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[bioontology-support] BioPortal down for upload ontologies

John Graybeal jgraybeal at stanford.edu
Mon Jun 14 12:45:07 PDT 2021


Jennifer, he sent me an image on slack, I'm forwarding that here.

John

[cid:623E654E-7EF2-40B6-A14C-3B938955D186]
On Jun 14, 2021, at 11:42 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi again Nikola,

I realized that your account name was displayed in the screenshot you sent. I queried our system for ontologies that you’re listed as an administrator for, and found the following:

DSVOC
FDC-GDMT
RNR-VOCAB
ROCKNROLLTEST
WETAXTOPICS
ZONMW-SUBJECT
ZONMW-SUBJECTS

Is RNR-VOCAB the ontology entry that you’re referring to? If so, it appears that the entry was created in our backend, but the submission failed to upload. You should be able to use the following steps to attempt another submission upload:

1. Log into BioPortal
2. Navigate to the ontology summary page (https://bioportal.bioontology.org/ontologies/RNR-VOCAB)
3. Click the “Add submission” button (plus sign) at the top of the Submissions table
4. Fill out the “Add new submission” form, and click the Add submission button.

If you’re still having difficulty, please send me the ontology source file, and I’ll try to troubleshoot from this end. Or, if you’re referring to some other ontology than what I listed above, let me know.

Kind regards,
Jennifer



On Jun 14, 2021, at 10:42 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Nikola,

Do you remember the acronym of the ontology you were trying to create? Alternatively, do you know under what account name you tried to submit the ontology? I can check our system to see if the entry succeeded or not, and do any necessary repairs to the object.

Kind regards,
Jennifer


On Jun 14, 2021, at 3:50 AM, Nikola Vasiljevic <niva at dtu.dk<mailto:niva at dtu.dk>> wrote:

Hi there,

We running a rapid M4M in Denmark.
One of the exercises is the registration of new ontology in BioPortal.

When doing the exercise we encountered the following screen once we pressed button submit new ontology:
<Screenshot 2021-06-14 at 12.31.45.png>

Any idea when this will be fixed?

We have the second day of the M4M workshop this Thursday and we are sort of desperate to register the ontology in BioPortal so we can use it in CEDAR.


Best,

Nikola



Nikola Vasiljević, PhD
RDA Ambassador
Special consultant for Digitalization


ORCID: 0000-0002-9381-9693<https://orcid.org/0000-0002-9381-9693>
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Mobile: +45 5180 1452
Email: niva at dtu.dk<mailto:niva at dtu.dk>



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========================
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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