Demonstrate using TAXRANK for ranks and properties

[cthoyt]

Closes #96, closes #97

This PR does the following:

1. Replaces the ad-hoc NCBITaxon identifiers for tax ranks with terms defined in the TAXRANK ontology
2. Replaces the ad-hoc NCBITaxon relation ncbitaxon:has_rank with TAXRANK:1000000
3. Extends missing tax ranks using terms defined in the TAXRANK ontology
4. Explicitly handles the no rank rank

It depends on phenoscape/taxrank#5, where I added the remaining 12 ranks that weren't already represented. That PR was merged and released on November 28th, 2024. Related: that PR included adding a tax rank for "strain", which was the point of discussion also in #107

[matentzn]

I personally very much like this change, and I approve of it, but I will request changes so that it is not accidentally merged before I can get some community feedback (and we can use my disapproval as a blocker until the taxrank PR is released).

Thank you very much!

[jplfaria]

@matentzn, are there any updates on "community feedback" for this change? Is this issue the best place to provide feedback?

I have been working to create ontology descriptions of other taxonomy sources (gtdb and silva) where I include TAXRANK per @cthoyt suggestion. Using TAXRANK to define taxonomic ranks will vastly facilitate comparison and mapping between different taxonomies.

[cmungall]

I’m I favor of this change

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On Sun, Feb 16, 2025 at 7:56 PM jplfaria ***@***.***> wrote: @matentzn <https://github.com/matentzn>, are there any updates on "community feedback" for this change? Is this issue the best place to provide feedback? I have been working to create ontology descriptions of other taxonomy sources (gtdb and silva) where I include TAXRANK per @cthoyt <https://github.com/cthoyt> suggestion. Using TAXRANK to define taxonomic ranks will vastly facilitate comparison and mapping between different taxonomies. — Reply to this email directly, view it on GitHub <#120 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOPXHBWA4EYBCPP55G32QFMWDAVCNFSM6AAAAABSTUPRXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNRRHEYTANRWGQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> [image: jplfaria]*jplfaria* left a comment (obophenotype/ncbitaxon#120) <#120 (comment)> @matentzn <https://github.com/matentzn>, are there any updates on "community feedback" for this change? Is this issue the best place to provide feedback? I have been working to create ontology descriptions of other taxonomy sources (gtdb and silva) where I include TAXRANK per @cthoyt <https://github.com/cthoyt> suggestion. Using TAXRANK to define taxonomic ranks will vastly facilitate comparison and mapping between different taxonomies. — Reply to this email directly, view it on GitHub <#120 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOPXHBWA4EYBCPP55G32QFMWDAVCNFSM6AAAAABSTUPRXWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNRRHEYTANRWGQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jamesaoverton]

We discussed this in the OBO Community Slack on November 27, but unfortunately the discussion did not get back here.

The current version of this PR drops the ncbitaxon:has_rank predicate and classes that we've been using for 20+ years, and so breaks any system that queries for or displays the old ranks.

If the PR just added new TAXRANK stuff without dropping the old stuff, it wouldn't be a breaking change.

[cmungall]

I think having an interim period with both would be fine, but can we start a survey of people who are using the old properties with a view to declaring EOL?

We use ncbitaxon heavily but this change would not break things for us AFAICT, but others use cases may differ