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[bioontology-support] bioontology-support Digest, Vol 66, Issue 12

Oravec, Thomas oravect at ccf.org
Mon Oct 7 04:53:14 PDT 2013


If the system was "useable" the subject line would not be so difficult
to figure out.

How do I get to CUI's?

Thomas J Oravec | Data Coordinator
Genomics Medicine Institute
Cleveland Clinic Foundation
Tel: 216-445-4030
Email: oravect at ccf.org
 
-----Original Message-----
From: bioontology-support-bounces at lists.stanford.edu
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Sent: Friday, October 04, 2013 3:07 PM
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Subject: bioontology-support Digest, Vol 66, Issue 12

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Today's Topics:

   1. Re: Search by UMLS CUI (Paul R Alexander)


----------------------------------------------------------------------

Message: 1
Date: Fri, 4 Oct 2013 11:46:37 -0700
From: Paul R Alexander <palexander at stanford.edu>
To: Fran?ois Schiettecatte <fschiettecatte at gmail.com>
Cc: support at bioontology.org
Subject: Re: [bioontology-support] Search by UMLS CUI
Message-ID: <FBC9AA3D-79F7-4BC1-92C5-DE964597E815 at stanford.edu>
Content-Type: text/plain; charset=iso-8859-1

This is now working, sorry for the trouble.

Paul


On Oct 1, 2013, at 10:56 AM, Paul R Alexander <palexander at stanford.edu>
wrote:

> Fran?ois,
> 
> This is a bug that we are currently working to resolve.
> 
> Best,
> Paul
> 
> 
> On Oct 1, 2013, at 10:49 AM, Fran?ois Schiettecatte
<fschiettecatte at gmail.com> wrote:
> 
>> Hi
>> 
>> I am the software developer working on OMIM.
>> 
>> Last year these searches worked, but they don't work anymore, have
they changed?
>> 
>>
http://bioportal.bioontology.org/search?q=C0221581&searchproperties=true
>> 
>> Cheers
>> 
>> Fran?ois
>> 
>> 
>> 
>> On Aug 15, 2012, at 1:55 PM, Paul R Alexander
<palexander at stanford.edu> wrote:
>> 
>>> Yes, we can do that.
>>> 
>>> To just search the properties, use this URL:
>>>
http://bioportal.bioontology.org/search?q=C0221581&searchproperties=true
>>> 
>>> If you need exact matches, you can add:
>>> exactmatch=true
>>> 
>>> If you want to show the advanced options in the UI (which will show
the checkboxes), then add this:
>>> opt=advanced
>>> 
>>> You can also limit the search to particular ontologies by adding:
>>> ontologyids=1032,1104,1007
>>> 
>>> Let me know if you have questions.
>>> 
>>> Paul
>>> 
>>> 
>>> 
>>> On 8/15/12 9:56 AM, Fran?ois Schiettecatte wrote:
>>>> Paul
>>>> 
>>>> I spoke too soon, the form is driven by a POST, what I am looking
for is to link out to your website and have it run the search on the ID
for me, something along the lines of :
>>>> 
>>>>
http://bioportal.bioontology.org/search?search=C0221581&search[include_p
rops]=1
>>>> 
>>>> For example Peter Robinson of HPO provides this format:
>>>> 
>>>>
http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0001511
>>>> 
>>>> It this possible?
>>>> 
>>>> 
>>>> Cheers
>>>> 
>>>> Fran?ois
>>>> 
>>>> 
>>>> On Aug 14, 2012, at 8:58 PM, Paul R Alexander
<palexander at stanford.edu> wrote:
>>>> 
>>>>> Fran?ois,
>>>>> 
>>>>> The process for searching via a property value like CUI is
different depending on whether or not you are using the REST service or
the Web UI.
>>>>> 
>>>>> If you are using the UI, then click "advanced options" and select
"Property values" to include them in your search. Searching on a CUI id
(EX: C0221581) should return matching terms. You can also restrict
results to particular ontologies.
>>>>> 
>>>>> You can achieve the same results on the REST service by using the
"includeproperties" query parameter, documented here:
>>>>>
http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Search
_BioPortal
>>>>> 
>>>>> Let me know if you have other questions.
>>>>> 
>>>>> Paul
>>>>> 
>>>>> 
>>>>> On 8/14/12 6:30 AM, Fran?ois Schiettecatte wrote:
>>>>>> Hi
>>>>>> 
>>>>>> I was wondering if it was possible to search by UMLS CUI?
>>>>>> 
>>>>>> I am working on both OMIM and the Baylor-Hopkins Center for
Mendelian Genomics and am trying to find a decent link out for UMLS CUIs
and was hoping that BioOntology would be able to provide me that.
>>>>>> 
>>>>>> Thanks
>>>>>> 
>>>>>> Fran?ois
>>>>>> 
>>>>>> 
>>> 
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 



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End of bioontology-support Digest, Vol 66, Issue 12
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