Reactome hierarchy

Question

[ceboral]

Hi! I did an enrichment analysis in Reactome and I got a list of pathways from my dataset. I would like to group the pathways considering their function and I have seen that in the website, when you search for a pathway, it is displayed the ascending hierarchy of the pathway (for example, if you search for "decin 2 family", you get in the website the information that it comes from immune system>innate immune system>c-type lectin receptors). Is there any way to get this information in an automated way? I have tried to search a function that would give me this information using R (ReactomePA and ReactomeDB), but so far no luck... Thanks a lot!!

Answer 1

[Robin Haw]

The pathway information files on our data download page consist of tab-separated tables that provide information about Reactome pathway hierarchy:

The "Complete list of pathways" file maps the Reactome Stable identifier (ST_ID) to a pathway name and corresponding species. The "Pathway hierarchy relationship" file consists of two columns of Reactome Stable identifiers (ST_ID), defining the relationship between pathways within the pathway hierarchy. The first column provides the parent pathway stable identifier, whereas the second column provides the child pathway stable identifier.

Link: https://reactome.org/download-data

Answer 2

[Muiz Khan]

rbioapi is a package that can provide you the hierarchy of reactome database. Here is the documentation: https://cran.r-project.org/web/packages/rbioapi/vignettes/rbioapi_reactome.html