[bioontology-support] bioportal and 30gigs ontology

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

[bioontology-support] bioportal and 30gigs ontology

Alexander Garcia Castro
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? 

--

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
Reply | Threaded
Open this post in threaded view
|

Re: [bioontology-support] bioportal and 30gigs ontology

John Graybeal-2
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 <[hidden email]> 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? 

--
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632



_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
Reply | Threaded
Open this post in threaded view
|

Re: [bioontology-support] bioportal and 30gigs ontology

Alexander Garcia Castro
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 <[hidden email]> wrote:
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 <[hidden email]> 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? 

--
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632




--

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support