Skip to main content

Parsing, validation, compilation, and data exchange of Biological Expression Language (BEL)

Project description

PyBEL is a pure Python package for parsing and handling biological networks encoded in the Biological Expression Language (BEL). It also facilitates data interchange between common formats and databases such as NetworkX, JSON, CSV, SIF, Cytoscape, CX, NDEx, SQL, and Neo4J.

Its companion package, PyBEL Tools, contains a suite of functions and pipelines for analyzing the resulting biological networks.

We realize there we have a name conflict with the python wrapper for the cheminformatics package, OpenBabel. If you’re looking for their python wrapper, see here.

Citation

If you find PyBEL useful for your work, please consider citing:

Getting Started

This example illustrates how the Selventa Small Corpus can be loaded.

>>> import pybel
>>> graph = pybel.from_url('http://resources.openbel.org/belframework/20150611/knowledge/small_corpus.bel')
>>> graph.number_of_nodes()  # Will be smaller than expected because we have the most strict settings enabled
1207

More examples can be found in the documentation and in the PyBEL Notebooks repository.

PyBEL also installs a command line interface with the command pybel for simple utilities such as data conversion. In this example, a BEL document is compiled then exported to GraphML for viewing in Cytoscape.

$ pybel compile ~/Desktop/example.bel
$ pybel serialize ~/Desktop/example.bel --graphml ~/Desktop/example.graphml

In Cytoscape, open with Import > Network > From File.

Installation Current version on PyPI Stable Supported Python Versions Apache 2.0 License

PyBEL can be installed easily from PyPI with the following code in your favorite terminal:

$ pip install pybel

or from the latest code on GitHub with:

$ pip install git+https://github.com/pybel/pybel.git

See the installation documentation for more advanced instructions. Also, check the change log at CHANGELOG.rst.

Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.rst for more information on getting involved. Please add your name to AUTHORS.rst!

Acknowledgements

Project details


Release history Release notifications | RSS feed

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pybel-0.13.1.tar.gz (327.6 kB view details)

Uploaded Source

Built Distribution

pybel-0.13.1-py3-none-any.whl (295.3 kB view details)

Uploaded Python 3

File details

Details for the file pybel-0.13.1.tar.gz.

File metadata

  • Download URL: pybel-0.13.1.tar.gz
  • Upload date:
  • Size: 327.6 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.12.1 pkginfo/1.4.2 requests/2.21.0 setuptools/40.6.3 requests-toolbelt/0.8.0 tqdm/4.29.0 CPython/3.7.0

File hashes

Hashes for pybel-0.13.1.tar.gz
Algorithm Hash digest
SHA256 eb71effcfc92fa541a5104db1b59c6de11b030f2aa09e26664b3932eff5d00f7
MD5 f8974caeccdba3c02851ba20cc9a6fd0
BLAKE2b-256 58c3319362a7313499299f8290e003fc533213e8c34776b9f175ba24ab7463c2

See more details on using hashes here.

Provenance

File details

Details for the file pybel-0.13.1-py3-none-any.whl.

File metadata

  • Download URL: pybel-0.13.1-py3-none-any.whl
  • Upload date:
  • Size: 295.3 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.12.1 pkginfo/1.4.2 requests/2.21.0 setuptools/40.6.3 requests-toolbelt/0.8.0 tqdm/4.29.0 CPython/3.7.0

File hashes

Hashes for pybel-0.13.1-py3-none-any.whl
Algorithm Hash digest
SHA256 aea36a3cc92f628c25ab68116133bafa379bfdcc8da4a27beb9c4ba95f0122ce
MD5 63813c7a59b4b33239f0df262d0b0b30
BLAKE2b-256 c2a1cedc46922d1b221d32f7091816bf71e599096ec6455ccc3e891e5f7440e3

See more details on using hashes here.

Provenance

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page