Add anti-slims for various taxonomic groupings

[cmungall]

Add antislims that can be applied that should be excluded from specific releases

E.g.

• exclude_from_mammal_release
• exclude_from_vertebrate_release

These are formally weaker than never-in-taxon. In particular, they are safe for intermediate classes and they are safe for classes that may be excluded due to being "too specific" for a use case without worrying about whether there is an existential linking to it

Examples

• the grouping "limb/fin" is not relevant for any tetrapod subset, despite being satisfiable
• highly specific skeletal terms such as various notches of limb bones may be less relevant for cell-centric atlases. Placing a never in taxon would be wrong, and would have the side effect of excluding existential dependents (e.g a major muscle with an insertion site on that notch)

The antislim would be applied after logic-based subset extraction (regardless of which logic-based strategy is used here: #2137)

The relevant owltools command is --extract-ontology-subset

HOWEVER, this only supports specifying a positive subset. Options

1. have a SPARQL or obo-sed.pl that creates an inclusion slim from an antislim
2. add a few lines of java to owltools
3. implement functionality in robot https://github.com/ontodev/robot/issues/497

Assuming 1, the command would be

owltools uberon-post-logic-filtering-euarch.owl --extract-ontology-subset -s include_in_euarch_release -o euarch.owl

Make sure that relax is first executed.

Some curation guidelines for using the subset

• no need to add on things that would be filtered by logic strategy
• be careful when applying to broad intermediate classes like limb/fin, as you can lose logical definitions
• the assumption is that the antislim is geared towards a use case. the various notches of bones may be relevant for skeletal annotation and may be useful for some HCA use cases, but the assumption is that being too strict as a first pass is better than being too inclusive, as unlike with reasoning strategy it doesn't propagate

[matentzn]

Add to tech board @shawntanzk

Thanks a lot @cmungall

[matentzn]

Should these antislims be created or generated? i.e. how will we know that fin/limb should be excluded from human-view? Manual curation?

[anitacaron]

From tech group meeting: we won't act on this ticket yet because we need to figure out how to implement the GAP filling over existential (Anitas comment edited by @matentzn )

[dosumis]

From tech group meeting: we won't act on this ticket yet because we need to figure out how to implement the GAP filling over existential (Anita's comment edited by @matentzn )

@anitacaron - we should discuss progress on this (as tested on scAtlas)

[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.

[anitacaron]

We can close this issue when the new ROBOT subset command is released.

[matentzn]

Are you sure? Robot subset will not allow removing "paw or hand” type classes without an anti slim approach. Maybe I am wrong though.

[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.