Convert Reactome Protein IDs to Pathway IDs?

On Reactome website they have at the download page mapping files (uniprot, ensembl, etc.), but unfortunately not for the protein IDs you are using (stable identifiers).

I had contact with their helpdesk, and they sent me a file containing all protein IDs to the pathways. Exactly what you need. I have asked them if they wanted to put it on their download page as well, but not sure if they want to do this. Meanwhile you can ask for the file as well, or get it from my google drive.

I assume you know how to get your Protein IDs and pathways from this file, using e.g., R?

If you don't mind hitting it 50k times and are OK with python3...

from urllib import request
import json

def getPathways(proteinID):
    baseURL = 'http://reactome.org/ContentService/data/query'
    PathwayIDs = set()
    try:
        response = request.urlopen('{}/{}'.format(baseURL, proteinID)).read().decode()
        data = json.loads(response)
        if 'consumedByEvent' in data:
            for event in data['consumedByEvent']:
                PathwayIDs.add(event['stId'])
        if 'producedByEvent' in data:
            for event in data['producedByEvent']:
                PathwayIDs.add(event['stId'])
    except:
        pass
    return PathwayIDs

Usage would then be something like:

l = ['R-HSA-49155', 'R-HSA-199420', '']
for rid in l:
    ids = getPathways(rid)
    for _ in ids:
        print("{}\t{}".format(rid, _))

Which would produce:

R-HSA-49155 R-HSA-110239
R-HSA-49155 R-HSA-110240
R-HSA-49155 R-HSA-110238
R-HSA-49155 R-HSA-110356
R-HSA-199420    R-HSA-8948800
R-HSA-199420    R-HSA-6807106
R-HSA-199420    R-HSA-6807206
R-HSA-199420    R-HSA-6807126
R-HSA-199420    R-HSA-8847968
R-HSA-199420    R-HSA-8850997
R-HSA-199420    R-HSA-2321904
R-HSA-199420    R-HSA-8948775
R-HSA-199420    R-HSA-8944497
R-HSA-199420    R-HSA-6807134
R-HSA-199420    R-HSA-8850945
R-HSA-199420    R-HSA-8873946

Note that this will silently ignore invalid or missing IDs such as '' (that's the try and except above. Note also that these are different pathway IDs than what you provided in your example. The main reason is that the protein IDs you showed are not always involved in the pathways IDs you showed (in my example, they always are).