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[bioontology-support] *bump* subtree search in the new API

Ray Fergerson ray.fergerson at stanford.edu
Thu Oct 24 14:35:02 PDT 2013


Sorry for not getting back to you. Yes, search in subtree is not
implemented in the new API. It should be. I have created a tracker item
for it. Note that, if you are in a real hurry, you can roll your own with
something like:

 

Search for <string>

Foreach <returned class>

                If class.get_ancestors().contains(subtree_root)

                                Do something

 

This is essentially our internal algorithm as well.

 

Ray

 

 

From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Lee M
Surprenant
Sent: Thursday, October 24, 2013 11:55 AM
To: support
Subject: [bioontology-support] *bump* subtree search in the new API

 

Any chance someone could look into this?

----- Forwarded by Lee M Surprenant/Raleigh/IBM on 10/24/2013 02:50 PM
-----

From: Lee M Surprenant/Raleigh/IBM
To: support <support at bioontology.org>
Date: 10/17/2013 04:02 AM
Subject: subtree search in the new API

  _____  



Does the new REST API support subtree search?

For instance, the v1 API supported it via subtreerootconceptid parameter
(when used with a single ontologyids value):
 
<http://rest.bioontology.org/bioportal/search/?query=history%20and%20physi
cal&ontologyids=1032&subtreerootconceptid=C43431&includeproperties=1&inclu
dedefinitions=true&pagesize=15&apikey=04631342-bf42-4906-8a13-3c12d2670f6c
>
http://rest.bioontology.org/bioportal/search/?query=history%20and%20physic
al&ontologyids=1032&subtreerootconceptid=C43431&includeproperties=1&includ
edefinitions=true&pagesize=15&apikey=YOUR_API_KEY_HERE


A potential substitute for subtree search for me would be the ability to
scope/filter a search by 'semantic type' but I couldn't figure that out
either.

In fact, I can't even get the search to include the semantic type in the
results.  For this information I must make a separate API call per search
result?

The documentation didn't make it clear if the 'Common Parameters' were
intended to work with search/annotator/resourceIndex endpoints or just the
resources themselves.  I assume the latter because using the 'include'
parameter on the search endpoint caused an "Internal Server Error":
 
<http://data.bioontology.org/search?q=melanoma&ontologies=NCIT&include=all
&apikey=YOUR_API_KEY>
http://data.bioontology.org/search?q=melanoma&ontologies=NCIT&include=all&
apikey=YOUR_API_KEY_HERE

thanks,

Lee Surprenant
IBM Emerging Technologies | jStart Team

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