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[bioontology-support] [BioPortal] Feedback from shruthichari

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Apr 27 11:52:59 PDT 2020


Hello Shruthi

Your ontology has been fully converted to standalone vs. a view. I’ve also reprocessed your ontology so that you can use it with the Annotator functionality.

Kind regards,
Jennifer



> On Apr 25, 2020, at 1:38 PM, Shruthi Chari <charis at rpi.edu> wrote:
> 
> Hi John,
> 
> Thanks a bunch the logs you sent me were a lifesaver. I was able to reupload our ontology and now the classes show up. I should have reached out to support a year earlier, but never too late.
> 
> I am still waiting on the ontology view fix as in to revert this to be a stand-alone ontology and not a view. This would then allow our ontology to be queryable by the BioAnnotator.
> 
> Thanks for your assistance and looking forward to getting this last issue resolved.
> 
> -Thanks,
> Shruthi
> 
> On 2020-04-24 19:48, John Graybeal 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 [4]) 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 [1] [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
>>> [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 [3] [1]
>>> [2] https://arxiv.org/abs/1907.04358 [1] [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/ [3]
>>> [2] https://arxiv.org/abs/1907.04358 [1]
>> <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
>> Links:
>> ------
>> [1] https://arxiv.org/abs/1907.04358
>> [2] https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> [3] http://2fbioportal.bioontology.org/
>> [4] http://librdf.org/raptor/rapper.html
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