adolescent stage?

[ANiknejad]

Hi Chris,

we would like to propose an 'adolescent stage' with the following draft definition: "A life cycle stage during which the completion of development and growth of the sexually mature organism occurs."

This will match with the design of Uberon (see below) and will precedes UBERON:0018241 ! prime adult stage [def: "A life cycle stage that starts at completion of development and growth of the sexually mature adult animal, and ends before senescence."]

currently in Uberon:

• post-juvenile adult stage (def: "The stage of being a sexually mature adult animal." [https://orcid.org/0000-0002-6601-2165]) -- prime adult stage -- late adult stage

Our suggestion is based on many references, here an example: http://www.ncbi.nlm.nih.gov/pubmed/15251870 "adolescence appears to be a highly conserved developmental stage, its characteristics sculpted to meet common evolutionary pressures that include the avoidance of inbreeding at this time of sexual emergence"

New proposition for Uberon design:

• post-juvenile adult stage -- adolescent stage -- prime adult stage -- late adult stage

For the usage of 'adolescent' in non-humain animals, please see:

http://www.ncbi.nlm.nih.gov/pubmed/21169902 http://www.ncbi.nlm.nih.gov/pubmed/24102398 http://www.ncbi.nlm.nih.gov/pubmed/15251892 http://www.ncbi.nlm.nih.gov/pubmed/25204637

Open to discussion, best regards,

Anne

[cmungall]

this one slipped - let me know if this is a priority or if you want to wait until the linked ticket is resolved

[fbastian]

Not a priority, as we already made the integration for the next release of Bgee, without using this stage.

[ANiknejad]

Could that be added please @cmungall ?

[ANiknejad]

I closed this issue, sounds like no more relevant to align HsapDv with HPO, see last comments here

https://github.com/obophenotype/human-phenotype-ontology/issues/5119

[tgbugs]

This has come up again for us. I think there are two cases that need to be considered (the 3rd is already handled).

1. After sexual maturity but before the end of growth. Most human beings reach sexual maturity before they finish growing. This the adolescent stage referred to by this issue. Behavorial maturity and other non-growth related phenotypes likely need to be ignored.
2. After the end of growth but before sexual maturity. The European eel is a classic example https://doi.org/10.1111/j.1095-8649.1982.tb03994.x.
3. The case where sexual maturity and the end of growth coincide. Many insects fall into this category.

@lzehl @UlrikeS91

[lzehl]

@tgbugs thanks for bringing this up again on our behalf. We (EBRAINS) have quite a number of researchers from human and rodent studies that would like to register an "adolescent stage" or "young adult stage".

The "prime adult stage" is defined as "A life cycle stage that starts at completion of development and growth of the sexually mature adult animal, and ends before senescence." which leaves at least for some species a life cycle stage within the "post-juvenile adult stage" undefined where sexual maturity is reached before the completion of development. Especially from the neuroscience perspective researchers want/need to point out that they are looking explicitly at subjects in that life cycle stage or not.

For this reason I strongly support @tgbugs suggestion.

[cmungall]

id: UBERON:0018241
name: prime adult stage
def: "A life cycle stage that starts at completion of development and growth of the sexually mature adult animal, and ends before senescence." [Bgee:AN, https://github.com/obophenotype/uberon/issues/496]
synonym: "adulthood stage" RELATED []
is_a: UBERON:0000105 ! life cycle stage
relationship: part_of UBERON:0000113 ! post-juvenile adult stage

how should the above be used for eels? The current def doesn't quite apply. What about changing to "starts at the onset of sexual maturity or the cessation of growth, whichever comes last"? cc @ANiknejad

once this is clarified it should be easy to fit in the two new terms

[tgbugs]

I like that definition, it makes it clear that both sexual maturity and growth must be complete and makes it more temporal so that it is easier to understand for the eel case.

[lzehl]

@cmungall I'm not sure if I understand correctly do you just want to redefine "prime adult stage" to include the missing period? That would not solve the problem that some researchers explicitly want to name that short period (sexual mature but not fully developed)

The eel case, if I got this correctly, would be fully developed but not sexually mature? would that not just mean that they are juvenile and then immediately merge into prime adults, because once the hit sexual maturity they are fully developed as well ?

[tgbugs]

@lzehl prime adult stage already does not contain the missing period, it is just that the current textual definition makes it hard to understand.

[lzehl]

@tgbugs yes, it does not contain the missing period. I was just not sure if the plan was to redefine "prime adult" to include the period or if the plan was to define the missing period separately and just refine all definitions. The latter is what we would need within our database. Our current solution is the following: openMINDS_controlledTerms PR 59 I hope this does not collide with the outcome of this issue

[lzehl]

To revive this issue a bit here is what we (openMINDS) defined so far for consecutive life cycle stages (in order):

• embryo: Life cycle stage of a subject that starts with fertilization and ends with the fully formed embryo.
• neonate: Life cycle stage of a subject that immediately follows birth.
• infant: Life cycle stage of subjects (mammals) that follows the neonate stage and ends at weaning.
• juvenile: Life cycle stage of a subject that starts with the independence of the nest and/or caregivers and ends with sexual maturity.
• adult: Life cycle stage of a subject that starts with sexual maturity and ends with death.
  • young_adult: Life cycle stage of a subject that starts with sexual maturity and ends with the cessation of growth (if this is reached after sexual maturity).
  • prime_adult: Life cycle stage of a subject that starts with sexual maturity or the cessation of growth, whichever comes last, and ends before senescence.
  • late_adult: Life cycle stage of a subject that follows the prime adult stage and ends with death.
• death: Life cycle stage of a subject that starts with death and ends with full decomposition of the subject's body.

Note that this list is incomplete and some definitions might need further adaptions. For now we did not had other use cases (therefore the incomplete list).

In addition, there was the need to have life cycle stages that are less clear biologically defined which are though often used to define the context of developmental stage of a subject:

• adolescent: Life cycle stage of a subject loosely defined by the transitional growth and development between childhood and adulthood, often described as ‘puberty’.
• perinate: Life cycle stage of a subject that starts right before and ends right after birth.

We link to UBERON where we can, however some terms are missing in UBERON and we tried to optimize some of the definitions.