Question

reactome.db: reactome IDs not mapped to pathway names

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Johannes Rainer ★ 2.1k

@johannes-rainer-6987

Last seen 9 weeks ago

Italy

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

annotation pathways • 4.0k views

ADD COMMENT • link updated 9.7 years ago by willem.ligtenberg ▴ 150 • written 10.1 years ago by Johannes Rainer ★ 2.1k

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Dan Du ▴ 210

@dan-du-5270

Last seen 11 months ago

Germany

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 COMMENT • link 10.1 years ago Dan Du ▴ 210

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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 REPLY • link 10.1 years ago Johannes Rainer ★ 2.1k

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willem.ligtenberg ▴ 150

@willemligtenberg-6989

Last seen 7.2 years ago

Netherlands

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 COMMENT • link 10.1 years ago willem.ligtenberg ▴ 150

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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 REPLY • link 10.1 years ago willem.ligtenberg ▴ 150

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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 REPLY • link 10.1 years ago Merienne Nicolas ▴ 120

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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 REPLY • link 9.9 years ago Merienne Nicolas ▴ 120

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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 REPLY • link 9.9 years ago Johannes Rainer ★ 2.1k

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Hi Johannes,

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

Thank you for your help.

Best,

Nico

ADD REPLY • link 9.9 years ago Merienne Nicolas ▴ 120

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Thomas Sandmann ▴ 90

@thomas-sandmann-6817

Last seen 16 months ago

USA

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 COMMENT • link 9.8 years ago Thomas Sandmann ▴ 90

score 1 · Accepted Answer · 2015-04-07

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willem.ligtenberg ▴ 150

@willemligtenberg-6989

Last seen 7.2 years ago

Netherlands

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 COMMENT • link 9.7 years ago willem.ligtenberg ▴ 150

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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 REPLY • link 9.7 years ago Dan Du ▴ 210

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

ADD REPLY • link 9.7 years ago willem.ligtenberg ▴ 150

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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 REPLY • link 9.7 years ago Dan Du ▴ 210

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Hi Dan,

did you try whether the package works now?

ADD REPLY • link 9.7 years ago Johannes Rainer ★ 2.1k

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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 REPLY • link 9.7 years ago willem.ligtenberg ▴ 150