Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
•
Formalities about the course
•
Database introduction
•
Data models and history
•
Course content
Lena Strömbäck
•
Research ad ADIT/DWIS
http://www.ida.liu.se/~TDDC94
•
Q/A
TDDC94 Database Technology
augusti 2008
1
1
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Todays lecture
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Course organisation
2
2
Course leadership
•
12 lectures (some together with TDDB77)
•
Examiner and Course leader:
•
Written exam
•
Course assistant
•
Lab exercises
•
Course administration:
•
Director of studies:
•
Teachers:
-
ƒ
ƒ
3 computer labs
1 paper lab
Mini project
ƒ
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augusti 2008
3
3
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
•
augusti 2008
5
José M Pena, jmp@ida.liu.se
Katarina Löfstrand, katlo@ida.liu.se
Lena Strömbäck, lestr@ida.liu.se
Tommy Ellkvist, g-tomel@ida.liu.se
He Tan, hetan@ida.liu.se
Patrick Lambrix patla@ida.liu.se
4
4
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Course literature
•
augusti 2008
Lena Strömbäck, lestr@ida.liu.se
Laboratory schedule
Elmasri, R., Navathe, S., Fundamentals of Database
Systems, 5th edition, Addison-Wesley, ISBN 0-32148506-X, 2006
•
Lab compendium: Databases, ADIT-1, version autumn
2008
•
Lab schedule on the course web-page.
ƒ One group have two rooms.
ƒ Paper lab scheduled in lecture rooms.
Mini-project: Less supervision.
ƒ One mandatory section discussing your data model.
5
augusti 2008
6
6
1
Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Laboratory information
•
You need a special database account
ƒ automatically created at course registration
ƒ e-mail system@ida.liu.se if any problems
Handing in labs
•
Each lab requires a written report
•
Labs can be handed in:
ƒ
ƒ
•
•
ƒ Students that retake the labs: discuss with Lena
augusti 2008
7
7
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Last day for handing in: Oct 15th
•
Next occasions: Jan 10th, August 2009
•
Later: Redo the labs!!!
9
9
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
•
augusti 2008
11
Dictionary – not electronic
No calculator
No books allowed
Registration to the exam
ƒ
ƒ
10
LiU: Disciplinary actions
• Any kind of academic dishonesty, such as
cheating, plagiarism, use of unauthorized
assistance, fraud and failure to comply with
University examination rules, may result in
the filing of a complaint to the University
Disciplinary Committee. The potential
penalties include expulsion, suspension,
and revocation of previously earned grade
or degree.
• LiU Rules and regulations
Theoretical and practical
Have to pass both parts
Equipment
ƒ
ƒ
ƒ
Lab policy
10
Two parts:
ƒ
ƒ
•
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Written exam
•
8
• You are expected to do the lab assignments by
yourself. Merely copying others solutions will not be
tolerated, even if you make cosmetic changes to the
code/solution. If we suspect that this, or any other
form of cheating, has happened we will report it to the
disciplinary board of the university.
• Be prepared to be asked questions by your laboration
assistant about detailed and specific code and also
inquiries about why you have selected a specific
solution. This applies to all lab group members.
• If you have problems meeting a deadline it is much
better to talk to the instructor about it than to cheat.
Lab1: Week 36
Lab2: Week 36
Lab3: Week 37
Lab4: Week 38
Project: Model Week 39
Project: Implementation Week 41
•
From the teacher at the lab
At the OUT box outside each teachers office
Remember to fetch your labs, it is your only proof that you have passed the
labs.
8
Lab reports are handed in:
ƒ
ƒ
ƒ
ƒ
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ƒ
augusti 2008
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Labs reports deadlines
•
Labs can be fetched:
ƒ
ƒ
ƒ
Subscribe for labs via course home page
To the teacher at the lab
At IDAs postboxes, opposite to Café Java
Studentportalen
Period: 2008-09-14 - 2008-10-05
11
augusti 2008
12
12
2
Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
•
Traditional Applications:
ƒ
•
13
•
Database:
•
Data:
•
Mini-world:
•
Database Management System (DBMS):
ƒ
ƒ
ƒ
•
•
A database consists of a logical coherent collection of
data with an underlying meaning.
•
A database is designed, built and filled with data with
respect to an underlying purpose.
14
14
Simplified database system environment
Known facts that can be recorded and have an implicit meaning.
Some part of the real world about which data is stored in a database. For example,
student grades and transcripts at a university.
A software package/ system to facilitate the creation and maintenance of a
computerized database.
The DBMS software together with the data itself. Sometimes, the applications are
also included.
15
augusti 2008
16
16
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Typical DBMS Functionality
Example of a Database
•
Define a particular database in terms of its data types,
structures, and constraints
•
Mini-world for the example:
•
Construct or Load the initial database contents on a secondary
storage medium
•
Some mini-world entities:
•
Manipulate the database:
•
17
A database represents some aspect of the real world, i.e.
a mini world.
A collection of related data.
15
ƒ
ƒ
ƒ
augusti 2008
•
Database System:
ƒ
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Basic Definitions
ƒ
augusti 2008
Multimedia Databases
Geographic Information Systems (GIS)
Data Warehouses
Real-time and Active Databases
Many other applications
13
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
What is a database? - Definition
Numeric and Textual Databases
More Recent Applications:
ƒ
ƒ
ƒ
ƒ
ƒ
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Types of Databases and Database
Applications
ƒ Part of a UNIVERSITY environment.
ƒ
ƒ
ƒ
ƒ
ƒ
Retrieval: Querying, generating reports
Modification: Insertions, deletions and updates to its content
Accessing the database through Web applications
STUDENTs
COURSEs
SECTIONs (of COURSEs)
(academic) DEPARTMENTs
INSTRUCTORs
Process and Share by a set of concurrent users and
application programs – yet, keeping all data valid and
consistent
17
augusti 2008
18
18
3
Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
•
Some mini-world relationships:
ƒ
ƒ
ƒ
ƒ
ƒ
ƒ
•
augusti 2008
Note: During the course you will learn how to express this as
an E/R model and translate the model into a data model.
19
ƒ
ƒ
Example of a simplified
database catalog
A DBMS catalog stores the description of a particular database (e.g. data
structures, types, and constraints)
The description is called meta-data.
This allows the DBMS software to work with different database applications.
Called program-data independence.
Allows changing data structures and storage organization without having to
change the DBMS access programs.
21
21
augusti 2008
Data Models
•
Data Abstraction:
Data Model:
ƒ
ƒ A data model is used to hide storage details and present the users
with a conceptual view of the database.
ƒ Programs refer to the data model constructs rather than data
storage details
•
22
22
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Main Characteristics of the Database
Approach (continued)
•
Example of a simplified database catalog
Insulation between programs and data:
ƒ
ƒ
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
20
20
Self-describing nature of a database system:
ƒ
•
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Main Characteristics of the Database
Approach
•
augusti 2008
SECTIONs are of specific COURSEs
STUDENTs take SECTIONs
COURSEs have prerequisite COURSEs
INSTRUCTORs teach SECTIONs
COURSEs are offered by DEPARTMENTs
STUDENTs major in DEPARTMENTs
19
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Example of a Database
ƒ
ƒ
Support of multiple views of the data:
A set of concepts to describe the structure of a database, the operations for
manipulating these structures, and certain constraints that the database
should obey.
Constraints specify some restrictions on valid data; these constraints must
be enforced at all times
For this example and throughout the course we will use the relational model
ƒ Each user may see a different view of the database, which
describes only the data of interest to that user.
augusti 2008
23
23
augusti 2008
24
24
4
Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Categories of Data Models
•
The three-schema architecture
Conceptual (high-level, semantic) data models:
ƒ Provide concepts that are close to the way many users perceive
data.
• (Also called entity-based or object-based data models.)
•
Implementation (representational) data models:
ƒ Provide concepts that fall between the above two, used by many
commercial DBMS implementations (e.g. relational data models
used in many commercial systems).
•
Physical (low-level, internal) data models:
ƒ Provide concepts that describe details of how data is stored in the
computer. These are usually specified in an ad-hoc manner
through DBMS design and administration manuals
augusti 2008
25
25
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
26
26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Data Independence
•
augusti 2008
Logical Data Independence:
Schemas versus Instances
•
ƒ The capacity to change the conceptual schema without having to
change the external schemas and their associated application
programs.
•
Database Schema:
ƒ The description of a database.
ƒ Includes descriptions of the database structure, data types, and
the constraints on the database.
Physical Data Independence:
ƒ The capacity to change the internal schema without having to
change the conceptual schema.
ƒ For example, the internal schema may be changed when certain
file structures are reorganized or new indexes are created to
improve database performance
•
Database State:
ƒ The actual data stored in a database at a particular moment in time.
This includes the collection of all the data in the database.
ƒ Also called database instance (or occurrence or snapshot).
• The term instance is also applied to individual database components,
e.g. record instance, table instance, entity instance
augusti 2008
27
27
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
augusti 2008
28
28
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Example of a Database Schema
Example
of a
database
state
augusti 2008
29
29
augusti 2008
30
30
5
Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Main Characteristics of the Database
Approach (continued)
•
Handling many users
Pelle
Sharing of data and multi-user transaction processing:
ƒ
ƒ
ƒ
ƒ
Allowing a set of concurrent users to retrieve from and to update the database.
Concurrency control within the DBMS guarantees that each transaction is
correctly executed or aborted
Recovery subsystem ensures each completed transaction has its effect
permanently recorded in the database
OLTP (Online Transaction Processing) is a major part of database
applications. This allows hundreds of concurrent transactions to execute per
second.
Sums total
salary costs
Kalle
Updates the
salary for 1000
employees
augusti 2008
31
31
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
augusti 2008
32
32
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Persistency and errors
Database
Database Users
•
Users may be divided into
ƒ Those who actually use and control the database content, and
those who design, develop and maintain database applications
(called “Actors on the Scene”),
Power failure
• Administrators
• Designers
• End-users
ƒ Those who design and develop the DBMS software and related
tools, and the computer systems operators (called “Workers
Behind the Scene”).
Kalle
Updates the
salary
for 1000
employees
augusti 2008
Database
33
33
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Data Definition Language (DDL)
•
Data Manipulation Language (DML)
34
34
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
DBMS Languages
•
augusti 2008
DBMS - benefits
ƒ
ƒ
ƒ
ƒ
ƒ
ƒ
ƒ
ƒ
ƒ
ƒ High-Level or Non-procedural Languages: These include the
relational language SQL
• May be used in a standalone way or may be embedded in a
programming language
ƒ Low Level or Procedural Languages:
Control of redundant information
Data access
Persistent data storage
Allow questions and inference
Allow several users
Representation of complex data relations
Efficient storage of data
Integrity Constraints
Backup and recovery.
• These must be embedded in a programming language
augusti 2008
35
35
augusti 2008
36
36
6
Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
When not to use a DBMS
•
Main inhibitors (costs) of using a DBMS:
ƒ
ƒ
•
ƒ
ƒ
•
High initial investment and possible need for additional hardware.
Overhead for providing generality, security, concurrency control, recovery,
and integrity functions.
•
Network Model
•
Hierarchical Model (introduced in the 60:s)
ƒ
If the database and applications are simple, well defined, and not expected to
change.
If there are stringent real-time requirements that may not be met because of
DBMS overhead.
If access to data by multiple users is not required.
If the database system is not able to handle the complexity of data because
of modeling limitations
If the database users need special operations not supported by the DBMS.
37
37
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Example of Network Model Schema
38
38
The Network Model
•
The first network DBMS was implemented by Honeywell in
1964-65 (IDS System).
•
Adopted heavily due to the support by CODASYL (Conference
on Data Systems Languages)
•
Advantages:
ƒ
ƒ
ƒ
•
39
39
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
augusti 2008
Network databases
•
Navigational and procedural nature of processing
Database contains a complex array of pointers that thread through a set of
records.
40
40
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
•
Network Model is able to model complex relationships.
Can handle most situations for modeling.
Language is navigational; uses constructs like FIND, FIND member, FIND
owner, FIND NEXT within set, GET, etc.
Disadvantages:
ƒ
ƒ
augusti 2008
(introduced in the 60:s)
When no DBMS may suffice:
ƒ
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
History of Data Models
When a DBMS may be unnecessary:
ƒ
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Hierarchical databases
The Hierarchical Data Model
•
Initially implemented in a joint effort by IBM and North
American Rockwell around 1965. Resulted in the IMS
family of systems.
•
Advantages:
ƒ Simple to construct and operate
ƒ Corresponds to a number of natural hierarchically organized
domains, e.g., organization (“org”) chart
ƒ Language is simple: Uses constructs like GET, GET UNIQUE, GET
NEXT, GET NEXT WITHIN PARENT, etc.
•
Disadvantages:
ƒ Navigational and procedural nature of processing
ƒ Database is visualized as a linear arrangement of records
augusti 2008
41
41
augusti 2008
42
42
7
Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
augusti 2008
augusti 2008
History of Data Models
•
Network Model
•
Hierarchical Model (introduced in the 60:s)
•
Relational Model (introduced in the 70:s)
43
•
Network Model
•
Hierarchical Model (introduced in the 60:s)
•
Relational Model (introduced in the 70:s)
•
Object-oriented Data Models (introduced in the 80:s)
•
Object-Relational Models (introduced in the 90:s)
47
Relational systems incorporate concepts from object
databases leading to object-relational.
•
Features: User defined types and Inheritance
•
Exemplified in the latest versions of Oracle, DB2, and
SQL Server and other DBMSs.
Standards included in SQL-99 and expected to be
enhanced in future SQL standards.
47
augusti 2008
•
Proposed in 1970 by E. F. Codd (IBM), first commercial system
in 1981-82.
•
Now in several commercial products (e.g. DB2, ORACLE, MS
SQL Server, SYBASE, INFORMIX). Several free open source
implementations, e.g. MySQL, PostgreSQL
•
Data model: Tables
•
Benefits: Easy to understand and use, Theoretical model,
declarative query language, query optimization can be efficient
•
SQL relational standards: SQL-89 (SQL1), SQL-92 (SQL2), SQL99, SQL3, …
44
Object-oriented Data Models
•
Enable concepts in persistent O-O Programming
Languages such as C++ (e.g., in OBJECTSTORE or
VERSANT), and Smalltalk (e.g., in GEMSTONE).
•
model: persistent objects, messages, encapsulation,
inheritance
•
Object Database Standard: ODMG-93, ODMG-version 2.0,
ODMG-version 3.0.
46
46
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Object-Relational Models
•
augusti 2008
The Relational Model
44
(introduced in the 60:s)
45
•
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
History of Data Models
45
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
augusti 2008
(introduced in the 60:s)
43
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
48
History of Data Models
•
Network Model
•
Hierarchical Model (introduced in the 60:s)
(introduced in the 60:s)
•
Relational Model (introduced in the 70:s)
•
Object-oriented Data Models (introduced in the 80:s)
•
Object-Relational Models (introduced in the 90:s)
•
XML databases and Hybrid models (2000 - )
48
8
Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Today:
•
Relational databases dominating.
•
Hierarchical and navigational databases still in use.
(Mainly in flight industry.)
•
Object-oriented databases in use, especially as objectrelational databases.
•
augusti 2008
Overview of Database Design Process
•
Two main activities:
ƒ Database design
ƒ Applications design
•
Focus in this chapter on database design
•
Applications design focuses on the programs and
interfaces that access the database
ƒ To design the conceptual schema for a database application
XML-databases – new, first commercial products
appearing.
ƒ Generally considered part of software engineering
49
49
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Over-view of Data-base Design Process
50
50
Course goals (1)
•
Understand the important concepts within databases and
database terminology
•
Design a database for a given application
•
Design and use a relational database
ƒ
ƒ
ƒ
ƒ
ƒ
augusti 2008
51
51
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Theoretical foundations behind relational databases
ƒ
ƒ
ƒ
•
52
Course goals (3)
•
Relational algebra
How these have impact on database implementation (Only TDDB38)
Query optimisation (Only TDDB38)
Understand how databases can support multiple users
ƒ
ƒ
ƒ
ƒ
Understand how the database is stored on the computer
ƒ
ƒ
ƒ
Concept of relations
Use SQL
Use MySQL
Decipher a new relational database system
52
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Course goals (2)
•
augusti 2008
EER-modelling
Basic technology, file structures, indexing
Impact on database performance
B-Trees, Hashing (Only TDDB38)
•
What problems occur
Views
Transactions
Serialisation (only TDDB38)
Understand how persistency can be guaranteed. (only
TDDB38)
ƒ Recovery
augusti 2008
53
53
augusti 2008
54
54
9
Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Course overview – Part1
•
Introduction (Lena)
•
The Relational Model and SQL (He)
•
ER-modelling (He)
•
EER and mapping ER/EER to relational, Intro to transactions (José)
ƒ
ƒ
ƒ
•
•
Lab1: SQL-queries and view
Lab2: Database Design and ER/modeling
Start with modeling part of the mini project!
Functional dependencies and normalization (José)
ƒ
Course overview - Part 2
•
Mini-project
•
Transactions and Concurrency Control (Patrick)
•
Database Recovery (NOT TDDI60) (Patrick)
•
Data structures for databases (He)
•
Data Structures for Databases II (He)
•
Query Processing and Optimization (Lena)
•
Summary and Research (Lena)
Lab3: Normalization
SQLPSM, triggers and stored procedures (José)
ƒ
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Lab4: Stored Procedures
55
55
augusti 2008
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Databases
56
56
DWIS – Databases and web
information systems
User 4
Real World
Model
Database
Database
management
system
Updates
UserQueries
3 Answers
Updates
UserQueries
2 Answers
UserQueries
1 Answers
Updates
Updates Queries Answers
Processing of
queries and updates
Access to stored data
Physical
database
augusti 2008
58
58
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Issues addressed
1. How is web data represented and
modelled?
Internet
2. How can the data be efficiently stored
and accessed?
3. How can we help a user to explore the
data?
augusti 2008
60
60
10
Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Available XML standards ….
Name
augusti 2008
Ver.
Year
Defined by
Purpose
Tools
Data
A computer-readable
format for representing
models of biochemical
reaction networks.
A standard for data
representation for proteinprotein interaction to
facilitate data comparison,
exchange and verification.
A collaborative effort to
create a data exchange
format for biological
pathway data.
Support the definition of
models of cellular and
subcellular processes.
Many tools available.
Data available from
many databases, for
instance, KEGG
and Reactome.
Datasets available
from many sources,
for instace IntAct,
DIP and MINT.
Interchange of chemical
information over the
Internet and other
networks.
More stability and finegrained modelling of
nucleotide sequence
information.
The purpose of INSDSeq is
to provide a near-uniform
representation for sequence
records.
NCBI uses ASN.1 for the
storage and retrieval of
data such as nucleotide and
protein sequences. Data
encoded in ASN.1 can be
transferred to XML.
Facilitate the interchange
of data for more efficient
communication within the
life sciences community.
A proteomics-oriented
markup language for
exchanging proteome data
between researchers.
SBML
2
2003
Systems Biology
Workbench
development group.
PSI MI
2.5
2005
Proteomics
Standards
Initiative.
BioPAX
2
2005
The BioPAX
group.
CellML
1.1
2002
CML
2.2
2003
University of
Auckland and
Physiome Sciences,
Inc.
Peter Murray-Rust,
Henry S. Rzepa.
EMBLxml
1.0
2005
EBI.
INSDseq
1.4
2005
Seqentry
n/a
International
Nucleotide
Sequence Database
Collaboration.
NCBI.
BSML
3.1
2002
Labbook.com.
HUP-ML
0.8
2003
JHUPO.
n/a
61
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Tools for viewing and
analysis.
Existing tools for OWL
such as Protégé.
Datasets available
from Reactome.
Tools for publication,
visualization, creation
and simulation.
CellML Model
Repository (~240
models).
Molecular browsers,
editors.
BioCYC.
API support in
BioJavaX.
EMBL.
API support in
BioJavaX.
EMBL, DBJ and
GenBank.
SRI's BioWarehouse and
ProteinStructureFactory's
ORFer.
Entrez.
Labbook's Genomic
Browser and Sequence
Viewer. Converters.
Previously
provided by
EMBL.
augusti 2008
Metabolism,
toxicology
Disease
models
63
What strategy to use?
474
1
16
25
48
1233
64
204
360
329
626
54186
831
1261
2165
2551
64574
Relational databases and XML
<model id="Tyson1991CellModel_6"
name="Tyson1991_CellCycle_6var">
<listOfSpecies>
+ <species id="C2" name="cdc2k" compartment="cell">
+ <species id="M" name="p-cyclin_cdc2" compartment="cell">
+ <species id="YP" name="p-cyclin" compartment="cell"> …
</listOfSpecies>
<listOfReactions>
<reaction id="Reaction1" name="cyclin_cdc2k dissociation">
<annotation>
<rdf:li rdf:resource="http://www.reactome.org/#REACT_6308"/>
<rdf:li
rdf:resource="http://www.geneontology.org/#GO:0000079"/>
</annotation>
<listOfReactants>
<speciesReference species="M"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="C2"/>
<speciesReference species="YP"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply> <times/> <ci> k6 </ci> <ci> M </ci> </apply></math>
<listOfParameters> <parameter id="k6" value="1“>
</listOfParameters>
</kineticLaw>
</reaction>
+ <reaction id="Reaction2" name="cdc2k phosphorylation">
... more reactions
</listOfReactions>
</model>
</sbml>
Clinical
trials
DISCOVERY
62
62
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
63
4
145
146
202
1690
immune response
i- acute-phase response
i- Allergic Response
i- anaphylaxis
i- Antigen Processing and Presentation
i- antigen presentation
i- antigen processing
i- cellular defense response
i- Complement Signaling
synonym complement activation
i- Cytokine Response
i- cytokine metabolism
i- cytokine biosynthesis
synonym cytokine production
…
p- regulation of cytokine_biosynthesis
…
…
i- B-cell activation
i- B-cell differentiation
i- B-cell proliferation
i- cellular defense response
…
i- T-cell activation
i- Natural Killer Cell Response
i- activation of natural killer cell activity
…
is-a relation
61
Target
structure
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
The New Ontology
Immune Response
i- Allergic Response
i- Antigen Processing and Presentation
i- B Cell Activation
i- B Cell Development
i- Complement Signaling
synonym complement activation
i- Cytokine Response
i- Immune Suppression
i- Inflammation
i- Intestinal Immunity
i- Leukotriene Response
i- Leukotriene Metabolism
i- Natural Killer Cell Response
i- T Cell Activation
i- T Cell Development
i- T Cell Selection in Thymus
HUP-ML Editor.
Chemical
structure
augusti 2008
SIGNAL-ONTOLOGY (SigO)
immune response
i- acute-phase response
i- anaphylaxis
i- antigen presentation
i- antigen processing
i- cellular defense response
i- cytokine metabolism
i- cytokine biosynthesis
synonym cytokine production
…
p- regulation of cytokine
biosynthesis
…
…
i- B-cell activation
i- B-cell differentiation
i- B-cell proliferation
i- cellular defense response
…
i- T-cell activation
i- activation of natural killer
cell activity
…
equivalent relations
Which?
Where?
How?
Disease
information
GENE ONTOLOGY (GO)
equivalent concepts
Information integration
Genomics
Ontology alignment
augusti 2008
Id
Name
C2
Compartment
cdc2k
cell
M
p-cyclin_cdc2
cell
YP
….
p-cyclin
….
cell
….
Id
Reaction1
Name
cyclin_cdc2k dissociation
Annotation
<annotation …..>
Formula
<kinetic_law …..>
Reaction2
cdc2k phosphorylation
<annotation ….>
<kinetic_law ….>
….
….
….
….
Id
Reaction1
Reaction2
….
Species
M
….
….
When the relational model works
well:
XML
Rel
SBML
3,2 M
1,9 M
PSI MI
31 M
9,1 M
64
64
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Integration of data:
• Can people benefit from each others
work?
63
390
719
1360
101438
509591 221705 2318 1154
Can we create tools that aid the user
in good database design for XML?
augusti 2008
65
65
augusti 2008
66
66
11
Responsible:
2000-01-26
Lena Strömbäck
lestr@ida.liu.se
IISLAB
IDA
Questions?
augusti 2008
67
67
12