1. Preliminary Definitions MySQL: An Open Source, Enterprise-level, multi-threaded, relational database management system that stores and retrieves data using the Structured Query Language o licensed with the GNU General public license http://www.gnu.org/ Structured Query Language (SQL): A standardized query language for getting information from a relational database. Relational Database: A database that stores data in the form of relational tables as 0pposed to flat files. Database Management System (DBMS): A system that manages relational databases; A collection of programs that enabling the storage, modification, and extraction of information from a database.

2. Main Features Fully multi-threaded using kernel threads. Works on many different platforms. Many column types Very fast joins using an optimized one-sweep multi-join Full operator and function support in the SELECT and WHERE parts of queries. You can mix tables from different databases in the same query. A privilege and password system that is very flexible and secure. Handles large databases. Tested with a broad range of different compilers. (C/C++) No memory leaks. Full support for several different character sets.

3. Cells, Rows, Tables and Databases Cell -- a single (scalar) value.

4. Cells, Rows, Tables and Databases Row -- a group of scalar values representing a single instance of an object or event.

5. Cells, Rows, Tables and Databases Table -- a series of rows describing separate objects or events.

6. Cells, Rows, Tables and Databases Database -- a collection of related tables describing various facets of a group of objects or events.

7. Relations -- One to One

8. Relations -- One to Many

9. Relations -- Many to Many

10. Relational Databases A database is a collection of tables Columns define attributes of the data o All data in a column must have the same data type A record is stored in a row table name column row

11. Use a Relational Database When… You have a very large dataset There is redundant data o Wastes disk space o Increases errors Information must be updated in multiple locations Security is important o Different users can be granted different permissions Strict enforcement of data types is important

12. Spreadsheet Example

13. Data is inconsistent! Now imagine you are designing the New York Public Library database which has tens of million books and well over a million cardholders.

14. Database Design Entity Relationship Design Entity (“thing”, “object”)Table Attributes (describe entity)Columns Entity InstanceRow Relationships between entities preserved in relationships between tables. If you are interested in learning more formal design methods look up “normalization” and/or “third normal form”.

15. Our data Ensembl Gene IDSymbol / Name Chromo some Start Position (bp) End Position (bp) LocusLink ID Taxonomy ID Common Name Species ENSG00000186891.3TNFRSF1811044947104814787849606humanHomo sapiens ENSG00000078808.4CAB45110583701073469511509606humanHomo sapiens ENSG00000176022.1B3GALT61107370310764761267929606humanHomo sapiens ENSG00000160087.5UBE2J21109535211152921184249606humanHomo sapiens ENSG00000162572.4SCNN1D11123634113346763399606humanHomo sapiens ENSG00000162576.4MGC3047111941301199973843089606humanHomo sapiens ENSG00000175756.3AKIP112151681216641549989606humanHomo sapiens ENSG00000131586.2MRPL20112887031294063550529606humanHomo sapiens ENSG00000179403.2WARP113223111327547648569606humanHomo sapiens ENSG00000160072.5ATAD3B113586111396091838589606humanHomo sapiens ENSG00000008128.5CDC2L21158261716040609859606humanHomo sapiens ENSG00000169911.4SLC35E211611978162572899069606humanHomo sapiens ENSG00000008130.3FLJ13052116309751659805652209606humanHomo sapiens ENSG00000078369.3GNB111665027177079227829606humanHomo sapiens ENSMUSG00000041954.1TNFRSF1841541397021541422512193610090mouseMus musculus ENSMUSG00000023286.1UBE2J24154057210154072296414049910090mouseMus musculus What entities or “objects” are defined here? Is there any redundant data? What happens if we want to add another species attribute (e.g. genus)?

16. Our tables How do we know which organism a gene belongs to? Do we have unique identifiers? Can the organism have more than one gene? Can the gene have more than one organism?

17. Our tables Means each gene has “one and only one” organism, but that each organism can have more than one gene. This is an example of an entity relationship diagram.

18. Our tables A primary key is a unique identifier for a record in a table. A foreign key in one table refers to the primary key of another. The gene table has a foreign key, Organism_ID. Each record in the gene table will have an organism id to link it to the correct species record in the organism table.

19. Database Design Caveat Sometimes design is “sacrificed” for speed.

20. Data Types float integer tinyint varchar(size) o stores strings o size can be between 0 - 255, inclusive datetime + more What data types should our attributes (columns) be?

21. Complete Design Gene ColumnData Type gene_idinteger ensembl_gene_idvarchar(50) organism_idinteger namevarchar(35) locuslinkvarchar(10) chromosometinyint chromo_startinteger chromo_endinteger descriptionvarchar(255 ) Organism ColumnData Type organism_idinteger taxonomy_idinteger common_namevarchar(35) speciesvarchar(35) Database name: ensmartdb

22. Connecting to MySQL from the Command Line mysql -uusername -p Example: >mysql -uroot To EXIT MySQL: EXIT;

23. Basic SQL Commands SQL statements end with a semicolon View databases SHOW DATABASES;

24. START A MYSQL CLIENT Without using passwords (when the password for the specified user is empty) mysql -u -h Using passwords mysql -u -h -p Example: mysql -u root -h localhost Exitting with the command quit or exit.

25. DATA MANAGEMENT SHOW DATABASES; USE databaseName; SHOW TABLES; DESCRIBE table; SELECT * FROM table; SELECT * FROM table \G CREATE DATABASE databaseName; DROP DATABASE databaseName; CREATE TABLE tableName(name1 type1, name2 type2,...); DROP TABLE tableName; INSERT INTO TABLE VALUES( value1, value2,...); SELECT field1, field2,... FROM tableName; SELECT * INTO OUTFILE 'C:/tmp/skr.txt' FROM skr; LOAD DATA INFILE /path/file.txt INTO TABLE skr;

26. Importing a Database Creating a database CREATE DATABASE trii; From the command line: mysql -uusername -ppassword databasename < filename.sql Example: o mysql -uroot trii < trii.sql

27. Use database databasename USE databasename; Display all tables in a database SHOW TABLES; Basic SQL Commands

28. Create Table CREATE TABLE organism ( organism_id INTEGER NOT NULL AUTO_INCREMENT, taxonomy_id INTEGER NOT NULL, common_name VARCHAR(35) NOT NULL, species VARCHAR(35) NOT NULL, PRIMARY KEY (organism_id), UNIQUE (taxonomy_id) ); database name column names

29. View column details for a table DESC tablename;

30. Selecting all data SELECT * FROM tablename;

31. Select only the columns you need (it will be faster) SELECT common_name, species FROM organism;

32. Limiting your data Get the species name for a specific organism (you have the id) SELECT species FROM organism WHERE organism_id=1; How do we select all the gene names for chromosome 1?

33. Insert Inserting a gene INSERT INTO gene (ensembl_gene_id, organism_id, name, chromosome, chromo_start, chromo_end) VALUES (‘MY_NEW_GENE’, 1, ‘MY GENE’, 1, 12345, 67890); Get the id of the gene: SELECT gene_id FROM gene WHERE name='MY GENE';

34. Delete/Update Deleting a gene DELETE FROM gene WHERE gene_id=19; Updating a gene UPDATE gene SET name=‘NEW NAME’ WHERE name=‘AKIP’;

37. Documentation http://www.mysql.com/documentation/ http://www.mysql.com/documentation/manual.ph p As text manual.txt As HTML manual_toc.html As GNU Infomysql.info As PostScript manual.ps http://www.turbolift.com/mysql

38. PHPMyAdmin Web application Makes it easier to use MySQL To launch: http://localhost/phpmyadmin/ Download it here: http://www.phpmyadmin.net/home_page/ downloads.php

39. Create Database Enter name of database here and click “Create” You are logged in as “root” To get back to this page at any time select “Databases”

40. Create Table SQL query used to create “ensmartdb” Enter table name and number of fields then click “Go” We are currently using this database

41. Define Columns Select “auto_increment” here Select “Primary” here since this is the primary key Don’t forget to click “Save”! We are defining the columns for table “gene”

42. View Database Select “ensmartdb” to view tables in database Click “gene” to view “gene” table Add another table here

43. Insert Data Don’t forget to save by clicking “Go”! Click on “insert” to add data to table

44. View/Delete/Edit Data Check rows to edit or delete Click here to edit checked rows Click here to delete checked rows Click on “Browse” to view/edit/delete data

45. Database Users To use MySQL you must have a username and password A user in MySQL has permissions set regarding o MySQL itself (ex. whether or not the user can create a database) o Specific databases within MySQL For example, user “guest” may have permission to view database “x” but not database “y” Multiple users can access a MySQL database simultaneously

46. Granting a User Privileges PHPMyAdmin is logged in as user “root”, and has permission to do anything You should NOT make a habit of connecting to your database as root Create a user with restricted permissions to your database instead Click “Add new User”

47. Granting a User Privileges (Continued) Enter “User name”, “Host”, and “Password” This are privileges the user will have on ALL databases

48. Granting a User Privileges (Continued) Select “ensmartdb” to edit user permissions for database “ensmartdb” On the next screen select ONLY the permissions the user must have After you save the “global” permissions, you may add database specific permissions

49. MySQL Access Privilege System

50. What the Privilege System Does? The primary function of the MySQL privilege system is to authenticate a user connecting from a given host, and to associate that user with privileges on a database such as SELECT, INSERT, UPDATE, and DELETE. When you connect to a MySQL server, your identity is determined by the host from which you connect and the username you specify. When you issue requests after connecting, the system grants privileges according to your identity and what you want to do.

51. How the Privilege System Works MySQL access control involves two stages: o Stage 1: The server checks whether it should allow you to connect. o Stage 2: Assuming that you can connect, the server checks each statement you issue to see whether you have sufficient privileges to perform it. For example, if you try to select rows from a table in a database or drop a table from the database, the server verifies that you have the SELECT privilege for the table or the DROP privilege for the database.

52. Grant Tables The server stores privilege information in the grant tables of the mysql database Access-control decisions are based on the in- memory copies of the grant tables o The MySQL server reads the contents of these tables into memory when it starts and re-reads them under some circumstances Normally, you manipulate the contents of the grant tables indirectly by using the GRANT and REVOKE statements to set up accounts and control the privilegee The server uses the user, db, and host tables in the mysql database at both stages of access control

53. Columns of user, db, and host Possible values in privilege columns are ‘Y’ and ‘N’, default to ‘N’

54. Columns of user, db, and host (Cont.)

55. Important Columns of table_priv and columns_priv The tables_priv and columns_priv tables provide finer privilege control at the table and column levels.

56. Scope Columns Case insensitive The default value for each is the empty string

57. Possible Values in tables_priv, and columns_priv

58. How the grant tables are used? The user table scope columns determine whether to reject or allow incoming connections. For allowed connections, any privileges granted in the user table indicate the user's global (superuser) privileges. These privileges apply to all databases on the server The db table scope columns determine which users can access which databases from which hosts. The privilege columns determine which operations are allowed. A privilege granted at the database level applies to the database and to all its tables The host table is used in conjunction with the db table when you want a given db table row to apply to several hosts. For example, if you want a user to be able to use a database from several hosts in your network, leave the Host value empty in the user's db table row, then populate the host table with a row for each of those hosts. o The host table is not affected by the GRANT and REVOKE statements. Most MySQL installations need not use this table at all.

59. How the grant tables are used? (Cont.) The tables_priv and columns_priv tables are similar to the db table, but are more finegrained: They apply at the table and column levels rather than at the database level. A privilege granted at the table level applies to the table and to all its columns. A privilege granted at the column level applies only to a specific column. The procs_priv table applies to stored routines. A privilege granted at the routine level applies only to a single routine.

60. How the grant tables are used? The user table grants privileges that are assigned to you on a global basis and that apply no matter what the current database is. o For example, if the user table grants you the DELETE privilege, you can delete rows from any table in any database on the server host! Wise to grant privileges in the user table only to superusers such as DBA. For other users, you should leave the privileges in the user table set to 'N' and grant privileges at more specific levels only. You can grant privileges for particular databases, tables, or columns. Global priv. OR (data priv. AND host priv.) OR table priv. OR column priv.

61. MySQL Privileges

62. Grant and Revoke Syntax

63. Grant Levels Global level o Global privileges apply to all databases on a given server. These privileges are stored in the mysql.user table. GRANT ALL ON *.* and REVOKE ALL ON *.* grant and revoke only global privileges Database level o Database privileges apply to all objects in a given database. These privileges are stored in the mysql.db and mysql.host tables. GRANT ALL ON db_name.* and REVOKE ALL ON db_name.* grant and revoke only database privileges Table level o Table privileges apply to all columns in a given table. These privileges are stored in the mysql.tables_priv table. GRANT ALL ON db_name.tbl_name and REVOKE ALL ON db_name.tbl_name grant and revoke only table privileges.

64. 64 Grant Levels (Cont.) Column level o Column privileges apply to single columns in a given table. These privileges are stored in the mysql.columns_priv table. When using REVOKE, you must specify the same columns that were granted Routine level o The CREATE ROUTINE, ALTER ROUTINE, EXECUTE, and GRANT privileges apply to stored routines. They can be granted at the global and database levels. Also, except for CREATE ROUTINE, these privileges can be granted at the routine level for individual routines and are stored in the mysql.procs_priv table.

65. Priv_type in Grant and Revoke

66. Priv_type in Grant and Revoke (Cont.)

67. When Privilege Changes Take Effect When MySQL starts, all grant table contents are read into memory and become effective for access control at that point. When the server reloads the grant tables, privileges for existing client connections are affected as follows: o Table and column privilege changes take effect with the client's next request. o Database privilege changes take effect at the next USE db_name statement. o Changes to global privileges and passwords take effect the next time the client connects.

68. When Privilege Changes Take Effect (Cont.) If you modify the grant tables using GRANT, REVOKE, or SET PASSWORD, the server notices these changes and reloads the grant tables into memory again immediately. If you modify the grant tables directly using statements such as INSERT, UPDATE, or DELETE, your changes have no effect on privilege checking until you either restart the server or tell it to reload the tables. To reload the grant tables manually, issue a FLUSH PRIVILEGES statement or execute a mysqladmin flush-privileges or mysqladmin reload command.

69. MySQL User Account Management

70. MySQL Usernames and Passwords A MySQL account is defined in terms of a username and the client host or hosts from which the user can connect to the server. The account also has a password. Difference from the MySQL username and OS username o Usernames, as used by MySQL for authentication purposes, have nothing to do with login names as used by Windows or Unix o MySQL usernames can be up to a maximum of 16 characters long o MySQL passwords have nothing to do with passwords for logging in to your OS o MySQL encrypts passwords using its own algorithm

71. Adding New User Accounts to MySQL You can create MySQL accounts in three ways: o By using GRANT statements o By using CREATE USER statement o By manipulating the MySQL grant tables directly Create a user without any privileges To specify the password as the hashed value as returned by the PASSWORD(), include the keyword PASSWORD

72. Example 1

73. Example 2

74. Example 2 (Cont.)

75. Removing User Accounts DROP USER ‘jeffrey’@’locahost’

76. Limiting Account Resources In MySQL 5.0, you can limit the following server resources for individual accounts: o The number of queries that an account can issue per hour o The number of updates that an account can issue per hour o The number of times an account can connect to the server per hour o The number of simultaneous connections to the server on a per-account basis To set or change limits for an existing account, use a GRANT USAGE statement at the global level (ON *.*) To reset the current counts to zero for all accounts, issue a FLUSH USER_RESOURCES statement

77. Example

78. Assigning Account Password