use the "insert" SQL command to add rows
to tables
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Usually, the special id column is initialized
automatically
INSERT INTO name (tax_id,name,name_class)
VALUES (9606,'H. sapiens','synonym');
SELECT * from name where tax_id = 9606;
Python and Relational
Databases
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Issue select statements from python and
iterate through the results
import sqlite3
conn = sqlite3.connect(‘taxa.db3')
c = conn.cursor()
c.execute("""
select * from name
where name like 'D%'
limit 10;
""")
for row in c:
print row
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Sometimes it is easiest to make Python do
some of the work!
Python and Relational
Databases
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Use parameter substitution for run-time
values
import sys
import sqlite3
tid = int(sys.argv[1])
conn = sqlite3.connect('taxa.db3')
params = [tid,'scientific name']
c = conn.cursor()
c.execute("""
select * from name
where tax_id = ? and name_class = ?;
""",params)
for row in c:
print row
Next-time:
Object-relational mappers
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Setup python to treat tables as classes, rows
as objects
# Set up data-model
from model import *
hs = Taxonomy.get(9606)
for n in hs.names:
print n.name, "|", n.nameClass
condition = Name.q.name.startswith('Da')
for n in Name.select(condition):
print n.name, "|", n.nameClass
Lab exercises
Read
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through an online course in SQL
sqlcourse.com, sql-tutorial.net, ...
Write
a python program to lookup the scientific
name for a user-supplied organism name.