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[bioontology-support] Help with downloading mappings from Bioportal

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed May 2 10:50:08 PDT 2018


Hello Irmgard,


On May 1, 2018, at 11:12 PM, Irmgard Teschke <irmgard.teschke at osthus.com<mailto:irmgard.teschke at osthus.com>> wrote:

Dear Jennifer,
Thanks for the tip…the link was helpful. I am not well-versed in using REST APIs and I was hoping to find an “easier” way to download the ontologies in a format such as owl. Your link at least provided me with a way to get the json format so I will see if I can find a workaround to transform it to owl.


I believe that you can download an OWL version of the DOID ontology from the OBO Foundry website:

http://www.obofoundry.org/ontology/doid.html

In BioPortal, we host the OBO version of the ontology, as this is the ontology author’s preference.

It’s the same situation for the HP ontology. An OWL version is available for HP on the OBO Foundry website:

 http://www.obofoundry.org/ontology/hp.html

On a related note, we do have a REST API call for most ontologies in BioPortal that allows you to download the ontology source files, e.g.:

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

Kind regards,
Jennifer


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