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[bioontology-support] ontology with OWL:Import

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Jan 12 17:57:58 PST 2017


Hello again Jacek,

Both of your ontologies are now parsed and available in BioPortal:

http://bioportal.bioontology.org/ontologies/ADALAB
http://bioportal.bioontology.org/ontologies/ADALAB-META

Apologies that it took some time to track down the issue of why neither of them parsed in our system upon initial submission.  It turns out that some of the values entered for the submission information created problems deep in the stack.  We don’t support the use of “local:” syntax when specifying alternatives to the property defaults:

[cid:8320829F-B8A9-4E2D-9AE7-81C765231C8F at stanford.edu]


These field values must be full URLs.  Our system should validate the contents of these fields on save, but currently doesn’t.  I’ll enter an issue in our tracker for this.

I changed the values of these fields back to the defaults for both of your ontologies, and re-parsed them.  The only reason to modify the defaults here would be adjust the way BioPortal displays your ontology content in our UI, e.g., on the classes tab:

http://bioportal.bioontology.org/ontologies/ADALAB?p=classes

Although SKOS properties are listed as the defaults, the system also checks in other common locations for things like preferred name (e.g., rdfs:label).

On another note, I removed the view from the AdaLab ontology as requested via private email.

Kind regards,
Jennifer



On Jan 11, 2017, at 1:30 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Jacek,

The use of imports is accepted.

I’m starting to look at the parsing errors in our log files for both of your ontology submissions.

In regard to your AdaLab-meta.owl file, I noticed that one of the import statements:

<Import>http://purl.org/dc/terms/dc_import.owl</Import>

… contains a URL that resolves to an HTML page instead of an OWL file:

http://dublincore.org/documents/2012/06/14/dcmi-terms/?v=terms#dc_import.owl

… which results in a missing import error in our log file.  Do you know what the direct link is to this dc_import.owl file?  I could edit your ontology file with the correct URL and try re-parsing.

I’ll need to follow up in a separate email about your other ontology, which I’m still investigating.

Kind regards,
Jennifer



On Jan 11, 2017, at 6:20 AM, Jacek Grzebyta <grzebyta.dev at gmail.com> wrote:

Dear Bioontology Team.

I have just submitted two ontologies which imports lot of classes using uses owl:Import property (ADALAB and ADALAB-META).

To make the ontologies pars-able by your engine do you want me either merge all imported ontologies in one file or using owl:Import is accepted.

best regards,
Jacek Grzebyta
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