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[bioontology-support] OpenMDR Integration

Paul R Alexander palexander at stanford.edu
Thu Sep 16 12:55:03 PDT 2010


  Here is documentation for the available URLs in the BioPortal User 
Interface:
http://www.bioontology.org/wiki/index.php/BioPortaul_UI_URLs

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


On 9/16/10 12:14 PM, Nigam Shah wrote:
> 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 
> <mailto: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 <mailto: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
>     <http://nigam@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 <http://Rakesh.Dhaval@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> <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>
>                 <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>
>                 <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=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>
>                     <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>
>                         <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>
>                         <http://nigam@stanford.edu> >
>                         Cc: "Wynden, Rob" <Rob.Wynden at ucsf.edu
>                         <http://Rob.Wynden@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>
>                         <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>
>                             <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>
>                                 <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>
>     <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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