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pato-ontology / pato

PATO - the Phenotype And Trait Ontology
https://pato-ontology.github.io/pato/
BSD 3-Clause "New" or "Revised" License
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changes to interdigitated #190

Open wdahdul opened 5 years ago

wdahdul commented 5 years ago

Regarding term 'interdigitated' PATO:0001960; def: A shape quality inhering in a bearer by virtue of the bearer's parts or projections being interlocked; for example, the fingers of two hands that are clasped.

Two proposed changes: 1) This is currently a subtype of 'shape'. I think it's more appropriately a subtype of 'structure' PATO:0000141, and more specifically a subtype of 'interlocked with' PATO:0002437

2) Add synonym 'interdigitated with'

nicolevasilevsky commented 5 years ago

Does anyone object to this change? @cmungall @dosumis @balhoff @mellybelly @matentzn, others?

matentzn commented 5 years ago

I have no strong opinion, but my tendency would be to not make too many assumptions about how annotators will interpret highly specific terms like this one, and perhaps add it under structure rather than anything more specific. Unless there is a strong reasoning case, I think we should be conservative when structuring PATO. Just my 5 cents.

dosumis commented 5 years ago

This seems reasonable: I think shape refers to external structure. Interdigitated sounds like either a description of internal structure (the long, slender cells in the tissue (E) are interdigitated with each other), or a relational quality describing one entity's structural relationship with another (the cuticular projections of the coxa (E1) are interdigitated with cuticular projections from trochanter (E2)).

But - I worry a bit about mixing what sound like absolute qualities (interdigitated, interlocked) with what sound like relational qualities (interdigitated_with; interlocked_with). In the latter case, we need a towards E2 to record what E1 is interdigitated with. Would it be better to have two hierarchies with some kind of logical relationship?

matentzn commented 5 years ago

+1 on what @dosumis said. There should be a clear separation!