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

Trish Whetzel whetzel at stanford.edu
Fri Mar 30 12:34:12 PDT 2012


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
> 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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