https://github.com/hemekg/hemekg
Modeling heme pathogenicity and pathway dysregulation in the context of hemolytic disorders
https://github.com/hemekg/hemekg
biological-expression-language heme knowledge-modeling networks-biology pathways pybel systems-biology
Last synced: 4 months ago
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Modeling heme pathogenicity and pathway dysregulation in the context of hemolytic disorders
- Host: GitHub
- URL: https://github.com/hemekg/hemekg
- Owner: hemekg
- License: cc0-1.0
- Created: 2019-08-15T05:58:38.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2023-02-21T10:51:27.000Z (over 3 years ago)
- Last Synced: 2025-09-22T15:37:12.388Z (8 months ago)
- Topics: biological-expression-language, heme, knowledge-modeling, networks-biology, pathways, pybel, systems-biology
- Language: Python
- Homepage: https://hemekg.github.io/hemekg/
- Size: 2.32 MB
- Stars: 3
- Watchers: 3
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
HemeKG
======
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
------------
The ``hemekg`` python package can be installed from `PyPI `_
with the following code in your shell:
.. code-block:: sh
$ pip install hemekg
The development version can be installed from `GitHub `_
with:
.. code-block:: sh
$ git clone https://github.com/hemekg/hemekg.git
$ cd hemekg
$ pip install -e .
Commands
--------
To see all the commands, simply run:
.. code-block:: sh
$ hemekg
Usage
-----
To get the BEL graph, use the following code:
.. code-block:: python
>>> 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.
More BEL Content
----------------
See `A Listing of Publicly Available Content in the Biological Expression Language (BEL)
`_ on Charles Tapley Hoyt's blog
for more BEL content.