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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>The documentation essentially is an example:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><a href="http://data.bioontology.org/documentation#nav_batch">http://data.bioontology.org/documentation#nav_batch</a><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>This call gets back prefLabel, Synonym, and semantic type. You can eliminate the last two (toward the end of the example) to just get prefLabel.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Ray<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='margin-left:.5in'><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Al Shapiro [mailto:als371@yahoo.com] <br><b>Sent:</b> Thursday, October 24, 2013 5:34 PM<br><b>To:</b> Ray Fergerson; bioontology-support@lists.stanford.edu; support@bioontology.org<br><b>Cc:</b> Mona Salem<br><b>Subject:</b> Re: *Second Request* - The annotations in the output report for the Annotator do Not always match the Annotations in the JSON file...<o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-left:.5in'><o:p> </o:p></p><div><div><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Ray,<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>When you have some time, can you send me an<b> example</b> of the batch call passing all classes, so that I can then get access to all the preferred names, because it is the "preferred names" that I consider to be the multiple annotations that I am looking for, for my project....<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>In other words, how does one do this process!<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Thank you for your quick response because I know you guys are swamped with support e-mails...<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Al Shapiro <o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p><div><div><div><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>On Thursday, October 24, 2013 4:40 PM, Ray Fergerson <<a href="mailto:ray.fergerson@stanford.edu">ray.fergerson@stanford.edu</a>> wrote:</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div><div><div id=yiv1973192132><div><div><div><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:11.0pt;font-family:"Helvetica","sans-serif";color:black'>Sorry about the delay. I think that I understand the question. I think that the service and the file are working correctly. I believe that the problem is that it is difficult to see the connection between what it displayed in the table and the contents of the json file. Perhaps this will help:</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:11.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:11.0pt;font-family:"Helvetica","sans-serif";color:black'>The first column in the table is the preferred name of the matched class. This name does not necessarily appear anywhere in the json output. We make another call to get the preferred name for all matched classes (a batch call passing all classes and getting back all preferred names). The “annotations text” in the result may or may not be the same as the preferred name. For example if the match was on a synonym then it will not be the same. Likewise if the match was a hierarchy or mapping match then it will not be the same.</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:11.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:11.0pt;font-family:"Helvetica","sans-serif";color:black'>Ray</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:11.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div><div id=yiv1973192132yqt69186><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><b><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>From:</span></b><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> Al Shapiro [<a href="mailto:als371@yahoo.com">mailto:als371@yahoo.com</a>] <br><b>Sent:</b> Thursday, October 24, 2013 12:20 PM<br><b>To:</b> Ray Fergerson; <a href="mailto:bioontology-support@lists.stanford.edu">bioontology-support@lists.stanford.edu</a>; <a href="mailto:support@bioontology.org">support@bioontology.org</a><br><b>Cc:</b> Al; Mona Salem<br><b>Subject:</b> *Second Request* - The annotations in the output report for the Annotator do Not always match the Annotations in the JSON file...</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div></div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-family:"Helvetica","sans-serif";color:black'> <o:p></o:p></span></p></div><div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Ray and support personnel,</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>I know you guys are busy but I would appreciate some <b>feedback </b>on the following BioPortal Annotator problem that I have outlined below the following:</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>a) Acknowledgement that it is or it is Not a problem;</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>b) If it is Not a problem, how can I locate (via the JSON output file) the matching annotations that display in the Annotation report;</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>c) If it is deemed a problem, <b>approximately </b>how long will it take for you guys to fix it.</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Thanks again - see details about this problem below,</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Al Shapiro</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div><div><div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>On Monday, October 21, 2013 5:17 PM, Al Shapiro <<a href="mailto:als371@yahoo.com" target="_blank">als371@yahoo.com</a>> wrote:</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div id=yiv1973192132><div><div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Hi there again,</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>The annotations in the output report for the Annotator do Not always match the Annotations in the JSON file...</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>The annotations from the output report in column 1 do Not always match the "annotations text" in the JSON file...</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><b><i><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Note: </span></i></b><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Over 60% of the Annotations on the displayed report do Not match what is in the JSON file...</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 1) column 1 of the report = NCI CTEP SDC Melanoma Sub-Category Terminology;</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the first "annotations text" entry in the JSON file  =  "<b>MELANOMA</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 2) column 1 of the report = Melanoma Pathway; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the second "annotations text" entry in the JSON file  =  "<b>MELANOMA</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 3) column  1 of the report = Melanoma; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the third "annotations text" entry in the JSON file  =  "MELANOMA"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 4) column  1 of the report = Mouse Melanoma; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the fourth "annotations text" entry in the JSON file  =  "<b>MELANOMA</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 5) column  1 of the report = Malignant Neoplasm; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the fifth "annotations text" entry in the JSON file  =  "<b>MALIGNANT TUMOR</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-top:1.2pt;margin-bottom:1.2pt'><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 6) column  1 of the report = Malignant Paraganglioma; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div style='margin-top:1.2pt;margin-bottom:1.2pt'><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the sixth "annotations text" entry in the JSON file  =  "<b>MALIGNANT</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 7) column  1 of the report = Anaplastic Oligodendroglioma; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div style='margin-top:1.2pt;margin-bottom:1.2pt;word-spacing:0px'><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the seventh "annotations text" entry in the JSON file  =  "<b>MALIGNANT</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div style='margin-top:1.2pt;margin-bottom:1.2pt;word-spacing:0px'><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 8) column  1 of the report = MALIGNANT; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the eighth "annotations text" entry in the JSON file  =  "MALIGNANT"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 9) column  1 of the report = Neoplasm; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the ninth "annotations text" entry in the JSON file  =  "<b>Tumor</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 10) column  1 of the report = Tumor Mass; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the tenth "annotations text" entry in the JSON file  =  "<b>Tumor</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 11) column  1 of the report = Melanocyte; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the eleventh "annotations text" entry in the JSON file  =  "MELANOCYTES"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 12) column  1 of the report = Murine Melanocytes; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the twelfth "annotations text" entry in the JSON file  =  "<b>MELANOCYTES</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 13) column  1 of the report = Present; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the thirteenth "annotations text" entry in the JSON file  =  "<b>FOUND</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 14) column  1 of the report = Skin; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the fourteenth "annotations text" entry in the JSON file  =  "SKIN"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 15) column  1 of the report = Murine Skin; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the fifteenth "annotations text" entry in the JSON file  =  "<b>SKIN</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 16) column  1 of the report = Mouse Skin; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the sixteenth "annotations text" entry in the JSON file  =  "<b>SKIN</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 17) column  1 of the report = Murine Intestines; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the seventeenth "annotations text" entry in the JSON file  =  "<b>BOWEL</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 18) column  1 of the report = Intestine; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the eighteenth "annotations text" entry in the JSON file  =  "<b>BOWEL</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 19) column  1 of the report = Murine Eye; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the nineteenth "annotations text" entry in the JSON file  =  "<b>EYE</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 20) column  1 of the report = Eye; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the twentieth "annotations text" entry in the JSON file  =  "EYE"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>entry 21) column  1 of the report = Mouse Eye; </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>and the twenty first "annotations text" entry in the JSON file  =  "<b>EYE</b>"</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Do the following to reproduce the above results:</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>1) Go to the  BioPortal Manual Annotator page;</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>2) Click on "insert sample text"; [Melanoma is a malignant tumor of melanocytes which are found predominantly in skin but also in the bowel and the eye.]</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>3) In the "Select Ontologies" box enter the National Cancer Institute Thesaurus (NCIT) ontology;</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>4) Click on "Get Annotations" button;</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>5) After the Annotations report displays on the screen, Click on Format Results As:     JSON link;</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>6) Examine results from both outputs.</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><b><i><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Note:</span></i></b><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> My company is developing an application system that needs to Annotate the Text contained in the biological software product abstracts located at The G6G Directory of Omics and Intelligent Software web-site: <a href="http://g6g-softwaredirectory.com/" target="_blank">http://g6g-softwaredirectory.com/</a></span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><i><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span></i><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Any insight would be greatly appreciated,</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><i><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span></i><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Thank you,</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>Al Shapiro</span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><i><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span></i><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><i><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span></i><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div style='margin-top:1.2pt;margin-bottom:1.2pt;word-spacing:0px'><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div style='margin-top:1.2pt;margin-bottom:1.2pt;word-spacing:0px'><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div style='margin-top:1.2pt;margin-bottom:1.2pt;word-spacing:0px'><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div style='margin-top:1.2pt;margin-bottom:1.2pt;word-spacing:0px'><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div style='margin-top:1.2pt;margin-bottom:1.2pt;word-spacing:0px'><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in;background:white'><span style='font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div></div><div><div style='margin-left:.5in'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><span style='font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div></div></div></div></div><div style='margin-left:.5in;margin-bottom:12.0pt'><p class=MsoNormal style='margin-left:.5in;background:white'><span style='font-family:"Helvetica","sans-serif";color:black'> <o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in;background:white'><span style='font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div></div></div></div></div></div></body></html>