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Harmonizing pathway databases using Biological Expression Language (BEL)

Project description

PathMe is a Python package aimed to convert KEGG [2] [3] [4], Reactome [5] [6], and WikiPathways [7] [8] [9] to Biological Expression Language (BEL).

It is the continuation of the ComPath web application aimed at exploring, analyzing, and curating pathway knowledge in a gene-centric view. This different approach involves converting all the pathways in these resources into BEL as a pivotal integration schema to harmonize entities and relationships in order across these multiple resources; thus, enabling a more comprehensive evaluation of pathway cross-talks, consensus, and boundaries. Additionally, PathMe is complemented with the PathMe-Viewer, a web application that enables querying, browsing, and navigating pathway knowledge assisted by a user-friendly visualization.

Citation

If you use PathMe in your work, please cite [1]:

[1]Domingo-Fernández, D., et al. (2018). PathMe: Merging and exploring mechanistic pathway knowledge. bioRxiv 451625.

Installation Current version on PyPI Stable Supported Python Versions Apache-2.0

  1. pathme can be installed with the following commands:
$ python3 -m pip install git+https://github.com/ComPath/PathMe.git@master
  1. or in editable mode with:
$ git clone https://github.com/ComPath/PathMe.git
$ cd pathme
$ python3 -m pip install -e .

How to Use

Before using PathMe, make sure you have installed and populated the Bio2BEL HGNC and Bio2BEL ChEBI databases (Simple run:”python3 -m bio2bel_hgnc populate” and “python3 -m bio2bel_chebi populate”) in your favourite terminal.

Each database has three main commands: download, bel, and summarize:

  1. Download content

PathMe first requires to download the raw files from the original pathway databases. This can be accomplished by running the command (‘database’ can be either KEGG, Reactome, or WikiPathways):

$ python3 -m pathme 'database' download
  1. Generate BEL Graphs

Once the raw files are downloaded, you can run the following to command to generate BELGraphs that will be exported as Python pickles files for further analysis. Furthermore, the conversion to BEL can be tuned differently for each database by using specific commands. For example, KEGG parameters are shown when running “python3 -m pathme kegg bel –help”. Finally, please bear in mind that converting the Reactome files take up to 8 hours due to the large amount of its RDF file.

$ python3 -m pathme 'database' bel
  1. Summarize

Summarizes the result of the conversion to BEL.

$ python3 -m pathme 'database' summarize

Advanced Parameters

KEGG Functionalities

The KEGG module of PathMe is able to handle KGML differently depending on the goal. By default, KEGG groups together the complex of nodes (e.g., gene families) into one node as it is depicted in the KEGG cartoons and represented in the KGML files. However, this behavior can be modified by adding the parameter –flatten=True in the exporting command. Example:

$ python3 -m pathme kegg bel --flatten

References

KEGG

PathMe makes use of KEGG KGML files that are downloaded via the KEGG API for academic purposes (see KEGG Terms and conditions.).

[2]Kanehisa, Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K.; KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353-D361 (2017).
[3]Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).
[4]Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).

Reactome

[5]Fabregat, Antonio et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 44.Database issue (2016): D481–D487. PMC. Web. 6 Oct. 2017.
[6]Croft, David et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 42.Database issue (2014): D472–D477. PMC. Web. 6 Oct. 2017.

WikiPathways

[7]Slenter, D.N., et al WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research Nucleic Acids Research, (2017) doi.org/10.1093/nar/gkx1064
[8]Kutmon, M., et al. WikiPathways: capturing the full diversity of pathway knowledge Nucl. Acids Res., 44, D488-D494 (2016) doi:10.1093/nar/gkv1024
[9]Kelder, T., et al. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2012 Jan;40(Database issue):D1301-7

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