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[bioontology-support] NCBO Annotator WebService

Eugenia Galeota eugenia.galeota at
Wed Jul 23 09:16:40 PDT 2014

To whom who may concern,
my name is Eugenia and I’m a post doc at the Center for genomic Science of the Italian Institute of Technology. I’m trying to annotate GEO metadata using BRENDA ontology and DISEASE ONTOLOGY and I would like to use the NCBO Annotator REST API. I spent some time looking at the documentation provided at and also found the Reccomender example R code. I managed to write some R code to query the Annotator, anyway I’ve not been able to find a more clear explanation of the tunable parameters. For example, when you specify exact_match=FALSE how many mismatches in the word are allowed? Is there a way to obtain matches for plurals or do I have to apply some stemming before? why mappings are always empty even if i set the parameter =“all”? Do you provide a way to exclude parent concepts where there is a more specific match? (As an example, in a sentence containing the words “BRAIN EMBRYONIC FIBROBLAST” i get “EMBRYO”, “FIBROBLAST”, “EMBRYONIC FIBROBLAST” and “BRAIN” but I would like to exclude “EMBRYO” and “FIBROBLAST”).
Below you can look at how I usually query the annotator. I would also like to ask if the apikey that I have obtained can be used by an application, since I’m writing an R package for bioconductor. 

  resultDF <- NULL		
  results_list <- NULL
  # Process each sentence
  # ----------------------------------------------------------------------------------------------------
  for (sentence_id in 1:length(samples_sentences)) {
  		curr_sentence <- as.character(samples_sentences[sentence_id]) # current sentence to process
		cat("#", sentence_id, "from", length(samples_sentences), ":", curr_sentence, "\n")  		
		JSONannotation <- postForm(REST_URL,
    		#"include" = "all"
    		"mappings"= "all",

I’m sorry for asking you all these questions by e-mail, but I didn’t find any alternative (even looking at the questions in the google group). Can you please help me? Thanks,


Eugenia Galeota, PhD 
Center for Genomic Science of IIT at SEMM
Computational Epigenomics
Email: eugenia.galeota at
Tel: +39 02 9437 5046
Via Adamello 16, 20139 Milan, Italy

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