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[bioontology-support] Mesh Ontology Annotation Produces no results

Marin, Marina Marina.Marin at nyumc.org
Fri Mar 19 08:37:04 PDT 2010


Hi Trish,

Here is a sample list of parameters that we use in our application. However, if you go directly to http://rest.bioontology.org/test_oba.html and input these parameters it would return nothing.
If you go directly to http://bioportal.bioontology.org/annotator, select MeSH Ontology (42142) and put “cancer” into the text to annotate field it would also produce nothing.


"longestOnly" : "false",
"wholeWordOnly" : "true",
"filterNumber" : "true",
"stopWords" : "",
 "withDefaultStopWords" : "true",
"isStopWordsCaseSenstive" : "",
"minTermSize" : "2",
"scored" : "true",
"withSynonyms" : "true",
"ontologiesToExpand" : "",
 "ontologiesToKeepInResult" : "42142",
"isVirtualOntologyId" : "false",
"semanticTypes" : "",
"levelMax" : "0",
"mappingTypes" : "",
textToAnnotate: “cancer”,
format: “xml”

Thanks a lot for your help.

Marina


On 3/19/10 11:26 AM, "Trish Whetzel" <whetzel at stanford.edu> wrote:

Can you send a list of parameters that your application uses to access the Annotator Web Service, e.g. longestOnly, stopWords, etc. as well as a small example of sample text?

Best regards,
Trish


On Mar 19, 2010, at 8:18 AM, Marin, Marina wrote:

Dear Sir or Madame,

We, at NYU Medical Center have just deployed an application that uses NCBO Annotator Web Service to generate MeSH terms from a medical course goals and objectives.
The tool worked great until very recently, when, the Mesh ontology (42142, former 40401) would not produce any results using either http://bioportal.bioontology.org/annotator or http://rest.bioontology.org/test_oba.html
Please, advise.

Thank you.

Marina Marin
Senior Applications Programmer
Division of Educational Informatics
New York University School of Medicine
550 First Avenue, Coles 202
New York, NY 10016
Tel: (212) 263-2058



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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org






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