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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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