Book Image

Bioinformatics with Python Cookbook

By : Tiago R Antao, Tiago Antao
Book Image

Bioinformatics with Python Cookbook

By: Tiago R Antao, Tiago Antao

Overview of this book

Table of Contents (16 chapters)
Bioinformatics with Python Cookbook
Credits
About the Author
About the Reviewers
www.PacktPub.com
Preface
Index

Geo-referencing GBIF datasets


Here, we will work with the geo-referenced data from the GBIF dataset. We will take this opportunity to see how to interface with OpenStreetMap (https://www.openstreetmap.org), a freely available mapping service. We will also use a Python image processing library called Pillow (http://python-pillow.github.io/, which is based on PIL). You may want to read a little bit on both before starting. Tile Map Services (http://wiki.openstreetmap.org/wiki/TMS) will be quite an important concept to get a basic grasp of. GBIF and OpenStreetMap tiles are available behind REST services.

In our example, we will try to extract information from GBIF using the geographic coordinates of the Galápagos archipelago.

Getting ready

You will need to install Pillow using conda install pillow or pip install pillow. You can find this content in the 07_Other/GBIF_extra.ipynb notebook.

How to do it...

Take a look at the following steps:

  1. First, let's define a function to get a map tile (a PNG image...