pypath-omnipath 0.16.17

OmniPath

Are you interested in OmniPath data? Check out our R package OmnipathR, the most popular and most versatile access point to OmniPath, a database built from more than 150 original resources. If you use Python and don’t need to build the database yourself, try our Python client. Read more about the web service here.

Do you need pypath?

Pypath is the database builder of OmniPath. For most people the data distributed in OmniPath is satisfying (see above), they don’t really need pypath. Typically you need pypath to:

• Build a custom or very fresh version of the OmniPath database(s)

• Use one of the utilities such as ID translation, homology translation, etc. (see the utils module)

• Access the raw or preprocessed data directly from the original resources (see the inputs module)

Installation

From PyPI:

pip install pypath-omnipath

From Git:

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

Docs

Read the reference documentation or check out the tutorials. The most comprehensive guide to pypath is The Pypath Book.

Get help

Should you have a question or experiencing an issue, please write us by the Github issues page.

Features

pypath is a Python module for processing molecular biology data resources, combining them into databases and providing a versatile interface in Python as well as exporting the data for access through other platforms such as R, web service, Cytoscape and BEL (Biological Expression Language).

pypath provides access to more than 100 resources! It builds 5 major combined databases and within these we can distinguish different datasets. The 5 major databases are interactions (molecular interaction network or pathways), enzyme-substrate relationships, protein complexes, molecular annotations (functional roles, localizations, and more) and inter-cellular communication roles.

pypath consists of a number of submodules and each of them again contains a number of submodules. Overall pypath consists of around 100 modules. The most important higher level submodules:

• pypath.core: contains the database classes e.g. network, complex, annotations, etc

• pypath.inputs: contains the resource specific methods which directly downlad and preprocess data from the original sources

• pypath.omnipath: higher level applications, e.g. a database manager, a web server

• pypath.utils: stand alone useful utilities, e.g. identifier translator, Gene Ontology processor, BioPax processor, etc

from pypath import omnipath
op = omnipath.db.get_db('omnipath')

from pypath.utils import mapping
mapping.map_name('P00533', 'uniprot', 'genesymbol')
# {'EGFR'}

from pypath.utils import homology
homology.translate('P00533', 10090) # translating the human EGFR to mouse
# ['Q01279'] # it returns the mouse Egfr UniProt AC

FAQ

Does it run on my old Python?

Most likely it doesn’t. The oldest supported version, currently 3.9, is defined in our pyproject.toml.

Is there something similar in R?

OmniPath’s R client, besides accessing data from OmniPath, provides many similar services as pypath: ID translation, homology translation, taxonomy support, GO support, and many more.

Questions about OmniPath

Contact

We prefer to keep all communication within the Github issues. About private or sensitive matters feel free to contact us by omnipathdb@gmail.com.

Impressum

The development of pypath is coordinated by Dénes Türei in the Saez Lab, with the contribution of developers and scientists from other groups:

• Erva Ulusoy, Melih Darcan, Ömer Kaan Vural, Tennur Kılıç, Elif Çevrim, Bünyamin Şen, Atabey Ünlü and Mert Ergün in the HU Biological Data Science Lab (PI: Tunca Doğan) created many new input modules in pypath;

• Leila Gul, Dezső Módos, Márton Ölbei and Tamás Korcsmáros in the Korcsmaros Lab contributed to the overall design of OmniPath, the design and implementation of the intercellular communication database, and with various case studies and tutorials;

• Michael Klein from the group of Fabian Theis developed the Python client for the OmniPath web service;

• Charles Tapley Hoyt and Daniel Domingo-Fernández added the BEL export module.

• From the Saez Lab, Olga Ivanova introduced the resource manager in pypath, Sophia Müller-Dott added the CollecTRI gene regulatory network, while Nicolàs Palacio, Sebastian Lobentanzer and Ahmet Rifaioglu have done various maintenance and refactoring works. Aurelien Dugourd and Christina Schmidt helped with the design of the metabolomics related datasets and services.

• The R package and the Cytoscape app are developed and maintained by Francesco Ceccarelli, Attila Gábor, Alberto Valdeolivas, Dénes Türei and Nicolàs Palacio;

• The first logo of OmniPath has been designed by Jakob Wirbel (Saez Lab), the current logo by Dénes Türei, while the cover graphics for Nature Methods is the work of Spencer Phillips from EMBL-EBI.

History and releases

See here a bird eye view of pypath’s development history. For more details about recent developments see the Github releases.