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WIP: Import workflow update

Open beckyjackson opened this issue 3 years ago • 1 comments

This switches the import workflow to use Gizmos.

This is using a version of gizmos in a branch here: https://github.com/ontodev/gizmos/pull/79

beckyjackson avatar Mar 31 '21 16:03 beckyjackson

For OBI developers wondering about this draft PR, it changes the import system from using the OntoFox web service to using locally installed files and tools. The key benefits are:

  1. A cleaner import configuration in two tables imports.tsv and config.tsv. This will also enable better tools and interfaces for managing imports.
  2. More control over which version of each ontology we import. When calling OntoFox we get whatever version they happen to have loaded in their triplestore, but with this system we can pick and choose exactly which OWL file to import from.
  3. Efficient processing of large ontologies, such as NCBITaxon and Protein Ontology.

The tools we're using to do this are very new. This draft PR is really meant as a thorough test of the tools against OBI's pretty diverse imports. We won't merge it into OBI until (1) the tools are stable, and (2) have the approval of OBI developers.

jamesaoverton avatar Mar 31 '21 18:03 jamesaoverton