OmniPath: literature curated human signaling pathways

data code install tutorials documentation article contact

Welcome to the home of OmniPath, a comprehensive collection of literature curated human signaling pathways. And pypath, a powerful Python module for molecular networks and pathways analysis.

Illustration by Spencer Phillips, EMBL-EBI. This cover artwork is the result of a collaboration between Spencer Phillips, Mary Todd-Bergman, Denes Turei, Tamas Korcsmaros and Julio Saez-Rodriguez, starting with the initial idea of using lenses by Jakob Wirbel (RWTH-Aachen). A modified version of this figure appeared in the Cover of Nature Methods Dec 2016

The article

click here for the paper

D Turei, T Korcsmaros and J Saez-Rodriguez (2016) OmniPath: guidelines and gateway for literature-curated signaling pathway resources. Nature Methods 13(12)

PMID: 27898060

How to access the data?

OmniPath data is available via a webservice. See example queries here.

What you can do with pypath?

pypath is a Python module for building molecular interaction networks. It is able to combine multiple resources, process custom files, and convert between different identifiers. Undirected and directed networks are supported. Once the network is constructed, you can load additional annotations and perform analysis tasks. A large collection of these are already included in pypath. Thanks to the flexibility and power of Python, you can handle and process many ways your network.

pypath code

Pypath is available under GPLv3 license. For the git repository, click here.

Forks, pull requests, bug reports and feature requests are welcome!

Installation

Linux:

pip install git+git://github.com/saezlab/pypath.git

OS X: Installation on Mac might be challenging, mainly because of cairo. Follow the scripts below, go step-by-step and watch out for errors. We tested these methods on several computers, but every system is different. We appreciate if you report any error you experience, and we will do our best to find a solution. Please contact omnipath@googlegroups.com.

pypath documentation

For the reference documentation of the pypath module click here.

Metainformation about signaling pathway resources

Find here a comprehensive list of signaling pathway resources.

Tutorials

Pypath allows to access and integrate dozens of bioinformatics resources in an easy way. Using the capabilities of Python you can handle them with a lot of flexibility. Just pop up a Python shell, and type:

import pypath

pa = pypath.PyPath()

pa.load_omnipath()

Check out our tutorials:

Quick start

Introduction (directions, enzyme-substrate, subnetworks)

ID conversion

Pathway annotations

Extracting signaling networks

Finding transcription factors

Special thanks for Luis Tobalina for providing some of the tutorials.

Miscellanous

OmniPath in meta-databases

OmniPath press releases

Contributing groups

Papers citing OmniPath



Dénes Türei, 2017. Feedback: omnipath@googlegroups.com

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