Suggestions to automate downloading the most current gmt files

[Krutik Patel]

Hello Wikipathways forum,

This query is a bit specific so I will give a short preamble. 

I have developed an R package (TimiRGeN -- final stages of bioconductor review)  that utilises wikipathways to identify microRNAs that may be effecting 

signalling pathways.

 

This package uses rWikipathways, Rcy3, clusterProfiler and a few other 

already published bioconductor tools to perform analysis on time series miRNA-mRNA

expression datasets. 

Ideally  I'd like to have my tool as up-to-data as possible, however this 

is a bit tricky as there is a new wikipathways update every month. 

Are there any suggestions as to how to automate downloading the most current, 

species specific versions of wikipathway gmt files, without having to change the code 

every month? 

My current method is to specify the exact gmt to download.

```

 download.file(paste("http://data.wikipathways.org/20200110/gmt/",

                        "wikipathways-20200110-gmt-Mus_musculus.gmt",

                        sep = ""),

                        "mus.gmt")

```

This leads onto my second query. If I cannot download the most up-to-date 

version of wikipathways, is it OK to use fairly recent older versions? 

For example the mouse 2020-01-10 version contains the Complement and Coagulation 

cascade, however more recent versions of the mouse wikipathways database do

not. 

I specifically highlight the Complement and Coagulation cascade pathway because

I was using this as my example in the vignette. I am a bit confused why this 

pathway was removed in the mouse database but not from the human database. 

Hopefully my queries make sense.

Best Wishes,

Krutik Patel  

PhD Student Newcastle University

[Martina Summer-Kutmon]

Dear Krutik,

You mention that you use the rWikiPathways package, right? 

You can use this function:

wp.hs.gmt <- rWikiPathways::downloadPathwayArchive(organism="Homo sapiens", format = "gmt") 

It always downloads the latest GMT file in the working directory. 

I will check the mouse pathway that you mention. Do you have the identifier? 

Best, Tina

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Martina Summer-Kutmon, PhD
email: mku...@gmail.com

[Krutik Patel]

Hi Tina,

Thank you for the suggestion, I will try this. 

The mouse pathway is WP449 and the human pathway is WP558. Now that I compare them, they are slightly different. 

Best wishes,

Krutik Patel  

PhD Student Newcastle University