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mgijax / mammalian-phenotype-ontology

Standard terms for annotating mammalian phenotypic data
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Review placement of all embryonic lethality terms with child term of incomplete and complete penetrance #4031

Closed anna-anagnostop closed 1 month ago

anna-anagnostop commented 2 months ago

Need to review all embryonic lethality terms that have child terms of incomplete and complete penetrance and revise their placement under the appropriate embryonic lethality parent terms.

For example:

embryonic lethality prior to organogenesis, complete penetrance MP:0014259 should be a child of embryonic lethality, complete penetrance MP:0011092

embryonic lethality prior to organogenesis, incomplete penetrance MP:0014260 should be a child of embryonic lethality, incomplete penetrance MP:0011102

embryonic lethality at implantation, complete penetrance MP:0011093 should be a child of embryonic lethality prior to organogenesis, complete penetrance MP:0014259

embryonic lethality at implantation, incomplete penetrance MP:0011103 should be a child of embryonic lethality prior to organogenesis, incomplete penetrance MP:0014260

None of these terms have EQs, except for embryonic lethality MP:0008762 which uses:

'has part' some ('lethal (sensu genetics)' and ('characteristic of' some embryo) and ('has modifier' some abnormal))

anna-anagnostop commented 1 month ago

Also, need to create complete and incomplete penetrance child terms of prenatal lethality prior to heart atrial septation MP:0013294

anna-anagnostop commented 1 month ago

Discuss placement of increased miscarriage rate MP:0031434 under prenatal lethality MP:0002080 and perinatal lethality MP:0002081; see definition of Fetal death from CDC and HPO term Miscarriage HP:0005268

@anna-anagnostop Miscarriage rate is where it is because we are talking about the phenotype of the mother (dependent on the maternal genotype) rather than the phenotype of the embryo or fetus (dependent on the embryo/fetus genotype). Technically all the prenatal lethality terms are miscarriages.

anna-anagnostop commented 1 month ago

Added new terms: prenatal lethality prior to heart atrial septation, incomplete penetrance MP:0031660 prenatal lethality prior to heart atrial septation, complete penetrance MP:0031661