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Mass Obsoletion: focus on branch 'disorder of development or morphogenesis' (MONDO:0021147) #6876

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sabrinatoro opened this issue Nov 16, 2023 · 5 comments
Closed

Mass Obsoletion: focus on branch 'disorder of development or morphogenesis' (MONDO:0021147) #6876

sabrinatoro opened this issue Nov 16, 2023 · 5 comments
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mass obsoletion

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sabrinatoro commented Nov 16, 2023 •
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branch: 'disorder of development or morphogenesis' (MONDO:0021147)

Terms to obsolete:

CURIE obsoletion candidate label
MONDO:0017961 46,XX disorder of gonadal development
MONDO:0020039 46,XX disorder of sex development induced by androgens excess
MONDO:0017963 46,XX disorder of sex development induced by endogenous maternal-derived androgen
MONDO:0017964 46,XX disorder of sex development induced by exogenous maternal-derived androgen
MONDO:0019593 46,XX disorder of sex development induced by fetal androgens excess
MONDO:0017962 46,XX disorder of sex development induced by fetoplacental androgens excess
MONDO:0019608 46,XX disorder of sex development induced by maternal-derived androgen
MONDO:0017966 46,XY disorder of gonadal development
MONDO:0019597 46,XY disorder of sex development due to isolated 17,20-lyase deficiency
MONDO:0017974 46,XY disorder of sex development induced by maternal-exposure to endocrine disruptors
MONDO:0017969 46,XY disorder of sex development of endocrine origin
MONDO:0019826 abnormal origin or aberrant course of coronary artery
MONDO:0017240 acrodysostosis with multiple hormone resistance
MONDO:0017422 adactyly of hand
MONDO:0019816 anomaly of the tricuspid subvalvular apparatus
MONDO:0020147 anophthalmia-microphthalmia syndrome
MONDO:0020286 aortic malformation
MONDO:0019822 arterial duct anomaly
MONDO:0020293 ascending aorta anomaly
MONDO:0019837 atrial appendage anomaly
MONDO:0020294 atrial defect and interatrial communication
MONDO:0020288 atrioventricular valve anomaly
MONDO:0017670 autosomal dominant diffuse mutilating palmoplantar keratoderma
MONDO:0020093 autosomal dominant isolated diffuse palmoplantar keratoderma
MONDO:0020096 autosomal recessive isolated diffuse palmoplantar keratoderma
MONDO:0016647 autosomal recessive Stickler syndrome
MONDO:0015334 branchial arch or oral-acral syndrome
MONDO:0044655 c12orf65-related combined oxidative phosphorylation defect
MONDO:0017104 central nervous system cystic malformation
MONDO:0015915 cerebellar malformation
MONDO:0016054 cerebral malformation
MONDO:0016170 chronic polyradiculoneuropathy
MONDO:0016034 cleft lip with or without cleft palate
MONDO:0017448 congenital absence/hypoplasia of fingers excluding thumb
MONDO:0017447 congenital absence/hypoplasia of thumb
MONDO:0019831 congenital anomaly of the coronary sinus
MONDO:0018185 congenital anomaly of the great veins
MONDO:0018771 congenital anomaly of ventricular septum
MONDO:0017428 congenital deformities of fingers
MONDO:0018292 congenital disorder of glycosylation-related bone disorder
MONDO:0015182 congenital enteropathy involving intestinal mucosa development
MONDO:0019054 congenital limb malformation
MONDO:0017710 congenital systemic veins anomaly
MONDO:0020375 coralliform cataract
MONDO:0020018 cranial malformation
MONDO:0020132 cranial nerve and nuclear aplasia
MONDO:0020145 developmental defect of the eye
MONDO:0020019 digestive tract malformation
MONDO:0020392 discrete fixed membranous subaortic stenosis
MONDO:0019619 duplication of the esophagus
MONDO:0018454 dysostosis of genetic origin
MONDO:0800075 dysostosis with predominant vertebral with and without costal involvement
MONDO:0019513 esophageal malformation
MONDO:0015385 external auditory canal aplasia/hypoplasia
MONDO:0018758 familial patent arterial duct
MONDO:0018262 fetal anticonvulsant syndrome
MONDO:0019998 gastroduodenal malformation
MONDO:0017114 global cerebellar malformation
MONDO:0020284 heart position anomaly
MONDO:0957024 hereditary 46,XX disorder of sex development
MONDO:0957025 hereditary 46,XY disorder of sex development
MONDO:0017131 hereditary cardiac anomaly
MONDO:0015961 hereditary head and neck malformation
MONDO:0018562 hereditary otorhinolaryngological malformation
MONDO:0957009 hereditary posterior fossa malformation
MONDO:0018187 hereditary syndromic Pierre Robin syndrome
MONDO:0016229 hereditary vascular anomaly
MONDO:0015497 hypoglossia/aglossia
MONDO:0017049 hypomyelination neuropathy-arthrogryposis syndrome
MONDO:0017420 intercalary limb defects
MONDO:0019999 intestinal malformation
MONDO:0018916 isolated anorectal malformation
MONDO:0018114 isolated brachycephaly
MONDO:0015337 isolated craniosynostosis
MONDO:0017667 isolated diffuse palmoplantar keratoderma
MONDO:0017673 isolated focal palmoplantar keratoderma
MONDO:0016805 isolated oxidative phosphorylation complex disorder
MONDO:0018113 isolated plagiocephaly
MONDO:0016518 isolated punctate palmoplantar keratoderma
MONDO:0018112 isolated scaphocephaly
MONDO:0017429 joint formation defects
MONDO:0036042 KAT6B-related multiple congenital anomalies syndrome
MONDO:0034024 kyphoscoliotic Ehlers-Danlos syndrome
MONDO:0015504 larynx anomaly
MONDO:0015418 lateral facial cleft
MONDO:0016815 Leigh syndrome with leukodystrophy
MONDO:0016816 Leigh syndrome with nephrotic syndrome
MONDO:0018731 lethal multiple congenital anomalies/dysmorphic syndrome
MONDO:0020146 major induction processes eye anomaly
MONDO:0020131 malformation of the cerebellar hemispheres
MONDO:0020130 malformation of the cerebellar vermis
MONDO:0017676 marginal papular palmoplantar keratoderma
MONDO:0016678 maternal disease-related embryofetopathy
MONDO:0016794 maternally-inherited mitochondrial myopathy
MONDO:0015412 median facial cleft
MONDO:0017950 microcephalic primordial dwarfism
MONDO:0017090 midline cerebral malformation
MONDO:0019758 midline interhemispheric variant of holoprosencephaly
MONDO:0016797 multiple mitochondrial DNA deletion syndrome
MONDO:0017059 neural tube closure defect
MONDO:0015219 non-syndromic central nervous system malformation
MONDO:0034671 non-syndromic complex polydactyly
MONDO:0017430 non-syndromic congenital joint dislocations
MONDO:0015217 non-syndromic developmental defect of the eye
MONDO:0015207 non-syndromic esophageal malformation
MONDO:0015209 non-syndromic gastroduodenal malformation
MONDO:0015211 non-syndromic intestinal malformation
MONDO:0015227 non-syndromic limb malformation
MONDO:0017431 non-syndromic limb overgrowth
MONDO:0019713 non-syndromic limb reduction defect
MONDO:0019714 non-syndromic polydactyly, syndactyly and/or hyperphalangy
MONDO:0034670 non-syndromic postaxial polydactyly
MONDO:0034669 non-syndromic preaxial polydactyly
MONDO:0019720 non-syndromic renal or urinary tract malformation
MONDO:0015221 non-syndromic respiratory or mediastinal malformation
MONDO:0017421 non-syndromic terminal limb defects
MONDO:0015619 non-syndromic urogenital tract malformation
MONDO:0015932 non-syndromic urogenital tract malformation of female
MONDO:0015933 non-syndromic urogenital tract malformation of male
MONDO:0015829 non-syndromic uterovaginal malformation
MONDO:0015213 non-syndromic visceral malformation
MONDO:0015503 nose and cavum anomaly
MONDO:0015415 oblique facial cleft
MONDO:0015482 otomandibular dysplasia
MONDO:0015330 overgrowth/obesity syndrome
MONDO:0015499 paralytic facial malformation
MONDO:0015478 paramedian facial cleft
MONDO:0019712 patellar dysostosis
MONDO:0035162 PIK3CA-related overgrowth syndrome
MONDO:0020133 posterior fossa malformation
MONDO:0016589 progressive cerebello-cerebral atrophy
MONDO:0020287 pulmonary artery or pulmonary branch anomaly
MONDO:0018580 PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome
MONDO:0020023 respiratory or mediastinal malformation
MONDO:0016355 semilobar holoprosencephaly
MONDO:0017218 septopreoptic holoprosencephaly
MONDO:0017423 split hand or/and split foot malformation
MONDO:0020148 syndromic aniridia
MONDO:0015246 syndromic anorectal malformation
MONDO:0034661 syndromic biliary atresia
MONDO:0015338 syndromic craniosynostosis
MONDO:0015208 syndromic esophageal malformation
MONDO:0015210 syndromic gastroduodenal malformation
MONDO:0016565 syndromic genetic obesity
MONDO:0015212 syndromic intestinal malformation
MONDO:0015222 syndromic respiratory or mediastinal malformation
MONDO:0015620 syndromic urogenital tract malformation
MONDO:0015214 syndromic visceral malformation
MONDO:0015323 teratogenic Pierre Robin syndrome
MONDO:0015505 tracheal anomaly
MONDO:0020285 transposition of the great arteries and conotruncal cardiac anomaly
MONDO:0015837 Unicervical bicornuate uterus
MONDO:0016803 unspecified inborn mitochondrial disorder
MONDO:0020020 visceral malformation of the liver, biliary tract, pancreas or spleen
MONDO:0018222 X-linked intellectual disability due to GRIA3 anomalies
@sabrinatoro sabrinatoro self-assigned this Nov 16, 2023
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sabrinatoro commented Nov 16, 2023 •
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The spreadsheet to review is here

@sabrinatoro sabrinatoro changed the title Mass Obsoletion: focus on branch 'disorder of development or morphogenesis' (MONDO:0021147) (MONDO:0002081) Mass Obsoletion: focus on branch 'disorder of development or morphogenesis' (MONDO:0021147) Nov 16, 2023
@sabrinatoro
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This branch is currently messy, and further review is necessary.
The terms seem to be used inconsistently:

'disorder of development or morphogenesis' (MONDO:0021147)
Any disease or disorder that disrupts the process development of an anatomical structure. Can be due to genetic or environmental causes. Typically happens during embryogenesis, but also includes post-embryonic development.
According to this definition, "any" abnormality that is congenital or found in newborns should be in this class. However, these abnormalities should be focused on an anatomical structure.
I found in this branch several diseases for which the etiology is an abnormal anatomical structure. Should these diseases be part of this branch? (that would probably be most diseases)

'developmental defect during embryogenesis'
A disease that has its basis in the disruption of embryonic morphogenesis.
This definition is very confusing. Does it mean "embryonic" or "in the fetus" or "before birth"? The diseases under this class include all of these. Therefore it brings the question "what is the difference between this class and the one above"?

In summary, this branch absolutely needs to be reviewed independently of the mass obsoletion. When reviewing the spreadsheet I:

  • kept the diseases that were clearly "morphological anomalies" that happened during gestation (e.g. dysplasia, aplasia, clefs,...)
  • I didn't keep any syndromes unless the phenotypic features were fully or mostly "morphological phenotypes".
    Note: my thought process evolved as I was going through the spreadsheet, so there might be inconsistencies.

@katiermullen
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@sabrinatoro nice work! I recommended a few more terms stay in the branch on the basis that they can be considered abnormalities in anatomical structures that arose during development or morphogenesis. Feel free to take them or leave them. I agree that future review is needed to improve the consistency of the terms in this branch.

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Thank you @katiermullen !

sabrinatoro added a commit that referenced this issue Nov 20, 2023
@sabrinatoro
mass obsoletion: focus on 'disorder of development or morphogenesis' …
bea94e4 
…(MONDO:0021147)

Addresses #6876
@sabrinatoro sabrinatoro mentioned this issue Nov 20, 2023
Merged
sabrinatoro added a commit that referenced this issue Nov 20, 2023
@sabrinatoro
mass obsoletion: focus on 'disorder of development or morphogenesis' … (
d5cb748 
#6893)

* mass obsoletion: focus on 'disorder of development or morphogenesis' (MONDO:0021147)

Addresses #6876

* term obsoletion

terms obsoleted:
MONDO:0015334
MONDO:0017428
MONDO:0020018
MONDO:0020019
MONDO:0018262
MONDO:0019998
MONDO:0017131
MONDO:0015961
MONDO:0019999
MONDO:0018916
MONDO:0018731
MONDO:0016678
MONDO:0017430
MONDO:0015209
MONDO:0015211
MONDO:0015227
MONDO:0017431
MONDO:0015221
MONDO:0015619
MONDO:0015213
MONDO:0015330
MONDO:0035162
MONDO:0016589
MONDO:0020023
MONDO:0015214
MONDO:0020020

* Added GH issue to already obsoleted terms

terms giving the GH issue:
MONDO:0019054
MONDO:0017961
MONDO:0020039
MONDO:0017963
MONDO:0017964
MONDO:0019593
MONDO:0017962
MONDO:0019608
MONDO:0017966
MONDO:0019597
MONDO:0017974
MONDO:0017969
MONDO:0019826
MONDO:0017240
MONDO:0017422
MONDO:0019816
MONDO:0020147
MONDO:0020286
MONDO:0019822
MONDO:0020293
MONDO:0019837
MONDO:0020294
MONDO:0020288
MONDO:0017670
MONDO:0020093
MONDO:0020096
MONDO:0016647
MONDO:0044655
MONDO:0017104
MONDO:0015915
MONDO:0016054
MONDO:0016170
MONDO:0016034
MONDO:0017448
MONDO:0017447
MONDO:0019831
MONDO:0018185
MONDO:0018771
MONDO:0018292
MONDO:0015182
MONDO:0017710
MONDO:0020375
MONDO:0020132
MONDO:0020145
MONDO:0020392
MONDO:0019619
MONDO:0018454
MONDO:0800075
MONDO:0019513
MONDO:0015385
MONDO:0018758
MONDO:0017114
MONDO:0020284
MONDO:0957024
MONDO:0957025
MONDO:0018562
MONDO:0957009
MONDO:0018187
MONDO:0016229
MONDO:0015497
MONDO:0017049
MONDO:0017420
MONDO:0018114
MONDO:0017667
MONDO:0017673
MONDO:0016805
MONDO:0018113
MONDO:0016518
MONDO:0018112
MONDO:0017429
MONDO:0036042
MONDO:0034024
MONDO:0015504
MONDO:0015418
MONDO:0016815
MONDO:0016816
MONDO:0020146
MONDO:0020131
MONDO:0020130
MONDO:0017676
MONDO:0016794
MONDO:0015412
MONDO:0017950
MONDO:0017090
MONDO:0019758
MONDO:0016797
MONDO:0017059
MONDO:0015219
MONDO:0034671
MONDO:0015217
MONDO:0015207
MONDO:0019714
MONDO:0034670
MONDO:0034669
MONDO:0019720
MONDO:0017421
MONDO:0015932
MONDO:0015933
MONDO:0015829
MONDO:0015503
MONDO:0015415
MONDO:0015482
MONDO:0015499
MONDO:0015478
MONDO:0019712
MONDO:0020133
MONDO:0020287
MONDO:0018580
MONDO:0016355
MONDO:0017218
MONDO:0017423
MONDO:0020148
MONDO:0015246
MONDO:0034661
MONDO:0015208
MONDO:0015210
MONDO:0016565
MONDO:0015212
MONDO:0015222
MONDO:0015620
MONDO:0015323
MONDO:0015505
MONDO:0020285
MONDO:0015837
MONDO:0016803
MONDO:0018222
@sabrinatoro
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There are some comments from the community that should be reviewed, but this is future work. This issue can be closed for now.

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