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[bioontology-support] Bioportal REST services

Trish Whetzel whetzel at stanford.edu
Sat Sep 5 12:07:15 PDT 2009


The search is a string based search. Given the concept Id that is in  
the search result, additional information about the concept can be  
requested via the Concept web service, http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Concept_services 
.

The BioPortal project is an open source project.

Trish


On Sep 3, 2009, at 8:58 AM, Sridevi Polavaram wrote:

> Hi Trish:
> I have a implementation related question. For the search services, I  
> am curious to know when I search for a concept such as "mouse", does  
> the service do normal string search on "preferred names" and  
> "synonyms" to return the concept IDs in ncbi_taxonomy ontology or  
> does it actually locate the concept by other features such as genus,  
> family, etc.,
> Also, is this an open source code?
> Thanks
> Sridevi
>
> ----- Original Message -----
> From: Sridevi Polavaram <spolavar at gmu.edu>
> Date: Thursday, September 3, 2009 9:00 am
> Subject: Re: RE: RE: RE: RE: [bioontology-support] Bioportal REST  
> services
>
>>
>> Hi Trish:
>> I am trying to access conceptIds programmatically, but this URL:
>> http://rest.bioontology.org/bioportal/search/mouse/?ontologyids=1132&isexactmatch=1&email=example@example.org
>>
>> which is trying to find the ID for the concept mouse in
>> ncbi_taxonomy gives me this result:
>> <success>
>> <accessedResource>/bioportal/search/mouse/
>> <accessDate>2009-09-03 05:56:27.488 PDT
>> <data/>
>> </success>
>>
>> I am think, I am giving the URL right this time!
>> Thanks
>> Sridevi
>>
>> ----- Original Message -----
>> From: Trish Whetzel <whetzel at stanford.edu>
>> Date: Wednesday, September 2, 2009 4:46 pm
>> Subject: RE: RE: RE: RE: [bioontology-support] Bioportal REST  
>> services
>>
>>> The value that is needed in the URL is the concept id, which for
>>> mouse is
>>> NCBITaxon:10090. The resulting URL to get the parents of this
>> term
>>> is:
>>>
>> http://rest.bioontology.org/bioportal/concepts/parents/38802/NCBITaxon:10090 
>> > ?email=example at example.org
>>>
>>> The concept id can be found via the web browser in the term
>>> metadata page in
>>> the id field or programmatically in the conceptId attribute from
>> other> services such as the search service.
>>>
>>> Trish
>>>
>>>
>>>> -----Original Message-----
>>>> From: Sridevi Polavaram [mailto:spolavar at gmu.edu]
>>>> Sent: Wednesday, September 02, 2009 12:51 PM
>>>> To: Trish Whetzel
>>>> Cc: support at bioontology.org
>>>> Subject: Re: RE: RE: RE: [bioontology-support] Bioportal REST
>>> services>
>>>> Hi Trish and others,
>>>> I have been successful in configuring the dependencies for
>>> HttpClient>3.1 and get my program to run. However, here is what I
>>> get as output.
>>>> I have also printed the URL in the first line.
>>>>
>>>> I am trying to access ncbi_taxonomy ontology hierarchy services
>>> and I
>>>> have tried different species terms like Cavia, mouse, mus musculus,
>>>> rattus, all gave the same result!?
>>>> I would really appreciate your response to this.
>>>> Thanks
>>>> Sridevi
>>>>
>>>> ********************* NCBO ANNOTATOR CLIENT TEST
>>>> *************************
>>>>
>>>
>>> URL:http://rest.bioontology.org/bioportal/concepts/parents/38802/mouse?e 
>>> > >mail=example at example.org
>>>>
>>>> <?xml version="1.0" encoding="UTF-8"?>
>>>> <errorStatus>
>>>>
>>>> <accessedResource>/bioportal/concepts/parents/38802/mouse>rce>
>>>> <accessDate>2009-09-02 12:34:54.686 PDT
>>>> <shortMessage>Internal Server Error</shortMessage>
>>>> <longMessage>Error. No parent in hierarchy found.</longMessage>
>>>> <errorCode>500</errorCode>
>>>> </errorStatus>
>>>>
>>>>
>>>> ----- Original Message -----
>>>> From: Trish Whetzel <whetzel at stanford.edu>
>>>> Date: Monday, August 31, 2009 3:50 pm
>>>> Subject: RE: RE: RE: [bioontology-support] Bioportal REST services
>>>>
>>>>> The import (import
>>>>> org.apache.commons.httpclient.methods.GetMethod;) is from
>>>>> Commons HttpClient (3.1). A different method may be needed for
>> use> >> withHttpCore (4.0.1).
>>>>>
>>>>> Trish
>>>>>
>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Sridevi Polavaram [mailto:spolavar at gmu.edu]
>>>>>> Sent: Saturday, August 29, 2009 2:32 PM
>>>>>> To: Trish Whetzel
>>>>>> Cc: support at bioontology.org
>>>>>> Subject: Re: RE: RE: [bioontology-support] Bioportal REST
>> services> >> >
>>>>>> Hi Trish:
>>>>>> I have downloaded the source tar of HttpCore4.0.1 and compiled
>>>>> the jar
>>>>>> files. I have the following jar's:
>>>>>> httpcore-4.0.1-sources.jar
>>>>>> httpcore-4.0.1.jar
>>>>>> httpcore-nio-4.0.1-sources.jar
>>>>>> httpcore-nio-4.0.1.jar
>>>>>> I have included them in my application classpath. However,
>>> still the
>>>>>> following import is not recognized:
>>>>>> import org.apache.commons.httpclient.methods.GetMethod;
>>>>>>
>>>>>> also my client calls are not recognized:
>>>>>> HttpClient client = new HttpClient();
>>>>>> GetMethod method = new
>>>>>> GetMethod(PARENT_URL+inName+"?email=example at example.org");
>>>>>>
>>>>>> I am trying to access the hierarchy services as described here:
>>>>>
>>>
>>>> http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Hierarchy_ 
>>>> > >S
>>>>>> ervices
>>>>>>
>>>>>> Please let me know if I am missing something.
>>>>>> Thanks
>>>>>> Sridevi
>>>>>>
>>>>>> ----- Original Message -----
>>>>>> From: Trish Whetzel <whetzel at stanford.edu>
>>>>>> Date: Wednesday, August 26, 2009 3:55 pm
>>>>>> Subject: RE: RE: [bioontology-support] Bioportal REST services
>>>>>>
>>>>>>> The files can be downloaded from Apache:
>>>>>>> http://hc.apache.org/downloads.cgiand will need to be added
>>> to the
>>>>>>> classpath as you mentioned. The import to
>>>>>>> use for GET methods is: import
>>>>>>> org.apache.commons.httpclient.methods.GetMethod;
>>>>>>>
>>>>>>> Trish
>>>>>>>
>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Sridevi Polavaram [mailto:spolavar at gmu.edu]
>>>>>>>> Sent: Wednesday, August 26, 2009 12:22 PM
>>>>>>>> To: Trish Whetzel
>>>>>>>> Subject: Re: RE: [bioontology-support] Bioportal REST
>> services> >> >> >
>>>>>>>> Hi Trish,
>>>>>>>> Thanks for responding. I have looked at the example, seems
>>>>> like I
>>>>>>> have>to import certain packages.
>>>>>>>> import org.apache.commons.httpclient.HttpClient;
>>>>>>>> import org.apache.commons.httpclient.methods.PostMethod;
>>>>>>>>
>>>>>>>> Since I am interested in hierarchy services, I am not sure
>>> if I
>>>>>>> should>replace the second import with an appropriate import!?
>>>>>>>>
>>>>>>>> If I have to import, I should probably download some jar
>>> files and
>>>>>>> have>them available in my classpath, can you please point
>> me
>>> where>> >> can I find
>>>>>>>> them?
>>>>>>>> Thanks
>>>>>>>> Sridevi
>>>>>>>>
>>>>>>>> ----- Original Message -----
>>>>>>>> From: Trish Whetzel <whetzel at stanford.edu>
>>>>>>>> Date: Wednesday, August 26, 2009 2:41 pm
>>>>>>>> Subject: RE: [bioontology-support] Bioportal REST services
>>>>>>>>
>>>>>>>>> Hi Sridevi,
>>>>>>>>>
>>>>>>>>> There are example clients in Java and Perl for the
>> Annotator> >> >> service,>>
>>>>>>>
>>>>>
>>>
>>>> http://www.bioontology.org/wiki/index.php/ 
>>>> Annotator_Client_Examples.>Th> >e
>>>>>>>>> main difference between that service and the others is
>>> that that
>>>>>>> the>> Annotator uses POST (includes additional parameters not
>>>>>>> specified>> in the
>>>>>>>>> URL) while the other services are GET requests with all
>>>>> parameters>> >> specifiedin the URL. In addition, the results
>> from> >> the GET services
>>>>>>>>> are returned as
>>>>>>>>> XML, as seen when calling the service via the browser,
>> and
>>> will>> >> >> need to be
>>>>>>>>> parsed in the client.
>>>>>>>>>
>>>>>>>>> Trish
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> -----Original Message-----
>>>>>>>>>> From: bioontology-support-bounces at lists.stanford.edu
>>>>>>>>>> [mailto:bioontology-support-bounces at lists.stanford.edu] On
>>>>>>> Behalf Of
>>>>>>>>>> Sridevi Polavaram
>>>>>>>>>> Sent: Wednesday, August 26, 2009 10:30 AM
>>>>>>>>>> To: support at bioontology.org
>>>>>>>>>> Subject: [bioontology-support] Bioportal REST services
>>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>> Is there a clear documentation about how to call the
>>> Bioportal>> >> >> REST web
>>>>>>>>>> services. e.g., I am interested to invoke the hierarchy
>>> service>> >> >> from my
>>>>>>>>>> Java application. The documentation available at:
>>>>>>>>>
>>> http://www.bioontology.org/wiki/index.php/NCBO_REST_services> >>
>>>>>>> explain about the services but not about how to invoke them!
>>>>>>>>>> Thanks
>>>>>>>>>> Sridevi
>>>>>>>>>> _______________________________________________
>>>>>>>>>> bioontology-support mailing list
>>>>>>>>>> bioontology-support at lists.stanford.edu
>>>>>>>>>
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-
>>>>> support>> >>
>>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>
>>>
>>




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