compath-resources 0.1.0

ComPath Resource Utilities

This repository contains the different resources derived or generated using ComPath. Among these resources, there are Jupyter notebooks outlining possible analyses that can be made using ComPath plugins as well as the results of the curation effort (see the mappings folder) where pathway mappings between three of the major pathway databases (see below) are stored. As of March 2020, PathBank 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. 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

• KEGG - Reactome

• WikiPathways - Reactome

• PathBank - KEGG

• PathBank - Reactome

• PathBank - WikiPathways

[*]

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 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. Please direct contributions to that repository following its curation guidelines.

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 with:

pip install compath_resources

Download the most recent code from GitHub with:

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

💪 Usage

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

• Daniel Domingo-Fernández

• Yojana Gadiya