Refactoring

[zhengj2007]

1. Renamed 'Ontofox input' -> Ontofox_input

2. Updated NCBITaxon_import_input.txt by providing correct settings of: [Low level source term URIs] and [Top level source term URIs and target direct superclass URIs]

3. Replaced OntoRat with Robot to generate the modules based on design patterns, change the term prefix from OccO to OCCO

   • Top_abilities_annotations: 1) OccO_00000002 has two labels 'occupation abilities', 'top occupation abilities', keep 'top occupation abilities' 1) Abilities of occupation were added using Annotation Property. It made more sense to be object Property since all abilities have been defined in the OccO, so generated a version using object Property ‘has ability’ (not used anywhere in the OccO yet). Now keep both annotation properties ('top occupation abilities') and objectProperty (has ability)for occupation abilities. 1) SOC ID is added using annotation property ‘editor preferred term’, changed to ‘US SOC ID’
   • Top_skills_annotations: 1) Similar issues as Top_abilities_annotations 1) Keep both annotation properties ('top occupation skills') and objectProperty (has skill) for occupation skills.
   • Add a new template for OCCO terms 1) The template including all OCCO terms except subclasses of OCCO:ability and OCCO:skill 1) Standardize the term editors, all using full name. 1) The code was added as ‘editor preferred term’. It doesn’t look correct. Changed to ‘US SOC ID’ 1) The definition source in the OccO-edit.owl for the occupation holders are not same as those in annotations.xlsx files that seems more accurate. Added more accurate ones in the template.
   • Add a new template for equivalent axioms
   • Update occo-edit.owl 1) Import various OWL files include Ontofox import and Robot modules files 1) Added declarations requested by OBO Foundry or update the existing ones using OBO Foundry recommended terms

4. Add makefile for term import, module generation and make release

[zhengj2007]

@yongqunh @smithGit Could you please review the updated occo files? After you approve the changes, I will merge it to the master. Thanks!

[smithGit]

谢谢

Thanks! I will look at tomorrow. Really appreciate your digging into the OccO data structure. Sam

From: jie zheng @.> Sent: Sunday, August 20, 2023 11:02 PM To: Occupation-Ontology/OccO @.> Cc: Sam Smith @.>; Mention @.> Subject: Re: [Occupation-Ontology/OccO] Refactoring (PR #5)

@yongqunh https://github.com/yongqunh @smithGit https://github.com/smithGit Could you please review the updated occo files? After you approve the changes, I will merge it to the master. Thanks!

— Reply to this email directly, view it on GitHub https://github.com/Occupation-Ontology/OccO/pull/5#issuecomment-1685550924 , or unsubscribe https://github.com/notifications/unsubscribe-auth/ABQ2PKA5HKUYVRBRQEZMM7DXWLFRBANCNFSM6AAAAAA3XXIKHU . You are receiving this because you were mentioned. https://github.com/notifications/beacon/ABQ2PKG3B2INNLRY6DYQLG3XWLFRBA5CNFSM6AAAAAA3XXIKHWWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTTEO53UY.gif Message ID: @. @.> >

[smithGit]

Re the refactoring # 5 topics:

1. ok good
2. ok good
3. Top_abilities and skills - Ok, good 3-new template: ok but I would like to see how 'editor preferred term' was incorrectly assigned - we need to have the SOC unchanged term preserved (plural and capitalized) re new templat/axioms / update occo-edit.owl sound good - I have no concerns but not fully on top of these topics Re makefile: great; I have not done a makefile in the last decade or two, so thanks for taking this on! Overall: Great - really appreciate the care you have taken in you review and update!

[zhengj2007]

@smithGit Thanks a lot for taking time reviewing the changes I made. Regarding 'editor preferred term', I may not describe the issues clearly. The SOC ID was add in the OWL format using annotation property 'editor preferred term'. I changed it to ‘US SOC ID’ now. So, you cannot find any 'editor preferred term' annotations in the occo OWL file any more. You can see It showed in the occo-edit.owl in the master branch.