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[bioontology-support] I need the json file output sent to an actual file, not to the screen

Mona Salem monasalem123 at
Thu Nov 14 15:50:15 PST 2013

I need help in retrieving results.

Using the following call:

How can I get the json file sent to an actual file, and not dumped to the
screen?  I wish to capture the preferred names (for the project I am working


-----Original Message-----
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Sent: Tuesday, November 12, 2013 12:08 PM
To: bioontology-support at
Subject: bioontology-support Digest, Vol 67, Issue 23

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Today's Topics:

   1. Re: Form widget problem (Beck, Tim  (Dr.))
   2. Extracting parent child relationships using	the web service
      (Mark Gerard)


Message: 1
Date: Tue, 12 Nov 2013 12:16:09 +0000
From: "Beck, Tim  (Dr.)" <tb143 at>
To: Ray Fergerson <ray.fergerson at>
Cc: "support at" <support at>
Subject: Re: [bioontology-support] Form widget problem
Message-ID: <7365B4E6-7B0B-46C9-948A-67725FE7FFC9 at>
Content-Type: text/plain; charset="us-ascii"

Thanks Ray.

Regarding the form widget again: I get the same values for both the
"a_bioportal_concept_id" and "a_bioportal_full_id" attributes.

For example, from if I type the
term "Neoplasms" into the "Example 3" box I get: 

<input id="c_bioportal_concept_id" type="hidden"
<input id="c_bioportal_full_id" type="hidden"

However, I would expect the concept id to have a value of "D009369".

This duplication of values also seems to occur for the other ontologies I'm
interested in.

Is this a fault or have I misunderstood what the concept id relates to?

Thanks for your help.


On 1 Nov 2013, at 18:57, Ray Fergerson <ray.fergerson at> wrote:

> This appears to be working now.
> Ray
> -----Original Message-----
> From: bioontology-support-bounces at
> [mailto:bioontology-support-bounces at] On Behalf Of 
> Paul R Alexander
> Sent: Monday, October 28, 2013 11:15 AM
> To: Beck, Tim (Dr.)
> Cc: support at
> Subject: Re: [bioontology-support] Form widget problem
> Tim,
> This is a (hopefully) temporary problem with HPO. We are reprocessing 
> the ontology today.
> Also, Trish is no longer with NCBO. You can continue to email the 
> support list to get assistance.
> Paul
> On Oct 25, 2013, at 4:21 AM, Beck, Tim (Dr.) <tb143 at>
> wrote:
>> Hi BioPortal team, hi Trish,
>> The "Term-selection field on a form" widget works fine for other
> ontologies I'm interested in, however I'm not seeing any terms from 
> the Human Phenotype Ontology when I attempt to list terms from all 
> ontologies
> (class="bp_form_complete-all-uri") or specifically HPO.
>> Also, the "Form Autocomplete" demo on your website doesn't seem to be
> working:
>> Is this a temporary problem with HPO?
>> Thanks for your help.
>> Regards,
>> Tim
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at


Message: 2
Date: Tue, 12 Nov 2013 21:49:14 +0300
From: Mark Gerard <mark.gerard at>
To: bioontology-support at
Subject: [bioontology-support] Extracting parent child relationships
	using	the web service
	<CALbVH61Jj7BAbUBz5OLEuwXvj5aYM7KD3fB_+iHUMR7iN9Lo6A at>
Content-Type: text/plain; charset="utf-8"

Hi all -

I have been trying to get the hierarchical information as displayed on the
web interface @"" when a term is searched
in a given ontology -

This is what I intend to achieve =>


Given the information returned by the web service, we intend to
programmatic-ally build this hierarchy (really, display the fields as shown
in the screen shot above) in another system (open source application =>
clincapture) which is using bio-portal as the end point for medical coding.

What I have done so for:

1. I am able to use the old "" (I am yet to get
acquainted with the new web service) to extract the coded term for a given
verbatim term entered by the user in our system

2. I have tried to work with the view extraction service but it seems to me
that it only returns one subclass of the concept (the immediate sub class)
- I am looking for the entire hierarchy

3. I have also tinkered with the RDF term service but it would appear that
the generated xml does not have the entire hierarchy - It would seem that
the returned xml cannot allow me to walk back to the root element (as
depicted on the UX)

I know I am missing something or have probably not looked somewhere, can
anyone give me some leads as to how I can retrieve the information in the
tree view (With the hierarchy)? I will really appreciate the help!


*Mark Gerard*
 Software Developer
 *mark.gerard at <sophie.mccallum at>*
  *Cell*: (256) 794323934
 *Tel*: (256) 794323934
 * <>*

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