Chris Mungall comments

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                                            Chris Mungall

Design pattern for absent X has complex OWL definitions that has unintended entailments

I’m pretty confident this approach isn’t going to scale. I also think the pattern could be simplified - what does the second clause do? I also don’t understand the use...

add example table of different property types

Add CURIEs/URIs and descriptions then should be ready to review

[pydanticgen] Embed extra metadata in modules, classes, and fields

How about adding some command line options to control - whether metadata is included (off by default, to avoid surprises?) - the extent of the metadata - whether the base...

[pydanticgen] Embed extra metadata in modules, classes, and fields

let's save the inlined vs runtime as a separate PR. Incremental is good! (as is preserving default behavior)

docgen should use alias field when reporting slots for a class

@turbomam check you are OK with my restructing your issue

NTR: 'has gene template' to replace either 'gene product of' or 'has gene product' (difficult to tell)

> In so doing, we came across two similar relations, one of which presumably means the same thing (I can't tell which). These are inverses You can see this in...

NTR: 'has gene template' to replace either 'gene product of' or 'has gene product' (difficult to tell)

I am happy to change the label, obsolete and make a new ID, etc. But I agree completely with David. In general shortcut relations in RO should reuse existing definitions...

Optional OWL reasoner tests are failing

Actually the short term problem is immediately fixed by running the tests `--with-output`. But this defeats the purpose of the original optimization. We really only need to materialize outputs for...

plantuml: hide circle and empty members, remove quotes

Thanks! The corresponding test should be fixed too - let us know if you want one of us to take over from here or if you're able to make the...

plantuml: hide circle and empty members, remove quotes

lgtm. We can circle back on escaping issues