The document is a training guide on MySQL, covering installation, schema design, SQL commands for inserting, updating, and deleting rows, and using Perl for database automation. It details how to use MySQL Workbench for schema design and provides examples of SQL statements and Perl DBI for executing database commands. The content is geared towards users in bioinformatics looking to manage biological data efficiently.

1. Introduction to MySQL
● Introduction
● Installation
● SQL
● Schema design
● Perl
BITS/VIB Bioinformatics Training – Jun 29, 2011 – Luc Ducazu <luc@daphnia.com>

2. Database schema
● Although you can execute DDL commands from
the MySQL monitor directly, this is not often
done
● There are tools that allow you to design a schema
graphically and generate the CREATE TABLE ...
statements
● Examples:
– MySQL workbench
– Dia

3. MySQL workbench
● Available as a standard package on some Linux
distros (eg Fedora)
● Available as Windows MSI, Linux DEB or RPM
package or source archive from
http://dev.mysql.com/downloads/workbench/
● To install a DEB package:
# dpkg ­i package.deb
● To install a RPM package:
# rpm ­Uvh package.rpm

4. MySQL workbench ­ demo

5. Database schema
● Once the schema is designed, MySQL workbench
can generate a 'script' containing all SQL
statements to create the tables and other objects:
File ­>
Export ­>
Forward Engineer SQL CREATE Script
● This 'script' can be executed as usual from the
MySQL monitor

6. Inserting rows
● To populate tables, use the INSERT SQL
statement:
mysql> insert into tbl
(col1, col2, ...)
values
(val1, val2, ...) [,
(valx, valy, ...) , ...]
● With:
– tbl the name of the table
– col1, col2, ... a list (subset) of column names
– val1 value for col1
– val2 value for col2

7. Inserting rows ­ examples
● Example (biodb version 1)
insert into modorg
(id, class, genus, species,
nchr, gsize, draft)
values
(1, “Bacteria”, “Escherichia”, “coli”,
1, 4.639, “1997­09­05 00:00:00”)
● Note that strings and dates have to be properly
quoted

8. Inserting rows
● You can leave out the column list if
– a value is given for all columns
– the values are specified in the order dictated by the
schema
mysql> insert into tbl
values
(val1, val2, ...) [,
(valx, valy, ...) , ...]

9. Changing rows
● To change one or more rows, use the UPDATE
SQL statement:
mysql> update tbl
set col1=expr1 [, col2=expr2, ...]
[where cond]
● With:
– tbl the name of the table
– col1 the column to change
– expr1 the new value
– cond the row filter ­ if unspecified, all rows of the
table will be updated

10. Changing rows ­ examples
● To change the C elegans number of
chromosomes to 7:
update modorg
set nchr = 7
where genus = “caenorhabditis”
and species = “elegans”;
● To change the draft date to the current date:
update modorg
set draft = now();

11. Deleting rows
● To remove rows, you use the DELETE SQL
statement:
delete from tbl
[where cond]
● With:
– tbl the name of the table
– cond the row filter ­ if unspecified, all rows of the
table will be deleted
– note: since you can only remove entire rows, there is
no need to specify column names

12. Deleting rows ­ examples
● To remove all in model organisms with a genome
publishing date before 2000:
delete from modorg
where year(draft) < 2000;

13. Introduction to MySQL
● Introduction
● Installation
● SQL
● Schema design
● Perl
BITS/VIB Bioinformatics Training – Jun 29, 2011 – Luc Ducazu <luc@daphnia.com>

14. Perl
● Perl is a scripting language that has excellent text
manipulation capabilities
● Many biological 'databases' are available as flat
text files
● Perl is very handy in the automation of the
population of MySQL databases

15. Automated population
● There are basically two ways Perl can help to
insert data into tables:
– The Perl script generates USE, INSERT, ... SQL
statements. You can than execute these statements
using the MySQL monitor:
$ perl myscript.pl | mysql
– The Perl script connects to the database and executes
SQL statements directly: DBI

16. Perl DBI
● Perl DBI provides a programming interface that
abstracts most of the RDBMS specifics
● In principle it should be possible to port scripts,
written for other RDBMS's (like PostgreSQL), to
MySQL with only minimal effort: all you have to
do is change the connection string
● Packages to install (Ubuntu)
– libdbi­perl: Perl DBI
– libdbd­mysql­perl: MySQL driver for DBI

17. Perl DBI ­ connecting
● Here is a minimal program:
#!/usr/bin/perl ­w
use strict;
use DBI;
my $dbh = DBI­>connect(
“DBI:mysql:host=localhost;database=biodb”,
“user”,
“password”) or die;
...
$dbh­>disconnect();

18. Perl DBI ­ connecting
● Some highlights:
– use DBI;
Load Perl DBI library
– DBI­>connect(connection string);
Connect to a database
● it is a MySQL database server
● the DB server is running on the local machine
● you can provide the name of the database
● you can provide a user name and password
The connect() function returns
● a database handle ($dbh) on success
● false on failure
– $dbh­>disconnect() to clean up resources

19. Perl DBI
● To execute a SQL statement that does not return a
result set, eg INSERT, DELETE, use do():
my $n = $dbh­>do(stmt);
● This function
– requires a valid database handle
– returns the number of rows affected, if no rows are
affected, a special value is returned: 0E0 (evaluates
true)
– false in case of an error
● You can use execute() as well

20. Perl DBI
● To execute a SQL statement that returns a result
set, eg SELECT use the following recipe:
1. Prepare a statement:
my $sth = $dbh­>prepare(stmt);
2. Send the query to the database server:
$sth­>execute();
3. Read the result, row by row:
my @row = $sth­>fetchrow_array();
my $ref = $sth­>fetchrow_hashref();
4. Clean up resources:
$sth­>finish();

21. Perl DBI ­ examples
● To list all classes in modorg:
...
my $qry = “select distinct class ”
. “from modorg ”
. “order by class”;
my $sth = $dbh­>prepare($qry);
$sth­>execute();
while(my @row = $sth­>fetchrow_array())
{
print “$row[0]n”;
};
$sth­>finish();
...

22. Perl DBI ­ examples
● To list all organisms in modorg:
...
my $qry = “select genus, species ”
. “from modorg ”
. “order by genus”;
my $sth = $dbh­>prepare($qry);
$sth­>execute();
while(my $ref = $sth­>fetchrow_hashref())
{
print $ref­>{“genus”} . “ “
. $ref­>{“species”} . “n”;
};
$sth­>finish();
...

23. Perl DBI ­ examples
● To insert a bunch of rows into modorg:
...
my $qry = “insert into modorg ”
. “(id, class, genus, species) ”
. “values (?, ?, ?, ?)”;
my $sth = $dbh­>prepare($qry);
$sth­>execute(11, “Mammels”,
“Sus”, “scrofa”);
...

24. Quoting
● Never allow arbitrary user input in SQL
statements