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[bioontology-support] Help Loading my ontology to the

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Apr 29 16:20:28 PDT 2019


Hello Dan,


On Apr 28, 2019, at 7:14 AM, Daniel Hier <dbhier at dbhier.com<mailto:dbhier at dbhier.com>> wrote:

Thank you for helping me with my ontology NEO (neurological examination ontology).  I have decided to rebuild it from scratch in PROTEGE and my partial version with 400 classes and it will now load properly.  I will finish it with 650 classes.  I particularly like the download feature of CSV file--that is a very nice feature that I will use when I post-process my file.

Thanks again for your help.  There must have been subtle errors in my original ontology.  I am about 60% done rebuilding it.


OK - thanks for letting us know that you’ve made additional uploads.

Nonetheless, I did want to track down why your previous submissions were failing. The problem occurred fairly deep in our stack in some code where we use a 3rd party library to load / parse ontologies. Normally this library produces helpful error messages, but in this particular case, we weren’t getting any indication of failure, so it took some digging around and testing before i was able to isolate the issue.

It turns out there’s a syntax error on line 1033 of your ontology (shown in bold below):

<!-- http://webprotege.stanford.edu/R95MZmrikwqzrjl7N1cShdN -->

<owl:Class rdf:about="http://webprotege.stanford.edu/R95MZmrikwqzrjl7N1cShdN">
  <rdfs:subClassOf rdf:resource="http://webprotege.stanford.edu/RCAfDthAKPwhOppuDOBzZo2"/>
  <webprotege:R8JlHtLpsj8hW18voM8qfVy><apraxic gait><Bruns apraxia><magnetic gait><frontal gait>|</webprotege:R8JlHtLpsj8hW18voM8qfVy>
  <webprotege:R9erWLcZm8MU17huk4CFMwy>|30767006|</webprotege:R9erWLcZm8MU17huk4CFMwy>
  <BbHRvdgdu3Y4vbyVxXTwfu:UMLS>C1510417</BbHRvdgdu3Y4vbyVxXTwfu:UMLS>
  <rdfs:label>gait apraxia</rdfs:label>
  <skos:definition rdf:resource="apraxia for walking, accompanied by inability to make skilled walking movements with the legs.gait apraxia; unexplained by weakness, sensory loss, or incoordination (n.d.) Farlex Partner Medical Dictionary. (2012). [Retrieved April 21 2016 from http://medical-dictionary.thefreedictionary.com/gait+apraxia]"/>
</owl:Class>

… where a skos:definition has an opening tag, but no closing tag. I added an end tag, i.e.:

 <skos:definition>apraxia for walking, accompanied by inability to make skilled walking movements with the legs.gait apraxia; unexplained by weakness, sensory loss, or incoordination (n.d.) Farlex Partner Medical Dictionary. (2012). [Retrieved April 21 2016 from http://medical-dictionary.thefreedictionary.com/gait+apraxia]</skos:definition>

... and tested uploading this fixed version of your ontology in our staging environment, and it succeeded.

I’m wondering - did you hand edit your ontology file before you submitted it to BioPortal? Or, did you simply upload the file that you exported from WebProtege? If it’s the latter, I recommend notifying the Protege team that your ontology was exported without an end tag for that particular skos definition.

Kind regards,
Jennifer

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