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[bioontology-support] Bioportal REST services

Trish Whetzel whetzel at stanford.edu
Wed Sep 2 13:46:38 PDT 2009


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</accessedResou
>rce>
>  <accessDate>2009-09-02 12:34:54.686 PDT</accessDate>
>  <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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