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[bioontology-support] [BioPortal] Feedback from marwa811

John Graybeal jgraybeal at
Mon Aug 24 16:01:27 PDT 2020

If you want them on your Windows PC, there are fewer choices for working with semantic content, but I think a few richly functional tools are available. Protege of course can work with them, it's an advanced tool focusing on single ontologies at a time.

If you are only working with a few ontologies, you can download many of them directly from BIoPortal's UI (see the summary page for each ontology, lower left side), and you can even download their classes (at least) in CSV format.


On Aug 24, 2020, at 2:57 PM, Jennifer Leigh Vendetti <vendetti at<mailto:vendetti at>> wrote:

Hello Marwa,

Here are some options for you to consider:

1). We have a virtual appliance distribution of the application. You could run it on your local PC and upload only those ontologies that interest you. More information here:

2). You can use the BioPortal REST API to access data from ontologies of interest to your application. That API is documented here: The same type of REST API functionality is available to you if you choose to install a virtual appliance. We provide example code for working with the REST API in various programming languages in our GitHub organization:

3). You could download ontology source files for ontologies of interest and work with them programmatically using a 3rd party API, e.g., the OWL API:

Kind regards,

On Aug 24, 2020, at 3:57 AM, support at<mailto:support at> wrote:

Name: marwa811

Email: marwa.abdelrehem at<mailto:marwa.abdelrehem at>



I want to use the information about bioportal ontologies in my research project. could you advise me on how to save the ontologies and their related information such as classes, definition, properties, etc, locally in my PC to easily access them for my application?what is the best data store that could fit here?


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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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