Metadata-Version: 2.1
Name: compath-resources
Version: 0.0.3
Summary: ComPath Resource Utilities.
Home-page: https://github.com/compath/resources
Author: Daniel Domingo-Fernández
Author-email: daniel.domingo.fernandez@scai.fraunhofer.de
Maintainer: Daniel Domingo-Fernández
Maintainer-email: daniel.domingo.fernandez@scai.fraunhofer.de
License: MIT
Keywords: KEGG,Reactome,WikiPathways,Biological Networks,Pathway Analysis,Networks Biology
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.6
Requires-Dist: pybel (>=0.12.0)
Requires-Dist: click
Requires-Dist: pandas

ComPath Resources
=================
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/resources/tree/master/notebooks>`_
outlining possible analyses that can be made using ComPath plugins as well as the results of the curation effort
`('mappings' folder) <https://github.com/ComPath/resources/tree/master/mappings>`_ where we generated pathway mappings
between three of the major pathway databases (see below).

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

Domingo-Fernández, D., *et al.* (2018). ComPath: An ecosystem for exploring, analyzing, and curating mappings across
pathway databases. bioRxiv 353235.

Curation (Pathway Mappings)
~~~~~~~~~~~~~~~~~~~~~~~~~~~
The aim of this exercise was to generate mapping files across pathway databases in order to establish relationships
between similar pathways in three of the major pathway databases:

- `KEGG <http://www.kegg.jp/>`_
- `Reactome <http://reactome.org/>`_
- `WikiPathways <https://www.wikipathways.org/index.php/WikiPathways>`_

*We recommend to download the mappings directly from the ComPath website since the pathways in WikiPathways are not
stable and might have been changed. However, the mapping file distributed by the website contains stable identifiers
from all resources.*

Mapping Between Pathway Databases
---------------------------------
A total of 3 mapping files are stored in this package, one for each pairwise comparison:

- `KEGG - WikiPathways <https://github.com/ComPath/curation/blob/master/mappings/kegg_wikipathways.xlsx>`_
- `KEGG - Reactome <https://github.com/ComPath/curation/blob/master/mappings/kegg_reactome.xlsx>`_
- `WikiPathways - Reactome <https://github.com/ComPath/curation/blob/master/mappings/wikipathways_reactome.xlsx>`_

*It is important to mention that even more mappings are stored in the database thanks to the ComPath inference system.
For example, when a KEGG to WikiPathways pathway is assigned as equivalent to a Reactome pathway, ComPath uses the
Reactome hierarchy to infer new hierarchical mappings and map the super/sub pathways of the Reactome pathway to this
corresponding equivalent pathway.*

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

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

Mapping Types
-------------
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


