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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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