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[bioontology-support] Bioportal REST services

Trish Whetzel whetzel at stanford.edu
Thu Sep 3 14:56:15 PDT 2009


It looks like since mouse is a synonym the isexactmatch parameter needs to
be set to 0. I am confirming with the developers on the documentation for
this service.

Trish 


>-----Original Message-----
>From: Sridevi Polavaram [mailto:spolavar at gmu.edu]
>Sent: Thursday, September 03, 2009 6:00 AM
>To: Trish Whetzel
>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&ise
>xactmatch=1&email=example at 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/</accessedResource>
><accessDate>2009-09-03 05:56:27.488 PDT</accessDate>
><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:1
>0090
>> ?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.>T
>h
>> >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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