I 'upgraded' my BioC installation today, including the annotation packages, and also installed reactome.db which I would like to use for pathway analyses of a dataset in the near future. However, I am confused on whether the content of reactome.db is still up to date. I am asking because I cannot really find which version of Reactome is packaged.

I assumed it would be the latest version (i.e. V58 [released September 28 2016], or maybe V57 [from June 27 2016]). However, when I check the help pages from reactome.db, I noticed that the time stamp for all annotation objects (e.g. reactomeEXTID2PATHID) is 2010-Dec-21(= ~6 yrs ago...). On the other end, in the description file it is mentioned that it was packed on 2016-04-14, which rather suggests the content is based on the V56 release [from March 24 2016]...

I also noticed on the list that there were some problems with reactome.db that prevented the incorporation of new data, but it was suggested these were solved ~2 years ago (see this thread from the archive: reactome.db is not updated?).

Anyway, I am lost, so any insights on this (or alternatives)  would be appreciated.

Thanks, Guido

<<edit>> Added sessionInfo()

<<edit2>> also found this informative thread: A: Reactome pathway names from IDs?.

> sessionInfo()
R version 3.3.1 Patched (2016-10-18 r71535)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
[1] reactome.db_1.55.0   AnnotationDbi_1.36.0 IRanges_2.8.0        S4Vectors_0.12.0    
[5] Biobase_2.34.0       BiocGenerics_0.20.0  BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] DBI_0.5-1     tools_3.3.1   RSQLite_1.0.0
>

Hi Guido,

Yes, we will have a new version of reactome.db but it's not ready yet. It's built and being tested now - should be available early next week.

Valerie