Question: help with KEGG or KEGGSOAP
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gravatar for ALAN SMITH
12.8 years ago by
ALAN SMITH40
ALAN SMITH40 wrote:
Hello, I would like to access the KEGG database from R and a create list of compound IDs from neutral masses. Does anyone know if this is possible in R and if so how one could perform it in R. I also am not able to get the examples to work in KEGGSOAP. The error is this examples occurs in the other expampes ########################################################## > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: KEGGSOAP SSOAP RCurl XML KEGG "1.8.0" "0.4-0" "0.8-0" "1.2-0" "1.8.1" > if(require("SSOAP") && require("XML")){ + genes <- get.genes.by.pathway("path:eco00020") + enzymes <- get.enzymes.by.pathway("path:eco00020") + compounds <- get.compounds.by.pathway("path:eco00020") + reactions <- get.reactions.by.pathway("path:eco00020") + } Error in curlPerform(postfields = txt, writeFunction = bodyDataFun$update, : couldn't connect to host > get.reactions.by.pathway("path:eco00020") Error in curlPerform(postfields = txt, writeFunction = bodyDataFun$update, : couldn't connect to host ############################################################## Currently, I have to query KEGG by hand and is taking considerable time. Any help will be greatly appreciated!!!!! Thank You, Alan Smith University of Wisconsin-Madison
keggsoap • 489 views
ADD COMMENTlink modified 12.8 years ago by Nianhua Li870 • written 12.8 years ago by ALAN SMITH40
Answer: help with KEGG or KEGGSOAP
0
gravatar for Nianhua Li
12.8 years ago by
Nianhua Li870
Nianhua Li870 wrote:
Dear Alan, It is possible to do it in R but not in a easy way. There are a data package "KEGG" and a software package "KEGGSOAP". Currently none of them can solve your problem. KEGG (the database in Japan) updated their Web Service API on Oct 4th, 2006, and added several new methods including "search_compounds_by_mass". We haven't updated KEGGSOAP correspondingly. The error you got with KEGGSOAP may also because of the API update. I will try update KEGGSOAP early next week. But if you are in a hurry, actually you can use SSOAP to access KEGG Web Service API. Sorry that I don't have a clear solution right now... thanks for the report and best wishes nianhua Nianhua Li Computational Biology, PHS, FHCRC
ADD COMMENTlink written 12.8 years ago by Nianhua Li870
Answer: help with KEGG or KEGGSOAP
0
gravatar for Nianhua Li
12.8 years ago by
Nianhua Li870
Nianhua Li870 wrote:
Dear Alan, I have updated KEGGSOAP (1.9.1) in bioconductor 2.0 repository so that it is compatible with KEGG API version 6.0. It should work in R 2.4 (with either SSOAP 0.3 or 0.4) as well. I add functions: * search.compounds.by.name * search.glycans.by.name * search.compounds.by.mass * search.glycans.by.mass * search.compounds.by.composition * search.glycans.by.composition * search.compounds.by.subcomp * search.glycans.by.kcam * bget (useful for generating queries for search.compounds.by.subcomp etc) KEGG API changelog: http://www.genome.jp/kegg/soap/changelog.html KEGG API reference: http://www.genome.jp/kegg/docs/keggapi_manual.html PS: I will send you windows binary offline cheers nianhua
ADD COMMENTlink written 12.8 years ago by Nianhua Li870
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