Skip to main content
Help the Python Software Foundation raise $60,000 USD by December 31st!  Building the PSF Q4 Fundraiser

A package for generating curation sheets for rationally enriching a BEL graph using INDRA and PyBEL.

Project description

A package for generating curation sheets for rationally enriching a BEL graph.

If you find bel_enrichment useful in your work, please consider citing [1]:

[1]Hoyt, C. T., et al (2019). Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language. Database, Volume 2019, 2019, baz068.

Additionally, this package also heavily builds on INDRA [2] and PyBEL [3].

Installation Current version on PyPI Stable Supported Python Versions License

bel_enrichment can be installed from PyPI with the following command:

$ pip install bel_enrichment

The latest version can be installed from GitHub with:

$ pip install git+https://github.com/bel-enrichment/bel-enrichment.git

You’ll need to set the INDRA_DB_REST_URL and INDRA_DB_REST_API_KEY in the ~/.config/indra/config.ini file. Please contact the INDRA team for credentials.

Rational Enrichment

Generate a folder full of curation sheets based on the given BEL graph that has been pre-compiled by PyBEL. Use --info-cutoff to specify the minimum information density cutoff. 1.0 means that the node has no edges, .5 means one edge, and so on. Use --belief-cutoff to specify the minimum belief score from INDRA for adding the statement to the sheet. Higher belief means the more chance a statement is already right.

$ bel-enrichment from-graph zhang2011.bel --directory ~/Desktop/zhang-enrichment

Generate a ranking for genes based on the information content in a given BEL graph that has been pre-compiled by PyBEL.

$ bel-enrichment ranks zhang2011.bel

Document-Based Curation

If you want to make a curation sheet based on a PubMed identifier (or list of them) do this:

$ bel-enrichment from-pmids 20585587 20585588 > ~/Desktop/document_based.tsv

Topic-Based Curation

If you want to make a curation sheet based on an entity, do this:

$ bel-enrichment from-agents MAPT GSK3B > ~/Desktop/topic_based.tsv

References

[2]Gyori, B. M., et al. (2017). From word models to executable models of signaling networks using automated assembly. Molecular Systems Biology, 13(11), 954.
[3]Hoyt, C. T., Konotopez, A., Ebeling, C., (2017). PyBEL: a computational framework for Biological Expression Language. Bioinformatics (Oxford, England), 34(4), 703–704.

Project details


Download files

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

Files for bel-enrichment, version 0.0.5
Filename, size File type Python version Upload date Hashes
Filename, size bel_enrichment-0.0.5-py3-none-any.whl (17.6 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size bel_enrichment-0.0.5.tar.gz (17.3 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page