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[bioontology-support] value sets

Trish Whetzel whetzel at stanford.edu
Mon Sep 27 15:01:50 PDT 2010


Hi Rakesh

I checked OCRe in Protege, however I don't see a definition for this property term. 

Trish 


On Sep 27, 2010, at 1:22 PM, Dhaval, Rakesh wrote:

> I am still encountering a few errors. Please check the following URL’s. Any idea why this might be so? 
> 
> Search: 
> http://rest.bioontology.org/bioportal/search/Gender?email=rakesh.dhaval@osumc.edu&ontologyids=1076
> 
> For definition:
> http://rest.bioontology.org/bioportal/virtual/ontology/1076/research:gender_restriction
> 
> 
> 
> On 9/27/10 1:33 PM, "Trish Whetzel" <whetzel at stanford.edu> wrote:
> 
> Hi Rakesh, 
> 
> The definitions for OCRe are now fixed. I can't get my hands on the documentation for Views, but Natasha (cc'd here) can help answer your questions on Views.  One item the Views do not include is datatype information. 
> 
> Trish
> 
> 
> On Sep 24, 2010, at 8:56 AM, Dhaval, Rakesh wrote:
> 
> It might be the same concept. Can you point me to the documentation for views?
> Also, would you let me know when the definitions for OCRe are fixed. Can you keep me in loop while communicating with Samson.
> 
> Thanks,
> Rakesh
> 
>  
> 
> On 9/23/10 5:48 PM, "Trish Whetzel" <whetzel at stanford.edu <x-msg://74/whetzel@stanford.edu> > wrote:
> 
> BioPortal supports "views" or subsets of 1 or more ontologies. Is this the same as value sets?
> 
> Trish
> 
> PS - cc'ing our support mailing list for logging 
> 
> 
> On Sep 23, 2010, at 2:37 PM, Dhaval, Rakesh wrote:
> 
> Thanks.
>  
>  Can value sets be loaded on bioportal, or is that something only LexEVS can do?
>  
>  On 9/23/10 5:29 PM, "Trish Whetzel" <whetzel at stanford.edu <x-msg://74/whetzel@stanford.edu> > wrote:
>  
>  
> If the ontology term has a definition and if the property was specified by the ontology author then yes, the definitions will at the same location. I've started some QA on this, but may not have this fully resolved until next week.  Unfortunately we do not have any XSD schema definition files for the web service output. I've added this as a feature request though. 
>  
>  Trish 
>  
>  
>  On Sep 23, 2010, at 2:11 PM, Dhaval, Rakesh wrote:
>  
>  
> Thanks this is much better. 
>   I am assuming I can find the “definitions” at the same location in all results from bioportal. Is there a schema associated to the result set that I can refer to?
>   
>   Thanks,
>   Rakesh
>   
>   On 9/23/10 4:36 PM, "Trish Whetzel" <whetzel at stanford.edu <x-msg://74/whetzel@stanford.edu> > wrote:
>   
>   
>  
> Ah, it is fixed now.  Although it looks like there is some extra formatting information tagged to the end of the definition, e.g. 
>   http://rest.bioontology.org/bioportal/virtual/ontology/1076/clinical:Treatment 
>   
>   Trish 
>   
>   
>   On Sep 23, 2010, at 12:57 PM, Dhaval, Rakesh wrote:
>   
>   
>  
> Looks like definition for OCRe is in synonyms.
>    http://rest.bioontology.org/bioportal/virtual/ontology/1076/clinical:Event
>    
>    
>    
>    On 9/23/10 3:44 PM, "Trish Whetzel" <whetzel at stanford.edu <x-msg://74/whetzel@stanford.edu> > wrote:
>    
>    
>   
>  
> PS - it looks like the term Adverse Event does not include a definition:
>    http://bioportal.bioontology.org/visualize/40688/?conceptid=clinical%3AAdverseEvent
>    
>    Trish 
>    
>    
>    On Sep 23, 2010, at 12:36 PM, Trish Whetzel wrote:
>    
>    
>   
>  
> Hi Rakesh, 
>    
>    Thanks for pointing out this error. The properties id, label, fullid, type, synonyms, definitions should all be "first-class" properties in that they are returned via a common XML attribute shared across ontologies. In the case of NCIt and OCRe the definition property was not specified in BioPortal. 
>    
>    I was able to identify the definition property for NCIt and update the ontology metadata, therefore the definition property is now returned as a "first-class" property [1]. However, I was not able to identify which property is used for the definition in OCRe. I emailed Samson to request this information. 
>    
>    Trish   
>    
>    
>    [1]
>    <classBean>
>    <id>Male_Gender</id>
>    −
>    <fullId>
>    http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Male_Gender
>    </fullId>
>    <label>Male Gender</label>
>    <type>Class</type>
>    −
>    <synonyms>
>    <string>Male</string>
>    <string>Male Gender, Self Reported</string>
>    <string>Male Gender, Self Report</string>
>    </synonyms>
>    −
>    <definitions>
>    −
>    <string>
>    An individual who reports belonging to the cultural gender role distinction of male.
>    </string>
>    </definitions>
>    −
>    <relations>
>    
>    
>    On Sep 23, 2010, at 9:08 AM, Dhaval, Rakesh wrote:
>    
>    
>   
>  
>  Thanks Trish.
>     I performed a couple of queries against NCI Thesaurus(Adverse Event) and OCRe (Male Gender) both from Bioportal resource. 
>     I have attached 2 files for queries to both these resources to find concept details and definition. I am trying to understand the difference in the results returned by NCIThesaurus and OCRe for definition (2nd url in each file).
>     It does not look like both these results follow the same schema as I don’t seee a consistent way to extract definition from the output. Can you please let me know your thoughts or suggestions on this.
>     
>     Thanks,
>     Rakesh
>     
>     
>     
>     On 9/20/10 2:30 PM, "Trish Whetzel" <whetzel at stanford.edu <x-msg://74/whetzel@stanford.edu> > wrote:
>     
>     
>    
>   
>  
> Hi Rakesh,
>     
>     OCRe is loaded in BioPortal and is available via the same web service calls. Based on the metadata ( http://bioportal.bioontology.org/ontologies/40688 ) it looks like the most recent version is 0.95.  
>     
>     Trish 
>     
>     
>     On Sep 20, 2010, at 9:42 AM, Dhaval, Rakesh wrote:
>     
>     
>    
>   
>   Hi Trish,
>      I am almost done integrating and testing the bioportal rest interface for consumption in openMDR. However,  I am wondering if OCRe has been loaded in bioportal in manner that I  can query it the same way as any other terminology/ontology.
>      Please let me know about the same. 
>      
>      Thanks,
>      Rakesh
>        
>      
>      
>      On 9/15/10 4:16 PM, "Trish Whetzel" <whetzel at stanford.edu <x-msg://74/whetzel@stanford.edu> > wrote:
>      
>      
>     
>    
>   
>  
> Sure thing. I too need to be packing up shop to head out as well.  Have a good trip back.
>      
>      Trish
>      
>      
>      On Sep 15, 2010, at 4:10 PM, Dhaval, Rakesh wrote:
>      
>      
>     
>    
>   Hey Trish,
>      I will have to leave because of the flight schedule. I guess we can catch up over emails.
>      
>      --Rakesh
>      Sent from my iPhone
>      
>      On Sep 15, 2010, at 11:28 AM, "Trish Whetzel" <whetzel at stanford.edu <x-msg://74/whetzel@stanford.edu> > wrote:
>      
>      
>     
>    
>   
>  
> I'll be around until about 4pm today if you'd like to chat in person. 
>      
>      BTW, is adding in the BioPortal search to openMDR still in the works?
>      
>      Trish
>      
>      Sent from my iPhone
>      
>      On Sep 14, 2010, at 2:23 PM, "Dhaval, Rakesh" < <mailto:Rakesh.Dhaval at osumc.edu> Rakesh.Dhaval at osumc.edu <x-msg://74/Rakesh.Dhaval@osumc.edu> > wrote:
>      
>      
>     
>     Hi Trish,
>       Thanks for your email. I am currently at the caBIG meeting. 
>       Probably we can catch up sometime today or tomorrow. I will try to get a hold of you in between sessions. 
>       
>       Thanks,
>       Rakesh
>         
>       
>       
>       On 9/14/10 2:15 PM, "Trish Whetzel" < <whetzel at stanford.edu <x-msg://74/whetzel@stanford.edu> >  <mailto:whetzel at stanford.edu> whetzel at stanford.edu <x-msg://74/whetzel@stanford.edu> > wrote:
>       
>       
>      
>     
>    Hi Rakesh,
>       
>       I'm not sure if you are at the caBIG meeting, but I'm attending in 
>       case you have any web service questions.
>       
>       Cheers,
>       Trish
>       
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>      <NCIThesaurusResults.txt><OCReResults.txt>
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