omnipath 1.0.12
Python client for the OmniPath web service
Requires Python: >=3.9
Keywords: ARN, Autophagy, BioGRID, BioPAX, CORUM, COSMIC, CPAD, Cancer Gene Census, CancerSEA, Cell Surface Protein Atlas, CellPhoneDB, ComPPI, Compleat, ComplexPortal, DEPOD, DGIdb, DIP, DNA, DisGeNet, DoRothEA, ELM, EMBRACE, Ensembl, Exocarta, GPCRdb, GSEA, Guide to Pharmacology, HGNC, HomoloGene, Human Plasma Membrane Receptome, Human Protein Atlas, ICELLNET, InnateDB, IntAct, IntOGen, KEGG, MPPI, MSigDB, Matrisome, MatrixDB, NCI-PID, NRF2ome, NetPath, ORegAnno, PANTHER, PAZAR, PPI, Phobius, Phosphatome, PhosphoPoint, PhosphoSite, Reactome, SIGNOR, SPIKE, STRING, SignaLink, Surfaceome, TRED, TRRD, TopDB, UniProt, Vesiclepedia, activity flow, adhesion, annotations, cancer, complexes, dephosphorylation, directed graph, disease, gene, gene symbol, iTALK, integrin, intercellular communication, ion channel, kinase, ligand, mRNA, miRNA, mouse, pathway, phosphatase, phospho.ELM, phosphorylation, protein, rat, receptor, regulation, signaling, signaling pathway, subcellular localization, transcription, transporter

|PyPI| |Downloads| |CI| |Docs| |Coverage|

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.

.. |PyPI| image:: https://img.shields.io/pypi/v/omnipath.svg
    :target: https://pypi.org/project/omnipath
    :alt: PyPI

.. |Downloads| image:: https://pepy.tech/badge/omnipath
    :target: https://pepy.tech/project/omnipath
    :alt: Downloads

.. |CI| image:: https://img.shields.io/github/actions/workflow/status/saezlab/omnipath/ci.yml?branch=master
    :target: https://github.com/saezlab/omnipath/actions?query=workflow:CI
    :alt: CI

.. |Coverage| image:: https://codecov.io/gh/saezlab/omnipath/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/saezlab/omnipath
    :alt: Coverage

.. |Docs|  image:: https://img.shields.io/readthedocs/omnipath
    :target: https://omnipath.readthedocs.io/en/latest
    :alt: Documentation

.. _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