1. SQL

2. What is a database?
 a collection of data
 Usually consists of entities and
relations
 An entity is an individual “object” that exists and is
distinguishable from other individuals.
Example: specific person, company, event, plant
 Entities have attributes
Example: people have names and addresses
 A relationship is an association among several entities

3. Database Management System
(DBMS)
 A computerized record-keeping system
 Allows operations such as:
 Adding new files
 Inserting data into existing files
 Retrieving data from existing files
 Changing data
 Deleting data
 Removing existing files from the database

4. Data Models
 A data model is a collection of concepts for
describing data.
 A schema is a description of a particular
collection of data, using the given data
model.
 The relational model of data is the most
widely used model today.
 Main concept: relation, basically a table with
rows and columns.
 Every relation has a schema, which describes
the columns, or fields.

5. Levels of Abstraction

6. Relational Databases
 Data is logically perceived as a two-
dimensional table
 Relational databases are sets of tables
 tables are relations

7. Example Table

8. Relational Database Query
 A relational database query is a question
about the data, and the answer consists of a
new relation containing the result.
 Queries are one part of the Data
Manipulation Language of a DBMS (we also
need to create, update, insert data)
 Language: Structured Query Language (SQL)

9. Example SQL query
 Select G.Accession, G.Medline
 From Genebank G
 Where G.source=`baker’s yeast’;

10. No explicit links between
tables
 Of course, there may be implicit links
in that two tables share the same
attribute (like the accession number)
 In fact, in a relational DB, this is the
only way to connect distinct tables, at
the logical level anyway
 A link between one table and another
is called a foreign key

12. Why use a DBMS
 Data independence and efficient
access.
 Reduced application development
time.
 Data integrity and security.
 Uniform data administration.
 Concurrent access, recovery from
crashes.

13. Example
 Suppose you created a file to hold names, ID
numbers and faculty/student status
 This was a flat file that resembled a table in
a database
 What if you wanted to now add new data for
some of the faculty with credit card
information?
 How would you connect the two tables?

14. Example
Fred 1234567
Mark 2345678
George 3456789
Quinn 4567890
ID Credit Card
1234567 44444444
4567890 55555555

15. How to use MySQL
 Connect to MySQL Server
shell> ~clement/mysqlbin/bin/mysql -h pathogen.cs.byu.edu –u
cs360 <Enter>
Welcome to the MySQL monitor.
Type 'help' for help.
mysql>

16. How to use MySQL
Data Definition 1
mysql> SHOW DATABASES;
Database
mysql
test
tmp

17. Creating Tables
 CREATE TABLE image (
image_id INT,
image_type CHAR(3),
filename CHAR(40),
url CHAR(128),
Primary Key(image_id));
 creates a table with 4 columns and no
rows

18. Another table
 create table image_decoder
(image_type CHAR(3),
decoder_program varchar(20),
args varchar(20));

19. Basic Data Types
 INT - signed integer value. Implementation-dependent
# bits
 NUMERIC(total length, number of decimal places)
 NUMERIC(8,4) - 3 digits, a decimal point, 4 decimal places
 REAL - floating point number
 BIT - single boolean value
 DATE - year, month, day
 TIME
 TIMESTAMP - date/time
 VARCHAR(length) - variable length string <= length
 BLOB - Binary Large Object

20. How to use MySQL
 INSERT INTO image
( image_id, image_type, filename, url)
VALUES
( 1, ‘jpg’, ‘image1’, ‘http://host/dir/image1’)
Values must be in the right order and fill all columns
Values must be the order specified.
But, you don’t need to fill all columns.

21. More
 insert into image_decoder
values('jpg','/usr/bin/jpgview’,’’);

22. Selecting Rows
 SELECT image_type from image
WHERE filename=‘image1’
 SELECT image_decoder.decoder_program FROM
image_decoder, image
WHERE image.filename=‘image1’
AND
image.image_type=image_decoder.image_type
 The Join operation can be viewed as creating a virtual table
on the fly from rows in two or more tables
 SELECT * from image GROUP by image_type

23. Basic Where Clauses
 Operators
 =, <, >, <=, >=, != (or <>)
 WHERE image_id = 2
 LIKE - wildcard comparison
 WHERE decoder_program LIKE ‘c:%’
 ISNULL - checks for null value
 IN - contained in a set (usually for subqueries)
 WHERE image_id IN (1,2)
 WHERE image_id IN
SELECT image_id FROM Image

24. Updating Rows
 UPDATE Image
SET url=‘http://newhost/image1’
WHERE filename=‘image1’
 The where clause may select multiple rows
e.g. WHERE image_id < 50
 If the WHERE clause is excluded, the SET
operation is applied to every row in the
table

25. Deleting Rows
 DELETE from Image
WHERE image_id=2
 Entire row is removed from the table
 DELETE from Image
 Every row is removed from the table!!!

26. How to use MySQL
 Data manipulation 2
mysql> SELECT * FROM seqs;
+-------+-----------+----------+
| title | accession | sequence |
+-------+-----------+----------+
| Human | u235 | cgatcagt |
+-------+-----------+----------+
mysql> insert into seqs
-> values('Dog','u222','ccgtacgt');
mysql> SELECT * FROM seqs;
+-------+-----------+----------+
| title | accession | sequence |
+-------+-----------+----------+
| Human | u235 | cgatcagt |
| Dog | u222 | ccgtacgt |
+-------+-----------+----------+

27. Add data from file
 mysql> load data local infile
’/users/faculty/snell/CS360/sample.txt' into
table seqs;
 Delete it
 mysql> delete from seqs
 Redo load with up arrow
 select title, accession from seqs;
 update seqs set accession = 'H0794' where
title = 'Human-01';
 select * from seqs order by title;

28. More commands
 mysql> select * from seqs where title
like 'Human%';

29. More commands
 use mysql;
 show tables;
 describe db;

30. PERL DBI
$dbh = DBI->connect("dbi:mysql:
database=sequences;
host=paintball:1236;",
"phylo","")
or die("Couldn't connect");
$SQL= "select * from seqs";
$Select = $dbh->prepare($SQL);
$Select->execute();
while($Row=$Select->fetchrow_hashref)
print "title $Row->{title}, sequence $Row->{sequence} n";
$dbh->disconnect();

31. What Is the Perl DBI?
 The standard Database Interface for
Perl
 “A perl module and specification that
defines a consistent database interface
independent of the actual database being
used”

32. Why the Perl DBI?
 Once upon a time…
 One language, many database interfaces
 Perl 5 - A new way
 Modules and Objects. The DBI is born.
 The future is now…
 ODBC, Oracle, Informix, Ingres, mSQL, mysql, DB2, Solid,
Sybase, Postgress, Quickbase, Empress, Fulcrum, ...
 The same database interface

33. Making simple things easy
and difficult things possible
 Goals
 Be simple to use for simple applications
 Have sufficient flexibility to accommodate unusual
functionality and non-SQL databases
 Conform to applicable standards (ODBC etc.)
 Enable the creation of database-independent Perl scripts
without being limited to the lowest functionality
 Be free.
 A ‘higher-level’ interface than ODBC/JDBC

34. Under the Hood
 DBI defines and implements an interface
 Driver modules do much of the real work
 DBI provides default methods, functions, tools etc for
drivers
 Not limited to the lowest common denominator -
mechanism provided for driver specific extensions
 Designed and built for speed
 Valuable detailed call tracing/debugging built-in

36. So why use the Perl DBI?
 Because...
 It delivers what it promises
 It’s here, there and everywhere
 It’s fast, flexible and well proven
 It’s free, with source
 Commercial support is available
 It has a large user base and a strong
future