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obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
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Obsolete brokenAnatomicalEntity pattern in favour of fracturedAnatomicalEntity #705

Open matentzn opened 4 years ago

matentzn commented 4 years ago

This is mainly important for @ybradford @sbello and @nicolevasilevsky @drseb

We have recently introduced the fracturedAnatomicalEntity to represent fractured bones etc, with a much neater classification that PATOs "broken". @sbello @ybradford can you check whether you would consider swapping the brokenAnatomicalEntity in MP/ZFIN from fracturedAnatomicalEntity (i.e. getting rid of PATO:broken altogether in favour of the more precisely defined "fractured")?

sbello commented 4 years ago

We use broken for a number of non-bone terms. For example: ocular rupture (MP:0006225) uterus rupture (MP:0003571) ruptured lens capsule (MP:0008841) I don't think I would want to use fractured for these.

It would be okay to switch the bone and cartilage terms to use fractured. Although I'll have to think about this one "fragmented Meckel's cartilage"

nicolevasilevsky commented 4 years ago

Looks like HPO is only using 'broken' for broken bone terms, so this could/should be replaced by 'fractured'.

From what @sbello noted above, sounds like we need both terms.

nicolevasilevsky commented 4 years ago

Fractured is a child of broken in PATO. So I think we could keep the broken pattern and if broken is a variable, we could use 'fractured' right? I changed my mind, I don't think we need both after all.

matentzn commented 4 years ago

I think we should try and use the fractured patterns for fractures, and review all the other classes using the more generic broken. Seems to me that maybe a new PATO quality is order for "ruptured"..

The broken pattern does not allow variables for the quality, just for the anatomical entity!

mellybelly commented 4 years ago

It does seem like there is more than one way to be broken!

pnrobinson commented 4 years ago

https://www.youtube.com/watch?v=1BjQYQ5p2Ko [https://www.bing.com/th?id=OVP.Idj-fpuupmpv_N2ZYnapkwHgFo&pid=Api]https://www.youtube.com/watch?v=1BjQYQ5p2Ko The Rolling Stones- Shatteredhttps://www.youtube.com/watch?v=1BjQYQ5p2Ko From Some Girls (1978) (Lyrics) Shattered, shattered Love and hope and sex and dreams Are still surviving on the street Look at me, I'm in tatters! I'm a shattered Shattered Friends are so alarming My lover's never charming Life's just a cocktail party on the street Big Apple People dressed in plastic bags Directing traffic Some kind of fashion ... www.youtube.com

Peter Robinson Professor and Donald A. Roux Chair, Genomics and Computational Biology The Jackson Laboratory for Genomic Medicine 860.837.2095 t | peter.robinson@jax.org | https://robinsongroup.github.io/ Peter Robinson

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It does seem like there is more than one way to be broken!

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sbello commented 4 years ago

ruptured is currently a synonym for broken in PATO

ybradford commented 4 years ago

ZP uses broken in many terms which are not bone or cartilage related. I agree we should use fractured for fractured bone terms and review other uses of broken as @matentzn has suggested.