Annotator R Client

2013-12-19T17:41:14Z

Andrew Su: /* Example */ minor tweaks for clarity

=== Example ===

<pre>
#
# sample client for NCBO Annotator in R
# Author: Andrew Su
#

annotate.it <- function( queryText, yourAPIKey ) {

library(RCurl)
library(XML)

# Login to BioPortal to get YourAPIKey
res<- postForm('http://rest.bioontology.org/obs/annotator',
"textToAnnotate"=queryText,
"apikey"=yourAPIKey,
"style"="POST",
"longestOnly"="false",
"wholeWordOnly"="true",
"filterNumber"="true",
"withDefaultStopWords"="true",
"isStopWordsCaseSensitive"="false",
"minTermSize"="3",
"scored"="true",
"withSynonyms"="true",
"ontologiesToExpand"="1353,1032,1351,1009",
"ontologiesToKeepInResult"="1353,1032,1351,1009",
"isVirtualOntologyId"="true",
"semanticTypes"="T017,T047,T191,T999",
"levelMax"="0",
"mappingTypes"="null",
"format"="xml",
"email"="YourEmail@Somewhere.com")

x <- xmlInternalTreeParse(res)

matchedConcepts <- list()
conceptNodes <- getNodeSet(x,"/success/data/annotatorResultBean/annotations/annotationBean/concept")
for( concept in conceptNodes ) {
localConceptId <- xmlValue(getNodeSet(concept,"./localConceptId")[[1]])
print( paste( "ID = ",localConceptId ))

preferredName <- xmlValue(getNodeSet(concept,"./preferredName")[[1]])
print( paste( "Name = ",preferredName ))

semanticType <- xmlValue(getNodeSet(concept,"./semanticTypes/semanticTypeBean/semanticType")[[1]])
print( paste( "Type = ",semanticType ))

description <- xmlValue(getNodeSet(concept,"./semanticTypes/semanticTypeBean/description")[[1]])
print( paste( "Type name = ",description ))

matchedConcepts[[localConceptId]] <- preferredName
}

matchedPhrase <- list()
resultNodes <- getNodeSet(x, "/success/data/annotatorResultBean/annotations/annotationBean/context")
for( result in resultNodes ) {
localConceptId <- xmlValue(getNodeSet(result,"./term/concept/localConceptId")[[1]])
print( paste( "ID = ", localConceptId ) )

term.name <- xmlValue(getNodeSet(result,"./term/name")[[1]])
print( paste( "Match = ", term.name ) )

from <- xmlValue(getNodeSet(result,"./from")[[1]])
print( paste( "From = ", from ) )

to <- xmlValue(getNodeSet(result,"./to")[[1]])
print( paste( "To = ", to ) )

matchedPhrase[[localConceptId]] <- term.name
}

for( key in names(matchedConcepts) ) {
print(paste(key,matchedConcepts[[key]],"matched",matchedPhrase[[key]]))
}
}

queryText <- "Melanoma is a malignant tumor of melanocytes which are found predominantly in skin but also in the bowel and the eye"

# Instructions on getting an API key are at http://www.bioontology.org/wiki/index.php/Annotator_User_Guide#Annotator_Web_service_Validation
yourAPIKey <- "XXXXXXXXXXXXX"

annotate.it( queryText, yourAPIKey )

</pre>

Annotator R Client

2013-03-22T00:52:04Z

Andrew Su: fix xpath

=== Example ===

<pre>
#
# sample client for NCBO Annotator in R
# Author: Andrew Su
#

AnnotatorURL <- "http://rest.bioontology.org/obs/annotator"

queryText <- "Melanoma is a malignant tumor of melanocytes which are found predominantly in skin but also in the bowel and the eye"

annotate.it( queryText )

annotate.it <- function( queryText ) {

library(RCurl)
library(XML)

# Login to BioPortal to get YourAPIKey
res<- postForm('http://rest.bioontology.org/obs/annotator',
"textToAnnotate"=queryText,
"apikey"=YourAPIKey,
"style"="POST",
"longestOnly"="false",
"wholeWordOnly"="true",
"filterNumber"="true",
"withDefaultStopWords"="true",
"isStopWordsCaseSensitive"="false",
"minTermSize"="3",
"scored"="true",
"withSynonyms"="true",
"ontologiesToExpand"="1353,1032,1351,1009",
"ontologiesToKeepInResult"="1353,1032,1351,1009",
"isVirtualOntologyId"="true",
"semanticTypes"="T017,T047,T191,T999",
"levelMax"="0",
"mappingTypes"="null",
"format"="xml",
"email"="YourEmail@Somewhere.com")

x <- xmlInternalTreeParse(res)

matchedConcepts <- list()
conceptNodes <- getNodeSet(x,"/success/data/annotatorResultBean/annotations/annotationBean/concept")
for( concept in conceptNodes ) {
localConceptId <- xmlValue(getNodeSet(concept,"./localConceptId")[[1]])
print( paste( "ID = ",localConceptId ))

preferredName <- xmlValue(getNodeSet(concept,"./preferredName")[[1]])
print( paste( "Name = ",preferredName ))

semanticType <- xmlValue(getNodeSet(concept,"./semanticTypes/semanticTypeBean/semanticType")[[1]])
print( paste( "Type = ",semanticType ))

description <- xmlValue(getNodeSet(concept,"./semanticTypes/semanticTypeBean/description")[[1]])
print( paste( "Type name = ",description ))

matchedConcepts[[localConceptId]] <- preferredName
}

matchedPhrase <- list()
resultNodes <- getNodeSet(x, "/success/data/annotatorResultBean/annotations/annotationBean/context")
for( result in resultNodes ) {
localConceptId <- xmlValue(getNodeSet(result,"./term/concept/localConceptId")[[1]])
print( paste( "ID = ", localConceptId ) )

term.name <- xmlValue(getNodeSet(result,"./term/name")[[1]])
print( paste( "Match = ", term.name ) )

from <- xmlValue(getNodeSet(result,"./from")[[1]])
print( paste( "From = ", from ) )

to <- xmlValue(getNodeSet(result,"./to")[[1]])
print( paste( "To = ", to ) )

matchedPhrase[[localConceptId]] <- term.name
}

for( key in names(matchedConcepts) ) {
print(paste(key,matchedConcepts[[key]],"matched",matchedPhrase[[key]]))
}
}

</pre>

NCBO Wiki - User contributions [en]

Annotator R Client

Annotator R Client