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

John Graybeal jgraybeal at stanford.edu
Tue Feb 20 17:35:28 PST 2018


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 bioontology.org<mailto:support at bioontology.org> wrote:


Name: Alsayed Algergawy

Email: alsayed.algergawy at uni-jena.de<mailto:alsayed.algergawy at uni-jena.de>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%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

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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