Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Bulk Downloading Ontologies

John Graybeal jgraybeal at stanford.edu
Mon Jun 17 18:34:53 PDT 2019


Hello Maleeha,

It is possible to download some of the ontologies, namely those that are publicly available for download.

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

To download multiple source files, you can 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

There is also a Ruby script (referenced in the Virtual Appliance FAQ at https://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_migrate_ontologies_from_BioPortal_or_previous_NCBO_Virtual_Appliance_versions_into_a_new_Appliance.3F) that was built for downloading ontologies into a Bioportal repository.  Even if you don't code in Ruby, it illustrates the API method got get all the ontology information, including the pull location.

  https://github.com/ncbo/ncbo_rest_sample_code/blob/master/ruby/bioportal_ontologies_import.rb, 

If you want to download the UMLS content, which makes up most of the ontologies that are *not* available for download, you'll have to transform the original content into ontologies yourself using the UMLS2RDF software (https://github.com/ncbo/umls2rdf), using a UMLS key obtained from National Libraries of Medicine (see https://www.nlm.nih.gov/research/umls/). We can not promise this will always work, as sometimes updating the script for the latest UMLS changes may be required. 

John



> On Jun 16, 2019, at 8:13 AM, Maleeha Arif Yasvi <maleeha18112 at iiitd.ac.in> wrote:
> 
> Respected Sir/Ma'am,
> I am currently doing masters thesis and my topic is related to ontologies. Is it possible to bulk download the ontologies (downloading all the ontologies in one go ) from this site?
> 
> Eagerly waiting for your reply.
> 
> Thank You and Regards
> Maleeha Arif Yasvi
> Mtech-IIITD
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632





More information about the bioontology-support mailing list