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[bioontology-support] bioportal.bioontology.org looks like it's down

John Graybeal jgraybeal at stanford.edu
Fri Nov 23 09:53:43 PST 2018


Thank you Faisal for this report. We had a system outage this morning that we just now fixed. (It's a holiday weekend here, so service may be a little slow. :->)  Everything should be working now.

Regarding your question, thank you for thinking of our system strain!  We have noticed an additional load recently, but searching for a single item (as this query was) should not cause any problem. If you are repeatedly using the Annotator with large bodies of text, using the Recommender, downloading large ontologies via API by walking their pages, or searching within large branches, we request you self-monitor the responses (in addition to our internal 15 messages per second throttle) to avoid creating more work than the system can handle. We encourage anyone in these situations to avoid parallelizing their requests, instead waiting for one to complete before issuing the next. (Considering that a number of other people may also be making expensive requests at the same time.)

We also invite people who are going to be using BioPortal extensively to install their own BioPortal Virtual Appliance [1].

Specifically to your question, I am not sure exactly what  you mean by 'get a dump of the API's dataset'. There are multiple datasets served by BioPortal's API and they are all large (the ontologies have 9 million terms at this point) or very large (there are a whole lot of mappings). If you still want to pursue this, contact us with the specifics of your API calls so we can understand what you would need—while we don't have a bundle that we ship maybe we can recommend a good alternative.

Hope this helps, and again appreciate your reaching out.

John



[1] https://www.bioontology.org/wiki/Category:NCBO_Virtual_Appliance


On Nov 23, 2018, at 6:39 AM, Al-Quaddoomi Faisal Sabah <alquaddoomi at nexus.ethz.ch<mailto:alquaddoomi at nexus.ethz.ch>> wrote:

Hello,

I wasn’t sure what the proper channel was to report this, but as of around 2:30pm CET it appears that https://bioportal.bioontology.org/account is throwing a 500 server error. I encountered it while following the advice from a 401 error I got while querying http://data.bioontology.org/search?q=splice_region_variant&apikey=x. (I thought my API was valid — it was working for previous requests — but perhaps not anymore? In any case, I can’t get to the account page to check.)

On a mildly related note, is there someplace where I can get a dump of the API’s dataset so that I don’t have to query your server so much? I’m writing a variant aggregation pipeline, and during its development I’ve been running the pipeline pretty frequently. I’m hoping this isn’t putting any undue strain on your server(s), and I’d like to reduce my contribution to it if possible.

Thanks,

Faisal Alquaddoomi
Software Developer
ETH Zürich, NEXUS, Switzerland
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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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