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[bioontology-support] [BioPortal] Feedback from Selen BOZKURT

John Graybeal jgraybeal at
Wed Jun 21 15:19:52 PDT 2017


Ah, I understand your issue better now.

The way I see if that particular endpoint is working, and learn about possible queries, is to start with this page:
and the executable examples it points to:

If clicking on 'run query' does not produce answers, generally within 5-10 seconds, then the endpoint is probably down (or at least so busy it isn't useful).

We'll bounce the endpoint as soon as we get a chance, please try it a bit later if you get the chance.

Hope this helps.


On Jun 21, 2017, at 3:01 PM, Selen Bozkurt <selenb at<mailto:selenb at>> wrote:

Thank you very much for your kind response.

I could not even see the results of example queries whole day today, so it looks like SPARQL server is down (I guess).

Since learning and applying SPARQL queries became extremely painful to me, I seek any help and thank you very much for your suggestions.


"You must be the change you wish to see in the world"

Selen Bozkurt, PhD

Department of Biostatistics and Medical Informatics
Akdeniz University Faculty of Medicine
Antalya, Turkey

2017-06-21 14:32 GMT-07:00 John Graybeal <jgraybeal at<mailto:jgraybeal at>>:
Hi Selen,

I am sorry you are having trouble with the beta SPARQL endpoint.

One of the reasons we have left that endpoint as a *beta* service is that it is relatively easy to write SPARQL queries that can take a very long time to execute, effectively freezing the server. I'm afraid that means the system may become unavailable for many stretches, as students and other learners often generate these kinds of complex queries, and send them often when they don't seem to work!

So you may want to try some tests to see if basic queries are failing as often as more complex queries, just to be confident your queries are well formed.

If you do decide that your queries should be optimized, you might want to ask the Protege list if you need assistance; that list may have more SPARQL expertise than this list does. (If anyone has knowledge of a SPARQL list, that would be another good place to try.)

Conversely, if it seems the SPARQL server is down, you can email this list to ask us to restart it. We will get to it as soon as we can.


On Jun 21, 2017, at 10:26 AM, support at<mailto:support at> wrote:

Name: Selen BOZKURT

Email: selenb at<mailto:selenb at>



It is very helpful for me since I can not use Protege effective on my computer, but it freezes many times and I can not see my query results :(.

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>


John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
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