bel-enrichment / results

An application of the rational enrichment workflow to ten subgraphs from NeuroMMSig for the Human Brain Pharmacome project (https://pharmacome.scai.fraunhofer.de)

BEL Enrichment

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

If you find bel_enrichment useful in your work, please consider citing¹:

Additionally, this package also heavily builds on INDRA² and PyBEL³.

Installation

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

---

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

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.↩

results's Issues

Add requirements.txt

Add content from GitLab

Add the whole folder from hbp/curation/indra here. Consider reorganizing all curation rounds into a single folder (rounds/). Consider reorganizing all excel sheets into a single folder (data/).

CC @ddomingof

Make pip installable

Add sheets.py

Update /notebooks README

Add description of all notebooks

Add .travis.yml

On every commit, all of the sheets should be syntax checked and a summary of the contents should be written

Add table of contents to the README