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Question: Is reactome.db still updated?
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gravatar for Guido Hooiveld
13 months ago by
Guido Hooiveld2.1k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.1k wrote:

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
>
ADD COMMENTlink modified 13 months ago • written 13 months ago by Guido Hooiveld2.1k
0
gravatar for Valerie Obenchain
13 months ago by
Valerie Obenchain ♦♦ 6.4k
United States
Valerie Obenchain ♦♦ 6.4k wrote:

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

ADD COMMENTlink written 13 months ago by Valerie Obenchain ♦♦ 6.4k

Hi Valerie,

Great! Also thanks for your prompt reply!

ADD REPLYlink written 13 months ago by Guido Hooiveld2.1k

I'm running the push scripts now, version 1.58 should be online tomorrow.

Valerie

ADD REPLYlink written 13 months ago by Valerie Obenchain ♦♦ 6.4k

Thanks! I just tried to install, but biocLite() (still?) refers to v1.55. I assumed this is the way to install it, or not?
 

ADD REPLYlink written 13 months ago by Guido Hooiveld2.1k

For the archive: got the update package (v1.58); the update was automatically found (and installed) using biocLite()when installing another library .

ADD REPLYlink written 13 months ago by Guido Hooiveld2.1k

OK good. I just tried with a fresh install of release and devel and got 1.58 in both cases.

Valerie

ADD REPLYlink written 13 months ago by Valerie Obenchain ♦♦ 6.4k
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