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

Carlo Torniai torniai at ohsu.edu
Tue Dec 7 17:07:35 PST 2010


Hi Trish and thanks for your support so far.
I was having a look at the owl file I've downloaded using your URL and I  have noticed that no definition for term is available, while i can see those in bioportal  (for instance for the term http://bioportal.bioontology.org/visualize/44776/?conceptid=D001423) and also when accessing the rest service for that (http://rest.bioontology.org/bioportal/rdf/44776/D001423<http://rest.bioontology.org/bioportal/rdf/44776/D001423%5D>)
There is any way that you know to have definitions included in the generated file?
Thanks
Carlo

On Dec 5, 2010, at 5:46 PM, Trish Whetzel wrote:

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<mailto: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<mailto: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>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>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> 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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