HsapDv:0000080 - Githubissues

obophenotype / developmental-stage-ontologies

Source files for various species-specific stage ontologies

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HsapDv:0000080 #62

Open fbastian opened 5 years ago

fbastian commented 5 years ago

UBERON:0034920 'infant stage' does not seem to be connected to HsapDv:0000080 'immature stage' (mapped to UBERON:0000112 'sexually immature stage')

('neonate stage' and 'juvenile stage' are part of 'sexually immature stage'. 'infant stage' is not)

ping @ANiknejad

ANiknejad commented 5 years ago

late answer, sorry. UBERON:0034920 'infant stage' has a definition that involves 'weaning time' and we did not put this socially fluctuating timing in our human ontology, (while we have such weaning definition in other primate dev ontologies..) so there is actually none UBERON corresponding to HsapDv:0000083 infant stage, and none 'UBERON:0018685 nursing stage' equivalent in our human ontology so far....

UBERON:0018685 nursing stage -- UBERON:0007221 neonate stage (GCI taxon restrictions) -- UBERON:0034920 infant stage

AND

UBERON:0000112 sexually immature stage -- UBERON:0007221 neonate stage -- UBERON:0034919 juvenile stage

Any help to understand how to solve this issue will be welcome, @fbastian

ANiknejad commented 4 years ago

We think doing:

UBERON:0000112 sexually immature stage -> to map HsapDv:0000080 immature stage (DONE IN hsapdv_3.obo)
|__UBERON:0018685 nursing stage -> TO CREATE and map new class in Hsapdv
|        |___UBERON:0007221 neonate stage -> to map HsapDv:0000082 new born human stage (change definition to relax and put age in comments)
|    |___UBERON:0034920 infant stage  -> to map HsapDv:0000083 infant stage (change definition to relax and put age in comments)
|
|__UBERON:0034919 juvenile stage -> to map HsapDv:0000081 child stage (change definition to relax and put age in comments)(mapping DONE IN hsapdv_3.obo)

ANiknejad commented 4 years ago

UBERON:0000112 sexually immature stage -> to map HsapDv:0000080 immature stage (DONE IN hsapdv_3.obo)

@fbastian Done on /develop, see https://github.com/obophenotype/developmental-stage-ontologies/commit/fd8289239a583b7ae035850e13b6eec29082b236#diff-f9da9f01dbacb2632673f7a620cf5f64

ANiknejad commented 4 years ago

UBERON:0018685 nursing stage -> TO CREATE and map new class in Hsapdv

@fbastian Done on my fork (/ANiknejad/developmental-stage-ontologies/develop), this is HsapDv:0000260 nursing stage see https://github.com/obophenotype/developmental-stage-ontologies/pull/70/commits/c1cf4022657fe4625a3b5542deb21c2ce2899420

ANiknejad commented 4 years ago

|___UBERON:0007221 neonate stage -> to map HsapDv:0000082 new born human stage (change definition to relax and put age in comments)>

@fbastian Done on my fork (/ANiknejad/developmental-stage-ontologies/develop), see https://github.com/obophenotype/developmental-stage-ontologies/pull/70/commits/f90e1d2d49b645e5061afd6f3b790c5cd533a45c

ANiknejad commented 4 years ago

|___UBERON:0034920 infant stage -> to map HsapDv:0000083 infant stage (change definition to relax and put age in comments)

@fbastian Done on my fork (/ANiknejad/developmental-stage-ontologies/develop) , see https://github.com/obophenotype/developmental-stage-ontologies/pull/70/commits/82d80758da98b5e6e3b1a0d856dfc6f4be1c13db

fbastian commented 3 years ago

UBERON:0034919 juvenile stage -> to map HsapDv:0000081 child stage (change definition to relax and put age in comments)

Actually, UBERON:0034919 juvenile stage has been mapped to HsapDv:0000271 juvenile stage (part_of HsapDv:0000264 ! pediatric stage, immediately_preceded_by HsapDv:0000265 ! child stage) Is that correct @ANiknejad?