Hi,<div><br></div><div>I got similar error messages:</div><div><br></div><div><div class="error">   BioPortal returned an error: Error Parsing Ontologies: [(Id: 
1004) - Ontology version with the given id does not exist] </div><div class="error"><br></div><div class="error">any suggestions where to check?  log files or so?</div><br>cheers,</div><div>erick</div><div><br><div class="gmail_quote">
On 25 January 2013 22:29, Holt, Jonathan <span dir="ltr"><<a href="mailto:jonathan.holt@vanderbilt.edu" target="_blank">jonathan.holt@vanderbilt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">





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When I tried to upload the ontology manually, I got the error, 
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<div>Jonathan Holt, DO, MS</div>
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<font color="#7F7F7F" size="3"><span style="font-size:12px">Assistant Professor of Biomedical Informatics and Medicine</span></font></div>
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<span style="font-size:12px;color:rgb(127,127,127);font-family:Calibri,sans-serif">Departments of Biomedical Informatics & </span><span style="color:rgb(127,127,127);font-family:Calibri,sans-serif">Medicine, Division
 of Genetic Medicine<br>
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<div><span style="color:rgb(127,127,127);font-family:Calibri,sans-serif;font-size:12px">Vanderbilt University Medical Center</span></div>
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<font color="#7F7F7F" size="3"><span style="font-size:12px"><a href="mailto:jonathan.holt@vanderbilt.edu" style="color:purple" target="_blank">jonathan.holt@vanderbilt.edu</a></span></font></div>
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<font color="#7F7F7F" size="3"><span style="font-size:12px"><a href="http://dbmi.mc.vanderbilt.edu/people/holt.html" style="color:purple" target="_blank">http://dbmi.mc.vanderbilt.edu/people/holt.html</a></span></font></div>

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<div>On Jan 25, 2013, at 3:02 PM, "Lian, Zonghui" <<a href="mailto:Lian.Zonghui@mayo.edu" target="_blank">Lian.Zonghui@mayo.edu</a>></div>
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<span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">One you uploaded the files, you can run the parser through this page:<span> </span><a href="http://rest.bioontology.org/bioportal_admin/parseontologies.jsf" style="color:purple;text-decoration:underline" target="_blank">http://rest.bioontology.org/bioportal_admin/parseontologies.jsf</a><u></u><u></u></span></div>

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<b><span style="font-size:10pt;font-family:Tahoma,sans-serif">From:</span></b><span style="font-size:10pt;font-family:Tahoma,sans-serif"><span> </span>Holt, Jonathan [mailto:<a href="mailto:jonathan.holt@" target="_blank">jonathan.holt@</a><a href="http://Vanderbilt.Edu" target="_blank">Vanderbilt.Edu</a>]<span> </span><br>

<b>Sent:</b><span> </span>Friday, January 25, 2013 2:38 PM<br>
<b>To:</b><span> </span>Lian, Zonghui<br>
<b>Cc:</b><span> </span>Paul R Alexander (<a href="mailto:palexander@stanford.edu" target="_blank">palexander@stanford.edu</a>);
<a href="mailto:support@bioontology.org" target="_blank">support@bioontology.org</a> Support<br>
<b>Subject:</b><span> </span>Re: [bioontology-support] parsing error<u></u><u></u></span></div>
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any update?<u></u><u></u></div>
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Thanks,<u></u><u></u></div>
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Jonathan<u></u><u></u></div>
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<span style="font-size:13.5pt;font-family:Helvetica,sans-serif">Jonathan Holt, DO, MS<u></u><u></u></span></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)"><a href="mailto:jonathan.holt@vanderbilt.edu" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">jonathan.holt@vanderbilt.edu</span></a></span></span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>

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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)"><a href="http://dbmi.mc.vanderbilt.edu/people/holt.html" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">http://dbmi.mc.vanderbilt.edu/people/holt.html</span></a></span></span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>

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On Jan 21, 2013, at 11:01 AM, "Jonathan Holt, DO, MS" <<a href="mailto:jonathan.holt@vanderbilt.edu" style="color:purple;text-decoration:underline" target="_blank">jonathan.holt@vanderbilt.edu</a>> wrote:<u></u><u></u></div>

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sure, <u></u><u></u></div>
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mine is in a slightly different place. <u></u><u></u></div>
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for ICD-9 is is located in: /srv/ncbo/bioportal_resources/uploads/1101/1<u></u><u></u></div>
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see below: <u></u><u></u></div>
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root@ncbo 1]# pwd<u></u><u></u></div>
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/srv/ncbo/bioportal_resources/uploads/1101/1<u></u><u></u></div>
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[root@ncbo 1]# ls -hal<u></u><u></u></div>
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total 25M<u></u><u></u></div>
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drwxr-xr-x 2 tomcat tomcat 4.0K Jan 18 13:30 .<u></u><u></u></div>
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drwxr-xr-x 3 tomcat tomcat 4.0K Jan 18 13:30 ..<u></u><u></u></div>
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-rw-r--r-- 1 tomcat tomcat  25M Jan 18 13:30 icd9cm.rrf<u></u><u></u></div>
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<Screen Shot 2013-01-21 at 11.01.05 AM.png><u></u><u></u></div>
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Thanks,<u></u><u></u></div>
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<u></u> <u></u></div>
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Jonathan <u></u><u></u></div>
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<span style="font-size:13.5pt;font-family:Helvetica,sans-serif">.................................<u></u><u></u></span></div>
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<span style="font-size:13.5pt;font-family:Helvetica,sans-serif">Jonathan Holt, DO, MS<u></u><u></u></span></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Assistant Professor of Biomedical Informatics and Medicine</span></span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>

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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Departments of Biomedical Informatics & </span></span><span><span style="font-size:13.5pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Medicine,
 Division of Genetic Medicine</span></span><span><span style="font-size:13.5pt;font-family:Helvetica,sans-serif"><u></u><u></u></span></span></div>
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<span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Vanderbilt University Medical Center</span><u></u><u></u></div>
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<span style="font-size:13.5pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">2209 Garland Ave<br>
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<span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">412 Eskind Biomedical Library</span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Nashville, TN  37232-8340</span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Phone:  615-322-8683</span></span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Fax: 615-875-1424</span></span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)"><a href="mailto:jonathan.holt@vanderbilt.edu" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">jonathan.holt@vanderbilt.edu</span></a></span></span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>

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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)"><a href="http://dbmi.mc.vanderbilt.edu/people/holt.html" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">http://dbmi.mc.vanderbilt.edu/people/holt.html</span></a></span></span><span style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>

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On Jan 21, 2013, at 10:35 AM, "Lian, Zonghui" <<a href="mailto:Lian.Zonghui@mayo.edu" style="color:purple;text-decoration:underline" target="_blank">Lian.Zonghui@mayo.edu</a>><u></u><u></u></div>
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 wrote:<u></u><u></u></div>
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<span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Dr Holt,</span><u></u><u></u></div>
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<span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">The error may be caused by the file uploader. Can you check if the file was uploaded correctly? For example, for the below ontology, its ontology id is (1290).</span><u></u><u></u></div>

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<span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">In the linux box, you can find its uploaded files are under</span><u></u><u></u></div>
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<span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Please use this method to check the file for your case. As what I know, the file uploader is not stable when the file size is big. Once you find this file you can manually
 replace them with the right one.  (For rrf format, you need to unzip the zipped file) .</span><u></u><u></u></div>
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<span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Thanks,</span><u></u><u></u></div>
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<span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">-Lian</span><u></u><u></u></div>
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<b><span style="font-size:10pt;font-family:Tahoma,sans-serif">From:</span></b><span><span style="font-size:10pt;font-family:Tahoma,sans-serif"> </span></span><span style="font-size:10pt;font-family:Tahoma,sans-serif">Holt,
 Jonathan [mailto:<a href="mailto:jonathan.holt@" target="_blank">jonathan.holt@</a><a href="http://vanderbilt.edu/" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">Vanderbilt.Edu</span></a>]<span> </span><br>

<b>Sent:</b><span> </span>Friday, January 18, 2013 4:09 PM<br>
<b>To:</b><span> </span>Lian, Zonghui<br>
<b>Cc:</b><span> </span><a href="mailto:support@bioontology.org" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">support@bioontology.org</span></a><span> </span>Support<br>
<b>Subject:</b><span> </span>Re: [bioontology-support] parsing error</span><u></u><u></u></div>
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Lian,<u></u><u></u></div>
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After trying to up load the zipped file i get, <u></u><u></u></div>
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 <u></u><u></u></div>
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"we are sorry, but something has gone wrong. We have been notified of this error."  (see below) <u></u><u></u></div>
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<image003.jpg><u></u><u></u></div>
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if i try from the import_ontologies.rb script and point to Stanford's server with my apikey,  I get a parsing error as shown below. <u></u><u></u></div>
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Of note, this does NOT happen when I import an ontology in a different format, such as OWL or OBO, as shown in my other ontologies that I have successfully imported using the script. <u></u><u></u></div>
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I've tried getting a new build using: <u></u><u></u></div>
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but that does help things either. <u></u><u></u></div>
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Thanks,<u></u><u></u></div>
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Jonathan <u></u><u></u></div>
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<span style="font-size:13.5pt;font-family:Helvetica,sans-serif">Jonathan Holt, DO, MS</span><u></u><u></u></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Assistant Professor of Biomedical Informatics and Medicine</span></span><u></u><u></u></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Departments of Biomedical Informatics & </span></span><span><span style="font-size:13.5pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Medicine,
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<span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Vanderbilt University Medical Center</span><u></u><u></u></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)"><a href="mailto:jonathan.holt@vanderbilt.edu" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">jonathan.holt@vanderbilt.edu</span></a></span></span><u></u><u></u></div>

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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)"><a href="http://dbmi.mc.vanderbilt.edu/people/holt.html" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">http://dbmi.mc.vanderbilt.edu/people/holt.html</span></a></span></span><u></u><u></u></div>

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On Jan 18, 2013, at 10:26 AM, "Lian, Zonghui" <<a href="mailto:Lian.Zonghui@mayo.edu" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">Lian.Zonghui@mayo.edu</span></a>><u></u><u></u></div>

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 wrote:<u></u><u></u></div>
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<span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Hi Dr Holt,</span><u></u><u></u></div>
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<span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">It looks like the rrf files you used may be not correct(in the figure 2, the icd9cm.rrf was incorrect). Can you download the rrf zip from<span> </span><a href="http://bioportal.bioontology.org/ontologies" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">http://bioportal.bioontology.org/ontologies</span></a>?
 After that, you can unzip them into the upload folder and overwrite the old one. Please let me know if it works. Thanks.</span><u></u><u></u></div>
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<span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">-Lian</span><u></u><u></u></div>
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<b><span style="font-size:10pt;font-family:Tahoma,sans-serif">From:</span></b><span><span style="font-size:10pt;font-family:Tahoma,sans-serif"> </span></span><span style="font-size:10pt;font-family:Tahoma,sans-serif">Paul
 R Alexander [mailto:<a href="mailto:palexander@" target="_blank">palexander@</a><a href="http://stanford.edu/" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">stanford.edu</span></a>]<span> </span><br>

<b>Sent:</b><span> </span>Thursday, January 17, 2013 4:11 PM<br>
<b>To:</b><span> </span>Lian, Zonghui<br>
<b>Subject:</b><span> </span>Fwd: [bioontology-support] parsing error</span><u></u><u></u></div>
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Begin forwarded message:<u></u><u></u></div>
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<b><span style="font-size:13.5pt;font-family:Helvetica,sans-serif">From:<span> </span></span></b><span style="font-size:13.5pt;font-family:Helvetica,sans-serif">"Holt, Jonathan" <<a href="mailto:jonathan.holt@Vanderbilt.Edu" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">jonathan.holt@Vanderbilt.Edu</span></a>></span><u></u><u></u></div>

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<b><span style="font-size:13.5pt;font-family:Helvetica,sans-serif">Subject: [bioontology-support] parsing error</span></b><u></u><u></u></div>
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<b><span style="font-size:13.5pt;font-family:Helvetica,sans-serif">Date:<span> </span></span></b><span style="font-size:13.5pt;font-family:Helvetica,sans-serif">January 9, 2013 3:04:05 PM PST</span><u></u><u></u></div>
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<b><span style="font-size:13.5pt;font-family:Helvetica,sans-serif">To:<span> </span></span></b><span style="font-size:13.5pt;font-family:Helvetica,sans-serif">"<a href="mailto:support@bioontology.org" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">support@bioontology.org</span></a>"
 <<a href="mailto:support@bioontology.org" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">support@bioontology.org</span></a>></span><u></u><u></u></div>
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I have recently tried to get my ncbo virtual appliance back up and running. <u></u><u></u></div>
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So, I tried to import some ontologies from the bioportal to my own hosted vm, but got a parsing error. <u></u><u></u></div>
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I also tried to manually and still got a java error. <u></u><u></u></div>
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see attached.<u></u><u></u></div>
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Any thoughts?<u></u><u></u></div>
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Jonathan<u></u><u></u></div>
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<span style="font-size:13.5pt;font-family:Helvetica,sans-serif">Jonathan Holt, DO, MS</span><u></u><u></u></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Assistant Professor of Biomedical Informatics and Medicine</span></span><u></u><u></u></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Departments of Biomedical Informatics & </span></span><span><span style="font-size:13.5pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Medicine,
 Division of Genetic Medicine</span></span><u></u><u></u></div>
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<span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Vanderbilt University Medical Center</span><u></u><u></u></div>
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<span style="font-size:13.5pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">2209 Garland Ave<br>
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<span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">412 Eskind Biomedical Library</span><u></u><u></u></div>
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<span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Nashville, TN  37232-8340</span><u></u><u></u></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)">Phone:  615-322-8683</span></span><u></u><u></u></div>
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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)"><a href="mailto:jonathan.holt@vanderbilt.edu" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">jonathan.holt@vanderbilt.edu</span></a></span></span><u></u><u></u></div>

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<span><span style="font-size:9pt;font-family:Calibri,sans-serif;color:rgb(127,127,127)"><a href="http://dbmi.mc.vanderbilt.edu/people/holt.html" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">http://dbmi.mc.vanderbilt.edu/people/holt.html</span></a></span></span><u></u><u></u></div>

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_______________________________________________<br>
bioontology-support mailing list<br>
<a href="mailto:bioontology-support@lists.stanford.edu" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">bioontology-support@lists.stanford.edu</span></a><br>
<a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support" style="color:purple;text-decoration:underline" target="_blank"><span style="color:purple">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</span></a><u></u><u></u></div>

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<br>_______________________________________________<br>
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