-
Notifications
You must be signed in to change notification settings - Fork 5
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Mappability of HsapDv to Uberon #33
Comments
2 years ago...I was already trying to revamping this bloody hsapdv |
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.
I agree, that's why I propose to map new HsapDv:0000226 human prime adult stage to UBERON:0018241 prime adult stage |
please see also |
Of note, HsapDv:0000081 could be mapped to UBERON:0034919. HsapDv:0000081 child stage (human) UBERON:0034919 juvenile stage |
related to
I do find Oxford literature references with 'young people' defined as children of 16 and over to be allowed to consent to medical treatment. 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:
p. 700: Menarche 11-15 years (98th-2nd centiles); 10.3-15.7 year (99.6th-0.4th centile)
https://www.ncbi.nlm.nih.gov/books/NBK470280/ http://www.epi.umn.edu/let/pubs/img/adol_ch1.pdf
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] |
remodeling of hsapdv.obo, propositions below -immature stage 0-10 years (=first decade human stage) --> 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 |
see issue #33 could you please check, @cmungall? NB: this version does not take into account modifications managed in last issues, this is a version we (with Fred B.) refined beginning of the year, but not checked so far. So if you agree with this version, I will do the merge with the last issues from Amos B. (49, 50 and 52)
References to define adolescent stage: 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. AnAgedb Female sexual maturity WHO Age groups |
#33, -immature stage 0-10 years (=first decade human stage) --new born 0-1 month --infant 1-24months --child ---2-5 years ---6-9
HsapDv is not properly mappable to Uberon. Because we have:
Problem are:
(some background on prime/late adult stages: obophenotype/uberon#496)
What we would like to have is something like:
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:
=> So we loose the mapping to UBERON:0018241 prime adult stage
The text was updated successfully, but these errors were encountered: