https://bioconductor.org/developers/how-to/deprecation/

• Deprecate in 1.8 ( Apr 2020, r3.11)
• Defunct 1.10 (Oct 2020, r3.12)
• Remove in 1.12 (Apr 2021, r3.13)

Our plan to migrate data.wikipathways.org content to Toolforge required a Web Redirect (called Page Rule at Cloudflare) so that we (and everyone else) can keep using the same data.wikipathways.or URL.

The current downloadPathwaysArchive function, however, breaks when scraping the files in a dir.

The solution is to first RCurl::getURL with followlocation=TRUE and then pass that to readHTMLTable.

some of your https://github.com/wikipathways/rWikiPathways/blob/master/vignettes/Pathway-Analysis.Rmd vignette was adopted from clusterProfiler. You need to acknowledge it.

We shouldn't rely on clusterProfiler for read.gmt. It's a basic function and our version could include the % parsing that is unique to our files.

Suggestion: Add readPathwayGMT()

I am interested in downloading metabolic enzymes from pathways. For example in the omega3 senescence pathway (https://www.wikipathways.org/pathways/WP5424.html) there are various genes that are not directly linked to metabolism, including p21. I think it it should be possible to identify metabolism genes using all genes involved in conversion MIM interactions? Is there a method of just extracting these genes as opposed to all genes in the pathway using the R package?

Thanks

The rWikiPathways vignettes tell us how to do a gene enrichment analysis by the gmt file, which give the gene lists per pathway.

Now I want to do the enrichment analysis based on the metabolome data. Is there a metabolites list file like gmt?

From Tina:

rWikiPathways::downloadPathwayArchive() is currently not working. I get an error:

Error in function (type, msg, asError = TRUE) : SSL certificate problem: certificate has expired

with new clusterProfilier functions: https://yulab-smu.top/biomedical-knowledge-mining-book/wikipathways-analysis.html

From: Gabriel, https://github.com/egonw/rwikipathways/issues/7

Hi @AlexanderPico,

Error

I was unable to execute this code in a fresh R session:

library(rWikiPathways)
downloadPathwayArchive(
  organism = "Homo sapiens", format = "gmt"
)

This code returned the following error:

Error in readHTMLTable(paste0("http://data.wikipathways.org/current/",  : 
  could not find function "readHTMLTable"

Current Workaround

I called library(XML) before the downloadPathwayArchive() and it worked fine.

In this vignette, Section 4, when not explicitly loading BridgeDbR first, we get an error with getXrefList():

> library(rWikiPathways)
> getXrefList('WP554', getSystemCode('Ensembl'))
Error in getSystemCode("Ensembl") : 
  could not find function "getSystemCode"
> library(BridgeDbR)
Loading required package: rJava

Attaching package: ‘BridgeDbR’

The following object is masked from ‘package:methods’:

    getProperties

> getXrefList('WP554', getSystemCode('Ensembl'))
 [1] "ENSG00000092009" "ENSG00000100448" "ENSG00000100739" "ENSG00000105329"
 [5] "ENSG00000113889" "ENSG00000130234" "ENSG00000130368" "ENSG00000135744"
 [9] "ENSG00000143839" "ENSG00000144891" "ENSG00000151623" "ENSG00000159640"
[13] "ENSG00000164867" "ENSG00000168398" "ENSG00000179142" "ENSG00000180772"
[17] "ENSG00000182220"

getXrefList does not work for https://www.wikipathways.org/index.php/Pathway:WP3620
WP3620 has 148 metabolites, but getXrefList does not return those metabolite IDs.
In particular, this pathway contains many KNApSAcK IDs, but I got none of them.
If this issue is resolved, an exhaustive MSEA(Metabolite Set Enrichment Analysis) can be easily implemented.

I knew about this issue, so I implemented Biopax parsing script for Wikipathways (The Biopax of WP3620 had the KNApSAcK IDs).
https://github.com/afukushima/MSEAp/blob/master/R/read.wikipathways.R
But the Biopax does not have non-primary IDs, so I hope this issue is resolved.

> getXrefList('WP3620', 'Ca')
[1] "13306-05-3" "480-20-6"   "5071-40-9"  "520-18-3"   "58124-18-8" "73692-50-9"
> getXrefList('WP3620', 'Ce')
 [1] "15401"       "15413"       "27843"       "28499"       "52047"       "CHEBI:15401" "CHEBI:15413" "CHEBI:1813" 
 [9] "CHEBI:27843" "CHEBI:28499" "CHEBI:4567"  "CHEBI:52047"
> getXrefList('WP3620', 'Ch')
[1] "HMDB0005801" "HMDB0029631" "HMDB0040314" "HMDB05801"   "HMDB29631"   "HMDB40314"  
> getXrefList('WP3620', 'Ck')
[1] "C00223" "C00974" "C05903" "C05905" "C06561" "C15567"
> getXrefList('WP3620', 'Cpc')
[1] "11954208" "122850"   "128861"   "21932272" "5280863"  "5280960"  "90657396"
> getXrefList('WP3620', 'Cks')
[1] ""
> getXrefList('WP3620', 'Wd')
[1] "Q27089427" "Q27123131" "Q393336"   "Q417606"   "Q956217"  
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] rWikiPathways_1.0.0  BiocInstaller_1.30.0

loaded via a namespace (and not attached):
[1] httr_1.3.1     compiler_3.5.0 R6_2.2.2       tools_3.5.0    curl_3.2       RJSONIO_1.3-0  caTools_1.17.1 bitops_1.0-6  
> 

For a few months, I've struggled with getting this method to work (first issues relating to getting geneset names that later resolved itself, and now issues with getting the actual genes in the genesets), which is strange because the issues started after the last commit.

The code I use is:

# Get metadata.
pw <- listPathways("Mus musculus")

# Compile pathways.
gs <- list()
for (i in pw$id)
{
  print(i)
  gs[[length(gs)+1]] <- getXrefList(i, "L")
  print(gs[[length(gs)]])
}

This code used to work for me, but now it produces incomplete returns like this (I only copied the first few outputs):

[1] "WP1"
[1] ""
[1] "WP10"
 [1] "11651"  "12702"  "14784"  "16186"  "16198"  "16199"  "16367"  "16451"  "16453"  "18708"  "19247"  "20416"  "20846" 
[14] "20848"  "20850"  "20851"  "26395"  "26396"  "26413"  "26417"  "269523" "384783" "54721"  "81601" 
[1] "WP103"
[1] ""
[1] "WP108"
[1] ""
[1] "WP113"
[1] ""
[1] "WP116"
[1] ""
[1] "WP1241"
[1] ""
[1] "WP1242"
[1] ""
[1] "WP1243"
[1] ""
[1] "WP1244"
[1] ""

I was wondering if it had to do with calling bridgedb's datasources repo, as their datasources.tsv file has been moved from the path described in location in getXrefList(...)'s help page.

Please tell me if you need more information!

The reason is that the first uses a header file from json.org which has a MIT-no-evil license and therefore is only in Debian non-free. After we moved, our R package can go into Debian. cc @tillea

I’m trying to figure out how to extract edges from a network using the GPML file . I’m using the example of WP1589.gpml. I think I need to extract the information from the <Interaction> tag. These tags have <Point> child tags which I'm guessing will give me information about the edges.

Question 1 - See screenshot. If you see [[9]] and [[10]] in the list, they each have two <Point> tags that could represent the an edge from the “From node” to the “To node” . But see [[11]] in the list - it has 3 <Point> tags, and one <Anchor> tag. Which would be “From node” node and “To node” ? Can you clarify this ?
Link to screenshot here: https://drive.google.com/file/d/1nl3GnqLSbnQR5asWIkPqgcJKbjCh7tsH/view?usp=sharing

Question 2 - Attached is a csv file of the nodes I extracted with the help of Martin Morgan’s code in Slack. I found some GraphIDs (example “bf654”) which are in the <Interaction> section, but not defined previously in <DataNodes> section. So don’t know if this is a gene, or metabolite or anything else. How do I get around this ?
Link to csv file here: https://drive.google.com/file/d/1maGS4Im6jzkO2Tz1_4W9LkSTzpkp_N9T/view?usp=sharing

@AlexanderPico, the alternative is, of course, the remove the method altogether.

Hi, thank you for your work!
I was wondering if the data could be extracted in a format compatible with igraph.
Hope my question it's not too naive.
Thank you!

(This is not bug report. This is feature request.)

I created an automation Rmd for rWikipathways.
https://nrnb.org/gsod2019_kozo_nishida/html_documents/Rmd/wikipathways-app.html

I thought findPathwaysByText should return data.frame rather than list.
How do you think about this?

Hi all,

How do we color multiple xrefIDs in a single pathway. I am using the R package, "rWikiPathways".
Any suggestions would be appretiated.

Thanks

Alex, can you plz have a look at commit 2ba575e ? It undid the replacement of RJSONIO with rjson :(

Was that by accident?

It's cutoff in the PDF:

And wrong in the HTML of the vignette:
https://www.bioconductor.org/packages/release/bioc/vignettes/rWikiPathways/inst/doc/Overview.html

https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.txt

.txt was changed to .tsv I think.

Is it enough if I change it in the Rmd file or do I also need to change it in the HTML page?