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Question: reactome.db: reactome IDs not mapped to pathway names
0
gravatar for Johannes Rainer
3.0 years ago by
Johannes Rainer1.0k
Italy
Johannes Rainer1.0k wrote:

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 

ADD COMMENTlink modified 2.6 years ago by willem.ligtenberg150 • written 3.0 years ago by Johannes Rainer1.0k
1
gravatar for willem.ligtenberg
2.6 years ago by
Netherlands
willem.ligtenberg150 wrote:

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

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by willem.ligtenberg150

Hi Willem, glad to hear that a solution is in place. 

btw, the link you posted gives a '404 not found', could you please check it again?

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Dan Du210

Thanks, pydio didn't like the extra dot in the name I gave the link...
This one works.

ADD REPLYlink written 2.6 years ago by willem.ligtenberg150

Super! the link works now! Will try it out! Thanks a lot!

keep bugging... the name versioning seems odd, 

should it not be 'reactome.db_1.52.0.tar.gz' instead of 'reactome.db_1.0.52.tar.gz', of coz which wont interfere with the installation.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Dan Du210

Hi Dan,

did you try whether the package works now?

ADD REPLYlink written 2.6 years ago by Johannes Rainer1.0k

I defaulted back to my original versioning scheme, sorry about that.
That should not be an issue with the version that would get into Bioconductor.

ADD REPLYlink written 2.6 years ago by willem.ligtenberg150
0
gravatar for Dan Du
3.0 years ago by
Dan Du210
Germany
Dan Du210 wrote:

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

ADD COMMENTlink written 3.0 years ago by Dan Du210

hi Dan,

you're right, now we have to hope the developer sees this...

I had to manually install the old reactome.db package (1.48.1), which worked fine. but for now I even completely switched to the "graphite" package for the reactome data. They have a recent reactome within the package (although only human), and also provide the interactions between the genes (which is not available in reactome.db). still, would be fine if the reactome.db package would work again...

cheers, jo

ADD REPLYlink written 3.0 years ago by Johannes Rainer1.0k
0
gravatar for willem.ligtenberg
3.0 years ago by
Netherlands
willem.ligtenberg150 wrote:

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... :)

ADD COMMENTlink written 3.0 years ago by willem.ligtenberg150

I haven't received any response yet. I will see if I can rewrite my queries to only use the normalised database.
This might take a bit though.

ADD REPLYlink written 3.0 years ago by willem.ligtenberg150

Hi all,

I have the same problem with reactome.db for Mus Musculus. I don't know if it can help, but I found that the pathway ID are not the same betweem all the databases included in reactome.db. For example, for cholesterol biosynthesis for mice, the pathway ID in reactomePATHID2EXTID is '5605312'. However, the pathway ID in reactomePATHID2NAME and in reactomePATHNAME2ID is '5943571'. So, the correspondance between the path ID obtained with reactomePATHID2EXTID and the pathway name can not be done. However, for the moment, I didn't find a solution to manually change the path ID in reactomePATHID2EXTID...

For users who are needed path name quickly, the internet site from Genscript (plasmid provider for molecular biology) still present old reactome path ID in the descriptions of their plasmids. If you just copy the path ID from reactomePATHID2EXTID to an internet browser, there will be a link to the genscript website if they are providing gene synthesis for one gene of the pathway. So it is a solution to get the path name manually. This is not an elegant solution, but it can be usefull if one need to finish a reactome analysis in emergency...

Best,

Nicolas

ADD REPLYlink written 3.0 years ago by Merienne Nicolas120

Hello everybody,

 

Do you know if a solution to get pathway names from reactome.db has been found?

Thank you in advance.

Best,

Nicolas
 

ADD REPLYlink written 2.8 years ago by Merienne Nicolas120

Hi Nicolas,

I don't think so; my solution for now is to manually install an older version of the package (so a pre-1.50.0 version).

cheers, jo

ADD REPLYlink written 2.8 years ago by Johannes Rainer1.0k

Hi Johannes,

It works for me with manual installation of reactome.db_1.48.0

Thank you for your help.

Best,

Nico

ADD REPLYlink written 2.8 years ago by Merienne Nicolas120
0
gravatar for Thomas Sandmann
2.7 years ago by
USA
Thomas Sandmann60 wrote:

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. 

ADD COMMENTlink written 2.7 years ago by Thomas Sandmann60
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