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[bioontology-support] Fwd: Proxy error when calling text mining service

Paul R Alexander palexander at
Wed Oct 13 12:30:42 PDT 2010


I'm not an Annotator expert, but I did look into the problem and it 
appears that the file is just too big to be processed in one call (it 
timed out for me). I had no problem processing the entire thing so long 
as I split it up into chunks that were generally 6000-8000 characters long.

Is this test case something that you are normally able to process 
without difficulty? There's a possibility that if you set your timeout 
long enough it would eventually come back with a result. As far as I 
know, the Annotator isn't built to handle text from an entire article, 
which it appears this is (someone please correct me on this if I am wrong).

Let me know if this workaround is suitable for you.

Paul R Alexander
Web / UI Developer
NCBO BioPortal <>
Stanford Center for Biomedical Informatics Research

On 10/13/10 10:29 AM, Natasha F. Noy wrote:
> Marco,
> Forwarding this to support so that we can get more eyeballs on this. I 
> myself don't know what is going on.
> Natasha
> Begin forwarded message:
>> *From: *Marco Ocana <marco.ocana at 
>> <mailto:marco.ocana at>>
>> *Date: *October 13, 2010 8:22:46 AM PDT
>> *To: *"Natasha F. Noy" <noy at <mailto:noy at>>, 
>> Trish Whetzel <whetzel at <mailto:whetzel at>>
>> *Cc: *Paolo Ciccarese <paolo.ciccarese at 
>> <mailto:paolo.ciccarese at>>
>> *Subject: **Proxy error when calling text mining service*
>> Hi Natasha and Trish,
>> On one of my test cases I am consistently getting an error from the 
>> text mining service. I was able to reproduce it using the html form 
>> at Below is the text from 
>> the returned web page:
>>   Proxy Error
>> The proxy server received an invalid response from an upstream server.
>> The proxy server could not handle the request /POST /obs/annotator 
>> <>/.
>> Reason: *Error reading from remote server*
>> *
>> *
>> To reproduce from the online form, below are the steps:
>> 1. For ontologiesToKeepInResult:
>> 42584,42801,3083,13356,39183,40009,42672,44158,42983,13352,40724,40726,36430,44005,44006,44007,39976,42277,42571,40791,44163,40133,3093,39579,39577,44169,42685,13342,42971,44133,42504,38631,42502,39966,40917,42728,40216,40688,44079,36417,44170,42925,44171,44172,44173,42920,35686,44174,44175,40546,39509,44178,42651,40872,42791,39508,13404,42860,39580,42794,40483,40117,36425,25148,42456,44182,42915,42455,42912,40802,44180,42453,42452,40223,44112,42093,42993,44113,40937,44084,44016,42525,42998,44011,39624,37911,42545,42646,8056,40764,40660,44057,42117,13397,44108,42948,29684,40245,39215,44109,39933,40865,42828,40652,39343,40651,38873,40653,42736,42737,39734,13386,42931,42932,40958,42330,44448,42835,42838,42837,40238,42834,39927,42764,42622,40832,39331,44038,40649,40648,3905,40646,42768,44036,42765,40643,40642,14391,42367,40261,39815,42820,39336,39544,39038,40844,42752,13323,42758,40984,4531,40985,42184,38801,38802,38550 
>> ,42497,4525,38366,40358,42955,39804
>> 2. For textToAnnotate, I copied and pasted the text in attached file. 
>> Note: need to open in an editor that can read UTF-8 . The test for 
>> this is that you can find:  Aβ    in the document.
>> 3. For format, xml.
>> If this is something you can fix at your end and/or have a 
>> workaround, it would be greatly appreciated.
>> Thanks
>> Marco
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