<div dir="ltr"><div><div>Thank you Jennifer,<br><br></div><div>We want to submit this ontology in a journal on the 1st October so it has been just in time.<br></div><div><br></div>Kind regards,<br><br></div>Laia<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Aug 24, 2017 at 1:44 AM, Jennifer Leigh Vendetti <span dir="ltr"><<a href="mailto:vendetti@stanford.edu" target="_blank">vendetti@stanford.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



<div style="word-wrap:break-word">
Hello Laia,
<div><br>
</div>
<div>The issue that was preventing ORDO from parsing/loading in BioPortal has been fixed. I reprocessed your HORD ontology, which is now fully parsed and available.</div>
<div><br>
</div>
<div>Kind regards,</div>
<div>Jennifer</div><div><div class="h5">
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite">
<div>On Aug 17, 2017, at 10:59 PM, Laia Subirats <<a href="mailto:laia.subirats@gmail.com" target="_blank">laia.subirats@gmail.com</a>> wrote:</div>
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<div>
<div dir="ltr" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
Hi Jennifer,
<div><br>
</div>
<div>Thank you for your answer. </div>
<div><br>
</div>
<div>Kind regards,</div>
<div><br>
</div>
<div>Laia
<div class="gmail_extra">
<div class="gmail_quote">On Fri, Aug 18, 2017 at 3:06 AM, Jennifer Leigh Vendetti<span class="m_-3277356339281155306Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:vendetti@stanford.edu" target="_blank">vendetti@stanford.<wbr>edu</a>></span><span class="m_-3277356339281155306Apple-converted-space"> </span>wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div style="word-wrap:break-word">Hi Laia,
<div><br>
</div>
<div>You’re including the ORDO ontology, which doesn’t parse in BioPortal at the moment. Unfortunately, the problem is a bug in the OWL API, which is 3rd party software that we use to load / parse ontologies. I’ve been corresponding with the developer
 of the OWL API and he has released a bug fix version that may address the problem with ORDO. I plan to integrate this new version of the OWL API into BioPortal, but haven’t been able to get to it yet due to some other work that is higher priority at the moment.</div>
<div><br>
</div>
<div>I apologize that I don’t have an exact date for you when the problem with ORDO will be resolved, but it should be in the near future.</div>
<div><br>
</div>
<div>Kind regards,</div>
<div>Jennifer</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite"><span>
<div>On Aug 17, 2017, at 3:32 AM, Laia Subirats <<a href="mailto:laia.subirats@gmail.com" target="_blank">laia.subirats@gmail.com</a>> wrote:</div>
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<div>Dear Jennifer,<br>
<br>
</div>
I would like to ask you help about this issue. I am still lost about how can I solve this error.<br>
<br>
</div>
Best,<br>
<br>
</div>
Laia<br>
</div>
</span>
<div class="gmail_extra"><br>
<div class="gmail_quote"><span>On Tue, Aug 8, 2017 at 1:00 PM, Laia Subirats<span class="m_-3277356339281155306Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:laia.subirats@gmail.com" target="_blank">laia.subirats@gmail.<wbr>com</a>></span><span class="m_-3277356339281155306Apple-converted-space"> </span>wrote:<br>
</span>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div dir="ltr"><span>
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<div>Hello Jennifer,<br>
<br>
</div>
I change the imports. I uploaded the external ontologies in my Github webpage and pointed my ontology to them. I also changed the unamed.owl import.<span class="m_-3277356339281155306Apple-converted-space"> </span><br>
<br>
</div>
However, now I have this error: "<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-ontology_submission_status">(Uploaded, Error Rdf)<span>".<br>
<br>
</span></span></div>
<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-ontology_submission_status"><span>I have uploaded to webprotege and it works properly, and in my local Protégé as well.<br>
<br>
</span></span></div>
<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-ontology_submission_status"><span>Sorry for making you spend time helping me.<br>
<br>
</span></span></div>
<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-ontology_submission_status"><span>Best,<br>
</span></span></div>
<div><span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-ontology_submission_status"><span><br>
</span></span></div>
<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-ontology_submission_status"><span>Laia</span></span><br>
</span>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div class="gmail_extra">
<div>
<div class="m_-3277356339281155306m_7096496498380612188h5">
<div class="gmail_quote"><span>On Mon, Aug 7, 2017 at 6:46 PM, Jennifer Leigh Vendetti<span class="m_-3277356339281155306Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:vendetti@stanford.edu" target="_blank">vendetti@stanford.<wbr>edu</a>></span><span class="m_-3277356339281155306Apple-converted-space"> </span>wrote:<br>
</span>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div><span>Hello Laia,
<div><br>
</div>
<div>I looked at your latest ontology source file (HORD_all_2017_08_07_scenarios<wbr>.owl). There are still a number of problems with the import statements.</div>
<div><br>
</div>
<div>1). It’s not valid to use a BioPortal REST API call as a download URL for the location of an ontology that you’d like to import. The import statements on lines 21 and 23 in your ontology file will result in not found errors:</div>
<div><br>
</div>
<div><owl:imports rdf:resource="<a href="http://data.bioontology.org/ontologies/ICF/submissions/3/download?apikey=eb8ef13c-ae88-42a5-b6f5-39c93d736688" target="_blank">http://data.bioo<wbr>ntology.org/ontologies/ICF/sub<wbr>missions/3/download?apikey=eb8<wbr>ef13c-ae88-42a5-b6f5-39c93d736<wbr>688</a>"/></div>
<div>
<div>…</div>
<div><owl:imports rdf:resource="<a href="http://data.bioontology.org/ontologies/ORDO/submissions/11/download?apikey=eb8ef13c-ae88-42a5-b6f5-39c93d736688%E2%80%9D/" target="_blank">http://data.bioo<wbr>ntology.org/ontologies/ORDO/su<wbr>bmissions/11/download?apikey=e<wbr>b8ef13c-ae88-42a5-b6f5-39c93d7<wbr>36688”/</a>></div>
</div>
<div><br>
</div>
<div>This is true not only for BioPortal, but for other ontology editing environments as well. If I open your ontology in the Protege ontology editing environment [1], you will see errors for both of those imports:</div>
<div><br>
</div>
<div><br>
</div>
</span>
<div><span id="m_-3277356339281155306m_7096496498380612188cid:F229D349-E469-46E9-A15B-5D1CC5550BFA@stanford.edu"><Screenshot 2017-08-07 09.20.54.png></span><span id="m_-3277356339281155306m_7096496498380612188cid:27C78D6C-8B9A-4ADD-8CD1-A07D94EB0713@stanford.edu"><Screenshot
 2017-08-07 09.21.22.png></span></div>
<div>
<div class="m_-3277356339281155306h5">
<div><br>
</div>
<div><br>
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<div><br>
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<div>2). Line 26 contains another invalid import statement:</div>
<div><br>
</div>
<div>
<div><owl:imports rdf:resource="<a href="http://www.owl-ontologies.com/unnamed.owl" target="_blank">http://www.owl-o<wbr>ntologies.com/unnamed.owl</a>"/></div>
</div>
<div><br>
</div>
<div>… which has a URL that doesn’t resolve to anything.</div>
<div><br>
</div>
<div>Kind regards,</div>
<div>Jennifer</div>
<div><br>
</div>
<div>[1] <a href="http://protege.stanford.edu/products.php" target="_blank">http://protege.stanford.ed<wbr>u/products.php</a></div>
<div>
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<div><br>
</div>
<div>
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite">
<div>On Aug 6, 2017, at 10:21 PM, Laia Subirats <<a href="mailto:laia.subirats@gmail.com" target="_blank">laia.subirats@gmail.com</a>> wrote:</div>
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<div>
<div>Hi John,<br>
<br>
</div>
I changed the references and now there is not a parsing problem anymore. However, the metrics do not appear.<br>
<br>
</div>
Cheers,<br>
<div>
<div>
<div>
<div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Laia Subirats<br>
</div>
<div class="gmail_extra">
<div class="gmail_quote">On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:jgraybeal@stanford.edu" target="_blank">jgraybeal@stanford.e<wbr>du</a>></span><span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span>wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div>Hi Laia, 
<div><br>
</div>
<div>Sorry for the trouble you are having.  Usually that message indicates there has been a problem parsing the ontology, and you can try verifying the ontology parses with Protege or WebProtege as a next step.</div>
<div><br>
</div>
<div>In this case, a quick look at the error log indicated two issues:</div>
<div>
<div>* "OWL_IMPORT_MISSING:<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><a href="http://who.int/icf" target="_blank">http://wh<wbr>o.int/icf</a>"</div>
<div>* "OWL_IMPORT_MISSING:<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><a href="http://www.orpha.net/version2.4" target="_blank">http://ww<wbr>w.orpha.net/version2.4</a>"</div>
<div><br>
</div>
<div>A quick suggestion (sorry, no time today to verify myself) is to check to confirm that those two ontologies are indeed at those locations, and if they are not, change the references in the source ontology to point to correct locations.</div>
<div><br>
</div>
<div>If you are still having trouble after that, please send another note indicating your latest understanding, and our team will try to help. Thanks.</div>
<div><br>
</div>
<div>John</div>
<div><br>
</div>
<div><br>
</div>
<div>
<blockquote type="cite">
<div>
<div class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186h5">
<div>On Aug 5, 2017, at 9:52 PM, Laia Subirats <<a href="mailto:laia.subirats@gmail.com" target="_blank">laia.subirats@gmail.com</a>> wrote:</div>
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<div>Dear Sir/Madam,<br>
<br>
</div>
I would like to see the<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186m_8729106135744704153gmail-il">metrics</span><span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span>of
 my ontology in<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><a href="http://bioportal.bioontology.org/ontologies/PMR" target="_blank">http://bioportal.bioontolog<wbr>y.org/ontologies/HORD</a>,
 I do not know if there is any problem. I see that there is a "<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186m_8729106135744704153gmail-ontology_submission_status">(Uploaded, Error Rdf)" but I do not see the problem.<br>
</span>
<div><br>
</div>
Yours faithfully,<br>
--<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><br>
<div class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186m_8729106135744704153gmail_signature">
Laia Subirats </div>
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______________________________<wbr>_________________<br>
bioontology-support mailing list<br>
<a href="mailto:bioontology-support@lists.stanford.edu" target="_blank">bioontology-support@lists.stan<wbr>ford.edu</a><br>
<a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support" target="_blank">https://mailman.stanford.edu/m<wbr>ailman/listinfo/bioontology-su<wbr>pport</a><br>
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========================<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186HOEnZb"><font color="#888888">
<div>John Graybeal</div>
<div>Technical Program Manager</div>
<div>Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal</div>
<div>Stanford Center for Biomedical Informatics Research<br>
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--<span class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><br>
<div class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186gmail_signature">
Laia Subirats </div>
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<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline">______________________________<wbr>_________________</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline">bioontology-support
 mailing list</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<a href="mailto:bioontology-support@lists.stanford.edu" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">bioontology-support@lists.stan<wbr>ford.edu</a><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
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<span class="m_-3277356339281155306HOEnZb"><font color="#888888"><span class="m_-3277356339281155306m_7096496498380612188HOEnZb"><font color="#888888">--<span class="m_-3277356339281155306Apple-converted-space"> </span><br>
<div class="m_-3277356339281155306m_7096496498380612188m_-2659791965169619746gmail_signature">Laia Subirats </div>
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--<span class="m_-3277356339281155306Apple-converted-space"> </span><br>
<div class="m_-3277356339281155306m_7096496498380612188gmail_signature" data-smartmail="gmail_signature">
Laia Subirats </div>
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</blockquote>
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</blockquote>
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--<span class="m_-3277356339281155306Apple-converted-space"> </span><br>
<div class="m_-3277356339281155306gmail_signature" data-smartmail="gmail_signature">Laia Subirats </div>
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</blockquote>
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<br>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature">Laia Subirats </div>
</div>