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[bioontology-support] bioportal and 30gigs ontology

John Graybeal jgraybeal at
Thu Jun 27 10:31:49 PDT 2019

Hi Alexander,

We have not successfully loaded a document of that size. I do not believe our current limitation is due to any inherent limitation in BioPortal's software, but has to do with communication limits between BioPortal's modules. Unfortunately we haven't had time to investigate this in detail yet.

However, if you are unable to load the ontology in Protege, it is possible there is a size limitation in the parsing process. I assume you have tried massively increasing the memory allocated to Protege (I think its ontology parsing is heavily dependent on available memory). Have you discussed the Protege loading issue on the Protege mailing list?

If the ontology can be parsed by Protege, I expect we could help you find a workaround that would enable you to upload it into BioPortal's triple store, but it would be a stress test for the entire system that we have not tried yet.

Please contact me offline if you would like to discuss options further, I could provide more technical details if that is of interest.


On Jun 27, 2019, at 12:55 AM, Alexander Garcia Castro <alexgarciac at<mailto:alexgarciac at>> wrote:

Hi, I would like to run my own installation of bioportal but I have one ontology that is 30 gigas in size. is this loadable? I cant open it in protege and if the ontology is parsed on a line by line basis chances are it wont work. how big can the ontologies in bioportal be? can it load a 30 gigas ontology?

Alexander Garcia

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

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