Bioinformatics: Data Management

What is a database?

Is a repository of information that has a specific structure that enables enterimg and extracting data.

How is a database structured?

In tables or files, each containing numerous records with data distributed in fields

What are the different database types?

• Flat-file → GenBank

  • The simplest form

  • Large single text files or collection of different text files

• Relational → PFAM

• Object-Oriented

• Data warehouses

• Distributes

Which type of database is specifically used for distributing raw data and can be read by many different programs?

Flat-file databases

What is a key disadvantage of complex databse structures (like relational databases) compared to flat-files?

They often depend on specific, and often expensive, software to be read and analyzed.

What does indexing mean?

In bioinformatics, indexing is the process of creating a separate, optimized data structure (an index) that allows for extremely fast searching and retrieval of specific information from a large, primary dataset.

What is the primary purpose of creating and index for large biological database like GenBank?

To enable fast searching and retrieval of specific records without scanning the entire database.

What is eXtensivle Markup Language (XML)?

Is a general tool for the storage of data and information, it uses plain file format. Data is stored in identifiers, called tabs.

HTML is a type of - and what does it allow to do?

It is a type of XML, and it allows to create webs.

What is a significant advantage of XML databases that makes them a serious alternative to flat-file and relational databases?

Their great flexibility in designing specialized ways to classify data.

Data extraction is similar to relational databases (Xquery language)

Disadvantage?: lower complexity

In a relational database, what is the term for a unique field used to relate one table to another?

A key (or primary key). Data for a key must be unique in each record

How can data from different tables be combined?

Through queries, this allows the extraction of useful data.

What is the main advantage of a relational database over a flat-file database?

The ability to easily extract and combine related data from multiple tables + the consistency of the data.

Relational Databases are built on general or specific programming languages?

Specific

Which language is specifically designed for managing and querying data in a relational database?

SQL (Structured Query Language)

What are the different operators in relational databases?

• Mathematical (+,-,*,/)

• Data handling (queries)

• SQL

What is PFAM?

A relational database that includes a collection of protein domain families.

The process of gathering, cleaning and modeling data to reveal meaningful insights is known as:

Data Analysis

What is the scientific field that uses insights from data analysis to support decision-making processes?

Data Analytics

In the context of biological databases, why is database maintenance critically important?

To ensure data quality and have confidence in the accuracy of the extracted data.

True or false: Flat-file databases are the most efficient structure for complex queries across multiple, related data types.

False: Relational databases are better suited for combinig data from multiple tables with complex queries.

Which database format uses a plain text file with a structured but simple layout, as seen in a GenBank record?

A Flat-file database.