search

obophenotype / mouse-anatomy-ontology

Ontologies for mouse anatomy and development
Other
5 stars 3 forks source link

temporal range of germ layer #118

Closed cmungall closed 5 years ago

cmungall commented 5 years ago

We have a GO annotation to:

cytoplasm AND part_of some testis AND part_of some 'germ layer'

I am trying to figure out what this means and why someone would annotate to this

It looks like it's unsatisfiable due to conflicting temporal ranges:

But I am wondering if even TS26 is extending it too far, surely the germ layers end before this?

cc @ukemi @vanaukenk

tfhayamizu commented 5 years ago

RE: "surely the germ layers end before this?"

The EMAPA includes 'extraembryonic' endoderm, ectoderm and mesoderm as subclasses of germ layer. While this classification may be debatable, extraembryonic mesoderm, at least, is thought to arise during gastrulation. (See, e.g., https://onlinelibrary.wiley.com/doi/full/10.1111/dgd.12294.)

The EMAPA has terms for amnion ectoderm and yolk sac endoderm (with annotations) extending to TS26. Not saying these are necessarily correct, but they support the stage range for 'germ layer.'

cmungall commented 5 years ago

OK, and I heard from @ukemi that the curator actually intended to use 'germinal epithelium' rather than germ layer!