omnipath

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Python client for the OmniPath web service

Installation

You can install omnipath by running::

pip install omnipath

The OmniPath database

OmniPath is a database of:

• Protein-protein, TF target and miRNA-mRNA interactions
• Enzyme-PTM relationships
• Protein complexes
• Annotations of protein function, structure, localization, expression
• Intercellular communication roles of proteins

To learn more about OmniPath, you can visit its website, or read our recent preprint or our first paper from 2016, especially its supplementary material.

The Python client

The data is available through a web service hosted on this website_. This repository hosts a Python package for querying this web service and downloading data into data frames or dictionaries.

The Python package for OmniPath is pypath, isn't it?

pypath_ is a tool for building the OmniPath databases in a fully customizable way. We recommend to use pypath if you want to:

• Tailor the database building to your needs
• Include resources not available in the public web service
• Use the rich Python APIs available for the database objects
• Make sure the data from the original sources is the most up-to-date
• Use the methods in pypath.inputs to download data from resources
• Use the various extra tools in pypath.utils, e.g. for identifier translation, homology translation, querying Gene Ontology, working with protein sequences, processing BioPAX, etc.

Is there an R client?

Yes there is. The R/Bioconductor package OmnipathR you may find on GitHub <https://github.com/saezlab/OmnipathR>_ or in Bioconductor <http://bioconductor.org/packages/3.12/bioc/html/OmnipathR.html>_. The R client currently supports all features of the web service.

Cytoscape

We even have a Cytoscape plug-in_. With the plug-in you are able to load networks into Cytoscape and access certain (not all) annotations of the proteins.

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.. _website : https://omnipathdb.org/ .. _Cytoscape plug-in : https://apps.cytoscape.org/apps/omnipath .. _pypath : https://github.com/saezlab/pypath .. _preprint : https://www.biorxiv.org/content/10.1101/2020.08.03.221242v2 .. _paper from 2016 : https://www.nature.com/articles/nmeth.4077 .. _supplementary material : https://static-content.springer.com/esm/art%3A10.1038%2Fnmeth.4077/MediaObjects/41592_2016_BFnmeth4077_MOESM495_ESM.pdf