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Intro_to_data_base.pdf
1. Introduction To biological
Database System
Zainab Hassan Ali, Lecturer at Faculty of Artificial Intelligence, Kafrelshikh University, Email: zainabhassan@ai.kfs.edu.eg
Academic Year 2022-2023
First Term
Second Level
2. Agenda:
❑Part One: DNA database: Overview.
❑Part Two: Read DAN sequencing by
Python.
❑Part Three: Introduction to Database.
4. *DNA Database: Overview
There are two major components to bioinformatics:
A.Storing and retrieving information about DNA sequencing.
1. Biological databases.
2. Querying these to retrieve data
B. Manipulating the data–tools.
1. Finding features on sequences.
2. Sequence similarity searches. (DNA Alignment)
3. Protein families and function prediction.
4. Comparing sequences.
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5. *DNA Database: Overview
There are three main types of biological databases:
Database Types
Primary Databases Secondary Databases Composite Databases
Archival databases
• It archives the experimental results
submitted by the scientists.
• The data are given accession
numbers when they are entered into
the database.
• Nucleic Acid Databases are GenBank
and DDBJ or Protein database
These types of databases are the
analysed result of the primary database.
Computational algorithms are applied to
the primary database and meaningful and
informative data is stored inside the
secondary database.
Example of DB.
• InterPro (protein families, motifs, and
domains).
• UniProt Knowledgebase (sequence
and functional information on
proteins).
• This type of databases are first
compared and then filtered based on
desired criteria.
• The initial data are taken from the
primary database, and then they are
merged together based on certain
conditions.
• It helps in searching sequences
rapidly.
• Example: OWL, NRD, and
Swissport +TREMBL
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10. *DNA Database: Overview
*GI-Numbers
A GI number (for GenInfo Identifier, sometimes written in
lower case, " gi ") is a simple series of digits that are
assigned consecutively to each sequence record processed
by NCBI. The GI number bears no resemblance to the
Version number of the sequence record. Each time a
sequence record is changed, it is assigned a new GI number.
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13. *Read DNA Sequencing by Python
Open NCBI and search about the following accession number: NP_001318308
Download FASTA format from Graphics link.
Example -3:
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19. 19
* What is the Database? and what is the difference between
Database and Database System?
ID Name Birth
ID Name Birth
Database: Database System:
2
1
*Introduction to Database
20. 20
* What is the Database? and what is the difference between
Database and Database System?
Database: Database System:
2
1
A collection of related data
can be organized into a set of
records and build a
structured table.
A collection of related data
can be organized into a set of
records and build a
structured table into
computer.
*Introduction to Database
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* Database is an structured object can
be divided as metadata and data.
Database
Metadata
Data
❑ Data about Data.
❑ A specific data uses to describe other data.
Is an abstract word when stored in records it
gives descriptive information.
*Introduction to Database
22. 22
*Database properties:
❑ A database describes some aspect of the real world.
❑ A database is a logically coherent collection of data with some inherent
meaning.
❑ A database is designed, built, and populated with data for a specific purpose.
❑ A database can be of any size and of varying complexity.
❑ A database may be generated and maintained manually or by machine.
*Introduction to Database
23. 23
*Recommended reading:
• Silberschatz, A., Korth, H.F. & Sudarshan, S. (2002). Database system concepts.
McGraw-Hill (4th ed.).
Ullman, J. & Widom, J. (1997). A first course in database systems. Prentice Hall.
Date, C.J. (2004). An introduction to database systems. Addison-Wesley (8th ed.).
• Visit website 1:
https://www.ncbi.nlm.nih.gov/
• Visit website 2:
https://app.schoology.com/course/2374966686/materials
Course Code: JRM6-ZTT4-6P298
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B- Solve the Database questions
1. What is meant by the Data and Metadate in computer field?
2. What is relation between Data, information, and knowledge?
3. Write a short note about Database and its applications.
4. In the DB context, define the relation between Data and meta data?
5. List the different properties of the Database?
6. Give some example of the database applications in our daily life?
7. What Is a Database System? list its main items for each write a short note?
A- Write a program using python to read the DNA sequencing from the
following link:
https://www.ncbi.nlm.nih.gov/protein/AXY93794.1?report=graph
*Report:
