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[bioontology-support] FW: Question about Root Paths in BioPortal web services

Ray Fergerson ray.fergerson at stanford.edu
Mon Mar 14 15:05:19 PDT 2011


Pradip,

 

Can you look into this? This does sound strange. If it is a bug then
please create a tracker item. Thanks.

 

Ray

 

From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Anthony Wenzel
Sent: Monday, March 07, 2011 7:24 AM
To: support at bioontology.org
Subject: [bioontology-support] Question about Root Paths in BioPortal web
services

 

Hi,

 

My team is working on a research project that is leveraging the BioPortal
web services to gather terminology hierarchy information (specifically in
the SNOMED-CT ontology). Thus far, we have found it generally very easy to
use and understand, so thank you for that.

 

We are using the "rootpath" web service function to determine the path to
root for a given term, using a call such as:

http://rest.bioontology.org/bioportal/virtual/rootpath/1353/126885006?emai
l=example at example.org

 

That call returns 56 root paths, which is fine. Where I'm having
difficulty is in understanding why some "root paths" don't seem to go all
the way to the "root" of the hierarchy. For example, here are two root
paths that are returned from that call (with term names):

.         Neoplasm of trunk(126637008) > Neoplasm of pelvis(126644004) >
Neoplasm of urinary system(126879004) > Neoplasm of urinary tract
proper(254913005)

.         Mass of body structure(300848003) > Mass of body
region(300862005) > Mass of trunk(309524007) > Neoplasm of
trunk(126637008) > Neoplasm of abdomen(128050000)

 

The first root path has 126637008 as it's root element, yet in SNOMED,
that is not a hierarchy root element. In fact, in the second root path,
that same element has 3 parent elements. Can you help me understand why
the root paths don't seem to include elements all the way to one of the
SNOMED root elements? Perhaps I'm misunderstanding the concept of a root
path, in which case I would be grateful if you could provide some insight
to this.

 

Thank you.

Anthony

 

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