mysql/php workshop 2 mysql lectures 2 php lectures each lecture builds on concepts taught and...
TRANSCRIPT
MySQL/PHP WorkshopMySQL/PHP Workshop
• 2 MySQL lectures• 2 PHP lectures • Each lecture builds on concepts taught and learned in the
previous lectures.• The first two lectures discuss the concept of a relational
database such as MySQL and show you how to manipulate the data stored in the database from the command line. It is essential to learn this first because PHP makes use of the language of the database.
• The third and fourth lectures will introduce you to PHP, a server-side scripting language that allows you to interact with the MySQL database from a web browser and create fancy web pages to display the data. PHP is the go-between that fetches the data from the MySQL database and then spits it out dynamically as the nicely formatted HTML page that the browser expects.
http://www.trii.org/courses/mysql/
Class #1: Introduction to MySQLClass #1: Introduction to MySQL
• Relational databases• Database design• SQL
o Creating databaseso Creating tableso Selecting from, deleting, and updating tables
• Exercises
• You should haveo Class noteso Exercise handouto MySQL Pocket Reference
• Useful resource: http://dev.mysql.com/doc/
Manda Wilson, BIC, cBio, MSKCCTrii Training: Bioinformatics and Computational Methods
First Name Last Name PhoneNadia Li 2687Madhu Charu 7856Ajuma Kinsaka 4489Wade Randal 5257Helen Clark 2147
Employees
Relational DatabasesRelational 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 rowtable name
column
row
Use a Relational Database When…Use a Relational Database When…
• You have a very large dataset• There is redundant data
o Wastes disk spaceo Increases errors
• Information must be updated in multiple locations
• Security is importanto Different users can be granted different
permissions• Strict enforcement of data types is important
Spreadsheet ExampleSpreadsheet Example
Title Author Borrower PhoneA House for Mr. Biswas VS Naipaul Sarah 646.555.1234Midnight's Children Salman RushdieOn the Road Jack Kerouac
Spreadsheet ExampleSpreadsheet Example
Title Author Borrower PhoneA House for Mr. Biswas VS Naipaul Sarah 646.555.1234Midnight's Children Salman RushdieOn the Road Jack Kerouac
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.
One Flew Over the Cuckoo's Nest Ken Kesey Sarah 646.555.1244Sula Toni MorrisonVillette Charlotte Bronte Jim 646.555.4586
Database DesignDatabase DesignEntity Relationship Design
Entity (“thing”, “object”) Table
Attributes (describe entity) Columns
Entity Instance Row
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”.
Our dataOur dataEnsembl Gene ID Symbol
/ NameChromosome
Start Position (bp)
End Position (bp)
LocusLink ID
Taxonomy ID
Common Name
Species
ENSG00000186891.3 TNFRSF18 1 1044947 1048147 8784 9606 human Homo sapiens
ENSG00000078808.4 CAB45 1 1058370 1073469 51150 9606 human Homo sapiens
ENSG00000176022.1 B3GALT6 1 1073703 1076476 126792 9606 human Homo sapiens
ENSG00000160087.5 UBE2J2 1 1095352 1115292 118424 9606 human Homo sapiens
ENSG00000162572.4 SCNN1D 1 1123634 1133467 6339 9606 human Homo sapiens
ENSG00000162576.4 MGC3047 1 1194130 1199973 84308 9606 human Homo sapiens
ENSG00000175756.3 AKIP 1 1215168 1216641 54998 9606 human Homo sapiens
ENSG00000131586.2 MRPL20 1 1288703 1294063 55052 9606 human Homo sapiens
ENSG00000179403.2 WARP 1 1322311 1327547 64856 9606 human Homo sapiens
ENSG00000160072.5 ATAD3B 1 1358611 1396091 83858 9606 human Homo sapiens
ENSG00000008128.5 CDC2L2 1 1582617 1604060 985 9606 human Homo sapiens
ENSG00000169911.4 SLC35E2 1 1611978 1625728 9906 9606 human Homo sapiens
ENSG00000008130.3 FLJ13052 1 1630975 1659805 65220 9606 human Homo sapiens
ENSG00000078369.3 GNB1 1 1665027 1770792 2782 9606 human Homo sapiens
ENSMUSG00000041954.1 TNFRSF18 4 154139702 154142251 21936 10090 mouse Mus musculus
ENSMUSG00000023286.1 UBE2J2 4 154057210 1540722964 140499 10090 mouse Mus 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)?
Our tablesOur 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?
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
Our tablesOur tables
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and aTIFF (LZW) decompressorare needed to see this picture.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.
Our tablesOur tables
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
• 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.
Database Design CaveatDatabase Design Caveat
• Sometimes design is “sacrificed” for speed.
Data TypesData Types• float• integer• tinyint• varchar(size)
o stores stringso size can be between 0 - 255, inclusive
• datetime• + more What data types should our attributes (columns) be?
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
Complete DesignComplete DesignGene
Column Data Typegene_id integerensembl_gene_id varchar(50)organism_id integername varchar(35)locuslink varchar(10)chromosome tinyintchromo_start integerchromo_end integer
description varchar(255)
OrganismColumn Data Typeorganism_id integertaxonomy_id integer common_name varchar(35)species varchar(35)
QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.
Database name: ensmartdb
Connecting to MySQL from the Connecting to MySQL from the Command LineCommand Line
mysql -uusername -p
Example:>mysql -uroot
To EXIT MySQL:EXIT;
Basic SQL CommandsBasic SQL Commands
• SQL statements end with a semicolon• View databases
SHOW DATABASES;
Importing a DatabaseImporting a Database
• Creating a databaseCREATE DATABASE trii;
• From the command line:mysql -uusername -ppassword databasename < filename.sql
• Example:o mysql -uroot trii < trii.sql
• Use database databasenameUSE databasename;
• Display all tables in a databaseSHOW TABLES;
Basic SQL CommandsBasic SQL Commands
Create TableCreate 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
View column details for a tableView column details for a table
DESC tablename;
Selecting all dataSelecting all data
SELECT * FROM tablename;
Select only the columns you need Select only the columns you need (it (it will be faster)will be faster)
SELECT common_name, speciesFROM organism;
Limiting your dataLimiting 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?
InsertInsert
• Inserting a geneINSERT 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';
Delete/UpdateDelete/Update
• Deleting a geneDELETE FROM gene WHERE
gene_id=19;• Updating a gene
UPDATE gene SET name=‘NEW NAME’ WHERE name=‘AKIP’;
Table JoinsTable Joins
• Sometimes you want data from more than one table. To do this we join the tables. The result is a new (temporary) table.
Cross JoinCross Join
• SELECT gene.name, organism.speciesFROM gene, organism;
Note: There are only two records in the gene table with the name “TNFRSF18”. One is a mouse gene and the other is a human gene. What do you think happened?
Cross Join (Continued)Cross Join (Continued)
Each row of the gene table was joined with every row in the organism table.
Cross Join (Continued)Cross Join (Continued)
• We want to use the organism id to match a gene record with the correct organism record so that we get:
Remember there are two gene
records with the name
“TNFRSF18”.
Cross Join (Continued)Cross Join (Continued)
SELECT gene.name, organism.speciesFROM gene, organismWHERE
gene.organism_id=organism.organism_id;
Notice that we have 18 rows and that there are
18 rows in the gene table.
Class #2: Introduction to MySQL Class #2: Introduction to MySQL (Continued) (Continued)
• Table Joins• Where clause (continued)• Aggregate Functions• Backing up your database• Indexes (if time)• Importing large datasets (if time)