compath-resources 0.0.7

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.

Installation

python3 -m pip install compath_resources

python3 -m pip install git+https://github.com/ComPath/resources.git@master

Mapping Between Pathway Databases

A total of 3 mapping files are stored in this package, one for each pairwise comparison:

• KEGG - WikiPathways

• KEGG - Reactome

• WikiPathways - Reactome

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

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