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

Marco Ocana marco.ocana at balboasystems.com
Thu Oct 14 13:51:10 PDT 2010


Hi Paul,

Thanks for looking into this.
I have in the past gotten results for this document, but not sure what were the 
circumstances.
Do you guys have advice on on how big the chunks can be? If we need to split up 
the document, then we would like to keep the chunks as large as possible.

Regards,

Marco

________________________________
From: Paul R Alexander <palexander at stanford.edu>
To: Natasha F. Noy <noy at stanford.edu>
Cc: support Support <support at bioontology.org>; Marco Ocana 
<marco.ocana at balboasystems.com>; Paolo Ciccarese <paolo.ciccarese at gmail.com>
Sent: Wed, October 13, 2010 3:30:42 PM
Subject: Re: [bioontology-support] Fwd: Proxy error when calling text mining 
service

Marco,

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.

Best,
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 balboasystems.com>
>>Date: October 13, 2010 8:22:46 AM PDT
>>To: "Natasha F. Noy" <noy at stanford.edu>,                   Trish Whetzel 
>><whetzel at stanford.edu>
>>Cc: Paolo Ciccarese <paolo.ciccarese at gmail.com>
>>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 http://rest.bioontology.org/test_oba.html . 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
>>
>>
>>
>>
>>
>>
>
>
>
>
> _______________________________________________ bioontology-support mailing 
>list bioontology-support at lists.stanford.edu 
>https://mailman.stanford.edu/mailman/listinfo/bioontology-support 
>
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