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information artifact ontology
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Jzheng2007 #215

Closed zhengj2007 closed 5 years ago

zhengj2007 commented 5 years ago

IAO file changes and IAO release

zhengj2007 commented 5 years ago

@jamesaoverton @cmungall I made the IAO release and did some changed in IAO repository. Could you please review and provide the comments for finalizing the process? The details of changes I made (the most important part are highlighted in bold text) are listed as follow:

  1. Update OntoFox-input.txt

    • import PATO include all includeAllIntermediates classes, it will easy to keep the hierarchy consistent with other OBO Foundry ontologies that also import PATO terms, such as OBI.
    • import GAZ_00000448:geographic location that was manually imported in externalByHand.owl
    • import missing term, RO_0001900:temporal interpretation
    • update IRI of import-OBO.owl

  2. Update externalByHand.owl

    • Remove term GAZ_00000448:geographic location

  3. Clean up catalog-v001.xml

  4. Update iao-main.owl

  5. Rename iao.owl to iao-all.owl which includes iao-main.owl and IAO terms deprecated in early development stage.

    • iao.owl used as the release version name, rename for avoiding confusion
    • clean up the import statements in the OWL file

  6. Update Makefile

    • Use iao-all.owl not iao-edit.owl (named as iao-main.owl before) to include obsoleted IAO terms in the release file.
    • Remove import-OBO.owl IRI replacement in the file since the issue fixed in the OntoFox input file
    • Save all files generated during the release process under build or release directory rather than src/ontology directory
    • The IAO release file, iao.owl was saved under home directory, rather than src/ontology.

Known issues:

  1. In Makefile, it does not download ontology-metadata.owl and keeps copy in the release directory.
  2. Have not checked the pull request made in 2017 and merged to IAO for this release, will do if need.

Question: Since we are adopting git release process, the files used for release will be tagged. Shall we need to copy the files made each version under release directory? e.g. releases/2019-06-07

@rctauber I may need your help on updating the Makefile since I am not good at it.

jamesaoverton commented 5 years ago

Very good @zhengj2007. The only change that I suggest right now is to add a copy of iao-edit.owl to the release directory.

The various files look good. I also tried importing this IAO into OBI and reasoning, which worked fine.

I have a bunch of suggestions for a cleaner release process, which I'll put in a new issue, but that can wait for the next release.

zhengj2007 commented 5 years ago

Thanks @cmungall and @jamesaoverton for your comments.

I will merge the changes and following #216 to make the release.

@cmungall Not clear why the GAZ term imported in IAO. May consider it is a domain independent term and stayed in IAO when separated IAO from OBI.

@jamesaoverton I agree with you on cleaning up IAO repository and simplifying Makefile mentioned in #217. We can work on it after this release. And I need the help from @jamesaoverton and @rctauber for simplifying Makefile.