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Hello Emma,
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<div class="">I assume the screen shots you provided are from the Ontology Lookup Service (<a href="https://www.ebi.ac.uk/ols/ontologies/uberon" class="">https://www.ebi.ac.uk/ols/ontologies/uberon</a>)?</div>
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<div class="">One thing to note:</div>
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<div class="">As far as I can tell, BioPortal and OLS serve different distributions of UBERON. We’re serving the distribution of UBERON available at this URL:</div>
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<div class=""><a href="http://purl.obolibrary.org/obo/uberon/ext.owl" class="">http://purl.obolibrary.org/obo/uberon/ext.owl</a></div>
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<div class="">The OLS appears to be serving the distribution of UBERON from this URL:</div>
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<div class=""><a href="http://purl.obolibrary.org/obo/uberon.owl" class="">http://purl.obolibrary.org/obo/uberon.owl</a></div>
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<div class="">The OBO Foundry website describes the differences between the various distributions of UBERON:</div>
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<div class=""><a href="http://www.obofoundry.org/ontology/uberon.html" class="">http://www.obofoundry.org/ontology/uberon.html</a></div>
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<div class="">Another thing to note:</div>
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<div class="">With regard to the display of class hierarchies, there’s a distinct difference between an “asserted" hierarchy and an “inferred" hierarchy. BioPortal is displaying the asserted class hierarchy. If you open the uberon.owl file that OLS serves in
 the Protege ontology editor, you can see that the “venous blood” class is also show as a leaf term, i.e., in the position that it was manually defined in the asserted hierarchy (screen shot below). You can also see in the same screen shot that the “venous
 blood” class has a subClassOf axiom:</div>
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<div class="">'part of' some 'hematopoietic system’</div>
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<div class="">This means that "venous blood" will be shown as a subclass of "hematopoietic system” in any instance where an *inferred* hierarchy is displayed. In order to display an inferred hierarchy, you need to perform reasoning on an ontology. I don’t know
 the internal of the OLS software - however, I’m guessing that somewhere in their pipeline they perform a reasoning task that allows them to display terms in the context of an inferred hierarchy.</div>
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<div class="">The hierarchy that BioPortal displays isn’t incomplete and/or incorrect. The differences you see between the two pieces of software have to do with asserted vs. inferred hierarchies.</div>
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<div class="">Kind regards,</div>
<div class="">Jennifer</div>
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<div class=""><img apple-inline="yes" id="0EE170F5-A809-4ABD-96D3-8A52788D7695" width="1119" height="940" src="cid:526E261A-F25A-4C02-A8A4-42D926EA593D@stanford.edu" class=""></div>
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<div class="">On Aug 11, 2020, at 11:53 PM, 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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<font face="arial, sans-serif" class="">Thank you for your reply. Sorry for any confusion!<br class="">
I can give one example:<br class="">
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<div class=""><font face="arial, sans-serif" class=""><font class="">I was looking at some UBERON classes, like "venous blood" (UBERON:0013756). If I resolve the ID of this class (<a href="http://purl.obolibrary.org/obo/UBERON_0013756" class="">http://purl.obolibrary.org/obo/UBERON_0013756</a>),
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I see that that "venous blood" is a descendant of "hematopoietic system" (UBERON:0002390): </font></font></div>
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<div class=""><font face="arial, sans-serif" class=""><span id="cid:ii_kdr09jiv1"><image.png></span><br class="">
</font></div>
<div class=""><font face="arial, sans-serif" class="">But "venous blood" doesn't show up as one of the descendants of the "hematopoietic system" class in BioPortal.
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The descendants page of the "hematopoietic system" class is even completely empty: <br class="">
<a href="http://data.bioontology.org/ontologies/UBERON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0002390/descendants" class="">http://data.bioontology.org/ontologies/UBERON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0002390/descendants</a></font></div>
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Similar to when I look at ancestors of "venous blood", the "hematopoietic system" class doesn't show up as ancestor:<br class="">
</font><a href="http://data.bioontology.org/ontologies/UBERON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0013756/ancestors" class="">http://data.bioontology.org/ontologies/UBERON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0013756/ancestors</a>  <font face="arial, sans-serif" class=""><br class="">
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<div class="">So both the classes "venous blood" and "hematopoietic system" are present in BioPortal, but the hierarchy doesn't seem to be complete/correct.</div>
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<div class="">I hope I made it a bit more clear. Thank you for your quick response and help!</div>
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<div class="">Kind regards,</div>
<div class="">Emma</div>
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<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Aug 12, 2020 at 12:23 AM Jennifer Leigh Vendetti <<a href="mailto:vendetti@stanford.edu" class="">vendetti@stanford.edu</a>> wrote:<br class="">
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<div style="overflow-wrap: break-word;" class="">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=""><span id="cid:173e1640c50994129f81"><Screen Shot 2020-08-11 at 3.15.04 PM.png></span></div>
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<div class="">On Aug 10, 2020, at 2:58 AM, Emma Vos <<a href="mailto:emma@thehyve.nl" target="_blank" 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=""><br class="">
</span></font></div>
<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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</span></font></div>
<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" target="_blank" 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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<blockquote type="cite" class="">
<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="gmail-m_3546679974596620925cid:1738f0790713b94fd2c1" class=""><Screenshot 2020-07-16 14.36.38.png></span></div>
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<p class=""><span 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="">
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<span style="color:rgb(127,186,56)" class="">E.   </span><span style="color:rgb(17,85,204)" class=""><span 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="">
</span>
<p class=""><span style="color:rgb(127,186,56)" class="">T.</span><span style="color:rgb(34,34,34)" class="">   </span><span class="">+31(0)30 700 9713</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="">W.<span class="">  </span></span><span 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 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="">
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<span style="color:rgb(127,186,56)" class="">E.   </span><span style="color:rgb(17,85,204)" class=""><span 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 class="">+31(0)30 700 9713</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="">W.<span class="">  </span></span><span 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="">
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<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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