search

obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
Creative Commons Zero v1.0 Universal
76 stars 17 forks source link

Add pattern for normal fertility and viability #496

Open matentzn opened 5 years ago

Clare72 commented 5 years ago

Flybase has these 'normal' phenotypes so that researchers can see which alleles are homozygous viable and fertile to help plan genetic crosses. They are not currently defined to be either 'normal' or 'abnormal'.

Current pattern is PATO:['fertile'/'viable'] and 'inheres in' some 'anatomical entity' (we use FBbt:'organism')

We may wish to use 'normal fertility' from PATO as 'fertile' has 'increased/decreased/normal fertility' children. 'viable' in PATO does not have any assertion of normality and does not have any children.

FlyBase also has 'semi-fertile', currently asserted as a subclass of 'fertile' (not the case for PATO:'semi-fertile'), but this might need to be an 'abnormal' phenotype. If it no longer falls under fertile, it may be less useful to researchers...

Clare72 commented 5 years ago

The more I think about this, the more I think that asserting 'fertile' and 'viable' to be 'normal' would be a bad idea for us. Authors often state that flies are fertile and viable without any quantification, so it is not clear whether they are really normal or slightly sub-normal. This would make it hard for curators to choose between 'fertile' (normal) and 'semi-fertile' (abnormal), where currently 'fertile' covers both situations.

matentzn commented 5 years ago

Other opinions on how to do viable @obophenotype/phenotype-editors and normal fertility?

chris-grove commented 5 years ago

At WormBase, we would curate similar "normal" cases just as annotations to "sterile" and "lethal" with a "NOT" qualifier to indicate NOT sterile and NOT lethal (a.k.a. "fertile" and "viable"). We could have a potential explosion of ontology terms if we tried to make separate ontology terms for the unobserved case for all of our phenotypes.

Clare72 commented 5 years ago

We generally don't add CV terms for negative results, 'fertile' and 'viable' are exceptions because they provide useful information about stocks and help plan genetic crosses.