I just found out that in recent reactome.db version (1.59.0) there was a change of pathways IDs (PATHID column). Before there was 20800 pathways with pathways beeing specific to an organism. Now there are 2185 pathways, shared between organisms. I'm not sure what were the reasons for the change, but I don't have problems with both schemes. However, I find it inconsistent, that for a single pathway ID there are multiple pathway names.

With reactome.db 1.58.0:

> length(keys(reactome.db, keytype="PATHID"))
[1] 20800
> AnnotationDbi::select(reactome.db, keys=c("Bos taurus: Interleukin-6 signaling", "Homo sapiens: Interleukin-6 signaling"), columns=c("PATHID"), keytype=c("PATHNAME"))
'select()' returned 1:1 mapping between keys and columns
                               PATHNAME  PATHID
1   Bos taurus: Interleukin-6 signaling 5870529
2 Homo sapiens: Interleukin-6 signaling 1059683

With reactome.db 1.59.0:

> length(keys(reactome.db, keytype="PATHID"))
[1] 2185
> AnnotationDbi::select(reactome.db, keys=c("Bos taurus: Interleukin-6 signaling", "Homo sapiens: Interleukin-6 signaling"), columns=c("PATHID"), keytype=c("PATHNAME"))
'select()' returned 1:1 mapping between keys and columns
                               PATHNAME  PATHID
1   Bos taurus: Interleukin-6 signaling 1059683
2 Homo sapiens: Interleukin-6 signaling 1059683

As this behavior breaks build of my package (fgsea) and I need to fix it, I wonder is this transition final? If yes, may be it's better to remove organism specific prefix whatsoever? I'm pretty sure it's much better to have one-to-one map between pathway IDs and pathway names.

Best,
Alexey

No that change is not final.
I was alerted to that issue last weekend. I have already created a new version which results in a one-to-one mapping of pathway-id to pathway name.

Apparently, Reactome has changed their identifiers, and I have revised the way I am building the package.
I mistakenly thought that the R-HSA-<ID> thing was only in their exports, but they have made that change throughout the database and website. (When I started using Reactome the DB_IDs were always numeric.)
So I removed the R-<three letter species>- bit from all ids, which then resulted in the multi mapping issue.

When I was alerted to this, I now have made a package that does not remove the R-HSA- part. So all IDs are now of the form: R-<three letter abbreviation species>-<number>.
I then had the request to also include the old (full numeric) ids that were present previously, but I can only do that with up to date info for human, which I think is not what people would expect, since there are also users using Reactome with  non-human data.
Another option would be to include the mappings from the previous version, which would mean that that data is stale. (Also sub-optimal)

Any suggestions on the preferred way forward are welcome. I can build another version relatively quickly.

If you want to test that new version feel free to download it here.