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[bioontology-support] [BioPortal] Feedback from shaker

Michael Dorf mdorf at stanford.edu
Thu Mar 30 18:56:19 PDT 2017


Hi Shaker,

Thank you for your inquiry. I found two issues with your ontology, which prevented it from being parsed successfully by our OWLAPI based parser:

1. We don’t accept files with RAR extension. ZIP is our go-to format for processing ontologies with multiple input files. The ZIP filename should match the filename of the main ontology file (DMTO.owl). In your case, this would result in a file called DMTO.zip which, in it’s root (no additional directories) contain the files:

- DINTO adverse effects.owl
- DMTO.owl
- OntoFood.owl
- time.ttl

2. This is a tougher one. I’ve zipped your ontology correctly and run it through our parser. It came back with the following error:

org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName):
https://bioportal.bioontology.org/ontologies/DMTO.owl#DMTO:0000081
https://bioportal.bioontology.org/ontologies/DMTO.owl#DMTO:0001649
http://www.co-ode.org/ontologies/ont.owl#DDO:0000002
https://bioportal.bioontology.org/ontologies/DMTO.owl#DMTO:0000051
https://bioportal.bioontology.org/ontologies/DMTO.owl#DMTO:0000909
https://bioportal.bioontology.org/ontologies/DMTO.owl#DMTO:0000079

I’ll need to do some more investigating to figure out why these aren’t valid QNames. If this gives you enough clues, feel free to implement your fixes and re-submit. Otherwise, I’ll keep you posted after I’ve done some additional digging.

Thanks!

Michael


On Mar 30, 2017, at 7:58 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: shaker

Email: shaker_elsapagh at yahoo.com<mailto:shaker_elsapagh at yahoo.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500%3Fp%3Dclasses%26conceptid%3Droot

Feedback:

Dear all,
My email is: shaker_elsapagh at yahoo.com<mailto:shaker_elsapagh at yahoo.com>
I have uploaded an ontology in this URL: http://bioportal.bioontology.org/ontologies/DMTO
The ontology appeared on the main page; however I can not make browsing. I think there is an error.
The error message is: "We're sorry but something has gone wrong. We have been notified of this error."

Thank you.

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