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[bioontology-support] OpenMDR Integration

Nigam Shah nigam at stanford.edu
Thu Sep 16 12:14:16 PDT 2010


number (3) should be:
http://bioportal.bioontology.org/visualize/42838/?conceptid=Diabetes_Mellitus


There should be a way to link to this HTML page using the
virtual/ontology/1032 naming convention .. I can't find the documentation
(!) so cc'ing the support at bioontology.org.

Meanwhile, you can use the PURL signature *
http://purl.bioontology.org/ontology/NCIT/<<conceptIDShort>>* .. so for
example, http://purl.bioontology.org/ontology/NCIT/Diabetes_Mellitus but you
have to construct it (it's not in the XML output). The reason for that is
that really,
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Diabetes_Mellitus, should
redirect to the HTML page, but there is no PURL server at NCI to do that. So
for now just constructing it might be the way to go.

Regards,
Nigam.

On Thu, Sep 16, 2010 at 12:00 PM, Dhaval, Rakesh <Rakesh.Dhaval at osumc.edu>wrote:

>  Hi Nigam,
> Let me know if this looks fine to you.
> I would like to be able to query for a term(s) on bioportal and be able to
> show the preferred name, definition and a link to the details page for that
> specific concept details on the terminology/ontology web page.
>
> 1. Search for Diabetes in NCI Thesaurus (1032)
> *http://rest.bioontology.org/bioportal/search/Diabetes/?ontologyids=1032
> *
> 2. Get conceptIdShort element value (e.g. Diabetes_Mellitus) from xml
> and use it to generate the details query url
> *
> http://rest.bioontology.org/bioportal/virtual/ontology/1032/Diabetes_Mellitus
> *
>
> 3. Generate HTML link to the details page:
> Get conceptId element value
> *http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Diabetes_Mellitus
> *
>
> Thanks,
> Rakesh
>
>
> On 8/31/10 4:43 PM, "Nigam Shah" <nigam at stanford.edu> wrote:
>
> Two responses already. I think this is addressed :-).
>
> -Nigam.
>
> On Tue, Aug 31, 2010 at 1:28 PM, Dhaval, Rakesh <Rakesh.Dhaval at osumc.edu>
> wrote:
>
> Thanks Nigam. Please let me know if you get to hear anything about it.
>
> Thanks,
> Rakesh
>
>
>
>
> On 8/31/10 4:14 PM, "Nigam Shah" <nigam at stanford.edu <
> http://nigam@stanford.edu> > wrote:
>
> Hmm that is weird. URL encoding should not change the results! I am copying
> support at bioontology.org <http://support@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<
> http://Rakesh.Dhaval@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 <
> http://nigam@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>  <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>  <
> http://nigam@stanford.edu> >
> Cc: "Wynden, Rob" <Rob.Wynden at ucsf.edu <http://Rob.Wynden@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>  <
> 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>  <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>  <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>  <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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