Converting Reactome SMBL/Biopax to KGML format (mainly for EnrichmentBrowser)

Question

[v36nguyen]

Hello All, I am currently using the latest version of EnrichmentBrowser which is a great all-in-one package for RNAseq/Microarray experiments with simple contrast designs. However, the native functionality for pathways is limited to KEGG and the KGML format. I am by no means an expert coder (happy to learn) but would like to know if there is a

1) Format that already exists in Reactome that can be quickly parsed into KGML.

2) Coaxing Biopax organism .owl files into a similar .xml format as KEGG.

3) Repurposing existing 'converters'. Another user has asked this question before me previously but has not left a trail that I could follow (https://www.biostars.org/p/244434/). KEGG Translator (http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/) seems robust but I am not at a level where I can reverse engineer this program to do what I need. KCPAVs is reported to be able to handle this conversion but had 'connection failed' issues using their converter https://sites.google.com/a/cidms.org/kcpavs/home)

Many thanks

Answer 1

[ludwig.geistlinger]

Hi Nguyen,

I'm currently working on a general compileGRN function that will allow to compile a gene regulatory network also from other pathway databases than KEGG (including Reactome, Biocarta, Humancyc, NCI, and Panther).

This function will become available in the devel version of the EnrichmentBrowser this week:

http://www.bioconductor.org/packages/devel/bioc/html/EnrichmentBrowser.html

(supposedly version 2.9.14).

I'll keep you posted.

Let me know if this already fullfills your needs. Otherwise I would typically not convert from BioPax to KGML but rather read in networks directly from BioPax. I'll check on corresponding functionality in R / Bioconductor.

Answer 2

[ludwig.geistlinger]

Hi,

I have added the new compileGRN function which supports KEGG, Reactome, Biocarta, and NCI for human. For a number of additional model organisms there is also support for Reactome (in addition to KEGG, of course).

You can install the new version of the EnrichmentBrowser package (2.9.14) using a recent Rdevel directly from github via:

# install.packages("devtools")

devtools::install_github("lgeistlinger/EnrichmentBrowser")

Once installed and loaded, you can check on the usage via:

?compileGRN

as also given here:

https://github.com/lgeistlinger/EnrichmentBrowser/blob/3efb94fdad64c6a9e73d0996e6bec96422acc51b/man/compileGRN.Rd#L16

This version of the package will also become available directly from Bioconductor within 48 hours from the website given in my previous post.

Please let me know in case any issues arise.

Thanks!

Answer 3

[v36nguyen]

Thank you very much to Ludwig Geistlinger who has been incredibly helpful through here and emails:

The function works exactly as described and depends on graphite. Sometimes the default biocLite installer method for EnrichmentBrowser will install 2.8.6. You can follow Ludwig's instructions above to install from github or the EnrichmentBrowser development version, current 2.9.15

https://bioconductor.org/packages/devel/bioc/html/EnrichmentBrowser.html

install.packages("https://bioconductor.org/packages/3.7/bioc/src/contrib/EnrichmentBrowser_2.9.15.tar.gz", repos = NULL, type="source")

This greatly expands the functionality of the program and is fast becoming the most versatile single pipeline for downstream transcriptomics and proteomics (at least for me)!

Cheers,

Vinh Nguyen

Answer 4

[liuhaizhou]

Hi, all. I am meeting the same problem, how to convert sbml or biopax format to kgml? I would like to extract the node interaction in the pathways, up to now, I know that an R package "isubpathwayminer " can deal it for kgml format, but for sbml or biopax format, is there any tools to solve the problem? Or how to convert sbml or biopax format to kgml? Many thanks.