OmniPath

This package is a Python equivalent of an R package OmnipathR for accessing web service of OmniPath database developed by Saezlab.

Installation

Omnipath requires Python version >= 3.7 to run.

PyPI

Omnipath is also available on PyPI:

pip install omnipath

Additionally, omnipath may sometimes require networkx to create an interaction graph. This dependency can be installed as:

pip install omnipath[graph]

Development Version

To stay up-to-date with the newest version, run:

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

API

Import Omnipath as:

import omnipath as op

Requests

requests.Annotations()	Request annotations from [OmniPath].
requests.Complexes()	Request information about protein complexes from [OmniPath].
requests.Enzsub()	Request enzyme-substrate relationships from [OmniPath].
requests.Intercell()	Request intercell annotations from [OmniPath].
requests.SignedPTMs()	Request enzyme-substrate relationships and interactions from [OmniPath].

Interactions

interactions.AllInteractions([include, exclude])	Request all [OmniPath] interaction datasets.
interactions.Dorothea()	Request interactions from the dorothea dataset.
interactions.KinaseExtra()	Request interactions from the kinase extra dataset.
interactions.LigRecExtra()	Request interactions from the ligrec extra dataset.
interactions.OmniPath()	Request interactions from the omnipath dataset.
interactions.PathwayExtra()	Request interactions from the pathway extra dataset.
interactions.PostTranslational([exclude])	Request all post-translational interactions from [OmniPath] .
interactions.TFmiRNA()	Request interactions from the TF-miRNA dataset.
interactions.TFtarget()	Request interactions from the TF-target dataset.
interactions.Transcriptional()	Request all TF-target interactions from [OmniPath].
interactions.lncRNAmRNA()	Request interactions from the lncRNA-mRNA dataset.
interactions.miRNA()	Request interactions from the miRNA-target dataset.
interactions.import_intercell_network([...])	Import intercellular network combining intercellular annotations and protein interactions.

Other

Constants

constants.InteractionDataset(*args, **kw)	Available interaction datasets in [OmniPath].
constants.License(*args, **kw)	License types.
constants.Organism(*args, **kw)	Organism types.

Options

omnipath.clear_cache()	Remove all cached data from omnipath.options.cache.
omnipath.options	Class defining various omnipath options.

Release Notes

Version 1.0

1.0.5 2021-16-08

• Setting omnipath.options.cache to None will now disable it (use 'memory' instead)

• Fix writing empty values into cache

• Fix memory cache not copying data before storing it

• Fix various pandas warnings

• Remove redundant step from CI

1.0.4 2020-27-12

• Fix recursion error

• Remove duplicated PostTranslational class

• Add interactions tests

1.0.3 2020-08-12

• Add omnipath.interactions.PostTranslational

• Add possibility to download all omnipath.requests.Annotations

1.0.2 2020-29-11

• Fix small bug when converting boolean values

• Fix typos

• Add option to create interaction graphs

1.0.1 2020-29-11

• Fix bug of not correctly passing datasets in interactions

• Fix the way the progress bar is getting content size

• Add comparison tests with OmnipathR

1.0.0 2020-23-11

• Fix minor bugs

• Add options improvements

• Add tests

References

[OmniPath]

Türei, D., Valdeolivas, A. et al. (2020),
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis,
bioRxiv 2020.08.03.221242.

[OmniPath16]

Türei, D., Korcsmáros, T. & Saez-Rodriguez, J. (2016),
OmniPath: guidelines and gateway for literature-curated signaling pathway resources.,
Nat Methods 13, 966–967.