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

jbasco jbasco at rsna.org
Wed Jun 30 11:44:19 PDT 2010


Paul,

You are indeed correct - thanks so much.  I must admit that I had become 
somewhat blinded with using the Hierarchy services since it closely 
resembles our other implementations of trees, but by using the Term 
service with a full list of "relations" I can gather all the information 
I was looking for. I completely forgot that all of the "SubClass" and 
"SuperClass" entries return complete <classBean> objects.

And thanks for pointing me towards the Path service, that may be 
something we can use as well.

Sorry for the confusion and thanks!
James


Paul R Alexander wrote:
> 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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>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>     
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