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[bioontology-support] Extracting parent child relationships using the web service

Ray Fergerson ray.fergerson at stanford.edu
Wed Nov 20 16:57:15 PST 2013


Mark,



You should use the “tree” call instead. This is the call the UI uses to 
display the hierarchy. It is tuned to give exactly the necessary 
information.



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



Ray



From: bioontology-support-bounces at lists.stanford.edu 
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Mark 
Gerard
Sent: Tuesday, November 12, 2013 10:49 AM
To: bioontology-support at lists.stanford.edu
Subject: [bioontology-support] Extracting parent child relationships using 
the web service



Hi all -

I have been trying to get the hierarchical information as displayed on the 
web interface @"http://bioportal.bioontology.org/" when a term is searched 
in a given ontology -

This is what I intend to achieve => 
https://trac.clinovo.com/clincapture/attachment/ticket/741/howTo.jpg



Context:

Given the information returned by the web service, we intend to 
programmatic-ally build this hierarchy (really, display the fields as shown 
in the screen shot above) in another system (open source application => 
clincapture) which is using bio-portal as the end point for medical coding.

What I have done so for:

1. I am able to use the old "http://rest.bioontology.org" (I am yet to get 
acquainted with the new web service) to extract the coded term for a given 
verbatim term entered by the user in our system

2. I have tried to work with the view extraction service but it seems to me 
that it only returns one subclass of the concept (the immediate sub class) - 
I am looking for the entire hierarchy

3. I have also tinkered with the RDF term service but it would appear that 
the generated xml does not have the entire hierarchy - It would seem that 
the returned xml cannot allow me to walk back to the root element (as 
depicted on the UX)

I know I am missing something or have probably not looked somewhere, can 
anyone give me some leads as to how I can retrieve the information in the 
tree view (With the hierarchy)? I will really appreciate the help!

Mark



-- 


Mark Gerard

Software Developer

 <mailto:sophie.mccallum at clinovo.com> mark.gerard at clinovo.com

Cell: (256) 794323934

Tel: (256) 794323934

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