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Hello Laia,
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<div class="">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>
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<div class="">Kind regards,</div>
<div class="">Jennifer</div>
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<div class="">On Aug 17, 2017, at 10:59 PM, Laia Subirats <<a href="mailto:laia.subirats@gmail.com" class="">laia.subirats@gmail.com</a>> wrote:</div>
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Hi Jennifer,
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<div class="">Thank you for your answer. </div>
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<div class="">Kind regards,</div>
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</div>
<div class="">Laia
<div class="gmail_extra">
<div class="gmail_quote">On Fri, Aug 18, 2017 at 3:06 AM, Jennifer Leigh Vendetti<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:vendetti@stanford.edu" target="_blank" class="">vendetti@stanford.edu</a>></span><span class="Apple-converted-space"> </span>wrote:<br class="">
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<div style="word-wrap: break-word;" class="">Hi Laia,
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<div class="">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>
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<div class="">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>
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<div class="">Kind regards,</div>
<div class="">Jennifer</div>
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<blockquote type="cite" class=""><span class="">
<div class="">On Aug 17, 2017, at 3:32 AM, Laia Subirats <<a href="mailto:laia.subirats@gmail.com" target="_blank" class="">laia.subirats@gmail.com</a>> wrote:</div>
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<div class="">Dear Jennifer,<br class="">
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I would like to ask you help about this issue. I am still lost about how can I solve this error.<br class="">
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Best,<br class="">
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Laia<br class="">
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<div class="gmail_quote"><span class="">On Tue, Aug 8, 2017 at 1:00 PM, Laia Subirats<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:laia.subirats@gmail.com" target="_blank" class="">laia.subirats@gmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br class="">
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<div class="">Hello Jennifer,<br class="">
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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="Apple-converted-space"> </span><br class="">
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However, now I have this error: "<span class="m_7096496498380612188m_-2659791965169619746gmail-ontology_submission_status">(Uploaded, Error Rdf)<span class="">".<br class="">
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<span class="m_7096496498380612188m_-2659791965169619746gmail-ontology_submission_status"><span class="">I have uploaded to webprotege and it works properly, and in my local Protégé as well.<br class="">
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<span class="m_7096496498380612188m_-2659791965169619746gmail-ontology_submission_status"><span class="">Sorry for making you spend time helping me.<br class="">
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<span class="m_7096496498380612188m_-2659791965169619746gmail-ontology_submission_status"><span class="">Best,<br class="">
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<span class="m_7096496498380612188m_-2659791965169619746gmail-ontology_submission_status"><span class="">Laia</span></span><br class="">
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<div class="gmail_quote"><span class="">On Mon, Aug 7, 2017 at 6:46 PM, Jennifer Leigh Vendetti<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:vendetti@stanford.edu" target="_blank" class="">vendetti@stanford.edu</a>></span><span class="Apple-converted-space"> </span>wrote:<br class="">
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<div class=""><span class="">Hello Laia,
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<div class="">I looked at your latest ontology source file (HORD_all_2017_08_07_scenarios<wbr class="">.owl). There are still a number of problems with the import statements.</div>
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<div class="">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>
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<div class=""><owl:imports rdf:resource="<a href="http://data.bioontology.org/ontologies/ICF/submissions/3/download?apikey=eb8ef13c-ae88-42a5-b6f5-39c93d736688" target="_blank" class="">http://data.bioo<wbr class="">ntology.org/ontologies/ICF/sub<wbr class="">missions/3/download?apikey=eb8<wbr class="">ef13c-ae88-42a5-b6f5-39c93d736<wbr class="">688</a>"/></div>
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<div class="">…</div>
<div class=""><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" class="">http://data.bioo<wbr class="">ntology.org/ontologies/ORDO/su<wbr class="">bmissions/11/download?apikey=<wbr class="">eb8ef13c-ae88-42a5-b6f5-39c93d<wbr class="">736688”/</a>></div>
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<div class="">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>
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<div class=""><span id="m_7096496498380612188cid:F229D349-E469-46E9-A15B-5D1CC5550BFA@stanford.edu" class=""><Screenshot 2017-08-07 09.20.54.png></span><span id="m_7096496498380612188cid:27C78D6C-8B9A-4ADD-8CD1-A07D94EB0713@stanford.edu" class=""><Screenshot
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<div class="">2). Line 26 contains another invalid import statement:</div>
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<div class=""><owl:imports rdf:resource="<a href="http://www.owl-ontologies.com/unnamed.owl" target="_blank" class="">http://www.owl-o<wbr class="">ntologies.com/unnamed.owl</a>"/></div>
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<div class="">… which has a URL that doesn’t resolve to anything.</div>
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<div class="">Kind regards,</div>
<div class="">Jennifer</div>
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<div class="">[1] <a href="http://protege.stanford.edu/products.php" target="_blank" class="">http://protege.stanford.ed<wbr class="">u/products.php</a></div>
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<div class="">On Aug 6, 2017, at 10:21 PM, Laia Subirats <<a href="mailto:laia.subirats@gmail.com" target="_blank" class="">laia.subirats@gmail.com</a>> wrote:</div>
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<div class="">Hi John,<br class="">
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I changed the references and now there is not a parsing problem anymore. However, the metrics do not appear.<br class="">
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Cheers,<br class="">
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<div class="gmail_extra">Laia Subirats<br class="">
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<div class="gmail_quote">On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal<span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:jgraybeal@stanford.edu" target="_blank" class="">jgraybeal@stanford.e<wbr class="">du</a>></span><span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span>wrote:<br class="">
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<div class="">Hi Laia, 
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<div class="">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>
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<div class="">In this case, a quick look at the error log indicated two issues:</div>
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<div class="">* "OWL_IMPORT_MISSING:<span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><a href="http://who.int/icf" target="_blank" class="">http://wh<wbr class="">o.int/icf</a>"</div>
<div class="">* "OWL_IMPORT_MISSING:<span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><a href="http://www.orpha.net/version2.4" target="_blank" class="">http://ww<wbr class="">w.orpha.net/version2.4</a>"</div>
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<div class="">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>
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<div class="">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>
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<div class="">John</div>
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<div class="">On Aug 5, 2017, at 9:52 PM, Laia Subirats <<a href="mailto:laia.subirats@gmail.com" target="_blank" class="">laia.subirats@gmail.com</a>> wrote:</div>
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<div class="">Dear Sir/Madam,<br class="">
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I would like to see the<span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186m_8729106135744704153gmail-il">metrics</span><span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span>of
 my ontology in<span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><a href="http://bioportal.bioontology.org/ontologies/PMR" target="_blank" class="">http://bioportal.bioontolog<wbr class="">y.org/ontologies/HORD</a>,
 I do not know if there is any problem. I see that there is a "<span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186m_8729106135744704153gmail-ontology_submission_status">(Uploaded, Error Rdf)" but I do not see the problem.<br class="">
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Yours faithfully,<br class="">
--<span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><br class="">
<div class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186m_8729106135744704153gmail_signature">
Laia Subirats </div>
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______________________________<wbr class="">_________________<br class="">
bioontology-support mailing list<br class="">
<a href="mailto:bioontology-support@lists.stanford.edu" target="_blank" class="">bioontology-support@lists.stan<wbr class="">ford.edu</a><br class="">
<a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support" target="_blank" class="">https://mailman.stanford.edu/m<wbr class="">ailman/listinfo/bioontology-su<wbr class="">pport</a><br class="">
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========================<span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186HOEnZb"><font color="#888888" class="">
<div class="">John Graybeal</div>
<div class="">Technical Program Manager</div>
<div class="">Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal</div>
<div class="">Stanford Center for Biomedical Informatics Research<br class="">
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--<span class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186Apple-converted-space"> </span><br class="">
<div class="m_7096496498380612188m_-2659791965169619746gmail-m_-7054672035172090186gmail_signature">
Laia Subirats </div>
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