[bioontology-support] bioontology-support Digest, Vol 67, Issue 23

[Mona Salem]

Hello 
I need help in retrieving results.

Using the following call:
http://data.bioontology.org/annotator?apikey=4ea81d74-8960-4525-810b-fa1baab
576ff&text=Melanoma%20is%20a%20malignant%20tumor%20of%20melanocytes%20which%
20are%20found%20predominantly%20in%20skin%20but%20also%20in%20the%20bowel%20
and%20the%20eye.&max_level=0&ontologies=NCIT

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
on).  

Thanks
Mona

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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 leicester.ac.uk>
To: Ray Fergerson <ray.fergerson at stanford.edu>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] Form widget problem
Message-ID: <7365B4E6-7B0B-46C9-948A-67725FE7FFC9 at mail.cfs.le.ac.uk>
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
http://bioportal.bioontology.org/ontologies/MESH/?p=widgets if I type the
term "Neoplasms" into the "Example 3" box I get: 

<input id="c_bioportal_concept_id" type="hidden"
value="http://purl.bioontology.org/ontology/MSH/D009369">
<input id="c_bioportal_full_id" type="hidden"
value="http://purl.bioontology.org/ontology/MSH/D009369">

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.

Regards,
Tim


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

> This appears to be working now.
> 
> Ray
> 
> -----Original Message-----
> From: bioontology-support-bounces at lists.stanford.edu
> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of 
> Paul R Alexander
> Sent: Monday, October 28, 2013 11:15 AM
> To: Beck, Tim (Dr.)
> Cc: support at bioontology.org
> 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 leicester.ac.uk>
> 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: http://bioportal.bioontology.org/ontologies/HP/?p=widgets
>> 
>> Is this a temporary problem with HPO?
>> 
>> Thanks for your help.
>> 
>> Regards,
>> Tim
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support



------------------------------

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

Hi all -

I have been trying to get the hierarchical information as displayed on the
web interface @"http://bioportal.bioontology.org/" when a term is searched
in a given ontology -

This is what I intend to achieve =>
https://trac.clinovo.com/clincapture/attachment/ticket/741/howTo.jpg

Context:

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 "http://rest.bioontology.org" (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

--
*Mark Gerard*
 Software Developer
 *mark.gerard at clinovo.com <sophie.mccallum at clinovo.com>*
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