Mappability of HsapDv to Uberon

[fbastian]

HsapDv is not properly mappable to Uberon. Because we have:

HsapDv:0000086 adolescent stage
HsapDv:0000087 human adult stage
    po HsapDv:0000088 human early adulthood stage 
    po HsapDv:0000091 human late adulthood stage 
        po HsapDv:0000092 human middle aged stage 
        po HsapDv:0000093 human aged stage => mappable to UBERON:0007222 late adult stage

Problem are:

• HsapDv:0000087 human adult stage is NOT directly mappable to UBERON:0000113 post-juvenile adult stage, because HsapDv:0000087 starts at 19 yo, so, after sexual maturity is acquired. HsapDv:0000204 mature stage is mappable to UBERON:0000113 post-juvenile adult stage, so, also including HsapDv:0000086 adolescent stage.
• Is HsapDv:0000088 human early adulthood stage mappable to UBERON:0018241 prime adult stage? Or is UBERON:0018241 prime adult stage equivalent to HsapDv:0000086 adolescent stage + HsapDv:0000087 human adult stage @ANiknejad? How I understand it, since adolescent people are still "developing", HsapDv:0000086 adolescent stage should not be part of UBERON:0018241 prime adult stage. HsapDv:0000092 human middle aged stage is also part of prime adult stage, because it's before senescence, right?

(some background on prime/late adult stages: obophenotype/uberon#496)

What we would like to have is something like:

UBERON:0000113 post-juvenile adult stage (xref to HsapDv:0000204 mature stage)
    po HsapDv:0000086 adolescent stage
    po UBERON:0018241 prime adult stage (not equivalent to HsapDv:0000087 human adult stage, that includes late adulthood)
        po HsapDv:0000088 human early adulthood stage
        po HsapDv:0000092 human middle aged stage (because it's before senescence, so still part of prime adult stage, right?)
    po UBERON:0007222 late adult stage (with xref to HsapDv:0000093 human aged stage)

So HsapDv:0000087 human adult stage and HsapDv:0000091 human late adulthood stage just disappear in this schema, it is not mappable to any term.

=> We need to add a term equivalent to UBERON:0018241 prime adult stage in HsapDv.
=> And maybe we should completely revamp stages not based on "actual biology". This would fit nicely with #17 and #10, and with the refactoring by decades we need for GTEx (#34).

In the meantime, we can do:

UBERON:0000113 post-juvenile adult stage (xref to HsapDv:0000204 mature stage)
    po HsapDv:0000086 adolescent stage
    po HsapDv:0000087 human adult stage
        po HsapDv:0000088 human early adulthood stage
        po HsapDv:0000091 human late adulthood stage 
            po HsapDv:0000092 human middle aged stage 
            po UBERON:0007222 late adult stage (xref to HsapDv:0000093 human aged stage)
                po HsapDv:0000094 65-79 
                ...

=> So we loose the mapping to UBERON:0018241 prime adult stage

[ANiknejad]

2 years ago...I was already trying to revamping this bloody hsapdv
PropositionDevHuman_Mouse_toUberon.docx

[ANiknejad]

Is HsapDv:0000088 human early adulthood stage mappable to UBERON:0018241 prime adult stage? Or is UBERON:0018241 prime adult stage equivalent to HsapDv:0000086 adolescent stage + HsapDv:0000087 human adult stage @ANiknejad? How I understand it, since adolescent people are still "developing", HsapDv:0000086 adolescent stage should not be part of UBERON:0018241 prime adult stage. HsapDv:0000092 human middle aged stage is also part of prime adult stage, because it's before senescence, right?

At time we defined the hsapdv we considered 'adolescent' (over 13yr and under 19yr) as sexually mature individual, due to the fact that some individuals become already parents at that time. We considered this stage for sake of annotation facility, as 'adolescent' is a usual term for human description at this age.

HsapDv:0000086 adolescent stage should not be part of UBERON:0018241 prime adult stage.

I agree, that's why I propose to map new HsapDv:0000226 human prime adult stage to UBERON:0018241 prime adult stage

hsapdv_2.txt

[ANiknejad]

please see also
obophenotype/uberon#577

[fbastian]

Of note, HsapDv:0000081 could be mapped to UBERON:0034919.

HsapDv:0000081 child stage (human)
def: "Immature stage that refers to child who is over 2 and under 13 years old." [Bgee:curator]

UBERON:0034919 juvenile stage
def: "The stage of being no more dependent of the nest and/or from caregivers for subsistence while having not reach sexual maturity." [Bgee:AN, https://github.com/obophenotype/uberon/issues/645]

[ANiknejad]

related to
https://sourceforge.net/p/obo/human-phenotype-requests/273/

Peter N. Robinson - 2014-03-12

Young adult should have been defined as from 16 years on to 40.
I have adjust the definition of adult to begin with 16 years.
Obviously there is no good definition of this, but I think this age classification is the most reasonable compromise between biology and culture etc.

I do find Oxford literature references with 'young people' defined as children of 16 and over to be allowed to consent to medical treatment.
See Oxford Desk Reference - Clinical Genetics ISBN 978-0192628961

So far in HsapDv we consider 'adolescent stage' 13-18 years as the first child of mature stage (sexually mature human). If young adult is 16-40 years, we should redefine 'adolescent' as a stage younger than 16 years.

For redefining 'adolescent' stage, we will consider:

• Oxford Desk Reference - Clinical Genetics ISBN 978-0192628961

p. 700: Menarche 11-15 years (98th-2nd centiles); 10.3-15.7 year (99.6th-0.4th centile)

• Tanner Staging and Sexual Maturation Rating (SMR)

https://www.ncbi.nlm.nih.gov/books/NBK470280/

http://www.epi.umn.edu/let/pubs/img/adol_ch1.pdf

• Oxford Textbook of Rheumatology ISBN 978-0191666988

p.12 Section 1, there are 3 adolescent stage definitions, early 10-13 years, mid 14-16 years, late 17-19 years.

--> Our hsapdv adolescent stage can then maybe be redefined as 11-15 years, with this stage still being part of sexually mature stage, xref UBERON:0000113 post-juvenile adult stage

def: "The stage of being a sexually mature adult animal." [https://orcid.org/0000-0002-6601-2165]

[ANiknejad]

@fbastian

remodeling of hsapdv.obo, propositions below

-immature stage 0-10 years (=first decade human stage)
--new born 0-1 month
--infant 1-24months
--child
---2-5 years
---6-9
-mature stage (over 10 years)
--adolescent 10-15
--prime adult 16-59 (before senescence)
---young adult 16-39
---middle 40-59
--late adult over 60

--> this is the 'hsapdv_4_hpoOxford.obo' in my local file

P:\My Documents\MRR\2017_NEW\humanDevONTO_new

OR maybe this scheme below, please let me know

-immature stage
--new born 0-1 month
--infant 0-24months
--child
---2-5 years
---6-10
---11-12 PRE_ADOLESCENT STAGE (sexually immature)
-mature stage
--adolescent 13-15
--prime adult 16-60 (before senescence)
---young adult 16-40
---middle 40-60
--late adult over 60

[ANiknejad]

References to define adolescent stage:
The Minnesota Adolescent Community Cohort (MACC) Study is a population-based, longitudinal study that enrolled 3636 youth from Minnesota and 605 youth from comparison states age 12 to 16 years in 2000–2001.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089859/

In females, the normal onset of puberty ranges from 8 to 13 years old, averaging age 10 years in White Americans and age 8.9 years in African-Americans...In males, the onset of puberty ranges from 9 to 14 years of age.
https://www.ncbi.nlm.nih.gov/books/NBK470280/

AnAgedb
http://genomics.senescence.info/species/entry.php?species=Homo_sapiens

Female sexual maturity
4,745 days = 13 years
Male sexual maturity
5,110 days = 14 years

WHO
https://www.who.int/maternal_child_adolescent/documents/pdfs/9241591269_op_handout.pdf

Age groups
WHO defines adolescents as individuals in the 10-19-year age group and “youth” as the 15-24-year age group. These two overlapping age groups are combined in the group “young people”,covering the age range 10-24 years (1