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[bioontology-support] Bioportal REST services

Sridevi Polavaram spolavar at gmu.edu
Wed Sep 2 12:51:27 PDT 2009


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?email=example@example.org

<?xml version="1.0" encoding="UTF-8"?>
<errorStatus>
  <accessedResource>/bioportal/concepts/parents/38802/mouse</accessedResource>
  <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.>The
> >> >> 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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