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[bioontology-support] Help Loading my ontology to the

Michael Dorf mdorf at stanford.edu
Mon May 6 16:54:21 PDT 2019


Hi Dan,

As requested, I’ve converted NEO from a view of SNOMEDCT into a standalone ontology. The ontology has been re-processed and is now available for viewing:

http://bioportal.bioontology.org/ontologies/NEO

Please let us know if you require further assistance.

Thanks,

Michael




On May 3, 2019, at 4:46 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Dan,

Apologies for the delayed response. We’ve been in the process of importing a large number of UMLS ontologies into our system, which has required us to hold off on making changes to existing ontologies.

I’m out of the office next week, but my colleague Michael has kindly offered to make the modification you requested below. I’ve entered an issue in our tracker to that effect:

https://github.com/ncbo/bioportal-project/issues/116

Best regards,
Jennifer



On Apr 30, 2019, at 3:52 PM, Daniel Hier <dbhier at dbhier.com<mailto:dbhier at dbhier.com>> wrote:

Thank you again.  I pasted the definition into Web Protege.  I am pretty far along in rebuilding my ontology.  I feel I know more now and am using Protege correctly.  My prior attempts were a mix of different IRIs.  Now everything looks consistent and professional.
Is there any way for me to change my NEO ontology from "ontology view" back to "ontology"?  Thanks again for all of your expert help!  I will try to get a descriptive paper  published in NEUROINFORMATICS as a data project and I will cite the BIOPORTAL as the repository.

Dan

On Mon, Apr 29, 2019 at 6:20 PM Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
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



--
Daniel B Hier MD


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