Refining the Uberon Euarchontoglires subset -- part 2

[rays22]

Remaining tasks

• [x] UBERON:4x series in https://docs.google.com/spreadsheets/d/133F9PVxOk2lM8tkY_afjy7P_bwbZM1b_u1O2abyTvI8/edit#gid=1223601784

UBERON:4x --> mixed, I think this is a small enough subset to look over quickly and add TCs. There will be a handful applicable to human"

Originally posted by @rays22 in https://github.com/obophenotype/uberon/issues/2050#issuecomment-947820509

[paolaroncaglia]

@matentzn @rays22 cc @dosumis Now that the ~1772 taxon constraints added in #2050 are in Uberon, could someone please re-build the Euarch slim? (The old one was at https://github.com/obophenotype/uberon/blob/v2021-07-27/subsets/euarchontoglires-basic.owl.) Many thanks!

Note to self:

• [x] When revised slim is ready, discuss its import into the HCAO pipeline with Zoe

[paolaroncaglia]

Summing up the tasks we resolved to leave for a “second pass” at the Euarch slim:

• [ ] Need to refine the UBERON:4x series in https://docs.google.com/spreadsheets/d/133F9PVxOk2lM8tkY_afjy7P_bwbZM1b_u1O2abyTvI8/edit#gid=1223601784 @cmungall wrote: “UBERON:4x --> mixed, I think this is a small enough subset to look over quickly and add TCs. There will be a handful applicable to human" There are 369 non-obsolete UBERON:4x classes in the slim, copied in the spreadsheet above. I inspected 10 random terms among the 369, and at least 3 are applicable to human, so I'm not very comfortable with adding TCs en masse to this set. Is there someone who could take a closer look and advice on what terms are safe to restrict to never in mammals? Perhaps Wasila, who authored some terms in this set?

• [ ] Terms that were added TCs in #2050 may be scanned for FMA xrefs, and brought back into the slim if they have FMA xrefs.

• [ ] Are there any logically defined non-human terms left? Search for annotation property ‘never in taxon’ ‘Homo sapiens’ (e.g. ‘ampullary gland’, ‘bone of reproductive organ’). Some terms may need double-checking in case they are found in non-human Euarchontoglires.

• [ ] Are there any insect terms left? Insect terms may be retrieved by searching for database_cross_reference contains FBbt (e.g.: 'egg chorion’). This will also bring up a dozen terms whose label contains “insect” (e.g. 'insect ring gland’).

• [x] (Moved to https://github.com/obophenotype/uberon/issues/2194) Are the following random finds left? exoskeleton shell 'open circulatory system' feather rhinarium? honey

• [x] (Moved to https://github.com/obophenotype/uberon/issues/2194; 2x, 3x, 4x and 6x terms are addressed elsewhere) Are any terms left to check/add TCs from this list? (It comes from https://github.com/obophenotype/uberon/issues/1824)

Notes to self: Guidelines on adding TCs here. Jim Balhoff wrote "You all may find my OBO taxon constraints plugin for Protégé useful in seeing what effective taxon constraint the reasoner knows about for the selected term (and you can get explanations). Just keep in mind that it can be SLOW.”

[paolaroncaglia]

Update: the broader issue of taxon restrictions was discussed at the Uberon editors meeting on 22/11/21:

"We need more specific action items to deal with taxon stuff https://github.com/obophenotype/uberon/issues/2137 Chris suggested fix - Chris to add ticket! Roll back 2x, 3x, 4x general taxon constraint 2x, 3x, 4x all get new slim tag - used for anti-slim stripping of terms only with owltools. Curate to hold back a few. Suggestion: We need a taxon fix hackathon where we look at the ontology itself to work through a longer term strategy for fixing."

[matentzn]

Alright, this is how I understand this ticket.

• [x] "Roll back": We go to @rays22 original list of taxon constraints, and remove them using robot unmerge, and instead add a "never_in_euroglires" subset tag on them. EDIT: remove all 3x terms, keep the 6x ones as these are likely to be totally fine.
• [x] Create another ROBOT template with the 3x terms and a new column "AI oboInOwl:inSubset"
• [ ] "Anti-slim stripping". After the normal unsat-pipeline is run, we use SPARQL to remove the remaining "never_in_euroglires", the difficulty here is to tie together broken existential edges (i.e. part-of) edges. Maybe we can use some kind of Relationgraph style approach or something @cmungall outline in #2183.

[rays22]

• [ ] "Roll back": We go to @rays22 original list of taxon constraints, and remove them using robot unmerge, and instead add a "never_in_euroglires" subset tag on them.

Summary of 673 taxon constraints added as part of #2050

Here is my list of the #2050-related taxon constraints that are in UBERON currently.

• provenance: {source="https://github.com/obophenotype/uberon/issues/2050"}

• 660 classes : never_in_taxon-IDs.txt relationship: never_in_taxon NCBITaxon:n

  • 23 classes : UBERON:2x (likely Teleost)
  • 637 classes : UBERON:3x (likely Amphibia)

• 13 classes : UBERON:6x (Arthropods) relationship: in_taxon NCBITaxon:6656 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Arthropoda

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This issue has not seen any activity in the past 6 months; it will be closed automatically in one year from now if no action is taken.

[paolaroncaglia]

This is still in progress.

[github-actions[bot]]

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

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This issue has been closed automatically because it has not been updated in 18 months. Please re-open if you still need this to be addressed.