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[bioontology-support] [BioPortal] Feedback from Alsayed Algergawy

Dr. Ing. Algergawy alsayed.algergawy at
Wed Feb 21 04:31:27 PST 2018

Dear John,

many thanks for your reply. However, I expected the problem is not
related to available resources to your or our sides. Since I have
already one time to download the set of ontologies. Currently, the
process of downloading is not completed especially when the number of
downloaded ontologies reaches 110 with the following error message

" ERROR de.julielab.bioportal.ontologies.HttpHandler - Error when
posting a request to BioPortal Server: Internal server error"

actually I tried many times with different API keys (for me and my
colleagues), but the same problem remains.

I hope you can help me to discover what is the problem



On 2/21/2018 2:35 AM, John Graybeal wrote:
> Hi Alsayed,
> It's hard to say without more information.
> If you are using the API to load ontology content one page at a time, it can be extremely time consuming and resource-intensive to do that for an ontology with several hundred thousand to a million terms in it. While I expect some people have been successful, they probably took great care to space out their requests far apart, making sure one page came back before the next page was requested, and so on. (You might find useful tips searching the mail list, as similar questions have been addressed before.)
> So if there is a resource issue, I can't tell you who is more short of resources, BioPortal or your system. My guess would be your system just doesn't have enough resources allocated at some point, or there could be a memory leak in your code. But that's just a guess based on my understanding that others have successfully downloaded all the ontologies.
> In any case, the problem may be with ontology 110, than it is with the fact you have already downloaded 110 ontologies. But we don't know what ontology 110 is, so we can't tell you much about the possible issues.
> If you want more detailed answers, you might want to include examples of your source code, the last dozen or so API requests that your code made, and the last few transmissions from BioPortal before the downloads stopped. And if your application is actually crashing, the crash log would provide valuable insights too. (If your application is crashing, that's probably the first place you should look, is your application and system logs.)
> John
> On Feb 20, 2018, at 5:12 AM, support at<mailto:support at> wrote:
> Name: Alsayed Algergawy
> Email: alsayed.algergawy at<mailto:alsayed.algergawy at>
> Location:<>%2Faccounts%2Falsayed
> Feedback:
> dear all,
> I am trying to download the available set of ontologies on the Bioportal side using the available API. It works fine till downloading 110 ontologies, and the process crashes. Do you have any explanation for this behavior?
> thank you in advance!!
> yours,
> alsayed
> _______________________________________________
> 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
> 650-736-1632

Dr. Ing. Alsayed Algergawy

Institut für Informatik
Friedrich-Schiller-Universität Jena
alsayed.algergawy at 
T: +49(0)3641-946438

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