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[bioontology-support] Missing metrics in HORD ontology

Laia Subirats laia.subirats at gmail.com
Thu Aug 17 22:59:47 PDT 2017


Hi Jennifer,

Thank you for your answer.

Kind regards,

Laia
On Fri, Aug 18, 2017 at 3:06 AM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hi Laia,
>
> You’re including the ORDO ontology, which doesn’t parse in BioPortal at
> the moment. Unfortunately, the problem is a bug in the OWL API, which is
> 3rd party software that we use to load / parse ontologies. I’ve been
> corresponding with the developer of the OWL API and he has released a bug
> fix version that may address the problem with ORDO. I plan to integrate
> this new version of the OWL API into BioPortal, but haven’t been able to
> get to it yet due to some other work that is higher priority at the moment.
>
> I apologize that I don’t have an exact date for you when the problem with
> ORDO will be resolved, but it should be in the near future.
>
> Kind regards,
> Jennifer
>
>
>
> On Aug 17, 2017, at 3:32 AM, Laia Subirats <laia.subirats at gmail.com>
> wrote:
>
> Dear Jennifer,
>
> I would like to ask you help about this issue. I am still lost about how
> can I solve this error.
>
> Best,
>
> Laia
>
> On Tue, Aug 8, 2017 at 1:00 PM, Laia Subirats <laia.subirats at gmail.com>
> wrote:
>
>> 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.bioo
>>> ntology.org/ontologies/ICF/submissions/3/download?apikey=eb8
>>> ef13c-ae88-42a5-b6f5-39c93d736688"/>
>>>>>> <owl:imports rdf:resource="http://data.bioo
>>> ntology.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:
>>>
>>>
>>> <Screenshot 2017-08-07 09.20.54.png><Screenshot 2017-08-07 09.21.22.png>
>>>
>>>
>>>
>>> 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
>>
>
>
>
> --
> Laia Subirats
>
>
>


-- 
Laia Subirats
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