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IEDB / ONTIE

Ontology for Immune Epitopes
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Change ROBOT tree -> gizmos tree browser #32

Closed beckyjackson closed 3 years ago

beckyjackson commented 4 years ago

Note that I had to declare owl:Thing with a label in this PR in order for gizmos.tree to work properly - see related issue: https://github.com/ontodev/gizmos/issues/21

In order for this to run properly on DROID, ontodev-gizmos must be put into the DROID requirements.txt

jamesaoverton commented 4 years ago

Good. I'd also like to be able to browse the upstream ontologies that we're importing from. At least a few of them, but ideally all of them.

beckyjackson commented 4 years ago

Right now, gizmos.tree doesn't support a db param in the query string, so I think we'd have to write different bash scripts for each ontology. One solution is to have a bash script "template" and just fill in the ontology database, or to put the db param in the query string (https://github.com/ontodev/gizmos/issues/21)

jamesaoverton commented 4 years ago

Ok, let's wait.

Since the user will be able to specify the db parameter, tree.sh will have to validate that user input. We should only allow a db that's in our build/ directory (or wherever they are), not just any file on disk.

beckyjackson commented 4 years ago

Waiting on a release of gizmos containing these fixes: https://github.com/ontodev/gizmos/pull/23

beckyjackson commented 4 years ago

The tree view is implemented for ONTIE + imports. I want to remove the MIREOT script and change to gizmos.extract, but this depends on https://github.com/ontodev/gizmos/pull/27

Edit: The -n issue is fixed, but not released. Other than that, this PR is ready 🙂