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[bioontology-support] is-a transitive closure (path to root)

Adrian Bivol ABivol at
Mon Apr 2 21:46:17 PDT 2012

Hi Trish,

I tried you suggestion and I still have a few questions:

1. I believe the path to root is returned in this string, as multiple concept ids concatenated:

2. I believe this won't work for old (obsolete) concepts, such as:
This is 'Surfactant':

Is there any way to obtain the path to root for old/obsolete concepts?

3. In some cases, multiple paths are returned. I am assuming the is-a transitive closure includes all of them?

4. I am hoping that the returned path only uses the 'is-a' edges (relations) in the ontology tree.

Thank you,
Adrian Bivol.

From: Trish Whetzel [whetzel at]
Sent: Friday, March 30, 2012 12:34 PM
To: Adrian Bivol
Cc: support at; Tobias Wittkop
Subject: Re: is-a transitive closure (path to root)

Hi Adrian,

I am looking into this now. A quick question, the REST call you provide does not seem to be the call to get the path from the leaf to the root [1]. Do you mean to use a call such as:



On Mar 30, 2012, at 3:19 PM, Adrian Bivol wrote:

Adding Trish:

Hi Trish, can you help us with the question below?

FYI - I am working for the Mooney lab, and I attended the bio-ontology tutorial at Stanford this year.

Thank you,
Adrian Bivol.

From: Adrian Bivol
Sent: Wednesday, March 28, 2012 3:29 PM
To: support at<mailto:support at>
Subject: is-a transitive closure (path to root)


I would like to obtain the is-a transitive closure generated by the annotator as described here:

To get that, I am trying to get the path to the root for a concept (in an ontology), using the the is_a relations.

I found this:

But I do not know exactly how to extract & parse the path (list of nodes) from the XML returned.


This should get the path from concept ID 33934002 to root, in SNOMED.

Can you help?

Thank you,
Adrian Bivol.

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378

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