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[bioontology-support] Java client for BioPortal REST services?

Trish Whetzel whetzel at
Wed Sep 22 15:06:13 PDT 2010


You can load ontologies to our Stage BioPortal instance:  You may need to register for a separate  
login account on this instance. The only other caveat is that since  
this is a Stage server, the response time from the server may be slow  
at times or the server not accessible.  If you experience prolonged  
access problems, email support at  I've also looped this  
email back to the support mailing list.


On Sep 8, 2010, at 1:30 PM, ben leinfelder wrote:

> Ah, yes, versioning...
> On that topic, is there a development instance of BioPortal running  
> where I could upload an ontology and experiment with how versions  
> are handled and accessed? I'd rather not pollute the 'production'  
> instance with my cruft.
> Our plan is to include versioning information in the URI of the  
> ontology - each version would then have a new URI/namespace, so I'd  
> like to make sure this is possible/feasible. You comments about  
> ontologyId vs. Id were helpful in this respect. Also let me know if  
> I should be directing these sorts of questions to a larger audience.  
> I know how it is when you respond to one simple inquiry and then  
> become the de facto source of information for that person. Though it  
> is very nice to have access to your insight!
> -ben
> On Sep 8, 2010, at 7:30 AM, Trish Whetzel wrote:
>> Hi Ben,
>> Glad the examples helped. Comments inline.
>> On Sep 6, 2010, at 5:10 PM, ben leinfelder wrote:
>>> Trish -
>>> Thanks for putting those examples up. I'm using a few services now  
>>> - easy breezy.
>>> I did have a couple more questions:
>>> -What is the difference between "ontologyId" and "id"? It seems  
>>> like most of the services use "id" as a parameter, but the  
>>> "ontologyId" is displayed here:
>> The ontologyId (also sometimes referred to as the virtual id) is  
>> the identifier for the overall ontology entry.  For each ontology  
>> version, there is also an associated ontology version id. Most of  
>> the services can use either value, but for those that use the  
>> ontologyId there is usually an additional parameter in the web  
>> service signature /virtual/.  When using the web service with the  
>> virtual ontologyId, data is pulled from the most recent version of  
>> the ontology.  More information on the services is documented at:
>>> -Is there anyway to request more return fields be included in the  
>>> search results. Specifically it would be useful to have the 'urn'  
>>> field included when available in the ontology metadata. Perhaps  
>>> I'm not using this field correctly, but I have put the logical URI  
>>> there when registering my ontologies. I use this to refer to my  
>>> ontology when working with tools like OWL API etc... If there's a  
>>> better place to get this identifying URI, please point me in that  
>>> direction.
>> In the Search Bean below [1] from the Search Web service [2], the  
>> conceptId is the URI of the term, the conceptIdShort is the  
>> combination of the ontology namespace abbreviation and term name,  
>> and the preferredName is the name of the term.
>> [1]
>> <searchBean>
>> <ontologyVersionId>44257</ontologyVersionId>
>> <ontologyId>1523</ontologyId>
>> <ontologyDisplayLabel>OBOE SBC</ontologyDisplayLabel>
>> <recordType>RECORD_TYPE_PREFERRED_NAME</recordType>
>> <conceptId></ 
>> conceptId>
>> <conceptIdShort>oboe:Unit</conceptIdShort>
>> <preferredName>Unit</preferredName>
>> <contents>Unit</contents>
>> </searchBean>
>> [2]
>> Hope this helps,
>> Trish
>>> Thanks again!
>>> -ben
>>> On Sep 5, 2010, at 1:03 PM, Trish Whetzel wrote:
>>>> Hi Ben,
>>>> There is a very basic example of how to use the Search web  
>>>> service in Java posted to a new project in our Gforge site, NCBO  
>>>> Sample Code.  Access information is posted at: 
>>>>  and the example client is within /trunk/Java/ 
>>>> BioPortalTermSearch.  There are a few lines that include hard- 
>>>> coded values, but these are noted in the README file.  Let me  
>>>> know if you have any trouble accessing or using the code.    
>>>> Generally, the flow is to build up the set of parameters that are  
>>>> needed for the web service call, send the call (GET or POST), and  
>>>> then process the resulting XML.
>>>> Best regards,
>>>> Trish
>>>> On Sep 2, 2010, at 9:58 AM, ben leinfelder wrote:
>>>>> Hi Trish -
>>>>> It's be great to see what your approach has been. I'm so used to  
>>>>> using webservices with WSDLs and such that it'll be nice to try  
>>>>> something different - even if it is a bit more free-form.
>>>>> Thanks and hope to see something from you soon,
>>>>> -ben
>>>>> On Sep 1, 2010, at 11:17 PM, Trish Whetzel wrote:
>>>>>> Hi Ben,
>>>>>> I have a demo Java client that I use with the Search web  
>>>>>> service. With a bit of clean-up I can send this. We do not have  
>>>>>> an XSD schema for the web services, but example service calls  
>>>>>> and output are provided in the documentation:
>>>>>> .
>>>>>> Trish
>>>>>> On Sep 1, 2010, at 10:26 AM, ben leinfelder wrote:
>>>>>>> Hi,
>>>>>>> I'm wondering if there are any existing Java clients for  
>>>>>>> consuming the services described here:
>>>>>>> I've poked around the GForge repository ( 
>>>>>>> ) for possibilities, but haven't found anything conclusive.
>>>>>>> If I do need to develop my own Java client, are there standard  
>>>>>>> schema for the responses I can get from each service?
>>>>>>> Thanks,
>>>>>>> -ben
>>>>>>> _______________________________________________
>>>>>>> bioontology-support mailing list
>>>>>>> bioontology-support at
>>>>>>> support

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