BSc HONS DEGREE IN INFORMATICS

BIOINFORMATICS PRESENTATION(2024)
Tittle: Object-Oriented Databases and Their Application in Bioinformatics
GROUP MEMBERS
1. Nyabunze Praise N02132436W
2. Tsoka Esther N02133254J
3. Shonhai Sylvia N02128909Q
4. Chipara Ishewatida N02134275p
5. Nyahuku Tatenda N02127339A
6. Mukora Vallerie N02133319X
7. Mugaragumbo Devone N02160104H
 Introduction to Databases
What is a Database?
•A structured collection of data stored electronically for easy access.

Everyday Example:
Imagine a phone book, where each page has a list of names, phone numbers, and addresses. A
database organizes data in a similar way, making it easy to find information.
Types of Databases

• Relational Databases:
Organize data in tables (like a spreadsheet with rows and columns).

• Object-Oriented Databases (OODBs):

Organize data as "objects," like items in real life (e.g., a person, a book).

Example: In a relational database, a person would be stored in a table with columns for name, age,
and job. In an OODB, a person is stored as an “object” with all this information linked together.
What are Object-Oriented Databases (OODBs)?

Definition: OODBs store data as objects, which are digital versions of real-world items.

How It’s Different: OODBs organize data more like real life, making it useful for complex relationships.

Example: Imagine a "Patient" object with information like name, age, medical history, and current medications.
All these details are stored together as one object instead of separate pieces.

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Key Features of Object-Oriented Databases
• Object Identity: Each object is unique, like a patient ID that identifies a specific person.

• Complex Objects: Stores data with many parts.

Example: A "Gene Sequence" object might include details about the DNA sequence, associated proteins, and
functions.

• Inheritance: Allows similar data to share common features.

Example: A “Human” and a “Mammal” object could share characteristics like “cells” and “DNA structure.”

• Encapsulation: Keeps data organized by storing it all in one place.

• Polymorphism: Allows different objects to work together.

Example: A “Doctor” and a “Patient” object can both interact within the same system.
Architecture of Object-Oriented Databases

•Schemas and Instances:

A schema is like a template, defining what kind of information an object holds (e.g., a patient’s medical details).
An instance is a specific example, like an individual patient’s record.

• Query Language (OQL):

Used to search and retrieve data from OODBs, similar to asking specific questions about the data stored.
Advantages of Object-Oriented Databases

1. Better for Complex Data: Can handle large and interconnected information.
Example: In bioinformatics, an OODB can store entire protein structures, including each protein’s shape, function,
and relationships.

2. Flexibility: Easily adapt to changes, making it ideal for research.

Example: Adding new details to a gene sequence record, such as new findings about mutations.

3. Integration with Software: Works well with programming languages, making them ideal for software that deals
with complex data.
Disadvantages of Object-Oriented Databases
1. Complex to Design and Maintain: More complex than traditional databases.
Example: Setting up an OODB for a hospital’s patient records takes more time and expertise than a basic table.

2. Limited Standardization: Fewer tools available for OODBs compared to relational databases.

3. Compatibility Issues: Harder to connect with other database types.

Example: Integrating an OODB with a hospital’s existing patient database could require specialized software.
Comparison with Relational Databases (RDBMS)

1)

RDBMS: Organizes data in tables with rows and columns, like a spreadsheet.

Example: A table for “Patients” where each row is a patient and columns represent details like name, age, and diagnosis.

OODBs: Organizes data as objects with more detailed relationships.

Example: A "Patient" object linked to "Medical History," "Medications," and "Doctor" objects.

2)

RDBMS: Simple, structured data (e.g., a list of customers).

OODBs: Complex, interconnected data (e.g., biological data in bioinformatics).

Explanation
1. Data Representation:
OODM: Organizes data as objects, similar to object-oriented programming. Each entity (like a customer or
address) is an object with properties and can reference other objects directly.
RDM: Uses tables to represent data. Each entity (like customers, addresses, and bank accounts) is stored in a
separate table, with rows for each instance and columns for properties.
2. Relationships:
OODM: Relationships are represented by direct links between objects. In this example, the "Customer" object
has direct references to its "BankAccount" and "Address" objects.
RDM: Relationships are represented by foreign keys that link rows across tables. For instance, the "Addresses"
and "BankAccounts" tables reference the "Customers" table through the customer ID (CID) column.
3. Data Access:
OODM: Accessing related data is straightforward as objects directly reference other objects. This makes
navigating complex relationships intuitive.
RDM: Accessing related data requires joining tables based on foreign keys, which can become complex for
queries with many relationships.
Explanation continued......
4. Structure:
OODM: The structure is more flexible, allowing objects to contain nested or associated objects naturally.
RDM: The structure is tabular, with relationships normalized across tables to avoid redundancy, following a
structured schema.
5. Use Cases:
OODM: Suited for applications with complex data models where objects and their relationships are key, such as
CAD/CAM systems, real-time simulations, and object-oriented programming integration.
RDM: Ideal for applications needing strong consistency, atomic transactions, and standard query capabilities,
like business data processing (e.g., banking, e-commerce).
The main difference lies in how data and relationships are managed: OODM provides a more natural
representation of interconnected objects, while RDM emphasizes structure, consistency, and relational
querying.
Applications of OODBs in Bioinformatics
•Data Modeling for Biological Data: Supports complex structures like DNA, proteins, and genomes.
Example: A "Gene" object could store details like its sequence, function, and associated diseases.

•Genomic and Proteomic Data Storage: Suitable for storing entire genomes and proteins.
Example: Store detailed models of proteins, including each component’s shape and chemical properties.

•Efficient for Large Datasets: Handles large, complex data sets, ideal for research data.
Examples of Object-Oriented Databases and Tools

•Popular OODBMS:
db4o, ObjectDB, ZODB

•Bioinformatics-Specific Use:
Applications or research databases that manage complex genetic or protein information using OODBs.
ZODB
ZODB is a Python-specific OODBMS allowing direct storage of Python objects.

Key features:
Seamless Python integration
Transparent persistence
Complex object support
ACID transactions
Pluggable storage options

ZODB is well-suited for applications with complex data structures and frequent reads.
ObjectDB
ObjectDB is a high-performance OODBMS for Java applications.

Key features:
Native Java support
JPA compliance
Cache-based storage
ACID compliance
Scalability (vertical and horizontal)

ObjectDB is ideal for Java-centric organizations dealing with complex data models and
high-concurrency environments.
Real-World Examples in Bioinformatics

•Bioinformatics Databases: OODBs used in storing complex biological relationships.

•Workflow Example: Diagram showing how a "Protein Structure" object connects to related objects like "DNA
Sequence" and "Function".
Future of Object-Oriented Databases in Bioinformatics

•Trends: More bioinformatics applications are adopting OODBs.

•Emerging Applications: Useful for AI and complex modeling in biological research.

•Future Enhancements: Expected to improve storage and analysis for growing biological datasets.
Summary of Key Points

•Object-Oriented Databases: Ideal for storing complex, real-life data.

•Key Benefits in Bioinformatics: Allows for detailed, interconnected data storage.
•Comparison with RDBMS: OODBs suit complex data better, but are more complex to design.
 QUESTIONS AND ANSWERS
1. How does an Object-Oriented Database improve data handling for complex bioinformatics data
compared to a Relational Database?
An OODB allows complex data, like proteins, genes, and diseases, to be represented as
interconnected objects with attributes and methods. This structure directly mirrors real-world
relationships and reduces the need for complex joins, making it easier and faster to manage and
query bioinformatics data.

2.What are some challenges you might face when implementing an Object-Oriented Database in a
bioinformatics project?
Challenges include higher initial setup costs, the need for specialized development skills, and
potential compatibility issues with existing relational-based bioinformatics tools and datasets.
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