Regenerate import file

These instructions are specific to regenerating the NCBITaxom import but can be applied to other import files.

If you have Docker installed:

1. Navigate to your local ontology directory, for example: cd src/ontology
2. Work on a branch.
3. Run command: ./run.sh make imports/ncbitaxon_import.owl
   1. Note - if you don't have Docker installed but have Robot installed, run this command:
      make imports/ncbitaxon_import.owl
   2. Note - this can take a while to run.
   3. Note - if it failed with a message saying the source ontology is not available, try again later.
4. Do the diff on ncbitaxon_import. We expect new classes and some subClassOf changes. A new ncbitaxon_import.owl file will be created in the imports folder. Run command: git diff
5. If you are expecting new classes to be added, check to see if those were added. For example: check the coronovirus shows up in the new import
   1. grep 2697049 imports/ncbitaxon_import.owl
   2. 2697049 = ID for class I am trying to import.
6. Commit ncbitaxon_import.owl file (if you see changes on any other files, discard the changes on the other files):
   git add imports/ncbitaxon_import.owl
git status should only this file is to be committed.
   git commit
git push
7. Once you regenerated the new import, it could contain newly deprecatecd classes from the source ontology and this could affect the Mondo ontology by creating danglers/obsolete references. To fix this, follow the instructions in Repair axioms pointing to deprecated classes.