FBW

27-02-2018

Biological Databases

Wim Van Criekinge

Syllabi left

Project

Big Data Volumes

Data Levels in Biological Research

Primary dataDerived data

Primary dataDerived dataInterpreted data/

knowledge

Experimental metadata

Analytical metadata

Direct Queryability of Selected Bioinformatics Databases

Database Direct Querying? How? Modality DB Engine

ArrayExpressWarehouse Eventually http://www.ebi.ac.uk/aedw/ SQL Oracle

BioWarehouse Yeshttp://biowarehouse.ai.sri.com/

- need accountSQL Oracle/MySQL

Ensembl Yeshttp://www.ensembl.org/info/d

ata/download.htmlSQL MySQL

Mouse Genome Database Yes ask for account SQL Sybase

PharmGKB Yeshttp://www.pharmgkb.org/hom

e/projects/webservices/SOAP-based Oracle

Saccharomyces Genome

DatabaseEventuallyMaybe Oracle

Stanford Microarray Database No Oracle

Example 3-tier model in biological database

Rationale to study SQL

• Learning SQL to Query Biological Databases

• Are you getting too much data, or missing crucial data when querying via a Web interface? Many biological databases can be queried directly via SQL, thus bypassing the limitations of the database's interface. SQL is at the heart of biological databases as diverse as Ensembl, ArrayExpress and the Mouse Genome Database.

• Focus on understanding relational databases by studying a repository of biological data and learn how to query it using SQL.

SQL consists of only 4 statements, sometimes

referred to as CRUD:

–Create - INSERT - to store new data

–Read - SELECT - to retrieve data

–Update - UPDATE - to change or modify

data.

–Delete - DELETE - delete or remove data

Structured Query Language

Definitions

Definitions

• Database: Collection of tables • Table

– Collection of records that share a common fundamental characteristic

• E.g., patients and locations can each be stored in their own table

• Record

– Basic unit of information in a relation information

– A record is composed of fields

– E.g., 1 record per person

• Query

– Set of instructions to a database “engine” to retrieve, sort and format returning data.

• “find me all patients in my database”

Table Characteristics

• Two-dimensional structure with rows and columns

• Rows (tuples) represent single entity

• Columns represent attributes

• Row/column intersection represents single value

• Tables must have an attribute to uniquely identify each row

• Column values all have same data format

• Each column has range of values called attribute domain

• Order of the rows and columns is immaterial to the DBMS

Numeric Data Types

MySQL uses all the standard ANSI SQL numeric data types, so if you're coming to MySQL from a different

database system, these definitions will look familiar to you. The following list shows the common numeric data

types and their descriptions:

INT - A normal-sized integer that can be signed or unsigned. If signed, the allowable range is from -2147483648 to

2147483647. If unsigned, the allowable range is from 0 to 4294967295. You can specify a width of up to 11 digits.

TINYINT - A very small integer that can be signed or unsigned. If signed, the allowable range is from -128 to 127.

If unsigned, the allowable range is from 0 to 255. You can specify a width of up to 4 digits.

SMALLINT - A small integer that can be signed or unsigned. If signed, the allowable range is from -32768 to

32767. If unsigned, the allowable range is from 0 to 65535. You can specify a width of up to 5 digits.

MEDIUMINT - A medium-sized integer that can be signed or unsigned. If signed, the allowable range is from -

8388608 to 8388607. If unsigned, the allowable range is from 0 to 16777215. You can specify a width of up to 9

digits.

BIGINT - A large integer that can be signed or unsigned. If signed, the allowable range is from -

9223372036854775808 to 9223372036854775807. If unsigned, the allowable range is from 0 to

18446744073709551615. You can specify a width of up to 20 digits.

FLOAT(M,D) - A floating-point number that cannot be unsigned. You can define the display length (M) and the

number of decimals (D). This is not required and will default to 10,2, where 2 is the number of decimals and 10 is

the total number of digits (including decimals). Decimal precision can go to 24 places for a FLOAT.

DOUBLE(M,D) - A double precision floating-point number that cannot be unsigned. You can define the display

length (M) and the number of decimals (D). This is not required and will default to 16,4, where 4 is the number of

decimals. Decimal precision can go to 53 places for a DOUBLE. REAL is a synonym for DOUBLE.

DECIMAL(M,D) - An unpacked floating-point number that cannot be unsigned. In unpacked decimals, each

decimal corresponds to one byte. Defining the display length (M) and the number of decimals (D) is required.

NUMERIC is a synonym for DECIMAL.

String Data Type

• Although numeric and date types are fun, most data you'll store will be in string format. This list describes

the common string datatypes in MySQL.

• CHAR(M) - A fixed-length string between 1 and 255 characters in length (for example CHAR(5)), right-

padded with spaces to the specified length when stored. Defining a length is not required, but the default

is 1.

• VARCHAR(M) - A variable-length string between 1 and 255 characters in length; for example

VARCHAR(25). You must define a length when creating a VARCHAR field.

• BLOB or TEXT - A field with a maximum length of 65535 characters. BLOBs are "Binary Large Objects"

and are used to store large amounts of binary data, such as images or other types of files. Fields defined

as TEXT also hold large amounts of data; the difference between the two is that sorts and comparisons

on stored data are case sensitive on BLOBs and are not case sensitive in TEXT fields. You do not specify

a length with BLOB or TEXT.

• TINYBLOB or TINYTEXT - A BLOB or TEXT column with a maximum length of 255 characters. You do

not specify a length with TINYBLOB or TINYTEXT.

• MEDIUMBLOB or MEDIUMTEXT - A BLOB or TEXT column with a maximum length of 16777215

characters. You do not specify a length with MEDIUMBLOB or MEDIUMTEXT.

• LONGBLOB or LONGTEXT - A BLOB or TEXT column with a maximum length of 4294967295

characters. You do not specify a length with LONGBLOB or LONGTEXT.

• ENUM - An enumeration, which is a fancy term for list. When defining an ENUM, you are creating a list of

items from which the value must be selected (or it can be NULL). For example, if you wanted your field to

contain "A" or "B" or "C", you would define your ENUM as ENUM ('A', 'B', 'C') and only those values (or

NULL) could ever populate that field.

Built-in Data Types in SQL

• date: Dates, containing a (4 digit) year, month and

date

– Example: date ‘2005-7-27’

• time: Time of day, in hours, minutes and seconds.

– Example: time ‘09:00:30’ time ‘09:00:30.75’

• timestamp: date plus time of day

– Example: timestamp ‘2005-7-27 09:00:30.75’

• interval: period of time

– Example: interval ‘1’ day

– Subtracting a date/time/timestamp value from another gives

an interval value

– Interval values can be added to date/time/timestamp values

Build-in Data Types in SQL (Cont.)

• Can extract values of individual fields from

date/time/timestamp

– Example: extract (year from r.starttime)

• Can cast string types to

date/time/timestamp

– Example: cast <string-valued-expression>

as date

– Example: cast <string-valued-expression>

as time

User-Defined Types

• create type construct in SQL creates user-defined

type

create type Dollars as numeric (12,2) final

• create domain construct in SQL-92 creates user-

defined domain types

create domain person_name char(20) not null

• Types and domains are similar. Domains can have

constraints, such as not null, specified on them.

Large-Object Types

• Large objects (photos, videos, CAD files, etc.)

are stored as a large object:

– blob: binary large object -- object is a large

collection of uninterpreted binary data (whose

interpretation is left to an application outside of

the database system)

– clob: character large object -- object is a large

collection of character data

– When a query returns a large object, a pointer is

returned rather than the large object itself.

Creating a Table

• To create a table, use the CREATE TABLE command:

mysql> CREATE TABLE pet (

-> name VARCHAR(20),

-> owner VARCHAR(20),

-> species VARCHAR(20),

-> sex CHAR(1),

-> birth DATE, death DATE);

Query OK, 0 rows affected (0.04 sec)

Keys

• One or more attributes that

determine other attributes

– Key attribute

– Composite key

• Full functional dependence

• Entity integrity

– Uniqueness

– No ‘null’ value in key

Example Tables

Simple Relational Database

Keys (con’t.)

• Primary key

– Candidate key to uniquely identify all other

attributes in a given row

• Foreign key

– Values must match primary key in another

table

Integrity Rules

• Entity integrity

– Ensures all entities are unique

– Each entity has unique key

• Referential integrity

– Foreign key must have null value or match

primary key values

– Makes it impossible to delete row whose

primary key has mandatory matching foreign

key values in another table

Integrity Constraints

• Integrity constraints guard against

accidental damage to the database, by

ensuring that authorized changes to the

database do not result in a loss of data

consistency.

– A checking account must have a balance

greater than $10,000.00

– A salary of a bank employee must be at

least $4.00 an hour

– A customer must have a (non-null) phone

number

Referential Integrity

• Ensures that a value that appears in one relation for a given set of

attributes also appears for a certain set of attributes in another

relation.

– Example: If “Perryridge” is a branch name appearing in one of the

tuples in the account relation, then there exists a tuple in the

branch relation for branch “Perryridge”.

• Primary and candidate keys and foreign keys can be specified as part

of the SQL create table statement:

– The primary key clause lists attributes that comprise the primary

key.

– The unique key clause lists attributes that comprise a candidate

key.

– The foreign key clause lists the attributes that comprise the

foreign key and the name of the relation referenced by the foreign

key. By default, a foreign key references the primary key attributes

of the referenced table.

Install BIOSQL locally

• Get latest version of mysql (MAMP,

mariaDB)

• Download biosqldb-mysql.sql

• Remove type=innodb

• Launch database server

• Connect using toad (port 8889)

• Create database biosql;

• Set as active database

• Use worksheet to execute biosqldb-

mysql.sql

Typical ODBC Architecture

How ODBC Works?

• ODBC inserts a middle layer called a Client

Driver

• Purpose of the Client Driver is to translate the

applications queries into commands that the

DBMS understands

Other Parts of the Architecture

• Application – calls functions defined in the ODBC API to access a data source

• Driver Manager – implements the ODBC API and provides information to the application

• Database – contains all the data

Setting Up a Data Source in Windows

• A data source is just a database that ODBC connects to

• This allows the person to change database types without any changes to the program

• Step 1. Get a database.

– Using access for this example because it’s on this computer

Conclusion

The four parts that make up ODBC:

Conclusion

• Advantages:

– Allows access to different types of databases

– Uniform way of retrieving information

– Highly efficient

– Low memory requirements

• Disadvantages

– Complex and steep learning curve

– All data in database must look like a relational

database

Conclusion

• ODBC changed the way people code their programs

that have to interact with databases.

• The efficiency of programmers in the business world

has increased due to ODBC because they no longer

are wasting time to create multiple copies of a

program.

• ODBC has vastly improved the way programmers

deal with databases.

Application/utilities

Project