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[bioontology-support] [BioPortal] Feedback from shruthichari

Shruthi Chari charis at rpi.edu
Sat Apr 25 13:38:44 PDT 2020


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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