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[bioontology-support] Downloading ontology dumps

John Graybeal jgraybeal at stanford.edu
Fri Nov 25 08:57:08 PST 2016


I would assume you can use the script to fetch any ontology for which you (and your API) have access permission. Possibly the author can weigh in if you have more specific questions, as we on the staff have not used it ourselves, to my knowledge.

john

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

cheers
Ilya

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Saturday, 19 November 2016 at 02:34
To: Ilya Zaihrayeu <ilya.zaihrayeu at babylonhealth.com<mailto:ilya.zaihrayeu at babylonhealth.com>>
Cc: BioPortal Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] Downloading ontology dumps

Ilya,

I've re-read the support list thread on your original question -- was it answered?

If not, I wondered if the ontology transfer script at https://github.com/ncbo/ncbo_rest_sample_code/blob/master/ruby/bioportal_ontologies_import.rb
might be a partial solution to your needs?

John

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

Hi all,

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.

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

could you please advise what the best way for getting ontology dumps from the Bioontology portal would be?

many thanks
Ilya
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