WikiPathways to Biological Expression Language (BEL)

[ddom...@gmail.com]

Hi guys,

I am Daniel Domingo-Fernandez from Fraunhofer SCAI (Germany). We are currently working on converting KEGG, Reactome, and WikiPathways to a common schema

to perform a comparison across these resources. This comparison will be based on the mappings we have manually curated between these resources (see: https://www.biorxiv.org/content/early/2018/06/21/353235.article-metrics or https://compath.scai.fraunhofer.de/catalog). 

Since our lab works with Biological Expression Language (BEL), we used this schema for harmonizing the three resources, and thus, implemented a package that converts each database to BEL. The package is still a beta version and it is complemented with a web application where you can explore and overlap the graphs to find discrepancies/boundaries and so on... Here the link to the package: https://github.com/ComPath/PathMe (converter) and https://github.com/ComPath/PathMe-Viewer (web application).

We would like input and feedback on the way we haved used WikiPathways: we used WikiPathways RDF files and performed SPARQL queries to get all nodes/edges and metainformation. Then, each relationship/entity is converted to its corresponding translation in BEL (more details here https://pharmacome.scai.fraunhofer.de/index.php/2018/08/07/compath-reloaded-overlapping-the-content-of-biological-pathway-databases/).

Please be free to use our software and give any feedback or suggested improvements.

Regards

Daniel

[Anders Riutta]

Hi Daniel,

This is really cool! I'm eager to dig into it further and I'll let you know what I find.

Regards,

Anders

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Anders Riutta

anders...@gladstone.ucsf.edu | Bioinformatics Core | Institute of Data Science and Biotechnology

Gladstone Institutes | Science Overcoming Disease