Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] ontologies filter

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Sep 5 10:34:36 PDT 2017


Hello Mazen,

On Sep 5, 2017, at 9:49 AM, Mazen Alobaidi <malobaid at oakland.edu<mailto:malobaid at oakland.edu>> wrote:

Hi,
I'm using rest call as below, but I want to restricted it with only using MESH.  How I can do this?

http://data.bioontology.org/annotator?text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye.


To restrict search to a particular ontology, you use the “ontologies” parameter, as documented here:

http://data.bioontology.org/documentation#nav_search




if used the filter ontology  I get the below error in rest call using Java

java.io.FileNotFoundException: http://data.bioontology.org/annotator?ontologies=MESH&longest_only=false&exclude_numbers=false&whole_word_only=false&exclude_synonyms=false&text=Melanoma+is+a+malignant+tumor+of+melanocytes+which%2Bare+found+predominantly+in+skin+but+also+in+the+bowel+and+the%2Beye
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)


Without seeing your Java code, it’s difficult to say what’s going wrong. You used the “ontologies” parameter correctly (i.e. ontologies=MESH). Also, entering the above URL in a browser correctly returns results from the annotator endpoint. So, the URL doesn’t appear to be malformed in any way.

A Java error like this was reported on our mailing list previously. You may want to read the post in the archive and see if the suggested solution works for you:

http://ncbo-support.2288202.n4.nabble.com/bioontology-support-java-io-FileNotFoundException-http-data-bioontology-org-ontologies-NCIT-classes-9-td4652641.html

Kind regards,
Jennifer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20170905/c31c47e2/attachment.html>


More information about the bioontology-support mailing list