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[bioontology-support] concept service in BP

Tania Tudorache tudorache at stanford.edu
Tue Mar 16 23:32:41 PDT 2010


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
>>>
>>
>




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