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[bioontology-support] [BioPortal] Feedback from Krys Kochut

John Graybeal jgraybeal at
Tue Nov 12 14:39:25 PST 2019

Hi Krys,

Thank you for your question.

Yes, we have had some cases where it appears an ontology exceeded a limit in our system, though that was an experiment and we have not finished identifying the bottleneck.

It would be helpful if you submitted the ontology, and assuming it also has this problem, we will create a ticket describing the specific issue your ontology is having. As your submission is not experimental, we will look at it as quickly as we can (given available staff) to try to work out any submission issues.

I should note that BioPortal recognizes the individuals and can display them via the API, but does not have a user interface for examining individuals. (This has come up as an issue/feature request very rarely in BioPortal's history, to my understanding.)  If you would be willing, I would appreciate the chance to work with you offline to understand to what extent this is a concern, and what features for individuals you think would be important for your primary BioPortal use cases. I'll send you a separate email on that topic.


On Nov 12, 2019, at 7:42 AM, support at<mailto:support at> wrote:

Name: Krys Kochut

Email: kkochut at<mailto:kkochut at>



Our bioinformatics team is planning to submit to BioPortal an ontology on protein kinases. Is there a limit on the size of ontologies that can be submitted? Our ontology has many instances (individuals) and it's approximately 3GB when serialized in OWL.

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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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