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    Sanjay,<br>
    <br>
    There was a bug in some versions of the Virtual Appliance that may
    have made metrics calculation break from the BioPortal Admin UI.
    Unfortunately there's no easy fix for that. Metrics are not
    necessary to utilize the ontology via the REST service or UI,
    however, so the only thing you'll be missing are class count and
    related information on the summary page.<br>
    <br>
    Paul R Alexander<br>
    Web / UI Developer<br>
    NCBO BioPortal<br>
    Stanford Center for Biomedical Informatics Research<br>
    <br>
    <br>
    <div class="moz-cite-prefix">On 5/7/12 2:19 PM, Agravat, Sanjay
      wrote:<br>
    </div>
    <blockquote cite="mid:CBCDB48A.6AD4%25sagrava@emory.edu" type="cite">
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      <title>Re: [bioontology-support] Support request for the
        Cardiovascular Research Grid project</title>
      <font face="Calibri, Verdana, Helvetica, Arial"><span
          style="font-size:11pt">Hi Paul,<br>
          <br>
          So I tried doing this and was able to at least get some of the
          classes loaded, but when I go to Calculate Metrics, I get this
          error: “</span></font><font size="1"><font face="Trebuchet MS"><span
            style="font-size:9pt">BioPortal returned an error: The
            method specified in the request is not allowed for the
            resource identified by the request URI”.<br>
            <br>
            Do you know how to resolve this issue?<br>
            <br>
            Thanks,<br>
            <br>
            Sanjay<br>
          </span></font></font><font face="Calibri, Verdana, Helvetica,
        Arial"><span style="font-size:11pt"><br>
          <br>
          On 5/7/12 2:44 PM, "Paul R Alexander" <<a
            moz-do-not-send="true" href="palexander@stanford.edu">palexander@stanford.edu</a>>
          wrote:<br>
          <br>
        </span></font>
      <blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span
            style="font-size:11pt"> Unfortunately, we don't support
            loading ontologies from a Protege database. You can attempt
            to swap a Protege database back-end table with the one used
            in BioPortal, but it's not a straightforward process.
            However, if you want to give it a shot, you would need to:<br>
             <br>
          </span></font>
        <ol>
          <li><font face="Calibri, Verdana, Helvetica, Arial"><span
                style="font-size:11pt">Submit a dummy ontology file with
                all of the information for the real ontology. This file
                should be something small that will parse properly
              </span></font></li>
          <li><font face="Calibri, Verdana, Helvetica, Arial"><span
                style="font-size:11pt">Parse the dummy ontology
              </span></font></li>
          <li><font face="Calibri, Verdana, Helvetica, Arial"><span
                style="font-size:11pt"></span></font><br>
          </li>
          <li><font face="Calibri, Verdana, Helvetica, Arial"><span
                style="font-size:11pt">Find the version number for the
                dummy ontology
              </span></font></li>
          <li><font face="Calibri, Verdana, Helvetica, Arial"><span
                style="font-size:11pt">Go to the database on the Virtual
                Appliance and find the table that corresponds to the
                dummy version in the 'bioportal_protege' database
              </span></font></li>
          <li><font face="Calibri, Verdana, Helvetica, Arial"><span
                style="font-size:11pt">Note the table name (should be
                something like 'tbl_10000') and delete the table
              </span></font></li>
          <li><font face="Calibri, Verdana, Helvetica, Arial"><span
                style="font-size:11pt">Import your parsed version of the
                real ontology and rename the imported table to match the
                old dummy table name (ex: 'tbl_10000')
              </span></font></li>
          <li><font face="Calibri, Verdana, Helvetica, Arial"><span
                style="font-size:11pt"></span></font><br>
          </li>
          <li><font face="Calibri, Verdana, Helvetica, Arial"><span
                style="font-size:11pt">Using the BioPortal Admin tool:
                1) calculate metrics and 2) index the ontology
                <br>
              </span></font></li>
        </ol>
        <font face="Calibri, Verdana, Helvetica, Arial"><span
            style="font-size:11pt"><br>
            <br>
            Give that a shot and let me know if you run into problems.<br>
             <br>
             <br>
            <br>
            Paul R Alexander<br>
             Web / UI Developer<br>
             NCBO BioPortal<br>
             Stanford Center for Biomedical Informatics Research<br>
             <br>
             <br>
             <br>
            On 5/7/12 10:35 AM, Trish Whetzel wrote:<br>
             <br>
             <br>
          </span></font>
        <blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span
              style="font-size:11pt"><br>
              Hi Sanjay, <br>
               <br>
              <br>
               <br>
               <br>
              I believe there is a mechanism to swap in the Protege
              database table into the Protege backend for BioPortal.
              <br>
               <br>
              <br>
               <br>
               <br>
              Paul, is this what you would recommend and/or can help
              Sanjay with this item?<br>
               <br>
              <br>
               <br>
               <br>
              Trish <br>
               <br>
              <br>
               <br>
               <br>
              <br>
               <br>
               <br>
               <br>
               <br>
              On May 7, 2012, at 9:09 AM, Agravat, Sanjay wrote:<br>
               <br>
               <br>
            </span></font>
          <blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span
                style="font-size:11pt"> <br>
                 Hi,<br>
                 <br>
                 I have a local instance of bioportal running  and I’m
                having a problem loading my ontology into bioportal.
                  The ontology is stored in the protégé database so I
                tried uploading the .pprj file with the database located
                on the same server as bioportal and that didn’t work.  I
                also tried converting the .pprj to use .pins and .ponts
                but that didn’t work because the upload form doesn’t
                take the classes or instances file as input.<br>
                 <br>
                 I am not able to export the ontology to .owl since the
                ontology is  very large and protégé doesn’t seem to be
                able to do it.  Do you have any suggestions?<br>
                 <br>
                 Thanks,<br>
                 <br>
                 Sanjay <br>
                 <br>
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                <br>
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              </span></font></blockquote>
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               <br>
               <br>
               <br>
            </span></font></blockquote>
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            style="font-size:11pt"><br>
             <br>
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          </span></font></blockquote>
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