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[bioontology-support] Downloading ontology dumps

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Oct 25 14:42:14 PDT 2016


Hi Ilya,


On Oct 25, 2016, at 4:32 AM, Ilya Zaihrayeu <ilya.zaihrayeu at babylonhealth.com<mailto:ilya.zaihrayeu at babylonhealth.com>> wrote:

I am looking for a way to download ontology dumps from the bioontology portal and was wondering what the best way for it might be.


You can download the source file for a given ontology via our REST endpoint, e.g.:

http://data.bioontology.org/ontologies/BRO/download

Our REST API is documented here:

http://data.bioontology.org/documentation

If you’re interested in downloading multiple source files, you could programmatically loop through the ontology objects and download the source file for each.

We provide sample code in multiple languages for using our REST API  in this GitHub repository:

https://github.com/ncbo/ncbo_rest_sample_code



as I understood, there was an ontology download service but it was shut down a while ago for some reason.


Sorry - we’re not familiar with what you’re referring to here.  We haven’t shut down any download services.


Also, as I understood, ontologies in UMLS format are not available for download due licensing reasons (https://mailman.stanford.edu/pipermail/bioontology-support/2016-August/008925.html). there is an RDF Download Service, but it is limited: "the RDF Download Service to download the whole ontology in RDF. Note that the second service will provide only some basic information about each term, not all the relations that are defined in the ontology." (https://www.bioontology.org/wiki/index.php?title=RDF_in_BioPortal&redirect=no)


If you have a current UMLS license, please contact our program manager John Graybeal offline (jgraybeal at stanford.edu<http://stanford.edu>) for possibilities regarding UMLS downloads.

Kind regards,
Jennifer

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