Informatics tools in network science

seminar 2

Database handling

storing information

(local) filesmemory database

speed

capacity

technical features

pure databaseconcept

real-time database(transactions and concurrency)

data warehouse system(big, reporting and analysis)distributed database

in-memory database

off-topic: raid technologies

“striping” “mirroring” “byte level parity” “block level parity”

against SPOF (Single Point Of Failure)

relational database storing data in tables

terminology:

relational database storing data in tables data types

relational database storing data in tables data types table relations

ARTICLES

• title• keyword• authorstoring articles

relational database storing data in tables data types table relations

ARTICLES

• title• keyword1• keyword2• keyword3• author

more keyword? no problem…

relational database storing data in tables data types table relations

ARTICLES

• title• keyword1• keyword2• keyword3• author1• author2• author3

more author? why not…

relational database storing data in tables data types table relations

ARTICLES

• title• keyword1• keyword2• keyword3• author1• author2• author3• author1_contact• author2_contact• author3_contact

and what about the contacts?

relational database storing data in tables data types table relations

ARTICLES

• title• keyword1• keyword2• keyword3• author1• author2• author3• author1_contact• author2_contact• author3_contact

there is some serious problem here…

• what if there is a 4th author?• what if usually there are 2 authors (wasting memory)• contacts are redundant!

relational database storing data in tables data types table relations

KEYWORDS

• keyword

AUTHORS

• name• contact

ARTICLES

• title

relational database storing data in tables data types table relations

KEYWORDS

• keyword ID• keyword

AUTHORS

• author ID• name• contact

ARTICLES

• article ID• title

ARTICLES_KEYWORDS

• article ID• keyword ID

ARTICLES_AUTHORS

• article ID• author ID

relational database • storing data in tables

• data types

• table relationsKEYWORDS

AUTHORS

ARTICLES

ARTICLES_KEYWORDS

ARTICLES_AUTHORS

article ID title

1 “first title”

2 “other title”

article ID keyword ID

1 1

1 2

2 2

keyword ID keyword

1 “cell”

2 “neurology”

author ID name contact

1 “Bill” “555-2316”

2 “Joe” “joe@mit.edu”

article ID author ID

1 2

2 1

2 2

could be worse…

Database servers

MySQL(free / professional)

sqLite(easy)

Oracle(professional)

MS Access(MS Office)

MS SQL Server(professional)

postgre SQL(object oriented)

some example:

install MySQL Download MySQL Community Server 5.1 from:

http://dev.mysql.com/downloads/mysql/5.1.html

install MySQL Download MySQL GUI tools from: http://dev.mysql.com/downloads

SQL• SQL = Structured Query Language

SELECT * FROM BookWHERE price > 10.00 ORDER BY title;

Selecting all attributes of given data rows…

…of table called “Book”,

…where the price is higher than 100.

Give back this list ordered by the title of the title.

Title Author Price

Linked A. L. Barabási 12.5

The Lord of the Links J. K. Lowling 40.0

Weak Links P. Csermely 15.0

SQL SQL = Structured Query Language

SELECTisbn, title, price, price * 0.06 AS sales_tax

FROM Book WHERE price > 100.00 ORDER BY title;

INSERT INTO My_table (field1, field2, field3)VALUES ('test', 'N', NULL);

UPDATE My_tableSET field1 = 'updated value‘

WHERE field2 = 'N';

DELETE FROM My_tableWHERE field2 = 'N';

MySQL Query Browser

SQL – join tables

animals

id animal

1 “cat”

2 “dog”

3 “cow”

SELECT *

FROM animals, foods;

+------------+--------+----------+-------+| animals.id | animal | foods.id | food |+------------+--------+----------+-------+| 1 | cat | 1 | milk || 1 | cat | 2 | bone || 1 | cat | 2 | grass || 2 | dog | 1 | milk || 2 | dog | 2 | bone || 2 | dog | 2 | grass || 3 | cow | 1 | milk || 3 | cow | 2 | bone || 3 | cow | 2 | grass |+------------+--------+----------+-------+

CROSS JOIN

foods

id food

1 “milk”

2 “bone”

3 “grass”

Let us ask MySQL to list data from both table!

SQL – join tables

people

pid name phone

1 “Mr Brown” “01225 708225”

2 “Miss Smith”

“01225 899360 ”

3 “Mr Pullen” “01380 724040”

sellingspid sid selling

1 1 “Old House Farm”

3 2 “The Willows”

3 3 “Tall Trees”

3 4 “The Melksham Florist”

4 5 “Dun Roamin”

Let us ask MySQL to list data from both table!

mysql> select name, phone, sellingfrom people join sellings on people.pid = sellings.pid;+-----------+--------------+----------------------+| name | phone | selling |+-----------+--------------+----------------------+| Mr Brown | 01225 708225 | Old House Farm || Mr Pullen | 01380 724040 | The Willows || Mr Pullen | 01380 724040 | Tall Trees || Mr Pullen | 01380 724040 | The Melksham Florist |+-----------+--------------+----------------------+4 rows in set (0.01 sec)

mysql>

INNER JOIN

SELECT name, phone, selling

FROM people join sellingson people.pid = selling.pid;

SQL – join tables

people

pid name phone

1 “Mr Brown” “01225 708225”

2 “Miss Smith”

“01225 899360 ”

3 “Mr Pullen” “01380 724040”

sellingspid sid selling

1 1 “Old House Farm”

3 2 “The Willows”

3 3 “Tall Trees”

3 4 “The Melksham Florist”

4 5 “Dun Roamin”

Let us ask MySQL to list data from both table!

mysql> select name, phone, sellingfrom people, sellings where people.pid = sellings.pid;+-----------+--------------+----------------------+| name | phone | selling |+-----------+--------------+----------------------+| Mr Brown | 01225 708225 | Old House Farm || Mr Pullen | 01380 724040 | The Willows || Mr Pullen | 01380 724040 | Tall Trees || Mr Pullen | 01380 724040 | The Melksham Florist |+-----------+--------------+----------------------+4 rows in set (0.01 sec)

mysql>

INNER JOIN = cross join + WHERE but faster!!

SELECT name, phone, selling

FROM people join sellingson people.pid = selling.pid;

SELECT name, phone, selling

FROM people, sellings

WHERE people.pid = selling.pid;

SQL – join tables

people

pid name phone

1 “Mr Brown” “01225 708225”

2 “Miss Smith”

“01225 899360 ”

3 “Mr Pullen” “01380 724040”

sellingspid sid selling

1 1 “Old House Farm”

3 2 “The Willows”

3 3 “Tall Trees”

3 4 “The Melksham Florist”

4 5 “Dun Roamin”

Let us ask MySQL to list data from both table!

SELECT name, phone, selling

FROM people left join sellingson people.pid = selling.pid;

LEFT JOIN

mysql> select name, phone, selling from people left join sellings on people.pid = sellings.pid; +------------+--------------+----------------------+| name | phone | selling |+------------+--------------+----------------------+| Mr Brown | 01225 708225 | Old House Farm || Miss Smith | 01225 899360 | NULL || Mr Pullen | 01380 724040 | The Willows || Mr Pullen | 01380 724040 | Tall Trees || Mr Pullen | 01380 724040 | The Melksham Florist |+------------+--------------+----------------------+5 rows in set (0.00 sec)

mysql>

SQL – join tables

people

pid name phone

1 “Mr Brown” “01225 708225”

2 “Miss Smith”

“01225 899360 ”

3 “Mr Pullen” “01380 724040”

sellingspid sid selling

1 1 “Old House Farm”

3 2 “The Willows”

3 3 “Tall Trees”

3 4 “The Melksham Florist”

4 5 “Dun Roamin”

Let us ask MySQL to list data from both table!

SELECT name, phone, selling

FROM people right join sellingson people.pid = selling.pid;

RIGHT JOIN

mysql> select name, phone, selling from people left join sellings on people.pid = sellings.pid; +------------+--------------+----------------------+| name | phone | selling |+------------+--------------+----------------------+| Mr Brown | 01225 708225 | Old House Farm || Mr Pullen | 01380 724040 | The Willows || Mr Pullen | 01380 724040 | Tall Trees || Mr Pullen | 01380 724040 | The Melksham Florist || NULL | NULL | Dun Romain |+------------+--------------+----------------------+5 rows in set (0.00 sec)

mysql>

SQL – join tables

sellingspid sid selling

1 1 “Old House Farm”

3 2 “The Willows”

3 3 “Tall Trees”

3 4 “The Melksham Florist”

4 5 “Dun Roamin”

SELECT name, COUNT(sid) as selling_num

FROM people join sellingson people.pid = selling.pid

GROUP BY selling.pid;

people

pid name phone

1 “Mr Brown” “01225 708225”

2 “Miss Smith”

“01225 899360 ”

3 “Mr Pullen” “01380 724040”

mysql> select name, phone, sellingfrom people, sellings where people.pid = sellings.pid;+-----------+--------------+----------------------+| name | phone | selling |+-----------+--------------+----------------------+| Mr Brown | 01225 708225 | Old House Farm || Mr Pullen | 01380 724040 | The Willows || Mr Pullen | 01380 724040 | Tall Trees || Mr Pullen | 01380 724040 | The Melksham Florist |+-----------+--------------+----------------------+4 rows in set (0.01 sec)

mysql>

+-----------+--------------+| name | selling_num |+-----------+--------------+| Mr Brown | 1 || Mr Pullen | 3 |+-----------+--------------+

Use aggregated function and join:

SQL – join tables

sellingspid sid selling

1 1 “Old House Farm”

3 2 “The Willows”

3 3 “Tall Trees”

3 4 “The Melksham Florist”

4 5 “Dun Roamin”

SELECT name, COUNT(sid) as selling_num

FROM people left join sellingson people.pid = selling.pid

GROUP BY selling.pid;

people

pid name phone

1 “Mr Brown” “01225 708225”

2 “Miss Smith”

“01225 899360 ”

3 “Mr Pullen” “01380 724040”

+------------+--------------+| name | selling_num |+------------+--------------+| Mr Brown | 1 || Miss Smith | 0 || Mr Pullen | 3 |+------------+--------------+

mysql> select name, phone, selling from people left join sellings on people.pid = sellings.pid; +------------+--------------+----------------------+| name | phone | selling |+------------+--------------+----------------------+| Mr Brown | 01225 708225 | Old House Farm || Miss Smith | 01225 899360 | NULL || Mr Pullen | 01380 724040 | The Willows || Mr Pullen | 01380 724040 | Tall Trees || Mr Pullen | 01380 724040 | The Melksham Florist |+------------+--------------+----------------------+5 rows in set (0.00 sec)

mysql>

Use aggregated function and (left) join:

SQL – more info

http://www.w3schools.com/SQl/default.asp MySQL 5.1 Reference Manual:

http://dev.mysql.com/doc/refman/5.1/en/index.html http://en.wikipedia.org/wiki/SQL