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[bioontology-support] OpenMDR Integration

Paul R Alexander palexander at stanford.edu
Tue Aug 31 13:28:19 PDT 2010


  Rakesh,

You can't encode the ampersand used to delimit the parameters in the 
query string. You're getting 884 results because "email" is the only 
parameter that's getting captured, and the email address is being read 
as "rakesh.dhaval at osumc.edu&ontologyids=1032" with the ontologyids 
parameter getting ignored completely.

If you were encoding the parameters rather than the whole URL it should 
work (in Ruby, untested):
baseURL = "http://rest.bioontology.org/bioportal/search/Discharge?"
parameters = { :email => "rakesh.dhaval at osumc.edu", :ontologyids => "1032" }
parameters.each do |name, value|
   baseURL << name.to_s + "&" + URI.encode(value)
end

Let me know if you have any questions.

Paul R Alexander
Web / UI Developer
NCBO BioPortal <http://bioportal.bioontology.org>
Stanford Center for Biomedical Informatics Research


On 8/31/10 1:14 PM, Nigam Shah wrote:
> Hmm that is weird. URL encoding should not change the results! I am 
> copying support at bioontology.org <mailto: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 <mailto: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
>     <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
>     <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
>     <http://nigam@stanford.edu>> wrote:
>
>         Here is the message thread ..
>
>         regards,
>         Nigam.
>
>         ---------- Forwarded message ----------
>         From: *Dhaval, Rakesh* <Rakesh.Dhaval at osumc.edu
>         <http://Rakesh.Dhaval@osumc.edu>>
>         Date: Fri, Aug 13, 2010 at 11:17 AM
>         Subject: Re: OpenMDR Integration
>         To: Nigam Shah <nigam at stanford.edu <http://nigam@stanford.edu>>
>         Cc: "Wynden, Rob" <Rob.Wynden at ucsf.edu
>         <http://Rob.Wynden@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> <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
>             <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>
>             <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>
>                 <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>
>                     <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
>
>
>
>
>
>
>
>
>
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