Welcome to the home of OmniPath, a comprehensive collection of literature curated human and rodent signaling pathways and other database prior knowledge. And pypath, a powerful Python module for molecular networks and pathways analysis and prior knowledge processing.
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
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 .
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
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
OmniPath is available via a web service, an R package , 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.
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 is available under GPLv3 license from. this git repository.
Forks, pull requests, bug reports and feature requests are welcome!
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.
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 email@example.com.
For the reference documentation of the pypath module click here.
Find here a comprehensive list of signaling pathway resources.
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:
Drug target lookup with OmnipathR
Special thanks for Luis Tobalina for providing some of the tutorials.
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 us with private messages at firstname.lastname@example.org. If you have a question or issue which might be of public interest please open an issue on github .
Dénes Türei, Nicolàs Palacio, Olga Ivanova, Saez Lab 2016-2020. Feedback: email@example.com