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[bioontology-support] concept service in BP

Trish Whetzel whetzel at stanford.edu
Thu Mar 18 14:54:06 PDT 2010


 From my side, a target date of when this will be pushed to production  
allowing for at least 3 days from now for folks to update code. Once  
the date is set, I'll send email to bioportal-announce of the change  
and date when it will be in production.

Thanks
Trish


On Mar 18, 2010, at 2:29 PM, Michael Dorf wrote:

> Per my conversations with Natasha and Paul, I plan to remove the  
> property
> <instances/> from the service. We now have a dedicated "instances"  
> service
> that can display all instances for a given concept using pagination.
> Instead, I plan to add a "relation" called "InstanceCount" that will  
> display
> the number of instances for a particular concept.
>
> Tania, Trish, what's the best way to coordinate this release?
>
> Thanks,
>
> Misha
>
>
>
>
> -----Original Message-----
> From: bioontology-support-bounces at lists.stanford.edu
> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of  
> Tania
> Tudorache
> Sent: Tuesday, March 16, 2010 11:33 PM
> To: Trish Whetzel
> Cc: support at bioontology.org; Csongor Nyulas
> Subject: Re: [bioontology-support] concept service in BP
>
> Yes, I will have to set up some automated nightly checks of the
> BioPortal services, because otherwise I won't know when iCAT will  
> break
> because of signature changes in BP ...
>
> Tania
>
> On 03/16/2010 11:28 PM, Trish Whetzel wrote:
>> Ok, I was not aware of this. Do you have any suggestions on some
>> programatic QA to check for these kind of changes?
>>
>> Trish
>>
>>
>> On Mar 16, 2010, at 9:38 PM, Tania Tudorache wrote:
>>
>>> No, the concept service is not the same. A new tag "instances" was
>>> introduced. Here is an example:
>>>
>>> http://rest.bioontology.org/bioportal/concepts/42122/?conceptid=14162009
>>>
>>> <classBean>
>>> <id>420984000</id>
>>> <fullId>420984000</fullId>
>>> <label>Structure of first web space of foot</label>
>>> <type>Class</type>
>>>>>> <relations>
>>>>>> <entry>
>>> <string>ChildCount</string>
>>> <int>3</int>
>>> </entry>
>>> </relations>
>>> <instances/>
>>> </classBean>
>>>
>>> Unfortunately this broke the import in iCAT.
>>>
>>> Tania
>>>
>>> On 03/16/2010 09:35 PM, Trish Whetzel wrote:
>>>> Does this mean that the tag <type>, now has an additional value of
>>>> 'Individual'? There is a new, separate Instance service, but the  
>>>> old
>>>> Concept/Term service was left the same AFAIK.
>>>>
>>>> Trish
>>>>
>>>>
>>>> On Mar 16, 2010, at 9:30 PM, Tania Tudorache wrote:
>>>>
>>>>> The concept service has changed signature (added an "instances"
>>>>> tag) and I did not know about it, so iCAT does not import from BP
>>>>> again :(
>>>>>
>>>>> And this is right when several ICD editors try to create mappings
>>>>> to Snomed.. They'll have to wait until I upgrade the code to match
>>>>> the new signature..
>>>>>
>>>>> Sorry if I've missed the announcement... I was watching all the
>>>>> announcements, but I did not see anything about the concept  
>>>>> service.
>>>>>
>>>>> Unrelated: I am not sure whether including all instances in the
>>>>> class bean is a very good idea. Fortunately not many OWL  
>>>>> ontologies
>>>>> have instances, but the "real" ones that use instances, they
>>>>> usually have thousands of them.
>>>>>
>>>>> Tania
>>>>
>>>
>>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org



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