[BioC] KEGGsoap: Space required after the Public Identifier

[Martin Morgan]

Hi seth --

On 01/07/2012 09:58 AM, seth redmond wrote:
> I keep running into the same error when trying to do a genes-to-pathways request in the KEGGsoap package:
>
> I'm new to the package, but as I understand it I should be able to pass a vector of gene IDs and receive back a vector of pathway IDs, however I keep getting a 'xmlns: URI SOAP/KEGG is not absolute' error. This appears to be something to do with the URL for the SOAP server:
>
>>> genes
>> [1] "hsa:728819"    "hsa:100129239" "hsa:441150"    "hsa:440905"    "hsa:389493"    "hsa:645954"
>> [7] "hsa:283711"    "hsa:400645"    "hsa:100128416" "hsa:100128542"
>>> get.pathways.by.genes(genes)
>> xmlns: URI SOAP/KEGG is not absolute
>> xmlns: URI SOAP/KEGG is not absolute
>> character(0)

I think the xmlns: message is not the problem. Instead, I think (a) some 
of your id's do not map to any pathway and (b) get.genes.by.pathway is 
doing an intersection of pathways for each gene. For instance...

 > paths <- list.pathways("hsa")
 > (geneids <- get.genes.by.pathway(paths[[1]]@entry_id))
  [1] "hsa:1431"  "hsa:1737"  "hsa:1738"  "hsa:1743"  "hsa:2271" 
"hsa:3417"
  [7] "hsa:3418"  "hsa:3419"  "hsa:3420"  "hsa:3421"  "hsa:4190" 
"hsa:4191"
[13] "hsa:47"    "hsa:48"    "hsa:4967"  "hsa:50"    "hsa:5091"  "hsa:5105"
[19] "hsa:5106"  "hsa:5160"  "hsa:5161"  "hsa:5162"  "hsa:55753" "hsa:6389"
[25] "hsa:6390"  "hsa:6391"  "hsa:6392"  "hsa:8801"  "hsa:8802"  "hsa:8803"
 > get.pathways.by.genes(geneids[1])
[1] "path:hsa00020" "path:hsa00630" "path:hsa01100"
 > get.pathways.by.genes(geneids[2])
[1] "path:hsa00010" "path:hsa00020" "path:hsa00620" "path:hsa01100"
 > get.pathways.by.genes(geneids[1:2])
[1] "path:hsa00020" "path:hsa01100"

Martin



>>>
>>> KEGGserver<- SOAPServer("http://soap.genome.jp/keggapi/request_v6.0.cgi")
>>> .SOAP(KEGGserver, "get_pathways_by_genes",
>> +                   .soapArgs=list('genes_id_list' = genes),
>> +                   action = KEGGaction, nameSpaces = SOAPNameSpaces(version=1))
>> xmlns: URI SOAP/KEGG is not absolute
>> xmlns: URI SOAP/KEGG is not absolute
>> character(0)
>>>
>>>
>
> There does seem to have been a similar error in relation to the biomaRt package, but I can't see an obvious fix to apply here and I don't seem to be able to find where within the SOAP method this is coming from; if anyone's encountered this before and/or has any advice to offer I'd much appreciate it.
>
> thanks
>
> -s
>
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