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[bioontology-support] [Fwd: RE: RNSA and NCBO Web services]

Paul R Alexander palexander at stanford.edu
Wed Jun 30 11:28:25 PDT 2010


  James,

Unless I'm missing something I think you could just skip using the 
hierarchy service and instead rely on just the term service to build the 
tree. The term service will return all the information you need to 
construct the tree.

For example, looking at 
http://rest.bioontology.org/bioportal/concepts/42758/?conceptid=root:

The <classBean> element is a representation of a particular concept in 
the ontology. The <relations> element contains an <entry> (entries are 
essentially key/value pairs) with the key 'SubClass', which will be a 
list of <classBean>s that represent child concepts. Each <classBean> 
will also have an entry with the key 'ChildCount' that lists the number 
of children for that class. Using this you should be able to know 
whether a concept is a leaf node.

Also, we have something called the path service that will render a tree 
structure of nested <classBean> elements from any class to any other 
class. We use this for situations in which we might jump into the middle 
of the tree and want to render it properly. See 
http://rest.bioontology.org/bioportal/path/42758/?source=transmed%3ATMO_0028&target=root.

These are the two calls we use when building our tree navigation as they 
provide the most info for the least number of calls. Let me know if this 
would work in your situation or if I can provide any additional info.

Thanks.

Paul Alexander
Web / UI Developer
NCBO BioPortal


On 6/30/10 6:16 AM, jbasco wrote:
> Trish,
>
> Thank you for the info, but that approach would not work (well) when 
> creating a tree since it would require a first call to a Hierarchy 
> service - for all the children of a given concept - followed by 
> additional calls to the Term service for each of the initial results.  
> As you can imagine, the overhead involved in making a specific request 
> for each child would be prohibitive and would become quite taxing to 
> your servers.
>
> Thanks again,
> James
>
>
> Trish Whetzel wrote:
>> Hi James,
>>
>> The Term Web service contains an attribute to indicate how many 
>> children exist for a given term. For example, for the term RID13158 
>> the Term Web service call 
>> (http://rest.bioontology.org/bioportal/concepts/42801/RID13158?email=example@example.org) 
>> <http://rest.bioontology.org/bioportal/concepts/42801/RID13158?email=example@example.org%29> 
>> contains an element <string>ChildCount</string> that indicates that 
>> there are 5 children. Although this information is not in the 
>> Hierarchy Web service, does this element from the Term Web service 
>> meet your needs?
>>
>> Trish
>>
>>
>> On Jun 28, 2010, at 11:19 AM, jbasco wrote:
>>
>>> Hi Trish,
>>>
>>> I've recently returned to my work of integrating the NCBO 
>>> webservices into several RSNA web applications.  Our aim is to use 
>>> the "BioPortal REST services" (wonderfully described 
>>> athttp://www.bioontology.org/wiki/index.php/NCBO_REST_services) to 
>>> use the javascript library ExtJS to create similar functionality to 
>>> that of your existing "Term-selection field" and "Ontology Tree" 
>>> widgets.
>>>
>>> In attempting to create our version of the Tree Widget, I've run 
>>> across a small problem and would like to request an additional 
>>> attribute added to the XML response of one of the Hierarch/Concept 
>>> webservices.  I am populating the tree using the "Get 
>>> children/parents" service (see example link below) which - as it 
>>> should - returns only the concepts that should be currently 
>>> visible.  When a user activates one of these concepts, another AJAX 
>>> call will be made to retrieve the children of that concept and so 
>>> on.  The problem here lies in that the "Get children/parents" 
>>> services does not indicate whether a concept is a leaf node (does 
>>> not have children), so unnecessary requests are made.
>>>
>>> http://rest.bioontology.org/bioportal/concepts/children/42801/RID1?level=1&email=jbasco@rsna.org
>>>
>>> Would it be possible to add some sort of indicator in the response 
>>> of the "Get children/parents" service that determines if each 
>>> concept has a child, such as some sort of "isLeaf" or "hasChildren" 
>>> flag?  Also, if you'd like a further description of what we're doing 
>>> with the NCBO webservices or would like some examples of the code we 
>>> are using, please let me know.
>>>
>>> Thanks for your help in advance,
>>> James
>>>
>>>
>>>
>>> Steve Drew wrote:
>>>> Trish,
>>>>
>>>> As you can see from email thread below, RSNA is working toward 
>>>> integration of Bioportal webservices.  We'll keep you informed as 
>>>> things progress.
>>>>
>>>> Kind Regards, Steve
>>>>
>>>>
>>>>
>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>     Brian Kalbfleisch wrote:
>>>>>>>>      I know james has been looking to integrate bioportal calls
>>>>>>>>     into myRSNA, but I think it is only in development at this
>>>>>>>>     time.
>>>>>>>>
>>>>>>>>         On Tuesday, May 11, 2010 10:03 AM, Steve Drew wrote:
>>>>>>>>
>>>>>>>>         *Date:* Tue, 11 May 2010 10:03:50 -0500
>>>>>>>>         *From:* Steve Drew
>>>>>>>>         *To:* Brian Kalbfleisch <bkalbfleisch at rsna.org>, James
>>>>>>>>         Basco <JBasco at rsna.org>, Bobby Boden <rboden at rsna.org>,
>>>>>>>>         "John W. Basco" <jwbasco at rsna.org>
>>>>>>>>         *cc:* Steve Drew <sdrew at rsna.org>, David Pede
>>>>>>>>         <DPede at rsna.org>
>>>>>>>>         *Subject:* [Fwd: RE: RNSA and NCBO Web services]
>>>>>>>>
>>>>>>>>         Brian et al.,
>>>>>>>>
>>>>>>>>         The following msg is regarding RSNA
>>>>>>>>         using/making-calls-to the NCBO bioportal in lieu of
>>>>>>>>         itsRadLex web applet.  Who should speak with Trish
>>>>>>>>         about her specific questions.... James, Bobby, John, you?
>>>>>>>>
>>>>>>>>         Thanks, Steve
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>         -------- Original Message --------
>>>>>>>>         Subject: 	RE: RNSA and NCBO Web services
>>>>>>>>         Date: 	Mon, 10 May 2010 18:00:03 -0700
>>>>>>>>         From: 	Daniel Rubin <dlrubin at stanford.edu>
>>>>>>>>         To: 	'Trish Whetzel' <whetzel at stanford.edu>
>>>>>>>>         CC: 	<sdrew at rsna.org>
>>>>>>>>         References:
>>>>>>>>         <2D110BE9-9FF1-4EF6-87B5-0881DDEF9134 at stanford.edu>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>         By copying Steve Drew at RSNA he will be able to answer
>>>>>>>>         that question.
>>>>>>>>         -------------------------------------
>>>>>>>>         Daniel Rubin, MD, MS
>>>>>>>>         Assistant Professor, Department of Radiology
>>>>>>>>         Stanford University
>>>>>>>>         Richard M. Lucas Center
>>>>>>>>         1201 Welch Road, Office P285
>>>>>>>>         Stanford, CA 94305-5488
>>>>>>>>         Phone: 650-725-4936  Fax: (650) 723-5795
>>>>>>>>
>>>>>>>>         *From:* Trish Whetzel [mailto:whetzel at stanford.edu]
>>>>>>>>         *Sent:* Monday, May 10, 2010 4:46 PM
>>>>>>>>         *To:* Daniel Rubin
>>>>>>>>         *Subject:* RNSA and NCBO Web services
>>>>>>>>         Hi Daniel,
>>>>>>>>         Do you know of someone from RNSA that is using the NCBO
>>>>>>>>         Web services? I saw the email jbasco at rnsa.org
>>>>>>>>         <mailto:jbasco at rnsa.org> in the logs and thought I
>>>>>>>>         would check with you on this.  I am interested to know
>>>>>>>>         if they are still using the Web service, information
>>>>>>>>         about their project and how the Web services are
>>>>>>>>         used...information to collect for the 2-page supplement
>>>>>>>>         to submit for the NCBO grant renewal.
>>>>>>>>         Trish
>>>>>>>>         Trish Whetzel, PhD
>>>>>>>>         Outreach Coordinator
>>>>>>>>         The National Center for Biomedical Ontology
>>>>>>>>         Ph: 650-721-2378
>>>>>>>>         whetzel at stanford.edu <mailto:whetzel at stanford.edu>
>>>>>>>>         http://www.bioontology.org
>>>>>>>>
>>>>>>
>>>>>>     -- 
>>>>>>     *John Basco *
>>>>>>     /Managing Director, Web Strategy & Operations /
>>>>>>     /Marketing Department /
>>>>>>
>>>>>>     Radiological Society of North America
>>>>>>     820 Jorie Blvd, Oak Brook, IL 60523
>>>>>>     TEL 1-630-590-7745
>>>>>>     FAX 1-630-571-7837
>>>>>>     jwbasco at rsna.org
>>>>>>     RSNA.org <http://www.rsna.org/email.cfm>
>>>>>>
>>>>>>     <http://www.facebook.com/RSNAfans?v=wall&viewas=1429820057&ref=ts>
>>>>>>     <http://twitter.com/RSNA>
>>>>>>     <http://www.linkedin.com/companies/rsna?trk=co_search_results&goback=.cps_1271876483836_1>
>>>>>>
>>>>>>
>>>>>>     RSNA 2010 Annual Meeting <http://www.rsna.org/AnnualMeeting>
>>>>>>     November 28 – December 3
>>>>>>     McCormick Place, Chicago
>>>>>
>>>>>     -- 
>>>>>     *Steve Drew *
>>>>>     /Assistant Executive: /
>>>>>     /Scientific Assembly & Informatics /
>>>>>
>>>>>     Radiological Society of North America
>>>>>     820 Jorie Blvd, Oak Brook, IL 60523
>>>>>     TEL 1-630-571-7879
>>>>>     FAX 1-630-571-7837
>>>>>     sdrew at rsna.org
>>>>>     RSNA.org <http://www.rsna.org/email.cfm>
>>>>>
>>>>>     <http://www.facebook.com/RSNAfans?v=wall&viewas=1429820057&ref=ts>
>>>>>     <http://twitter.com/RSNA>
>>>>>     <http://www.linkedin.com/groups?gid=116568&trk=hb_side_g>
>>>>>
>>>>>     RSNA 2010 Annual Meeting <http://www.rsna.org/AnnualMeeting>
>>>>>     November 28 – December 3
>>>>>     McCormick Place, Chicago
>>>>>
>>>>
>>>> -- 
>>>> *Steve Drew *
>>>> /Assistant Executive: /
>>>> /Scientific Assembly & Informatics /
>>>>
>>>> Radiological Society of North America
>>>> 820 Jorie Blvd, Oak Brook, IL 60523
>>>> TEL 1-630-571-7879
>>>> FAX 1-630-571-7837
>>>> sdrew at rsna.org
>>>> RSNA.org <http://www.rsna.org/email.cfm>
>>>>
>>>> <mime-attachment.jpeg> 
>>>> <http://www.facebook.com/RSNAfans?v=wall&viewas=1429820057&ref=ts><mime-attachment.jpeg> 
>>>> <http://twitter.com/RSNA><mime-attachment.jpeg> 
>>>> <http://www.linkedin.com/groups?gid=116568&trk=hb_side_g>
>>>>
>>>> RSNA 2010 Annual Meeting <http://www.rsna.org/AnnualMeeting>
>>>> November 28 – December 3
>>>> McCormick Place, Chicago
>>
>
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