<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
I haven’t received a response from the ontology maintainers, so I fixed the small error in the ontology source file that was causing parsing issues and reprocessed it in our system. CMO is fully available in BioPortal now, including the ability to use with
 the Annotator.
<div class=""><br class="">
</div>
<div class="">Jennifer</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Apr 27, 2020, at 11:11 AM, Jennifer Leigh Vendetti <<a href="mailto:vendetti@stanford.edu" class="">vendetti@stanford.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi again Jay,
<div class=""><br class="">
</div>
<div class="">I found the error in the ontology source file that is causing the parsing error, and have asked the maintainers if they could repair it:</div>
<div class=""><br class="">
</div>
<div class=""><a href="https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues/3" class="">https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues/3</a></div>
<div class=""><br class="">
</div>
<div class="">If I don’t get a response shortly, I’ll attempt to fix it on our end and reprocess.</div>
<div class=""><br class="">
</div>
<div class="">Jennifer</div>
<div class=""><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Apr 27, 2020, at 10:26 AM, Jennifer Leigh Vendetti <<a href="mailto:vendetti@stanford.edu" class="">vendetti@stanford.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Jay,
<div class=""><br class="">
</div>
<div class="">I looked at CMO in our system and it appears that the latest version (uploaded on January 7th) failed to parse. The status is showing as "Error Rdf”. This is the underlying reason that the Annotator doesn’t include results from this ontology.
 I’ve entered an issue in our tracker:</div>
<div class=""><br class="">
</div>
<div class=""><a href="https://github.com/ncbo/bioportal-project/issues/164" class="">https://github.com/ncbo/bioportal-project/issues/164</a></div>
<div class=""><br class="">
</div>
<div class="">… and am looking into the parsing errors.</div>
<div class=""><br class="">
</div>
<div class="">Kind regards.</div>
<div class="">Jennifer</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Apr 25, 2020, at 2:19 PM, <a href="mailto:support@bioontology.org" class="">
support@bioontology.org</a> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">
<p class="">Name: Jay Franklin </p>
<p class=""><a href="mailto:frankj7@rpi.edu" class="">Email: frankj7@rpi.edu</a> </p>
<p class="">Location: http%3A%2F%<a href="http://2fbioportal.bioontology.org/" class="">2Fbioportal.bioontology.org</a>%2Fannotator
</p>
<p class=""><br class="">
<strong class="">Feedback:</strong> </p>
<p class="">Hi,</p>
<p class="">It seems as though the Clinical Measurements Ontology (CMO) is not working correctly with the Annotator tool right now. Although I can select CMO in the drop-down list of ontologies, when I input biomedical text to be annotated CMO is never returned.
 For example, "diastolic blood pressure" does not return its corresponding IRI "<a href="http://purl.obolibrary.org/obo/CMO_0000004" class="">http://purl.obolibrary.org/obo/CMO_0000004</a>".</p>
<p class="">Is this an error within the Annotator, or am I misusing the software somehow? I would like to use the Annotator with CMO, so please let me know if something can be done about this.</p>
<p class="">Thanks, <br class="">
Jay Franklin <br class="">
Rensselaer Polytechnic Institute</p>
<div class=""><br class="webkit-block-placeholder">
</div>
</div>
_______________________________________________<br class="">
bioontology-support mailing list<br class="">
<a href="mailto:bioontology-support@lists.stanford.edu" class="">bioontology-support@lists.stanford.edu</a><br class="">
<a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support" class="">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
_______________________________________________<br class="">
bioontology-support mailing list<br class="">
<a href="mailto:bioontology-support@lists.stanford.edu" class="">bioontology-support@lists.stanford.edu</a><br class="">
<a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support" class="">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
_______________________________________________<br class="">
bioontology-support mailing list<br class="">
<a href="mailto:bioontology-support@lists.stanford.edu" class="">bioontology-support@lists.stanford.edu</a><br class="">
https://mailman.stanford.edu/mailman/listinfo/bioontology-support<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</body>
</html>