johnymcb / biological_databases_api

An introduction to Biological Databases and how the API can be used to access data

Introduction to Biological databases and APIs

Introduction

Genomic research data generated by researchers has grown exponentially over the years. Often, a bioinformatics project would utilize a massive amount of data from a variety of databases. Data from these biological databases can be accessed over the web but can be time-consuming when dealing with huge data. In this session, we will briefly introduce biological databases, how to access the data programmatically, and how to submit sequences to GenBank.

This session assumes prior introduction to Biological databases. However, if this is all new to you, have a look at this presentation content developed by Etienne de Villiers.

Competencies

In this short course, we intend to impart knowledge and skills in the following competencies (See ISCB Competencies):

1. Knowledge and skills: Bioinformatics tools and their usage.
2. Knowledge and Skills: Command line and scripting based computing skills appropriate to the discipline.
3. Knowledge and skills: Data management

Learning Objectives

To attain the above competencies, the workshop participants should be able to:

1. Identify important Biological databases
2. Understand the different ways of accessing biological data and choose the best means of acquiring the data
3. Know how to use APIs to download Biological data

Learning Outcomes

From the above objectives, the workshop participant should acquire the following skills;

1. Be able to download data using APIs
2. Be prepared to submit sequence data to NCBI

Instructors

• Caleb Kibet
• Jean-Baka