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[bioontology-support] OpenMDR Integration

Nigam Shah nigam at stanford.edu
Tue Aug 31 13:14:34 PDT 2010


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<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=1032returns 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
>
>
>
>
>
>
>
>
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