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[bioontology-support] Downloading ontology dumps

Jennifer Leigh Vendetti vendetti at
Mon Nov 28 11:01:22 PST 2016

Hello Ilya,

On Nov 25, 2016, at 8:20 AM, Ilya Zaihrayeu <ilya.zaihrayeu at<mailto:ilya.zaihrayeu at>> wrote:

Hi John,

thanks for your message. Yes, my question was answered. Actually, I noticed that some datasets provide owl/rdf/etc dumps for download. for some others, as I understand, dumps can be found of the pages of dump publishers. Not sure we can always find a dump for any ontology.

can we use the script to fetch any ontology from BioPortal?

You can use scripts to fetch any *public* ontology from BioPortal.

BioPortal allows users to create private ontologies.  Your script would not be able to access these ontologies unless you are an owner or administrator of such an ontology.  There are also a few ontologies in BioPortal for which we aren’t allowed to provide the source files due to licensing restrictions, e.g., the UMLS ontologies (SNOMED CT, etc.).

Kind regards,

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