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

[sabrinatoro]

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]

The spreadsheet to review is here

[sabrinatoro]

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]

@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.

[sabrinatoro]

Thank you @katiermullen !

[sabrinatoro]

There are some comments from the community that should be reviewed, but this is future work. This issue can be closed for now.