Annotator R Client - Revision history

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

2013-12-19T17:41:14Z

Example: minor tweaks for clarity

Andrew Su: fix xpath

2013-03-22T00:52:04Z

fix xpath

Whetzel: /* Example */

2012-11-16T23:43:42Z

Example

Whetzel: /* Example */

2012-11-15T19:04:44Z

Example

Whetzel at 00:09, 25 May 2011

2011-05-25T00:09:37Z

Whetzel at 00:09, 25 May 2011

2011-05-25T00:09:16Z

Whetzel: New page: === Annotator Client in R ===

 # # sample client for NCBO Annotator in R # Author: Andrew Su (andrew.su@gmail.com) #  AnnotatorURL <- "http://rest.bioontology.org/obs/annotator"  que...

2011-05-25T00:08:43Z

New page: === Annotator Client in R === <pre> # # sample client for NCBO Annotator in R # Author: Andrew Su (andrew.su@gmail.com) # AnnotatorURL <- "http://rest.bioontology.org/obs/annotator" que...

New page

=== Annotator Client in R ===

<pre>
#
# sample client for NCBO Annotator in R
# Author: Andrew Su (andrew.su@gmail.com)
#

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"="true",
"wholeWordOnly"="true",
"filterNumber"="true",
"withDefaultStopWords"="true",
"isStopWordsCaseSensitive"="false",
"minTermSize"="3",
"scored"="true",
"withSynonyms"="true",
"ontologiesToExpand"="40403,40644,40401,44764",
"ontologiesToKeepInResult"="40403,40644,40401,44764",
"isVirtualOntologyId"="false",
"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/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>

← Older revision		Revision as of 00:09, 25 May 2011
Line 1:		Line 1:
−	=== ~~Annotator Client in R~~ ===	+	=== Example ===

	<pre>		<pre>

@@ Line 7: / Line 7: @@
+#
-queryText <- "Melanoma is a malignant tumor of melanocytes which are found predominantly in skin but also in the bowel and the eye"
+annotate.it <- function( queryText, yourAPIKey ) {
      library(RCurl)
@@ Line 22: / Line 16: @@
      res<- postForm('http://rest.bioontology.org/obs/annotator',
              "textToAnnotate"=queryText,
-			"apikey"=YourAPIKey,
+			"apikey"=yourAPIKey,
              "style"="POST",
              "longestOnly"="false",
@@ Line 83: / Line 77: @@
+     }
+}
 </pre>

@@ Line 64: / Line 64: @@
      resultNodes <- getNodeSet(x, "/success/data/annotatorResultBean/annotations/annotationBean/context")
      for( result in resultNodes ) {
-        localConceptId <- xmlValue(getNodeSet(result,"./term/localConceptId")[[1]])
+        localConceptId <- xmlValue(getNodeSet(result,"./term/concept/localConceptId")[[1]])
         print( paste( "ID = ", localConceptId ) )

@@ Line 32: / Line 32: @@
 			"scored"="true",
 			"withSynonyms"="true",
-             "ontologiesToExpand"="40403,40644,40401,44764",
+             "ontologiesToExpand"="1353,1032,1351,1009",
-             "ontologiesToKeepInResult"="40403,40644,40401,44764",
+             "ontologiesToKeepInResult"="1353,1032,1351,1009",
-			"isVirtualOntologyId"="false",
+			"isVirtualOntologyId"="true",
              "semanticTypes"="T017,T047,T191,T999",
              "levelMax"="0",

@@ Line 24: / Line 24: @@
 			"apikey"=YourAPIKey,
              "style"="POST",
-             "longestOnly"="true",
+             "longestOnly"="false",
              "wholeWordOnly"="true",
 			"filterNumber"="true",