help with KEGG or KEGGSOAP
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ALAN SMITH ▴ 40
@alan-smith-1941
Last seen 8.1 years ago
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 KEGGSOAP • 713 views
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
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
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
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
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