CODEWITHSUNDEEP
rxmlxpath
user5031866
user5031866

Reputation:

R XML xpath queries return NULL or list()

I would like to extract data as dataframes from an XML file available under: http://www.uniprot.org/uniprot/P43405.xml

I only get back empty string although I think that the xpath queries are okay. 

library(RCurl)
library(XML)
url <- "http://www.uniprot.org/uniprot/P43405.xml"
urldata <- getURL(url)
xmlfile <- xmlParse(urldata)

# some xpath queries
xmlfile["//entry/comment[@type='function']/text"]
xmlfile["//entry/comment[@type='PTM']/text"]

xpathSApply(xmlfile,"//uniprot/entry",xmlGetAttr, 'dataset')
xpathSApply(xmlfile,"//uniprot/entry",xmlValue)

Can anyone help me with this problem?

Thanks, Frank

Upvotes: 1

Views: 607

Answers (2)

user5031866
user5031866

Reputation:

Thanks for the help! YEs, the namespaces were missing. I added some additional code. Maybe that will help others to get familiar with XML.

library(RCurl)
library(XML)

url <- "http://www.uniprot.org/uniprot/P43405.xml"
urldata <- getURL(url)
xmlfile <- xmlParse(urldata)

getNodeSet(xmlfile, "//entry//comment")

# one needs the name space here
namespaces <- c(ns="http://uniprot.org/uniprot")

# extract all comments, make a data frame
comments.uniprot <- getNodeSet(xmlfile, "//ns:entry//ns:comment", namespaces)
comments.dataframe <- as.data.frame(sapply(comments.uniprot, xmlValue))
comments.attributes <- as.data.frame(sapply(comments.uniprot, xmlGetAttr,'type'))
comments.all <- cbind(comments.attributes,comments.dataframe)

# only extract PTM comments
PTMs <- getNodeSet(xmlfile, "//ns:entry//ns:comment[@type='PTM']/ns:text", namespaces)
PTMs2 <- sapply(PTMs, xmlValue)
PTMs2.dataframe <- as.data.frame(PTMs2)


xpathSApply(xmlfile,"//ns:uniprot/ns:entry",xmlGetAttr, 'dataset', namespaces=namespaces)
xpathSApply(xmlfile,"//ns:uniprot/ns:entry/ns:accession",xmlValue, namespaces=namespaces)

Upvotes: 0

renato vitolo
renato vitolo

Reputation: 1754

Namespaces are missing:

library(RCurl)
library(XML)

url <- "http://www.uniprot.org/uniprot/P43405.xml"
urldata <- getURL(url)
xmlfile <- xmlParse(urldata)

getNodeSet(xmlfile, "//entry//comment")
namespaces <- c(ns="http://uniprot.org/uniprot")
getNodeSet(xmlfile, "//ns:entry//ns:comment", namespaces)

getNodeSet(xmlfile, "//ns:entry//ns:comment[@type='PTM']/ns:text", namespaces)

xpathSApply(xmlfile,"//ns:uniprot/ns:entry",xmlGetAttr, 'dataset', namespaces=namespaces)
xpathSApply(xmlfile,"//ns:uniprot/ns:entry",xmlValue, namespaces=namespaces)

References:

?xpathApply

How can I use xpath querying using R's XML library?

Upvotes: 1

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