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[bioontology-support] [BioPortal] Feedback from shruthichari

Shruthi Chari charis at rpi.edu
Fri Apr 24 19:02:23 PDT 2020


Hi John,

Great thanks I will fix those issues. Thanks for the tool reference I will use it to test.

So just to confirm if I run my ontology through this tool, is Bioportal guaranteed to render it?

-Thanks,
Shruthi 

Sent from my iPhone

> On Apr 24, 2020, at 7:48 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
> 
>  Hi Shruthi,
> 
> I had a look at the logs.  There appear to be two locations in the file that say "rdf:resoure" (instead of rdf:resource). Just a warning in the OWLAPI parser, but our Rapper software (http://librdf.org/raptor/rapper.html) didn't like it.  See if fixing those makes it better, yes?
> 
> John
> 
> 
> 
>> On Apr 24, 2020, at 4:23 PM, Shruthi Chari <charis at rpi.edu> wrote:
>> 
>> Hi John,
>> 
>> I don't want it to be a view yes. Thanks for making the change.
>> 
>> As for the RDF parsing error, I am not sure what is happening. Can you send me the log as I don't see to it on my end. I don't see errors on Protege per se it opens there. I am attaching a screenshot for your reference.
>> 
>> However, I want to make some import clean up changes so I will work on that and hopefully it should render better?
>> 
>> Not sure why it doesn't render on Bioportal though.
>> 
>> -Thanks,
>> Shruthi
>> 
>>> On 2020-04-24 19:06, John Graybeal wrote:
>>> Ah, that explains it, thank you.
>>> I have changed the setting to not be View, and saved that. (It would
>>> have showed up previously, if you enabled the Views checkbox. But if
>>> it isn't a view that isn't what you want!)
>>> There may be some additional processing required as a result; I'll ask
>>> our expert on such things when she is back on Monday.
>>> I notice there are no classes being displayed, due to an RDF parsing
>>> error; do you understand why that is? Let us know if you need help
>>> figuring that out—my basic rule of thumb is to try opening it in
>>> Protege to see if that reports any errors, and fix all those first. If
>>> it works there but not in BioPortal, let us know and we'll try to hep.
>>> John
>>>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>>> Hi John,
>>>> Thanks so much for reassigning ownership to me, with this, I am
>>>> able to upload a new version. I have a problem in that my ontology
>>>> doesn't show up on Bioportal's main page as an ontology page as I
>>>> accidentally made it an ontology view. Can you help revert this
>>>> option and instead set it as an ontology?
>>>> -Thanks,
>>>> Shruthi
>>>> On 2020-04-24 18:09, John Graybeal wrote:
>>>> Hi Shruthi,
>>>> I am happy to help you, and just want to clarify the situation.
>>>> I can see a public ontology called SCO that fits your description,
>>>> with you as the contact, and it seems to be publicly visible. So if
>>>> you are still having trouble seeing this ontology, can you please
>>>> provide further details about what you are doing?
>>>> It appears the owner of the ontology may have been mis-assigned
>>>> (possibly an operator error on our side); I have re-assigned you as
>>>> the owner.
>>>> My apologies for this issue. Please try to access it and let me
>>>> know
>>>> if you have any difficulty.
>>>> john
>>>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote:
>>>> Name: shruthichari
>>>> Email: charis at rpi.edu
>>>> Location: https%3A%2F%2Fbioportal.bioontology.org [1]
>>>> [1]%2Fontologies
>>>> FEEDBACK:
>>>> Hi Sir/Madam,
>>>> I had an ontology on Bioportal under the name, Study Cohort
>>>> Ontology
>>>> and acronym, SCO. Not only can I not find it anymore but I can't
>>>> resubmit as somebody else has made a submission. I attest that I am
>>>> the author of this ontology and we even have a paper in the
>>>> International Semantic Web Conference (ISWC) last year:
>>>> https://arxiv.org/abs/1907.04358 [2] [2]. Can you please help me
>>>> resubmit my ontology?
>>>> Feel free to reach out to me at charis at rpi.edu
>>>> -Thanks,
>>>> Shruthi
>>>> _______________________________________________
>>>> 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
>>>> 650-736-1632 | ORCID 0000-0001-6875-5360
>>>> Links:
>>>> ------
>>>> [1] http://2Fbioportal.bioontology.org [1]
>>>> [2] https://arxiv.org/abs/1907.04358 [2]
>>> ========================
>>> John Graybeal
>>> Technical Program Manager
>>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>>> Stanford Center for Biomedical Informatics Research
>>> 650-736-1632 | ORCID 0000-0001-6875-5360
>>> Links:
>>> ------
>>> [1] http://2fbioportal.bioontology.org/
>>> [2] https://arxiv.org/abs/1907.04358
>> <Screenshot 2020-04-24 at 7.15.07 PM.png>
> 
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632  | ORCID  0000-0001-6875-5360
> 
> 
> 
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