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[bioontology-support] Bioportal REST services

Sridevi Polavaram spolavar at gmu.edu
Thu Sep 3 08:58:31 PDT 2009


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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