dear all,

I think there is a problem with the reactome.db package: in version 1.50.0 most of the pathway IDs are not mapped to pathway names:

library( reactome.db )
reactome.list <- as.list( reactomePATHID2EXTID )
have.name <- names( reactome.list ) %in% ls( reactomePATHID2NAME )
sum( have.name )
length( have.name )

In 3.1.2 with reactome.db 1.50.0 only 1518 of 10373 pathway IDs can be mapped to a pathway name, while in R 3.0.2 with reactome.db version all of the 10469 IDs can be mapped to pathway names.

cheers, jo

sessionInfo for 3.1.2:

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin14.0.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] reactome.db_1.50.0   RSQLite_1.0.0        DBI_0.3.1           
[4] AnnotationDbi_1.28.1 GenomeInfoDb_1.2.2   IRanges_2.0.0       
[7] S4Vectors_0.4.0      Biobase_2.26.0       BiocGenerics_0.12.0

and for 3.0.2 (without the problem above):

R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
[9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] reactome.db_1.46.1   RSQLite_0.11.4       DBI_0.2-7           
[4] AnnotationDbi_1.24.0 Biobase_2.22.0       BiocGenerics_0.8.0  

loaded via a namespace (and not attached):
[1] IRanges_1.20.7 stats4_3.0.2 

I can finally say that we have found a solution.

It was a long journey, and we will still need a long term solution, since this time they had to generate the file at Reactome, instead of me being able to do it myself. We will continue working together for a better long term solution.

I have submitted the package, and I hope it will make it in the next release. In the mean time, you can download the latest version here:
https://share.openanalytics.eu/data/public/reactome.php

Hi Johannes, 

I got bitten by the same problem recently, currently I have to patch a little to catch those unmapped IDs. 

Hopefully someone sees this... (it is not like you can now easily cc the maintainer like we were on mailing list...)

cheers,

Dan

Hi Dan and Johannes,

I am looking into this. The package was generated by a script and apparently the dumps that reactome made available changed. I have asked for clarification using the contact page on reactome.org.
Thank you for bringing it up, sorry that I missed the issue myself.

Kind regards,

Willem

PS: I didn't know this existed... :)

Marc Carlson seems to be working with reactome on this problem, which has been discussed in a A: reactome.db is not updated?. Unfortunately, there doesn't seem to be a solution, yet.