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[bioontology-support] [BioPortal] Feedback from shaker

John Graybeal jbgmeta1 at
Mon Dec 21 11:00:38 PST 2015


An update to the previous information — I can see that both ontology uploads have failed to parse correctly.

I can’t tell if this is an error with the file or our system, but I offer the following naive observation: When I try to open the file with Protege (5 beta-17), it reports a parsing error at the beginning of the file. Others on the list may be able to help further.



Your ontology is visible now in BioPortal.

Yes, it usually does take some time for an upload to become visible in BioPortal — we do a number of indexing and other activities before finally making it public, usually it is fully visible by the next morning.

I see that while I can download the ontology, it is still being indexed. This may just be a matter of time — the ontology is somewhat large at 3MB, and the indexing and other processes can take up to a day.

If it is not indexed within another day, it may have to be reviewed by our ontology experts, who will be available after the new year. (Also,  I’m not sure how common the use of functional OWL syntax is for BioPortal imports — so you could try conversion to another OWL syntax just to see if that works better. If you do, realize a day or two may be required again to complete all the upload-related processes.)


On Dec 19, 2015, at 11:51 PM, support at<mailto:support at> wrote:

Name: shaker

Email: shaker_elsapagh at<mailto:shaker_elsapagh at>



Thank you for accepting my ontology in your portal. Please I can not browse my ontology until now ( Are there any problem, or it will take some times to be available on the BioPortal?

Thank you very much.

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