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[bioontology-support] value sets

Trish Whetzel whetzel at stanford.edu
Thu Sep 23 14:48:09 PDT 2010


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> 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> 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> 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> 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> 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 
> > 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> 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>  <mailto:whetzel at stanford.edu 
> > whetzel at 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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