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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Need new term for post-embryonic/pre adult term for alliance #1447

Open cerivs opened 5 years ago

cerivs commented 5 years ago

Need to make sure there is a stage term that encompasses range of stages after embryo and before adult stage. To support expression data for C. elegans to mammals.

doughowe commented 5 years ago

Term could be something like "post-embryonic juvenile stage"

doughowe commented 5 years ago

Unclear (to me at least) why we can't use: embryonic = embryo stage uberon:0000068 post-embryonic = post-embryonic stage uberon:0000092 adult = post-juvenile adult uberon:0000113

oh...I see...post-juvenile adult is part of post-embryonic..so that doesn't wash for us. We need a three part series embryonic, post-embryonic pre-adult, adult

doughowe commented 5 years ago

What about: embryonic = embryo stage uberon:0000068 post-embryonic = juvenile stage uberon:0034919 adult = post-juvenile adult stage uberon:0000113

Seems like those work?

GAH...and nope. juvenile stage, as defined, doesn't include early postnatal/post hatching stuff.

doughowe commented 5 years ago

Looking for something like this:

  1. post-embryonic stage (UBERON:0000092)
  2. (p)post-embryonic juvenile [New] - intended to include larval and pupal stages so isn't part of fully formed stage. Spans birth/hatching to formation of sexually mature adult
  3. (p)sexually immature stage (UBERON:0000112) - remove (p) post-embryonic stage
  4. (p)larval stage (UBERON:0000069) - remove (p) post-embryonic stage
  5. (p)nursing stage (UBERON:0018685) - remove (p) post-embryonic stage
  6. (p)pupal stage (UBERON:0000070) - remove (p) post-embryonic stage
  7. (follows) post-juvenile adult stage (UBERON:0000113)
  8. (precedes) embryo stage (UBERON:0000068)
  10. life cycle stage (UBERON:0000105)
  11. (i)post-embryonic juvenile [New]

(i) = is_a (p) = part_of

cmungall commented 5 years ago

Minor nomenclature point: is it not odd to call a larva or a pupa "juvenile"

I can't think of a better name: "post-embryonic pre-mature" is a bit of a mouthful

@ANiknejad - thoughts? (note we should be able to infer membership of this in the 20 or so stage ontologies)

doughowe commented 5 years ago

Maybe "post-embryonic immature stage"?