OmniPath: literature curated
mammalian signaling pathways

article data code install tutorials documentation help contact

Welcome to the home of OmniPath, a comprehensive collection of molecular biology prior knowledge from 103 databases, with focus on literature curated human and rodent signaling pathways.

OmniPath is available via a web service, an R package, a Cytoscape plug-in (paper) and a Python module.

We also provide a large variety of software to analyze and integrate this prior knowledge. The pypath Python module builds the database segments in OmniPath and provides the most versatile API supported by many stand alone utilities. Saez Lab offers a software suite for functional omics data analysis and mechanistic modeling of intra- and inter-cellular signaling, find more details at saezlab.org .

New: combined metabolic and signaling network in MetaPKN – By Aurelien Dugourd. Available at https://metapkn.omnipathdb.org/ .

New: our paper about the OmniPath Cytoscape app F Ceccarelli, D Turei, A Gabor, J Saez-Rodriguez (2020) Bringing Data From Curated Pathway Resources to Cytoscape With OmniPath. Bioinformatics 36 (1).

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

Tweets by omnipathdb

What's new?

Since our last paper we added quite some new resources and features. Most importantly we largely extended the scope of the prior knowledge we cover, including annotations about protein functions and localizations, protein complexes and a comprehensive classification of protein roles in inter-cellular communication. Overall we build OmniPath using more than 115 databases. We also added homology translation to mouse and rat, transcriptional regulation from DoRothEA and other databases, miRNA-mRNA interactions, a number of ligand-receptor databases, improved processing of enzyme-substrate interactions and Gene Ontology, many other things. We even got a Cytoscape plug-in thanks to Francesco Ceccarelli . With Nicolàs Palacio and Olga Ivanova we improve pypath code quality, documentation and tests. On the figure below you can see the new parts highlighted by violet. Almost every couple of weeks we add new ones, stay tuned and follow our Twitter!

Overview of resources in pypath and OmniPath. New additions since Nov 2016 highlighted in violet. Expanded from Fig 1 of Turei et al. Nature Methods (2016). For high resolution PDF click here .

OmniPath publications

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

click here for the general paper

F Ceccarelli, D Turei, A Gabor, J Saez-Rodriguez (2020) Bringing Data From Curated Pathway Resources to Cytoscape With OmniPath. Bioinformatics 36 (1) PMID: 31886476

click here for the Cytoscape app paper

How to access the data?

OmniPath is available via a web service, an R package ( website ), a Cytoscape plug-in and a Python module . For the web service see example queries here.

For old versions of the web service content see the archive .

In the webservice you can access not only OmniPath but also TF-gene interactions from DoRothEA . See example queries in the readme at the DoRothEA git repo. The web service provides 5 main query types: interactions, enzyme-substrate relationships, protein complexes, annotations and inter-cellular communication roles. Here you can see examples for all of these query types.

What you can do with pypath?

pypath is a Python module which builds all of the five main database segments of OmniPath: the network, the enzyme-substrate relationships, the protein complexes, the annotations and the inter-cellular communication roles. If you use pypath instead of the web service you will be able (1) to customize the databases and (2) to access the data by a versatile and flexible API. In addition pypath provides many utility modules for example to convert between different identifiers, work with Gene Ontology, and many more.

pypath code

Pypath is available under GPLv3 license from. this git repository.

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

Installation

New: Since the beginning of 2020 igraph and cairo are not mandatory dependencies of pypath which makes the installation process much easier on Mac. We will updates the guides below soon.

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

New: Since the beginning of 2020 pypath has a new API for the network database. This new API is in "beta" phase at the moment and not covered yet in the Pypath Guide but we will include it soon.

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:

from pypath import network

op = network.Network.omnipath()

Check out our tutorials:

Comprehensive guide

Drug target lookup with OmnipathR

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

Help

If you have a question or experiencing issues with the data or pypath please open an issue in the git repo of pypath . We closed our support channel in Google Groups to eliminate the redundancy with the issues on github. If you have a private message which is not of public interest you can send us an email to the address below.

Contact

Contact us with private messages at omnipathdb@gmail.com. If you have a question or issue which might be of public interest please open an issue on github .

Miscellanous

OmniPath in meta-databases

OmniPath press releases

Contributing groups

Papers citing OmniPath



Dénes Türei, Nicolàs Palacio, Olga Ivanova, Saez Lab 2016-2020. Feedback: omnipathdb@gmail.com

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