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[bioontology-support] Missing metrics in HORD ontology

Laia Subirats laia.subirats at gmail.com
Tue Aug 8 04:00:48 PDT 2017


Hello Jennifer,

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.

However, now I have this error: "(Uploaded, Error Rdf)".

I have uploaded to webprotege and it works properly, and in my local
Protégé as well.

Sorry for making you spend time helping me.

Best,

Laia
On Mon, Aug 7, 2017 at 6:46 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Laia,
>
> I looked at your latest ontology source file (HORD_all_2017_08_07_scenarios.owl).
> There are still a number of problems with the import statements.
>
> 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:
>
> <owl:imports rdf:resource="http://data.bioontology.org/ontologies/
> ICF/submissions/3/download?apikey=eb8ef13c-ae88-42a5-b6f5-39c93d736688"/>
>> <owl:imports rdf:resource="http://data.bioontology.org/ontologies/
> ORDO/submissions/11/download?apikey=eb8ef13c-ae88-42a5-b6f5-39c93d736688”/
> >
>
> 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:
>
>
>
>
>
> 2). Line 26 contains another invalid import statement:
>
> <owl:imports rdf:resource="http://www.owl-ontologies.com/unnamed.owl"/>
>
> … which has a URL that doesn’t resolve to anything.
>
> Kind regards,
> Jennifer
>
> [1] http://protege.stanford.edu/products.php
>
>
>
> On Aug 6, 2017, at 10:21 PM, Laia Subirats <laia.subirats at gmail.com>
> wrote:
>
> Hi John,
>
> I changed the references and now there is not a parsing problem anymore.
> However, the metrics do not appear.
>
> Cheers,
>
> Laia Subirats
> On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal <jgraybeal at stanford.edu>
> wrote:
>
>> Hi Laia,
>>
>> 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.
>>
>> In this case, a quick look at the error log indicated two issues:
>> * "OWL_IMPORT_MISSING: http://who.int/icf"
>> * "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4"
>>
>> 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.
>>
>> If you are still having trouble after that, please send another note
>> indicating your latest understanding, and our team will try to help. Thanks.
>>
>> John
>>
>>
>> On Aug 5, 2017, at 9:52 PM, Laia Subirats <laia.subirats at gmail.com>
>> wrote:
>>
>> Dear Sir/Madam,
>>
>> I would like to see the metrics of my ontology in http://bioportal.
>> bioontology.org/ontologies/HORD
>> <http://bioportal.bioontology.org/ontologies/PMR>, I do not know if
>> there is any problem. I see that there is a "(Uploaded, Error Rdf)" but
>> I do not see the problem.
>>
>> Yours faithfully,
>> --
>> Laia Subirats
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>> ========================
>> John Graybeal
>> Technical Program Manager
>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>>
>
>
>
> --
> Laia Subirats
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>


-- 
Laia Subirats
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