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[bioontology-support] Missing metrics in HORD ontology

Laia Subirats laia.subirats at gmail.com
Wed Aug 23 23:11:22 PDT 2017


Thank you Jennifer,

We want to submit this ontology in a journal on the 1st October so it has
been just in time.

Kind regards,

Laia

On Thu, Aug 24, 2017 at 1:44 AM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Laia,
>
> The issue that was preventing ORDO from parsing/loading in BioPortal has
> been fixed. I reprocessed your HORD ontology, which is now fully parsed and
> available.
>
> Kind regards,
> Jennifer
>
>
>
>
> On Aug 17, 2017, at 10:59 PM, Laia Subirats <laia.subirats at gmail.com>
> wrote:
>
> 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=e
>>>> b8ef13c-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
>
>
>


-- 
Laia Subirats
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