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[bioontology-support] Question about the REST service for Mesh Extraction

Trish Whetzel whetzel at stanford.edu
Sun Dec 5 17:46:36 PST 2010


For the URIs, they should be in the form: http://purl.bioontology.org/ontology/MSH/{conceptid}.  There is also the parameter "filterrelations" you can try. 

Trish 



On Dec 5, 2010, at 5:00 PM, Carlo Torniai wrote:

> Great Trish, thanks.
> I've just downloaded the file and it look good.
> Few questions:
> what URI should we used to have each term resolved by bioportal (or at least pointing on the correspondent bioportal page)?
> There is any parameter to have just specific annotation properties extracted?
> Thanks
> Carlo
>  
> 
> 
> On Dec 5, 2010, at 4:46 PM, Trish Whetzel wrote:
> 
>> Thanks Carlo. To build-up the proper URL, here are the pieces to use with the View Extraction web service:
>> http://rest.bioontology.org/bioportal/viewextractor/  --> web service signature
>> 44776/  --> ontology version identifier
>> ?conceptid=U000006  --> concept identifier for parent term 
>> &ontologyname=http://example.org/testing.owl&delay=10  --> name of resulting ontology and timing parameter.
>> 
>> Therefore, the full URL is:
>> http://rest.bioontology.org/bioportal/viewextractor/44776/?conceptid=U000006&ontologyname=http://purl.biooontology.org/ontology/MSH/testing.owl&delay=10
>> 
>> Trish 
>> 
>> 
>> On Dec 2, 2010, at 9:40 AM, Carlo Torniai wrote:
>> 
>>> Hi Trish,
>>> please let me know if this helped or if you need more info.
>>> Carlo
>>> 
>>> 
>>> On Dec 1, 2010, at 5:28 PM, torniai at ohsu.edu wrote:
>>> 
>>>> I don't think so. It's the one with all disease subcategories. If you look for disease in the extractor is this one 
>>>> http://rest.bioontology.org/bioportal/rdf/44776/U000006
>>>> Carlo
>>>> 
>>>> 
>>>> On Dec 1, 2010, at 5:08 PM, "Trish Whetzel" <whetzel at stanford.edu> wrote:
>>>> 
>>>>> Hi Carlo, 
>>>>> 
>>>>> Is this the 'Disease' term you refer to in MeSH:
>>>>> http://bioportal.bioontology.org/visualize/44776/?conceptid=D004194
>>>>> 
>>>>> Trish
>>>>> 
>>>>> 
>>>>> On Dec 2, 2010, at 1:49 AM, Carlo Torniai wrote:
>>>>> 
>>>>>> Hi Trish,
>>>>>> yesterday I've played around a bit with the Extraction tool (very nice).
>>>>>> As you know we are trying to extract all the mesh disease branch.
>>>>>> You've pointed us to the documentation to use a rest service to have a whole branch extracted (http://www.bioontology.org/wiki/index.php/View_Extraction). 
>>>>>> I am trying to figure out what parameters to use (i.e. what the URL of the rest service would look like) in order to get   all the subclasses of Disease (Mesh category)  [see the superclass information here http://rest.bioontology.org/bioportal/rdf/44776/U000006]
>>>>>> It would be probably easier for you to send us the correct URL than me to figure out the correct  values of the parameters :-)
>>>>>> We can get in touch anytime if you need more info.
>>>>>> Thanks
>>>>>> Carlo
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>> 
>> 
> 

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