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[bioontology-support] [BioPortal] Feedback from shruthichari

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Apr 27 12:36:06 PDT 2020


Hello Shruthi,

No, you don’t need to take extra steps. BioPortal only serves data from the most recent version of an ontology.

Please note though - when you submit a new version of your ontology it goes into the queue for ontology processing, and there may be a time delay of an hour or two before the new version is fully processed and available in our system. If you notice any irregularities, feel free to contact us again via this support list.

Kind regards,
Jennifer



> On Apr 27, 2020, at 12:28 PM, Shruthi Chari <charis at rpi.edu> wrote:
> 
> Hi Jennifer,
> 
> Thanks so much for this update. I have a quick question if we resubmit a version of the ontology - do we need to take extra steps to ensure that it is usable via the Annotator functionality?
> 
> -Thanks,
> Shruthi
> 
> On 2020-04-27 14:52, Jennifer Leigh Vendetti wrote:
>> 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
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support



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