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[bioontology-support] concept service in BP

Trish Whetzel whetzel at stanford.edu
Mon Mar 22 23:50:15 PDT 2010


Has a date been set for when this change will be available on Stage?

Thanks,
Trish


On Mar 18, 2010, at 2:54 PM, Trish Whetzel wrote:

> 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
>
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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