Package: pathme
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).This project 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 thePathMe-Viewer, a web application that enables querying, browsing, and
navigating  pathway knowledge assisted by a user-friendly visualization.Database VersionsPathMe currently uses the following versions of the databases:KEGG: Up-to-date (KEGG does not have tag its releases)Reactome: 67 ReleaseWikiPathways: March 2020 ReleaseCitationIf you use PathMe in your work, please consider citing:[1]Domingo-Fernández, D.,et al.(2019).PathMe: Merging and exploring mechanistic pathway knowledge.BMC Bioinformatics, 20:243.Installationpathmecan be directly installed from PyPi with pip:$python3-mpipinstallpathmeTo use the latest version install directly from GitHub:$python3-mpipinstallgit+https://github.com/PathwayMerger/PathMe.gitor in editable mode with:$gitclonehttps://github.com/PathwayMerger/PathMe.git$cdpathme$python3-mpipinstall-e.How to UseBefore using PathMe, make sure you have installed and populated theBio2BEL HGNCandBio2BEL ChEBIdatabases (Simple run:”python3 -m bio2bel_hgnc populate” and
“python3 -m bio2bel_chebi populate”) in your favourite terminal.Each database has three main commands:download,bel, andsummarize:Download contentPathMe first requires to download the raw files from the original pathway databases. This can be accomplished by
running the command (‘database’ can be either KEGG, Reactome, or WikiPathways). E.g., python3 -m pathme kegg download$python3-mpathme<database>downloadGenerate BEL GraphsOnce 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.$python3-mpathme<database>belSummarizeSummarizes the result of the conversion to BEL.$python3-mpathme<database>summarizeAdvanced ParametersKEGG FunctionalitiesThe 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=Truein the exporting command. Example:$python3-mpathmekeggbel--flattenExport PathMeRun the following command to see the different formats that you can export PathMe to (e.g., CX, SPIA, etc.):$python3-mpathmeexport--helpDisclaimerPathMe is a scientific software that has been developed in an academic capacity, and thus comes with no warranty
or guarantee of maintenance, support, or back-up of data.ReferencesKEGGPathMe makes use of KEGG KGML files that are downloaded via the KEGG API for academic purposes (please make sure you comply theirTerms and Conditions).[2]Kanehisa,et al.(2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45,
D353-D361.[3]Kanehisa, M.,et al.(2016). KEGG as a reference resource
for gene and protein annotation. Nucleic Acids Res. 44, D457-D462.[4]Kanehisa, M. and Goto, S. (2000). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30.Reactome[5]Fabregat, Aet al.(2016). The Reactome Pathway Knowledgebase. Nucleic Acids Research 44. Database issue:
D481–D487.[6]Croft, Det al.(2014). The Reactome Pathway Knowledgebase.Nucleic Acids Research42.Database issue:
D472–D477.WikiPathways[7]Slenter, D.N.,et al.(2017). WikiPathways: a multifaceted pathway database bridging metabolomics to other omics
research.Nucleic Acids Research, doi.org/10.1093/nar/gkx1064[8]Kutmon, M.,et al.(2016). WikiPathways: capturing the full diversity of pathway knowledge Nucl. Acids Res., 44,
D488-D494.[9]Kelder, T.,et al.(2011). WikiPathways: building research communities on biological pathways. Nucleic Acids Res.
Jan;40(Database issue):D1301-7