compath-resources 0.1.1
ComPath Resource Utilities
License: MIT
Requires Python: >=3.7
Keywords: KEGG,Reactome,WikiPathways,PathBank,Biological Networks,Pathway Analysis,Networks Biology

ComPath Resources
=================
|tests| |pypi_version| |python_versions| |pypi_license| |zenodo|

This repository contains the different resources derived or generated using `ComPath <https://github.com/ComPath>`_.
Among these resources, there are `Jupyter notebooks <https://github.com/ComPath/compath-resources/tree/master/notebooks>`_
outlining possible analyses that can be made using ComPath plugins as well as the results of the curation effort
(see the `mappings <https://github.com/ComPath/compath-resources/tree/master/mappings>`_ folder) where pathway mappings between
three of the major pathway databases (see below) are stored. As of March 2020, `PathBank <https://pathbank.org/>`_
mappings are now available in ComPath.

Citation
--------
If you use ComPath in your work, please consider citing:

.. [1] Domingo-Fernández, D., *et al.* (2018). `ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases <https://doi.org/10.1038/s41540-018-0078-8>`_. *npj Syst Biol Appl.*, 4(1):43.

💾 Data
-------
A total of 6 mapping files are stored in this package, one for each pairwise comparison [*]_.
These data are available under the CC0 1.0 Universal License.

- `KEGG - WikiPathways <https://github.com/ComPath/compath-resources/blob/master/mappings/kegg_wikipathways.csv>`_
- `KEGG - Reactome <https://github.com/ComPath/compath-resources/blob/master/mappings/kegg_reactome.csv>`_
- `WikiPathways - Reactome <https://github.com/ComPath/compath-resources/blob/master/mappings/wikipathways_reactome.csv>`_
- `PathBank - KEGG <https://github.com/ComPath/compath-resources/blob/master/mappings/pathbank_kegg.csv>`_
- `PathBank - Reactome <https://github.com/ComPath/compath-resources/blob/master/mappings/pathbank_reactome.csv>`_
- `PathBank - WikiPathways <https://github.com/ComPath/compath-resources/blob/master/mappings/pathbank_wikipathways.csv>`_

.. [*] Pairwise mappings between KEGG, Reactome and WikiPathways were last updated in March of 2019. PathBank mappings
    were last updated in March of 2020.

Update: March 2020
~~~~~~~~~~~~~~~~~~
Mappings between `PathBank <https://pathbank.org/>`_ and the above-mentioned databases are now available in ComPath.

📊 Summary
----------
A summary is automatically generated nightly with GitHub Actions and deployed to
https://compath.github.io/compath-resources/.

🙏 Contributing
---------------
While it's possible to improve the files in this repository, they have been integrated into a more
general effort for identifying mappings between biological entities,
`Biomappings <https://github.com/biomappings/biomappings>`_. Please direct contributions to that repository
following its `curation guidelines <https://github.com/biomappings/biomappings#-contributing>`_.

Curation Guidelines
~~~~~~~~~~~~~~~~~~~
We have distinguished between two types of relationships between pathways (mappings): “equivalentTo” and “isPartOf”.

- equivalentTo. An undirected relationship denoting both pathways refer to the same biological process. The
  requirements for this relationship are:

  - Scope: both pathways represent the same biological pathway information.
  - Similarity: both pathways must share at minimum of one overlapping gene.
  - Context: both pathways should take place in the same context (e.g., cell line, physiology)

- isPartOf. A directed relationship denoting the hierarchical relationship between the pathway 1 (child) and 2
  (parent). The requirements are:

  - Subset: The subject (pathway 1) is a subset of pathway 2 (e.g., Reactome pathway hierarchy).
  - Similarity: same as above
  - Context: same as above

⬇️ Installation
---------------
Download the latest stable code from `PyPI <https://pypi.python.org/pypi/compath_resources>`_ with:

.. code-block:: python

   pip install compath_resources

Download the most recent code from `GitHub <https://github.com/ComPath/compath-resources>`_ with:

.. code-block:: python

   pip install git+https://github.com/ComPath/compath-resources.git

💪 Usage
--------
.. code-block:: python

   import compath_resources

   # get all mappings as a pandas dataframe
   df = compath_resources.get_df()

   # get all mappings as a PyBEL BEL graph
   bel_graph = compath_resources.get_bel()

   # get all mappings as an RDFLib graph.
   rdf_graph = compath_resources.get_rdf()

⚖️ License
----------
Code is licensed under the MIT License. Curated mappings are licensed under the CC-0 License.

Acknowledgements
----------------
Curation Team
~~~~~~~~~~~~~
The curation exercise was conducted under inter-curator agreement in a team formed by:

- Carlos Bobis-Álvarez
- `Josep Marín-Llaó <https://github.com/jmarinllao>`_
- `Daniel Domingo-Fernández <https://github.com/ddomingof>`_
- `Yojana Gadiya <https://github.com/YojanaGadiya>`_

.. |python_versions| image:: https://img.shields.io/pypi/pyversions/compath_resources.svg
    :alt: Stable Supported Python Versions
.. |pypi_version| image:: https://img.shields.io/pypi/v/compath_resources.svg
    :target: https://pypi.python.org/pypi/compath_resources
    :alt: Current version on PyPI
.. |pypi_license| image:: https://img.shields.io/pypi/l/compath_resources.svg
    :alt: MIT License
.. |zenodo| image:: https://zenodo.org/badge/132792765.svg
   :target: https://zenodo.org/badge/latestdoi/132792765
.. |tests| image:: https://github.com/ComPath/compath-resources/workflows/Tests/badge.svg
   :target: https://github.com/ComPath/compath-resources/actions?query=workflow%3ATests