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information-artifact-ontology / IAO

information artifact ontology
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Suggested repository clean up #217

Closed jamesaoverton closed 4 years ago

jamesaoverton commented 5 years ago

These suggestions are low priority and I don't think they should delay the release of #215.

The changes in #215 include an iao-all.owl file that imports iao-edit.owl and obsolete.owl. I suggest just importing obsolete.owl into iso-edit.owl and eliminating iao-all.owl.

Since #211 ROBOT is used to build IAO. I believe that src/tools is no longer used and can be removed. I think that these two scripts for OntoFox can also be removed: clean-ontofox-results.pl, get-ontofox-imports.

I don't understand the purpose of src/ontology/iao-examples.owl. Would it be better in src/examples/?

I'm confused about copying RO and BFO bits to this repository during releases. I suggest that IAO should instead owl:import dated versions of these dependencies.

The Makefile adds a license annotation that should just be asserted in iao-edit.owl. Between these changes and those suggested in #216, the Makefile would be greatly simplified.

zhengj2007 commented 5 years ago

@jamesaoverton I cleaned up the files under src/ontology directory based on your suggestion:

These suggestions are low priority and I don't think they should delay the release of #215.

The changes in #215 include an iao-all.owl file that imports iao-edit.owl and obsolete.owl. I suggest just importing obsolete.owl into iso-edit.owl and eliminating iao-all.owl.

  • imported obsolete.owl into iao-edit.owl and removed iao-all.owl

Since #211 ROBOT is used to build IAO. I believe that src/tools is no longer used and can be removed. I think that these two scripts for OntoFox can also be removed: clean-ontofox-results.pl, get-ontofox-imports.

  • moved clean-ontofox-results.pl, get-ontofox-imports from src/ontology/ontoFox to src/tools. I do not remove the src/tools directory now. It may be hard to find these old files if I removed them. I will do it if most of IAO developers prefer to do so. But I am planning to add a wiki page to describe the files in the IAO repository. Hope it is helpful for IAO users/developers.

I don't understand the purpose of src/ontology/iao-examples.owl. Would it be better in src/examples/?

  • moved the file, src/ontology/iao-examples.owl, to src/examples directory.

I'm confused about copying RO and BFO bits to this repository during releases. I suggest that IAO should instead owl:import dated versions of these dependencies.

The Makefile adds a license annotation that should just be asserted in iao-edit.owl. Between these changes and those suggested in #216, the Makefile would be greatly simplified.

  • added license to iao-edit.owl.

Will work on makeFile later.

zhengj2007 commented 4 years ago

MakeFile is added.