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[bioontology-support] API access to NCBITAXON

Erik Fäßler erik.faessler at uni-jena.de
Tue Dec 29 06:45:20 PST 2015


John,

holidays distractions actually sounds good, sorry to bother you at this time.

I did try again and it worked - for a few hours. I got my job nearly completed but than the very same error appeared again. I am getting in right now. It seems the system is up for some time and then down again. You described it yourself, first you get the error, then it is gone - and then it comes back.

I will continue to try. Thanks for your efforts!

Best,

Erik

> On 28 Dec 2015, at 07:36, John Graybeal <jbgmeta1 at stanford.edu> wrote:
> 
> Erik,
> 
> Sorry, not sure why I did not see this earlier. (Perhaps too much holiday distraction.)
> 
> Please try this request again. Just a little while I was getting the error you describe, but now I am no longer getting that error. 
> 
> I could not duplicate your issue with visiting the BIoPortal page at all — it worked consistently for me.
> 
> Happy holidays to you!
> 
> John
> 
>> On Dec 24, 2015, at 12:43 AM, Erik Fäßler <erik.faessler at uni-jena.de <mailto:erik.faessler at uni-jena.de>> wrote:
>> 
>> Dear BioOntologies team,
>> 
>> I try to access the classes of NCBITAXON via the BioPortal API for a few day now with always the same error.
>> 
>> Request: http://data.bioontology.org/ontologies/NCBITAXON/classes?include=prefLabel,synonym,definition,parents,obsolete,notation,semanticType,cui,xref&pagesize=100&no_context=true&no_links=true <http://data.bioontology.org/ontologies/NCBITAXON/classes?include=prefLabel,synonym,definition,parents,obsolete,notation,semanticType,cui,xref&pagesize=100&no_context=true&no_links=true>
>> Error:
>> <html>
>> <head><title>504 Gateway Time-out</title></head>
>> <body bgcolor="white">
>> <center><h1>504 Gateway Time-out</h1></center>
>> <hr><center>nginx/1.6.2</center>
>> </body>
>> </html>
>> 
>> Other ontologies could be accessed exactly like this. I also cannot visit the BioPortal page for the NCBITAXON, it says "We're sorry but something has gone wrong. We have been notified of this error.
>> 
>> I wish happy holidays despite my report ;-) Best, Erik
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632  
> skype: graybealski
> 
> 

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