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[bioontology-support] bioportal and 30gigs ontology

Alexander Garcia Castro alexgarciac at
Fri Jun 28 04:41:46 PDT 2019

I will start with a test, trying to load a simpler one. Geonames whic is in
RDF and has mostly individuals. Can Bioprotal deal with individuals?

On Thu, Jun 27, 2019 at 7:31 PM John Graybeal <jgraybeal at>

> 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.
> John
> On Jun 27, 2019, at 12:55 AM, Alexander Garcia Castro <
> 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
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632

Alexander Garcia
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