Download Introductory to database handling

Introductory to database handling
Endre Sebestyén
What is a database?
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A database is a bunch of information
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It is a structured collection of information
It contains basic objects, called records or entries
The records contain fields, which contain defined types of data,
somehow related to that record
A nuclotid sequence database would contain for example all
kinds of nucleotides as records, and nucleotide properties
(length, name, origin, etc) as fields.
What is a database?
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A database is searchable
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It is updated regularly (releases)
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It contains an index (table of content, catalog)
New data goes in
Obsolete, old data goes out
It is cross referenced
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To other databases
Why databases?
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The main purpose of databases is not only to collect and
organize data, but to allow advanced data retrieval and
analysis
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A database query is a method to retrieve information
from the database
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The organization of records into fields allows us to use
queries on fields
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Example : all mouse rna sequences between 1000-1500
bp length
Databases on the internet
WEBSERVERS
USER
DATABASE
SERVER
Databases on the internet
Information
system
Query
system
Storage
system
Data
Databases on the internet
Information
system
Query system
Storage
system
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Data
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Book
Book title
Sequence
Temperature
Picture
Video
Log files of web servers
etc
Databases on the internet
Information
system
Query system
Storage
system
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Data
Bookshelves
Boxes
Text files/directories
Binary files
MySQL database
Oracle database
Types of databases
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Hierarchical model
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Tree-like structures
Parent -> child
One to many relations
Types of databases
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Network model
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More complex than the previous
Parent -> child
One to many
Many to one
Types of databases
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Relational model
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Most widely used
Fast and efficient (if the data structure is designed correctly)
Databases on the internet
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Lists
Catalogues
Librarian
Index files
SQL language
grep command
Query systems for databases
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SQL query language
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Querying and modifying data
Managing the database
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Optimize queries
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SELECT * FROM sequence_feature WHERE sequence_primary_id LIKE
‘%$variable%’ SORT BY sequence_primary_id LIMIT 10;
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Multiple operating systems
Different programming languages
Different storage systems (MySQL, PostgreSQL, etc)
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Use SQL terminal
Throught programming languages
Databases on the internet
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Library
NCBI Entrez
Google
Lots of other general and
specialized databases with
search interfaces on the
web
Case study: the DoOP database
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Tries to collect and analyze the promoter regions of different
genes and orthologous gene clusters
http://doop.abc.hu
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2 main sections: plant and chordate
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Chordate: v1.4
Plant: v1.5, v1.6
Integrates different kinds of data
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Sequence data
Sequence annotation
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Cross-references to external databases
Multiple alignments
Conserved sequence regions
Goal: easily accessible and searchable interface on the web
Data processing
MySQL tables
MySQL tables
MySQL table
MySQL tables
Data processing
API for the MySQL database
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Application Programming Interface
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We want to convert the MySQL data into nice webpages
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MySQL query to get data:
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SELECT * FROM sequence_feature WHERE
sequence_primary_id LIKE ‘%$variable%’ SORT BY
sequence_primary_id LIMIT 10;
And so on…
Process the data
OR with n API
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$data = $sequence_feature_object->get_data;
Bio::DOOP API
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(More or less) simple representations of the sequence and
other data -> modules and objects
The API “hides” the MySQL queries and other stuff from us, so
we can concentrate on the web pages
It works well only if we have good API design with all the
necessary features
Bio::DOOP API modules
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Clusters
Subsets
Sequences
Sequence features
Motifs
Other modules for managing, sorting and filtering the data
Search page
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Search types
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Sequence ID
Gene ID
Keywords
Species
Sequence
Search results
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Cluster ID
Description
Conserved motifs
Taxonomical groups
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Download sequences
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Promoter cluster
Sequences
Gene annotation
Sequence alignment
Crossreferences
Conserved regions
Promoter cluster
UTR region
Species,
size
Motifs
Motifs
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Further search in the motif
collection
Similar table as in the
previous search results
Thank you for your attention!