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[bioontology-support] Bioportal REST services

Sridevi Polavaram spolavar at gmu.edu
Sun Sep 6 05:23:10 PDT 2009


Hi Trish: 
 Thanks for confirming on this. The link http://rest.bioontology.org/bioportal/search/mouse/?ontologyids=1132&isexactmatch=0&email=example@example.org returns results. But I guess since this is a string based search I get results like
Mouse parvovirus 1 (which is a virus)
But I am searching for mouse the animal not viruses or bacteria. 
Is there a way through web services to do such searches? filtering on species? 
If this is a open source where can I find the code for the search services?
Thanks
Sridevi 

----- Original Message -----
From: Trish Whetzel <whetzel at stanford.edu>
Date: Saturday, September 5, 2009 3:07 pm
Subject: Re: [bioontology-support] Bioportal REST services

> 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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