Document ObjectProperties/patterns for use in TC plugin

[cmungall]

Which OPs/patterns does the plugin work for?

This is a good opportunity to standardize across OBO

1. all instances of C must be in T: C SubClassOf in-taxon some T // no need for only-in-taxon if in-taxon is functional
2. no instances of C are in T: C SubClassOf in-taxon only not T
3. there exists some instance of C in T (currently only used in Uberon): keep as annotation assertion for now?

Will the PTC plugin would with 1 + 2?

Note for 2 we have historically used an AP. This will still be necessary if ontology maintained in .obo. But we can standardize to the most precise OWL for use with this tool

[matentzn]

+1

[cmungall]

Modification of the above, allowing for a canonical logical representation and a canonical shortcut

1. all instances of C must be in T:
   a. Logical: C SubClassOf in-taxon some T // no need for only-in-taxon if in-taxon is functional
   b. Shortcut: no need
2. no instances of C are in T:
   a. Canonical logical representation: C SubClassOf in-taxon only not T
   b. Alternative EL logical representation: C disjointWith in-taxon some T (depends on injecting GCIs into NCBITaxon)
   c. Canonical Shortcut: AnnotationAssertion: C never-in-taxon T
3. there exists some instance of C in T
   a. Canonical logical representation: [a C] Type in-taxon some T
   b. Canonical shortcut: C present-in-taxon T

[cmungall]

Note: none of the above can be considered to be statements about evolutionary gain or loss

It's important for us in GO to be able to indicate

• gain in ancestral node X
• lost in ancestral node X

@thomaspd's proposal here:

https://docs.google.com/presentation/d/1Z3d8SBz-BWHPV5a9oaniPypZIYzV7VzBwVcleLdpk_c/edit#slide=id.p

This essentially adds a qualifier to a TC such that it can be declared GLOBAL strengthening the meaning

• Only in = Gained at the specified branch in evolution
• Never in = Lost at the specified branch in evolution

These could be represented by paired statements. cc @balhoff