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

Adrian Bivol ABivol at buckinstitute.org
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:
<string>441900009.312415009.41175001.259554009.301861005</string>

2. I believe this won't work for old (obsolete) concepts, such as:
http://rest.bioontology.org/bioportal/virtual/rootpath/1353/73234000?apikey=XXX
This is 'Surfactant':
http://rest.bioontology.org/bioportal/search/?query=73234000&ontologyids=1353&apikey=XXX

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?
http://rest.bioontology.org/bioportal/virtual/rootpath/1353/422248006?apikey=XXX

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 stanford.edu]
Sent: Friday, March 30, 2012 12:34 PM
To: Adrian Bivol
Cc: support at bioontology.org; 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:
http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?apikey=YourAPIKey

Trish

[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology


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 bioontology.org<mailto:support at bioontology.org>
Subject: is-a transitive closure (path to root)

Hi,

I would like to obtain the is-a transitive closure generated by the annotator as described here:
http://www.bioontology.org/wiki/index.php/Annotator_User_Guide#The_is_a_transitive_closure_expansion_component

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:
http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Get_a_path_between_a_term_and_the_root
http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology

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

Example:
http://rest.bioontology.org/bioportal/path/46896/?source=33934002&target=root&apikey=XXX

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
http://www.bioontology.org

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