PDBe API Training

These interactive Python notebooks will guide you through various ways of programmatically accessing Protein Data Bank in Europe (PDBe) and Knowledge Bank (PDBe-KB) data using REST API

The REST API is a programmatic way to obtain information from the PDB and EMDB. You can access details about:

  • sample

  • experiment

  • models

  • compounds

  • cross-references

  • publications

  • quality

  • assemblies and more…

For more information, visit https://www.ebi.ac.uk/pdbe/pdbe-rest-api.

Recently we introduced a novel REST API that takes advantage of graph database Neo4J. This API contains a lot more value added annotations from PDBe and partner resources and is available from: https://www.ebi.ac.uk/pdbe/graph-api/pdbe_doc/

Getting Started

Either use Binder to use the notebooks:

Binder

Or

You will need to have Jupyter installed on your machine. For Linux/OSX machines, simply type:

pip3 install --upgrade pip
pip3 install jupyter

For Windows machines (optionally also for Linux/OSX) you can install Jupyter with Anaconda: https://www.anaconda.com/download/

Prerequisites

If installing using Anaconda, there is no additional prerequisites. If installing using pip3, you will need to have Python3 on your machine, and of course pip3

Installing

From command line on Unix machine these would be the steps setting up everyone:

mkdir pdbe_jupyter
cd pdbe_jupyter
git clone https://github.com/PDBeurope/pdbe-api-training .
jupyter notebook

Jupyter Notebook will open a window in your browser, and you can select the specific notebooks you would like to view.

Authors

  • Mihaly Varadi - Initial work - mvaradi

Acknowledgments

  • Thanks to the PDBe team for suggestions during creating these materials