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[bioontology-support] procedures CPT

Arvinder Choudhary achoudhary at kumc.edu
Tue May 25 09:53:49 PDT 2010


We trying to build CPT hierarchy table (umls) 
In the code (ComputeHierarchies.java) what Production service URL should put instead of the below serverURL
    private static final String serverUrl ="http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obs/";
 

>>> Nigam Shah <nigam at stanford.edu> 5/25/2010 10:35 AM >>>
Hey .. you are hitting the ncbolabs-dev2 machine ... that is our sandbox. Please use the production service URLs from the wiki links below. The prod boxes should not time out.

Also, if you run into issues on hitting prod, email support at bioontology.org .. I am out of town starting today (actually on vacation right now) so might not be able to respond.

Regards,
Nigam.


On Tue, May 25, 2010 at 8:18 AM, Arvinder Choudhary <achoudhary at kumc.edu> wrote:


Nigam:
While executing the step 5 to create a file we are getting time out issue (attaching the snapshot to the email). Please advice
Arvinder





1 - you specify an ontology to extract (or a root node that you want to extract the branch under)

2 - the code simply calls the services at: http://www.bioontology.org/wiki/index.php/NCBO_REST_services
 ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services )- specifically "get term" http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_term_for_latest_ontology_version_id
- and then recursively "get children" http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_parents.2Fchildren_of_a_given_concept_in_the_latest_version_of_a_given_ontology

 ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_parents.2Fchildren_of_a_given_concept_in_the_latest_version_of_a_given_ontology )3 - parses the XML using a few XPATH expressions and writes out the information the information in the i2b2 format.






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