Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] OpenMDR Integration

Natasha F. Noy noy at stanford.edu
Tue Aug 31 13:35:52 PDT 2010


Rakesh,

You should not be encoding "&" as "&" in the URL. You do this only  
inside an HTML page (see [1], for example). So, in the first call,  
BIoPortal simply ignores the ontologyid and hence your result set is  
not limited to 1032 (thus, far more results).

If you want to pass an encoded URL, it will look like this:
http%3A%2F%2Frest.bioontology.org%2Fbioportal%2Fsearch%2FDischarge 
%3Femail%3Drakesh.dhaval%40osumc.edu%26ontologyids%3D1032

Hope this helps.

Natasha

[1] http://htmlhelp.com/tools/validator/problems.html#amp


On Aug 31, 2010, at 1:14 PM, Nigam Shah wrote:

> Hmm that is weird. URL encoding should not change the results! I am  
> copying support at bioontology.org so that a bug gets logged for this.
>
> regards,
> nigam.
>
> On Tue, Aug 31, 2010 at 12:49 PM, Dhaval, Rakesh <Rakesh.Dhaval at osumc.edu 
> > wrote:
> Nigam,
> The url encoded url for example: http://rest.bioontology.org/bioportal/search/Discharge?email=rakesh.dhaval@osumc.edu&ontologyids=1032 
>  returns 884 results, whereas http://rest.bioontology.org/bioportal/search/Discharge?email=rakesh.dhaval@osumc.edu&ontologyids=1032 
>  returns 16 results. I am hoping to get 16 results since that is the  
> number of matches which ontology id 1032 has.
>
> Any thoughts on this?
>
> Thanks,
> Rakesh
>
>
>
>
> On 8/30/10 1:28 PM, "Nigam Shah" <nigam at stanford.edu> wrote:
>
> Here is the message thread ..
>
> regards,
> Nigam.
>
> ---------- Forwarded message ----------
> From: Dhaval, Rakesh <Rakesh.Dhaval at osumc.edu>
> Date: Fri, Aug 13, 2010 at 11:17 AM
> Subject: Re: OpenMDR Integration
> To: Nigam Shah <nigam at stanford.edu>
> Cc: "Wynden, Rob" <Rob.Wynden at ucsf.edu>
>
>
> Thanks Nigam.
> I will take a look at these and will let you know if I have any  
> questions.
>
> Thanks,
> Rakesh
>
>
>
>
> On 8/13/10 2:13 PM, "Nigam Shah" <nigam at stanford.edu <http://nigam@stanford.edu 
> > > wrote:
>
> Hi Rakesh,
>
> http://www.bioontology.org/wiki/index.php/NCBO_REST_services is the  
> place you want to look at. For example, if you wanted to query for  
> "melanoma" in SNOMEDCT. Here is what you would do:
>
> 1 - get a list of all ontologies in Bioportal
> http://rest.bioontology.org/bioportal/ontologies?email=example@example.org
>
>  <http://rest.bioontology.org/bioportal/ontologies?email=example@example.org 
> > 2 - find SNOMEDCT:
>
> <ontologyBean>
> <id>
> 42789
> </id>
> <ontologyId>
> 1353
> </ontologyId>
> <displayLabel>
> SNOMED Clinical Terms
> </displayLabel>
>    :
> </ontologyBean>
>
> 3 - pick the ontologyId (1353)
>
> 4 - Go to the search service and access:
>
> http://rest.bioontology.org/bioportal/search/Melanoma?email=example@example.org&ontologyids=1353
>
> (other parameters are:
> 	• ontologyids=<ontologyid>,<ontologyid>… - limits the search to  
> specific ontologies (default: all ontologies)
> 	• isexactmatch=[1/0] – match the entire concept name (default: 0)
> 	• includeproperties=[1/0] – include attributes in the search  
> (default: 0)
> 	• pagesize=<pagesize> - the number of results to display in a  
> single request (default: all)
> 	• pagenum=<pagenum> - the page number to display (pages are  
> calculated using <total results>/<pagesize>) (default: 1)
> 	• maxnumhits=<maxnumhits> - the maximum number of top matching  
> results to return (default: 1000)
> 	• subtreerootconceptid=<uri-encoded conceptid> - narrow the search  
> to concepts residing in a sub-tree, where the "subtreerootconceptid"  
> is the root node. This feature requires a SINGLE <ontologyid> passed  
> in using the "onotlogyids" parameter.
> )
>
> 5 - Once you have found the hit you want example:
>
>
> <searchBean>
> <ontologyVersionId>
> 42789
> </ontologyVersionId>
> <ontologyId>
> 1353
> </ontologyId>
> <ontologyDisplayLabel>
> SNOMED Clinical Terms
> </ontologyDisplayLabel>
> <recordType>
> RECORD_TYPE_SYNONYM
> </recordType>
> <conceptId>
> http://purl.bioontology.org/ontology/SNOMEDCT/2092003
> </conceptId>
> <conceptIdShort>
> 2092003
> </conceptIdShort>
> <preferredName>
> Malignant melanoma
> </preferredName>
> <contents>
> Melanoma
> </contents>
> </searchBean>
>
> You can then access its HTML at: http://purl.bioontology.org/ontology/SNOMEDCT/2092003
>
> or you can call another service on the search result using the  
> conceptIdShort (or the conceptId) fields. Example,
>
> http://rest.bioontology.org/bioportal/virtual/ontology/1353/2092003
>
> .. which will get you all the info you need to create a concept in  
> openMDR using Bioportal as as source.
>
> Note that this is just one example. The services at http://www.bioontology.org/wiki/index.php/NCBO_REST_services 
>  also allow you to get all terms, get a specific branch, get child  
> nodes, search a subtree etc. You could now create a data element  
> called "Melanoma" and store its "range" (e.g. severe, metastatic  
> etc) in openMDR and associate it with "Melanoma" for HOM and others  
> to use. (this is a cartoon example, but you get the idea).
>
> Regards,
> Nigam.
>
>
> On Fri, Aug 13, 2010 at 10:54 AM, Dhaval, Rakesh <Rakesh.Dhaval at osumc.edu 
>  <http://Rakesh.Dhaval@osumc.edu> > wrote:
> Hi Nigam,
> Currently, openMDR is able to query NCI Thesaurus and Metathesaurus  
> through their LexEVS REST interface. We would like to be able to  
> query terminologies and ontologies stored in BioPortal so as to make  
> it more applicable to the domain of translational research. At this  
> point of time,  we would like to be able to query Bioportal using  
> its REST interface. I believe it is a little different from what  
> LexEVS has, and you have your own wrapper sitting on top of the  
> LexBIG database. Any clarification and pointers to documentation  
> would help for a start.
>
> I had interacted with Trish previously and also had a chance to meet  
> her during the caBIG/VCDE meeting. I had expressed my interest in  
> using Bioportal as a source of concepts for data element creation in  
> openMDR. I know Philip has had a few talks with Trish regarding  
> using Bioportal too.
>
> Thanks,
> Rakesh
>
>
>
>
> On 8/11/10 2:42 PM, "Nigam Shah" <nigam at stanford.edu <http://nigam@stanford.edu 
> >  <http://nigam@stanford.edu> > wrote:
>
> Thanks Rob. Hi Rakesh!.
>
> Happy to answer questions as to what kind of integration you are  
> pursuing. Rakesh, by any chance, have you been interacting with  
> Trish Whetzel at all? Trish has been in contact with Phillip Payne  
> and Taylor Pressler for other projects at OSUMC that are interested  
> in using BioPortal.
>
> Regards,
> Nigam.
>
> On Wed, Aug 11, 2010 at 8:56 AM, Wynden, Rob <Rob.Wynden at ucsf.edu <http://Rob.Wynden@ucsf.edu 
> >  <http://Rob.Wynden@ucsf.edu> > wrote:
> Nigam,
>
> In order to support caGRID (with i2b2) we are also interested in the  
> integration of OpenMDR with NCBO Bioportal.  Rakesh Dhaval at OSU is  
> working on that issue.
>
> This email is intended as an introduction.  I think that Rakesh  
> could use some help on this if I'm not mistaken.
>
> Regards,
> Rob
>
>
>
>
>
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support




More information about the bioontology-support mailing list