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Hello Emma,
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<div class="">I reprocessed the UBERON ontology in our system. However, the "hematopoietic system” class is still shown as a leaf node with no children. As a secondary step, I downloaded the ontology source file and double checked against different software,
 i.e., I loaded the ontology into the Protege ontology editor. Protege displays the same hierarchy with this particular class as a leaf node (screen shot below).</div>
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<div class="">Could you be more specific with regard to why you think there are classes missing from the ontology, and/or why the structure isn’t what you’re expecting?</div>
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<div class="">Kind regards,</div>
<div class="">Jennifer</div>
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<div class="">On Aug 10, 2020, at 2:58 AM, Emma Vos <<a href="mailto:emma@thehyve.nl" class="">emma@thehyve.nl</a>> wrote:</div>
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<div dir="ltr" class="">Dear Jennifer,
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<div class=""><font face="arial, sans-serif" class="">As I was querying terms in the UBERON ontology, I figured there is a similar issue as with the Cell Ontology.
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I was looking for children/descendants of the class <span style="white-space:pre-wrap" class="">"hematopoietic system", but these are missing in BioPortal</span></font><span style="white-space: pre-wrap; font-family: arial, sans-serif;" class="">.
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<div class=""><span style="white-space: pre-wrap; font-family: arial, sans-serif;" class="">Other classes seem to be missing as
</span>well<span style="white-space: pre-wrap; font-family: arial, sans-serif;" class="">.
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<div class=""><font face="arial, sans-serif" class=""><span style="white-space:pre-wrap" class="">Would you be able to help me out with this as well?</span></font></div>
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<div class=""><font face="arial, sans-serif" class=""><span style="white-space:pre-wrap" class="">Kind regards,</span></font></div>
<div class=""><font face="arial, sans-serif" class=""><span style="white-space:pre-wrap" class="">Emma Vos</span></font></div>
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<div dir="ltr" class="gmail_attr">On Mon, Jul 27, 2020 at 8:48 AM Emma Vos <<a href="mailto:emma@thehyve.nl" class="">emma@thehyve.nl</a>> wrote:<br class="">
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<div dir="ltr" class="">Dear Jennifer,
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<div class="">That's great, thank you very much!</div>
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<div class="">Kind regards,</div>
<div class="">Emma</div>
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<div dir="ltr" class="gmail_attr">On Thu, Jul 16, 2020 at 11:40 PM Jennifer Leigh Vendetti <<a href="mailto:vendetti@stanford.edu" target="_blank" class="">vendetti@stanford.edu</a>> wrote:<br class="">
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<div class="">Hello Emma,
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<div class="">On Jul 15, 2020, at 10:57 AM, <a href="mailto:support@bioontology.org" target="_blank" class="">
support@bioontology.org</a> wrote:</div>
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<p class="">I wanted to annotate some cell types (e.g. "monocyte") with Cell Ontology terms, using the Annotator tool. Unfortunately, this didn't work. When browsing through the Cell Ontology, I saw that part of the ontology is missing in BioPortal. For example,
 Cell Ontology contains a term for "monocyte": <a href="http://purl.obolibrary.org/obo/CL_0000576" target="_blank" class="">
http://purl.obolibrary.org/obo/CL_0000576</a> . But this term is not included in the Cell Ontology on BioPortal. Hence why I couldn't annotate this "monocyte" properly using the Annotator tool.</p>
<p class="">Another issue I had was with downloading the CSV file of Cell Ontology. I get the following error:
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"Cannot read latest submission upload file: /srv/ncbo/repository/CL/73/CL.csv.gz"</p>
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<div class="">Apologies for the inconvenience. It appears there was an error that occurred during the processing of the latest submission of the Cell Ontology. I reprocessed the ontology and the issues you reported are resolved - the CSV file is downloadable
 again, and the classes page appears normal.</div>
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<div class="">Kind regards,</div>
<div class="">Jennifer</div>
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<div class=""><span id="cid:1738f0790713b94fd2c1"><Screenshot 2020-07-16 14.36.38.png></span></div>
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<p class=""><span style="" class="">Emma Vos | Data Engineer</span></p>
<p class=""><img src="https://docs.google.com/uc?export=download&id=1p1QmNUCB4EKQ-qI0YTgYN0eZt8b_bV0M&revid=0B7YE47A_Oq-IT1gyUTNvMk96Wk16Vy9JRDZmcG8yd1dReWl3PQ" class=""><br class="">
<span style="" class=""></span><span style="color:rgb(34,34,34)" class=""></span></p>
<span style="color:rgb(127,186,56)" class="">E.   </span><span style="color:rgb(17,85,204)" class=""><span style="" class=""><a href="mailto:emma@thehyve.nl" target="_blank" class="">emma@thehyve.nl</a></span></span><span style="color:rgb(127,186,56)" class=""><br class="">
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<p class=""><span style="color:rgb(127,186,56)" class="">T.</span><span style="color:rgb(34,34,34)" class="">   </span><span style="" class="">+31(0)30 700 9713</span><span style="color:rgb(127,186,56)" class=""><br class="">
</span></p>
<p class=""><span style="color:rgb(127,186,56)" class="">W.<span style="" class="">  </span></span><span style="" class=""><a rel="nofollow" href="http://www.thehyve.nl/" target="_blank" class="">www.thehyve.nl</a></span></p>
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<p class=""><span style="" class="">Emma Vos | Data Engineer</span></p>
<p class=""><img src="https://docs.google.com/uc?export=download&id=1p1QmNUCB4EKQ-qI0YTgYN0eZt8b_bV0M&revid=0B7YE47A_Oq-IT1gyUTNvMk96Wk16Vy9JRDZmcG8yd1dReWl3PQ" class=""><br class="">
<span style="" class=""></span><span style="color:rgb(34,34,34)" class=""></span></p>
<span style="color:rgb(127,186,56)" class="">E.   </span><span style="color:rgb(17,85,204)" class=""><span style="" class=""><a href="mailto:emma@thehyve.nl" target="_blank" class="">emma@thehyve.nl</a></span></span><span style="color:rgb(127,186,56)" class=""><br class="">
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<p class=""><span style="color:rgb(127,186,56)" class="">T.</span><span style="color:rgb(34,34,34)" class="">   </span><span style="" class="">+31(0)30 700 9713</span><span style="color:rgb(127,186,56)" class=""><br class="">
</span></p>
<p class=""><span style="color:rgb(127,186,56)" class="">W.<span style="" class="">  </span></span><span style="" class=""><a rel="nofollow" href="http://www.thehyve.nl/" target="_blank" class="">www.thehyve.nl</a></span></p>
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