hemekg 0.0.1

Mechanistic knowledge about heme and hemolytic disorders in Biological Expression Language with PyBEL

Assembling and modeling the knowledge around heme pathogenicity and pathway dysregulation in the context of hemolytic disorders. The data hosted in this repo was curated by Farah Humayun in context of her Master’s Thesis. The curated documents are located in the hemekg directory.

Citation

If you find HemeKG useful in your work, please consider citing:

[1]

Humayun, F., et al. (2020). A computational approach for mapping heme biology in the context of hemolytic disorders. Front. Bioeng. Biotechnol. 8:74.

Installation

To install the hemekg python package for programmatic access to the BEL files in this repository, use the following code in your shell:

$ git clone https://github.com/hemekg/hemekg.git
$ cd hemekg
$ pip install -e .

Commands

To see all the commands, simply run:

$ hemekg

Usage

To get the BEL graph, use the following code:

>>> import hemekg
>>> graph = hemekg.get_graph()
>>> graph.summarize()

Annotations

Auxiliary annotations are located in the hemekg/annotations directory. These include:

1. TimePoint.

2. Species.

3. Concentration.