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    Marco,<br>
    <br>
    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.<br>
    <br>
    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).<br>
    <br>
    Let me know if this workaround is suitable for you.<br>
    <br>
    Best,<br>
    Paul R Alexander<br>
    Web / UI Developer<br>
    <a href="http://bioportal.bioontology.org">NCBO BioPortal</a><br>
    Stanford Center for Biomedical Informatics Research<br>
    <br>
    <br>
    On 10/13/10 10:29 AM, Natasha F. Noy wrote:
    <blockquote
      cite="mid:EB8BDC12-FB55-4BFA-A7A3-3B8B4028F514@stanford.edu"
      type="cite">Marco,
      <div><br>
      </div>
      <div>Forwarding this to support so that we can get more eyeballs
        on this. I myself don't know what is going on.<br>
        <div>
          <div>
            <p style="margin: 0px; min-height: 14px;"><br>
            </p>
            <p style="margin: 0px;"><font style="font: 12px Helvetica;"
                face="Helvetica" size="3">Natasha</font></p>
            <br class="Apple-interchange-newline">
          </div>
        </div>
        <div><br>
          <div>Begin forwarded message:</div>
          <br class="Apple-interchange-newline">
          <blockquote type="cite">
            <div>
              <div style="margin: 0px;"><font style="font: 14px
                  Helvetica; color: rgb(0, 0, 0);" color="#000000"
                  face="Helvetica" size="4"><b>From: </b></font><font
                  style="font: 14px Helvetica;" face="Helvetica"
                  size="4">Marco Ocana <<a moz-do-not-send="true"
                    href="mailto:marco.ocana@balboasystems.com">marco.ocana@balboasystems.com</a>></font></div>
              <div style="margin: 0px;"><font style="font: 14px
                  Helvetica; color: rgb(0, 0, 0);" color="#000000"
                  face="Helvetica" size="4"><b>Date: </b></font><font
                  style="font: 14px Helvetica;" face="Helvetica"
                  size="4">October 13, 2010 8:22:46 AM PDT</font></div>
              <div style="margin: 0px;"><font style="font: 14px
                  Helvetica; color: rgb(0, 0, 0);" color="#000000"
                  face="Helvetica" size="4"><b>To: </b></font><font
                  style="font: 14px Helvetica;" face="Helvetica"
                  size="4">"Natasha F. Noy" <<a
                    moz-do-not-send="true"
                    href="mailto:noy@stanford.edu">noy@stanford.edu</a>>,
                  Trish Whetzel <<a moz-do-not-send="true"
                    href="mailto:whetzel@stanford.edu">whetzel@stanford.edu</a>></font></div>
              <div style="margin: 0px;"><font style="font: 14px
                  Helvetica; color: rgb(0, 0, 0);" color="#000000"
                  face="Helvetica" size="4"><b>Cc: </b></font><font
                  style="font: 14px Helvetica;" face="Helvetica"
                  size="4">Paolo Ciccarese <<a moz-do-not-send="true"
                    href="mailto:paolo.ciccarese@gmail.com">paolo.ciccarese@gmail.com</a>></font></div>
              <div style="margin: 0px;"><font style="font: 14px
                  Helvetica; color: rgb(0, 0, 0);" color="#000000"
                  face="Helvetica" size="4"><b>Subject: </b></font><font
                  style="font: 14px Helvetica;" face="Helvetica"
                  size="4"><b>Proxy error when calling text mining
                    service</b></font></div>
              <div style="margin: 0px; min-height: 14px;"><br>
              </div>
            </div>
            <span class="Apple-style-span" style="border-collapse:
              separate; color: rgb(0, 0, 0); font-family: Helvetica;
              font-style: normal; font-variant: normal; font-weight:
              normal; letter-spacing: normal; line-height: normal;
              orphans: 2; text-indent: 0px; text-transform: none;
              white-space: normal; widows: 2; word-spacing: 0px;
              font-size: medium;">
              <div>
                <div style="margin: 0px; font-family: 'times new
                  roman','new york',times,serif; font-size: 12pt; color:
                  rgb(0, 0, 0);">
                  <div style="margin: 0px;">Hi Natasha and Trish,</div>
                  <div style="margin: 0px;"><br>
                  </div>
                  <div style="margin: 0px;"><span>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 <a moz-do-not-send="true"
                        target="_blank"
                        href="http://rest.bioontology.org/test_oba.html">http://rest.bioontology.org/test_oba.html</a><span
                        class="Apple-converted-space"> </span>. Below is
                      the text from the returned web page:</span></div>
                  <div style="margin: 0px;"><br>
                  </div>
                  <div style="margin: 0px;">
                    <h1 style="font-family: Times; font-size: medium;">Proxy
                      Error</h1>
                    <div style="margin: 0px; font-family: Times;
                      font-size: medium;">The proxy server received an
                      invalid response from an upstream server.<br>
                      The proxy server could not handle the request <em><a
                          moz-do-not-send="true"
                          href="http://rest.bioontology.org/obs/annotator">POST /obs/annotator</a></em>.</div>
                    <div style="margin: 0px; font-family: Times;
                      font-size: medium;">Reason: <strong>Error reading
                        from remote server</strong></div>
                    <div style="margin: 0px; font-family: Times;
                      font-size: medium;"><b><br>
                      </b></div>
                  </div>
                  <div style="margin: 0px;">To reproduce from the online
                    form, below are the steps:</div>
                  <div style="margin: 0px;"><br>
                  </div>
                  <div style="margin: 0px;">1. For
                    ontologiesToKeepInResult:</div>
                  <div style="margin: 0px;">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</div>
                  <div style="margin: 0px;"><br>
                  </div>
                  <div style="margin: 0px;">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.</div>
                  <div style="margin: 0px;"><br>
                  </div>
                  <div style="margin: 0px;">3. For format, xml.</div>
                  <div style="margin: 0px;"><br>
                  </div>
                  <div style="margin: 0px;">If this is something you can
                    fix at your end and/or have a workaround, it would
                    be greatly appreciated.</div>
                  <div style="margin: 0px;"><br>
                  </div>
                  <div style="margin: 0px;">Thanks</div>
                  <div style="margin: 0px;"><br>
                  </div>
                  <div style="margin: 0px;">Marco</div>
                  <div style="margin: 0px;"><br>
                  </div>
                  <div style="margin: 0px;"><br>
                  </div>
                  <div style="margin: 0px;"><br>
                  </div>
                </div>
              </div>
            </span></blockquote>
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</pre>
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