compath-resources 0.0.9

Citation

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

Installation

python3 -m pip install compath_resources

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

Mapping Between Pathway Databases

A total of 6 mapping files are stored in this package, one for each pairwise comparison [*]:

• KEGG - WikiPathways

• KEGG - Reactome

• WikiPathways - Reactome

• PathBank - KEGG

• PathBank - Reactome

• PathBank - WikiPathways

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

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