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Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Mass Obsoletion: focus on branch 'hereditary disease' (MONDO:0003847) #6877

Closed sabrinatoro closed 5 months ago

sabrinatoro commented 9 months ago

branch: hereditary disease' (MONDO:0003847)

Terms to obsolete:

CURIE obsoletion candidate label
MONDO:0019597 46,XY disorder of sex development due to isolated 17,20-lyase deficiency
MONDO:0017240 acrodysostosis with multiple hormone resistance
MONDO:0017422 adactyly of hand
MONDO:0018239 aggrecan-related bone disorder
MONDO:0020343 alpha-crystallinopathy
MONDO:0016072 anomaly of puberty or/and menstrual cycle of genetic origin
MONDO:0100343 antenatal Bartter syndrome
MONDO:0017241 AP4-related intellectual disability and spastic paraplegia
MONDO:0015921 ARX-related epileptic encephalopathy
MONDO:0016980 ATR-X-related syndrome
MONDO:0017670 autosomal dominant diffuse mutilating palmoplantar keratoderma
MONDO:0015360 autosomal dominant hereditary axonal motor and sensory neuropathy
MONDO:0015359 autosomal dominant hereditary demyelinating motor and sensory neuropathy
MONDO:0015365 autosomal dominant hereditary sensory and autonomic neuropathy
MONDO:0020093 autosomal dominant isolated diffuse palmoplantar keratoderma
MONDO:0016224 autosomal dominant proximal spinal muscular atrophy
MONDO:0015088 autosomal dominant pure spastic paraplegia
MONDO:0016599 autosomal dominant secondary polycythemia
MONDO:0017270 autosomal ichthyosis syndrome
MONDO:0015089 autosomal recessive complex spastic paraplegia
MONDO:0016109 autosomal recessive distal myopathy
MONDO:0008406 autosomal recessive Emery-Dreifuss muscular dystrophy
MONDO:0015361 autosomal recessive hereditary demyelinating motor and sensory neuropathy
MONDO:0015366 autosomal recessive hereditary sensory and autonomic neuropathy
MONDO:0020096 autosomal recessive isolated diffuse palmoplantar keratoderma
MONDO:0016536 autosomal recessive lymphoproliferative disease
MONDO:0014753 autosomal recessive optic atrophy
MONDO:0015090 autosomal recessive pure spastic paraplegia
MONDO:0016647 autosomal recessive Stickler syndrome
MONDO:0015679 autosomal thrombocytopenia with normal platelets
MONDO:0018384 avascular necrosis of genetic origin
MONDO:0018775 axonal hereditary motor and sensory neuropathy
MONDO:0015586 benign familial mesial temporal lobe epilepsy
MONDO:0019138 bleeding diathesis due to a collagen receptor defect
MONDO:0044655 c12orf65-related combined oxidative phosphorylation defect
MONDO:0019213 cerebral organic aciduria
MONDO:0017448 congenital absence/hypoplasia of fingers excluding thumb
MONDO:0017447 congenital absence/hypoplasia of thumb
MONDO:0018888 congenital cornea plana
MONDO:0018292 congenital disorder of glycosylation-related bone disorder
MONDO:0018277 congenital muscular dystrophy with cerebellar involvement
MONDO:0018279 congenital muscular dystrophy without intellectual disability
MONDO:0018144 congenital myasthenic syndromes with glycosylation defect
MONDO:0015765 congenital myopathy with cores
MONDO:0018701 congenital nemaline myopathy
MONDO:0020375 coralliform cataract
MONDO:0017922 deafness-onychodystrophy syndrome
MONDO:0020118 dense granule disease
MONDO:0018318 disorder of asparagine metabolism
MONDO:0018579 disorder of ketone body transport
MONDO:0017709 disorder of lipid absorption and transport
MONDO:0017745 disorder of O-mannosylglycan synthesis
MONDO:0017743 disorder of O-N-acetylgalactosaminylglycan synthesis
MONDO:0017744 disorder of O-xylosyl/N-acetylgalactosaminylglycan synthesis
MONDO:0017742 disorder of O-xylosylglycan synthesis
MONDO:0017760 disorder of other vitamins and cofactors metabolism and transport
MONDO:0017756 disorder of pterin metabolism
MONDO:0016579 dominant hypophosphatemia with nephrolithiasis or osteoporosis
MONDO:0016899 Duchenne and Becker muscular dystrophy
MONDO:0018454 dysostosis of genetic origin
MONDO:0800094 dysostosis with brachydactyly with extraskeletal manifestations
MONDO:0800093 dysostosis with brachydactyly without extraskeletal manifestations
MONDO:0800085 dysostosis with predominant craniofacial involvement
MONDO:0800075 dysostosis with predominant vertebral with and without costal involvement
MONDO:0800090 ectrodactyly with and without other manifestations
MONDO:0020197 EEC syndrome and related syndrome
MONDO:0036192 EN1-related dorsoventral syndrome
MONDO:0035685 epidermolysis bullosa simplex with extracutaneous involvement
MONDO:0035684 epidermolysis bullosa simplex without extracutaneous involvement
MONDO:0015385 external auditory canal aplasia/hypoplasia
MONDO:0015470 familial isolated dilated cardiomyopathy
MONDO:0019150 familial isolated restrictive cardiomyopathy
MONDO:0013742 familial mesial temporal lobe epilepsy with febrile seizures
MONDO:0957024 hereditary 46,XX disorder of sex development
MONDO:0957025 hereditary 46,XY disorder of sex development
MONDO:0021034 hereditary alopecia
MONDO:0033947 hereditary angioedema with normal C1Inh
MONDO:0017132 hereditary ATTR amyloidosis
MONDO:0015509 hereditary biliary tract disease
MONDO:0800092 hereditary inflammatory or rheumatoid-like osteoarthropathy
MONDO:0018188 hereditary intestinal polyposis
MONDO:0018340 hereditary isolated aplastic anemia
MONDO:0957001 hereditary mixed dermis disorder
MONDO:0018562 hereditary otorhinolaryngological malformation
MONDO:0015508 hereditary parenchymatous liver disease
MONDO:0957009 hereditary posterior fossa malformation
MONDO:0017057 hereditary thrombocytopenia with normal platelets
MONDO:0016229 hereditary vascular anomaly
MONDO:0015975 hyper-IgM syndrome with susceptibility to opportunistic infections
MONDO:0015976 hyper-IgM syndrome without susceptibility to opportunistic infections
MONDO:0018779 hypercontractile muscle stiffness syndrome
MONDO:0017049 hypomyelination neuropathy-arthrogryposis syndrome
MONDO:0019505 hypomyelination-hypogonadotropic hypogonadism-hypodontia syndrome
MONDO:0016352 idiopathic inherited hypercalciuria
MONDO:0015132 immunodeficiency predominantly affecting antibody production
MONDO:0019224 inborn disorder of gamma-aminobutyric acid metabolism
MONDO:0019227 inborn disorder of glycerol metabolism
MONDO:0017129 inherited cardiac tumor
MONDO:0018538 inherited digestive cancer-predisposing syndrome
MONDO:0017128 inherited digestive tract tumor
MONDO:0035645 inherited gynecological cancer-predisposing syndrome
MONDO:0017263 inherited ichthyosis syndromic form
MONDO:0025511 inherited neuroendocrine tumor
MONDO:0017262 inherited non-syndromic ichthyosis
MONDO:0017234 inherited prion disease
MONDO:0017891 inherited renal cancer-predisposing syndrome
MONDO:0015950 inherited skin tumor
MONDO:0017127 inherited soft tissue tumor
MONDO:0020238 inherited vitreous-retinal disease
MONDO:0017420 intercalary limb defects
MONDO:0018114 isolated brachycephaly
MONDO:0018796 isolated constitutional thrombocytopenia
MONDO:0015337 isolated craniosynostosis
MONDO:0017667 isolated diffuse palmoplantar keratoderma
MONDO:0017673 isolated focal palmoplantar keratoderma
MONDO:0016361 isolated hereditary giant platelet disorder
MONDO:0035002 isolated inherited retinal disorder
MONDO:0016520 isolated Klippel-Feil syndrome
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:0034024 kyphoscoliotic Ehlers-Danlos syndrome
MONDO:0016815 Leigh syndrome with leukodystrophy
MONDO:0016816 Leigh syndrome with nephrotic syndrome
MONDO:0019718 lethal chondrodysplasia
MONDO:0017676 marginal papular palmoplantar keratoderma
MONDO:0016794 maternally-inherited mitochondrial myopathy
MONDO:0019697 mesomelic and rhizo-mesomelic dysplasia
MONDO:0017950 microcephalic primordial dwarfism
MONDO:0018575 microcephalic primordial dwarfism-insulin resistance syndrome
MONDO:0019758 midline interhemispheric variant of holoprosencephaly
MONDO:0019692 multiple epiphyseal dysplasia and pseudoachondroplasia
MONDO:0019693 multiple metaphyseal dysplasia
MONDO:0016797 multiple mitochondrial DNA deletion syndrome
MONDO:0022409 nephropathy-associated ciliopathy
MONDO:0034671 non-syndromic complex polydactyly
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:0017421 non-syndromic terminal limb defects
MONDO:0020275 oculocutaneous or ocular albinism
MONDO:0018385 osteochondrosis of genetic origin
MONDO:0020506 ovarioleukodystrophy
MONDO:0800091 overgrowth or tall stature syndrome with skeletal involvement
MONDO:0020178 palpebral lentiginosis
MONDO:0019712 patellar dysostosis
MONDO:0019689 perlecan-related bone disorder
MONDO:0018329 persistent combined dystonia
MONDO:0020345 presynaptic congenital myasthenic syndrome
MONDO:0800089 primary bone dysplasia with disorganized development of skeletal components
MONDO:0800084 primary bone dysplasia with increased bone density
MONDO:0800086 primary bone dysplasia with multiple joint dislocations
MONDO:0015485 primary hereditary glaucoma
MONDO:0015823 primary immunodeficiency due to a defect in adaptive immunity
MONDO:0015135 primary immunodeficiency due to a genetic defect in innate immunity
MONDO:0020524 primary parathyroid hyperplasia
MONDO:0017828 primary renal tubular acidosis
MONDO:0017914 pure or complex autosomal dominant spastic paraplegia
MONDO:0017915 pure or complex autosomal recessive spastic paraplegia
MONDO:0017916 pure or complex X-linked spastic paraplegia
MONDO:0016157 qualitative or quantitative defects of fukutin
MONDO:0016183 qualitative or quantitative defects of protein glycosyltransferase-like
MONDO:0016182 qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase
MONDO:0015133 quantitative and/or qualitative congenital phagocyte defect
MONDO:0034217 resistance to thyroid hormone due to a mutation in thyroid hormone receptor beta
MONDO:0022407 retinal ciliopathy due to mutation in Bardet-Biedl gene
MONDO:0022405 retinal ciliopathy due to mutation in nephronophthisis gene
MONDO:0022397 retinal ciliopathy due to mutation in the retinitis pigmentosa-1 gene
MONDO:0022399 retinal ciliopathy due to mutation in the RPGR gene
MONDO:0022400 retinal ciliopathy due to mutation in the RPGRIP gene
MONDO:0022404 retinal ciliopathy due to mutation in Usher gene
MONDO:0020216 secondary dysgenetic glaucoma
MONDO:0035075 secondary early-onset glaucoma of genetic origin
MONDO:0016355 semilobar holoprosencephaly
MONDO:0017218 septopreoptic holoprosencephaly
MONDO:0017146 sickle cell disease and related diseases
MONDO:0016667 sickle cell disease associated with an other hemoglobin anomaly
MONDO:0019699 slender bone dysplasia
MONDO:0017629 sodium channelopathy-related small fiber neuropathy
MONDO:0018550 spastic paraplegia-optic atrophy-neuropathy and spastic paraplegia-optic atrophy-neuropathy-related disorder
MONDO:0019688 sulfation-related bone disorder
MONDO:0020346 synaptic congenital myasthenic syndrome
MONDO:0800095 syndrome with synostosis or other joint formation defect
MONDO:0020148 syndromic aniridia
MONDO:0015338 syndromic craniosynostosis
MONDO:0016565 syndromic genetic obesity
MONDO:0020211 syndromic keratoconus
MONDO:0020240 syndromic retinitis pigmentosa
MONDO:0034954 syndromic vitreoretinopathy
MONDO:0019176 trichorhinophalangeal syndrome type I or III
MONDO:0018240 TRPV4-related bone disorder
MONDO:0800087 type 11 collagen-related bone disorder
MONDO:0016803 unspecified inborn mitochondrial disorder
MONDO:0020339 X-linked complex spastic paraplegia
MONDO:0018451 X-linked distal hereditary motor neuropathy
MONDO:0018222 X-linked intellectual disability due to GRIA3 anomalies
MONDO:0017912 X-linked pure spastic paraplegia
katiermullen commented 9 months ago

@sabrinatoro this branch is ready for review.

Please note my review process:

  1. Terms with OMIM xref's were kept in branch thanks @matentzn for helping with this!
  2. First, I assigned the terms with OMIM xrefs to the most specific parent as possible, then I realized this would take a long time, so I assigned these terms to the parent 'Hereditary Disease' MONDO:0003847.
  3. For the terms that did not have an OMIM xref, if the term or definition contained language to suggest that they were hereditary, e.g. genetic disease, inherited, hereditary, autosomal dominant or autosomal recessive, I assigned them the parent 'Hereditary Disease' MONDO:0003847.
  4. For the terms that did not have an OMIM xref and no terminology to suggest they were hereditary, I recommended that they leave the branch.
sabrinatoro commented 9 months ago

@katiermullen, Awesome job! Please review my comments.

In addition to your review process, and assuming we can trust the original classification (e.g all children of "MONDO:0016229 - TO_BE_OBSOLETED->hereditary vascular anomaly" are indeed hereditary), I suggest that we keep all the children of terms to be obsoleted in the branch when these terms to be obsoleted contain language like "inherited, autosomal dominant, hereditary".

katiermullen commented 9 months ago

@sabrinatoro thank you for the review! I agree with your comments and made the suggested changes.

sabrinatoro commented 9 months ago

Thank you @katiermullen. I will create a PR first thing on Monday.

sabrinatoro commented 5 months ago

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