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

Jennifer Leigh Vendetti vendetti at
Wed Feb 21 18:07:23 PST 2018

Hello Dr. Algergawy,

We don’t have enough information from you yet to offer help.

When you say “downloading ontologies”, what does this mean? Are you downloading ontology source files to disk? Or, are you retrieving class data from each ontology in Bioportal using the /classes endpoint?

Also, you say that your code fails reliably on the 110th ontology. Please add some log statements to your code that outputs which ontology you’re processing. We can’t do much if we don’t know which ontology is causing issues. In addition, please indicate the REST call that returns a 500 error. Also helpful would be some sort of a code snippet from you for the portion of the code that’s failing.

Kind regards,

On Feb 21, 2018, at 4:31 AM, Dr. Ing. Algergawy <alsayed.algergawy at<mailto:alsayed.algergawy at>> wrote:

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.)


On Feb 20, 2018, at 5:12 AM, support at<mailto:support at><mailto:support at><mailto:support at> wrote:

Name: Alsayed Algergawy

Email: alsayed.algergawy at<mailto:alsayed.algergawy at><mailto:alsayed.algergawy at><mailto:alsayed.algergawy at>



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!!

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

Dr. Ing. Alsayed Algergawy

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

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