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

Adrian Bivol ABivol at buckinstitute.org
Fri Mar 30 12:19:41 PDT 2012


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
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.


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