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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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New abnormal mobility patterns needed #536

Open matentzn opened 5 years ago

matentzn commented 5 years ago

We need to following patterns for XenBase:

increased mobility (PATO_0000051) decreased mobility (PATO_0002283) immobile (PATO_0000300)

Example: cilium in the lung

Range probably cellular component;

Please give examples everyone! Also help us to clearly distinguish mobile from motile.

@seger

matentzn commented 5 years ago

https://github.com/obophenotype/xenopus-phenotype-ontology/issues/58

nicolevasilevsky commented 5 years ago

is there a meaningful difference b/w mobility and motility?

nicolevasilevsky commented 5 years ago

do these patterns need to apply to anatomical entities as well? (I will look for examples)

ybradford commented 5 years ago

@nicolevasilevsky there is a meaningful difference between mobility and motility. As far as I know cilium are not ever referred to as being mobile, but rather motile. I believe the pattern should be for motility - cilium in the lung are motile - they move fluid, they do not move themselves away from the lung

nicolevasilevsky commented 5 years ago

thanks @ybradford! Sounds like we need two patterns. I'll work on this

nicolevasilevsky commented 5 years ago

For motility, in PATO there is: 'cellular motility' -> 'decreased cellular motility' ->'increased cellular motility'

HP uses these PATO terms in the logical defs for these terms: 'Abnormal sperm motility' Reduced sperm motility Reduction of neutrophil motility

The HPO terms follow these patterns:

'has part' some ('cellular motility' and ('inheres in' some %s) and ('has modifier' some abnormal))

'has part' some ('decreased cellular motility' and ('inheres in' some %s) and ('has modifier' some abnormal))

There are also GO terms related to motility and MP uses these: MP_0002674 'abnormal sperm motility' 'has part' some (quality and ('inheres in part of' some 'flagellated sperm motility') and ('has modifier' some abnormal))

MP_0002675 asthenozoospermia 'has part' some ('decreased rate' and ('inheres in' some 'flagellated sperm motility') and ('has modifier' some abnormal))

Which pattern should I create?

nicolevasilevsky commented 5 years ago

Are there any cases of increased cellular motility? I don't see any examples in MP or HP

matentzn commented 5 years ago

@seger @srobb1 @chris-grove @ybradford

What do you think? I think I am kind of liking the MP way of doing things, using a GO term instead of a PATO term. But I dont really mind. (abnormal motility, increased and decreased motility patterns)