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Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Update the mondo_release_diff.md #3923

Closed sabrinatoro closed 2 years ago

sabrinatoro commented 2 years ago

1) add a term label column for the following table/sections:

2) Update the table for "Number of terms who were previously candidate for obsoletion and are now not anymore"

matentzn commented 2 years ago

Apart from please update the column titles to "Previous release definition" and "New release definition" which would be a bit hacky (is this important to you?) i think its done.

I also tweaked some the tables to remove columns which may not be so useful to the user, like the "obsolete" status for new terms. This is how this all would look:

Overview:

New terms

Mondo ID Label Definition
MONDO:0023670 Bardet-Biedl syndrome 20
MONDO:0030258 pontocerebellar hypoplasia, type 14
MONDO:0030259 pontocerebellar hypoplasia, type 15
MONDO:0030260 pontocerebellar hypoplasia, type 1E
MONDO:0030261 pontocerebellar hypoplasia, type 1F
MONDO:0030263 leukodystrophy, hypomyelinating, 21
MONDO:0030266 immunodeficiency 80 with or without congenital cardiomyopathy
MONDO:0030268 developmental and epileptic encephalopathy 6B
MONDO:0030270 lymphatic malformation 9
MONDO:0030281 arthrogryposis multiplex congenita 6
MONDO:0030293 angioedema, hereditary, 5
MONDO:0030294 megacystis-microcolon-intestinal hypoperistalsis syndrome 3
MONDO:0030296 megacystis-microcolon-intestinal hypoperistalsis syndrome 4
MONDO:0030298 angioedema, hereditary, 8
MONDO:0030300 cardiomyopathy, dilated, 2D
MONDO:0030302 immunodeficiency 81
MONDO:0030307 spermatogenic failure 55
MONDO:0030308 immunodeficiency 82 with systemic inflammation
MONDO:0030309 Leber hereditary optic neuropathy, autosomal recessive
MONDO:0030311 combined oxidative phosphorylation deficiency 52
MONDO:0030312 spinocerebellar ataxia, autosomal recessive 29
MONDO:0030313 encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 10
MONDO:0030314 inflammatory bowel disease (infantile ulcerative colitis) 31, autosomal recessive
MONDO:0030316 lymphatic malformation 11
MONDO:0030317 cardiomyopathy, familial hypertrophic, 28
MONDO:0030318 spinocerebellar ataxia, autosomal recessive 30
MONDO:0030323 spinocerebellar ataxia, autosomal recessive 31
MONDO:0030326 mitochondrial dna depletion syndrome 16B (neuroophthalmic type)
MONDO:0030329 megacystis-microcolon-intestinal hypoperistalsis syndrome 5
MONDO:0030330 cardiomyopathy, familial restrictive, 6
MONDO:0030331 Ritscher-Schinzel syndrome 4
MONDO:0030332 ciliary dyskinesia, primary, 46
MONDO:0030333 immunodeficiency 84
MONDO:0030334 encephalitis, acute, infection (viral)-induced, susceptibility to, 11
MONDO:0030335 diarrhea 12, with microvillus atrophy
MONDO:0030337 cutis laxa, autosomal recessive, type 2E
MONDO:0030338 anencephaly 2
MONDO:0030339 microcephaly 28, primary, autosomal recessive
MONDO:0030341 myasthenic syndrome, congenital, 7B, presynaptic, autosomal recessive
MONDO:0030346 ciliary dyskinesia, primary, 47, and lissencephaly
MONDO:0030353 Joubert syndrome 38
MONDO:0030354 facioscapulohumeral muscular dystrophy 3, digenic
MONDO:0030355 facioscapulohumeral muscular dystrophy 4, digenic
MONDO:0030356 short-rib thoracic dysplasia 21 without polydactyly
MONDO:0030360 cholestasis, progressive familial intrahepatic, 6
MONDO:0030361 Aicardi-Goutieres syndrome 8
MONDO:0030362 Aicardi-Goutieres syndrome 9
MONDO:0030366 cardiomyopathy, dilated, 2E
MONDO:0100365 mucopolysaccharidosis or mucopolysaccharidosis-like disorder Any disease that presents as a mucopolysaccharidosis or mucopolysaccharidosis-like disorder.
MONDO:0100366 occupational disorder Any disorder that is realized in response to an exposure to occupation.
MONDO:0100367 port-wine nevi-mega cisterna magna-hydrocephalus syndrome A rare developmental defect during embryogenesis syndrome characterized by a glabellar capillary malformation, congenital communicating hydrocephalus, and posterior fossa brain abnormalities, including Dandy-Walker malformation, cerebellar vermis agenesis, and mega cisterna magna. Seizures are occasionally associated. There have been no further descriptions in the literature since 1979.
MONDO:0100429 intrahepatic cholestasis of pregnancy A cholestatic disorder characterized by (i) pruritus with onset in the second or third trimester of pregnancy, (ii) elevated serum aminotransferases and bile acid levels, and (iii) spontaneous relief of signs and symptoms within two to three weeks after delivery.
MONDO:0600030 B-cell acute lymphoblastic leukemia with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1) A B-cell acute leukemia characterized by the presence of lymphoblasts that carry a translocation between the E2A gene on chromosome 19 and the PBX1 gene on chromosome 1. It occurs in children and less often in adults.
MONDO:8000000 infectious discitis An infection of the intervertebral disc space.
MONDO:8000001 staphylococcus discitis Discitis caused by infection with Staphylococcus.
MONDO:8000002 escherichia coli discitis Discitis caused by infection with Escherichia coli.
MONDO:8000003 streptococcus pneumoniae discitis Discitis caused by infection with Streptococcus pneumoniae.
MONDO:8000004 salmonella discitis Discitis caused by infection with Salmonella.
MONDO:8000005 fungal discitis Discitis caused by infection with fungi.

Changed terms

Changed label

Mondo ID Label Previous release New release
MONDO:0007665 glaucoma 1, open angle, E primary open angle glaucoma glaucoma 1, open angle, E
MONDO:0019313 lymphatic malformation hereditary lymphedema lymphatic malformation
MONDO:0007883 periodic fever, immunodeficiency, and thrombocytopenia syndrome lazy leukocyte syndrome periodic fever, immunodeficiency, and thrombocytopenia syndrome
MONDO:0007919 lymphatic malformation 1 lymphedema, hereditary, 1A lymphatic malformation 1
MONDO:0007920 lymphatic malformation 5 Meige disease lymphatic malformation 5
MONDO:0007964 melanoma, cutaneous malignant, susceptibility to, 2 dysplastic nevus syndrome melanoma, cutaneous malignant, susceptibility to, 2
MONDO:0008233 pheochromocytoma phaeochromocytoma pheochromocytoma
MONDO:0010118 inherited threoninemia Threoninemia inherited threoninemia
MONDO:0010301 obsolete thrombocythemia, X-linked thrombocythemia, X-linked obsolete thrombocythemia, X-linked
MONDO:0011293 obsolete Homocysteinemia Homocysteinemia obsolete Homocysteinemia
MONDO:0012317 visceral neuropathy, familial, 3, autosomal dominant visceral neuropathy, familial, autosomal dominant visceral neuropathy, familial, 3, autosomal dominant
MONDO:0012765 lymphatic malformation 2 lymphedema, hereditary, 1B lymphatic malformation 2
MONDO:0012842 melanoma, cutaneous malignant, susceptibility to, 7 CMM7 melanoma, cutaneous malignant, susceptibility to, 7
MONDO:0012892 bone fragility with contractures, arterial rupture, and deafness connective tissue disorder due to lysyl hydroxylase-3 deficiency bone fragility with contractures, arterial rupture, and deafness
MONDO:0013278 lymphatic malformation 3 lymphedema, hereditary, 1C lymphatic malformation 3
MONDO:0013759 melanoma, cutaneous malignant, susceptibility to, 8 MITF-related melanoma and renal cell carcinoma predisposition syndrome melanoma, cutaneous malignant, susceptibility to, 8
MONDO:0013995 cholestasis, intrahepatic, of pregnancy, 3 cholestasis, intrahepatic, of pregnancy 3 cholestasis, intrahepatic, of pregnancy, 3
MONDO:0014393 lymphatic malformation 4 lymphedema, hereditary, 1D lymphatic malformation 4
MONDO:0014797 lymphatic malformation 6 lymphedema, hereditary, type III lymphatic malformation 6
MONDO:0014926 Bardet-Biedl syndrome 22 Bardet-Biedl syndrome 20 Bardet-Biedl syndrome 22
MONDO:0015009 lymphatic malformation 7 hydrops fetalis, nonimmune, and/or atrial septal defect, susceptibility to lymphatic malformation 7
MONDO:0015318 obsolete Pierre Robin syndrome associated with collagen disease Pierre Robin syndrome associated with collagen disease obsolete Pierre Robin syndrome associated with collagen disease
MONDO:0015320 obsolete Pierre Robin syndrome associated with a chromosomal anomaly Pierre Robin syndrome associated with a chromosomal anomaly obsolete Pierre Robin syndrome associated with a chromosomal anomaly
MONDO:0015321 obsolete Pierre Robin syndrome associated with branchial archs anomalies Pierre Robin syndrome associated with branchial archs anomalies obsolete Pierre Robin syndrome associated with branchial archs anomalies
MONDO:0015322 obsolete Pierre Robin syndrome associated with bone disease Pierre Robin syndrome associated with bone disease obsolete Pierre Robin syndrome associated with bone disease
MONDO:0015543 obsolete hemophagocytic syndrome associated with an infection hemophagocytic syndrome associated with an infection obsolete hemophagocytic syndrome associated with an infection
MONDO:0015633 obsolete Bazex syndrome Bazex syndrome obsolete Bazex syndrome
MONDO:0015750 obsolete amelogenesis imperfecta-gingival hyperplasia syndrome amelogenesis imperfecta-gingival hyperplasia syndrome obsolete amelogenesis imperfecta-gingival hyperplasia syndrome
MONDO:0015938 obsolete systemic disease systemic disease obsolete systemic disease
MONDO:0016148 obsolete qualitative or quantitative defects of collagen 6 qualitative or quantitative defects of collagen 6 obsolete qualitative or quantitative defects of collagen 6
MONDO:0016329 obsolete familial syndrome associated with hypertrophic cardiomyopathy familial syndrome associated with hypertrophic cardiomyopathy obsolete familial syndrome associated with hypertrophic cardiomyopathy
MONDO:0017133 obsolete genetic systemic or rheumatologic disease genetic systemic or rheumatologic disease obsolete genetic systemic or rheumatologic disease
MONDO:0017274 obsolete autosomal ichthyosis syndrome with other associated signs autosomal ichthyosis syndrome with other associated signs obsolete autosomal ichthyosis syndrome with other associated signs
MONDO:0019687 obsolete type 11 collagen-related bone disorder type 11 collagen-related bone disorder obsolete type 11 collagen-related bone disorder
MONDO:0020012 obsolete systemic or rheumatic disease systemic or rheumatic disease obsolete systemic or rheumatic disease
MONDO:0020272 obsolete connective tissue disease with eye involvement connective tissue disease with eye involvement obsolete connective tissue disease with eye involvement
MONDO:0020277 obsolete ectodermal malformation syndrome associated with ocular features ectodermal malformation syndrome associated with ocular features obsolete ectodermal malformation syndrome associated with ocular features
MONDO:0020764 Brown-Pearce carcinoma carcinoma, Brown-Pearce Brown-Pearce carcinoma
MONDO:0035354 obsolete IgG4-related systemic disease IgG4-related systemic disease obsolete IgG4-related systemic disease
MONDO:0035363 obsolete IRF2BPL-related regressive neurodevelopmental disorder-dystonia-seizures syndrome IRF2BPL-related regressive neurodevelopmental disorder-dystonia-seizures syndrome obsolete IRF2BPL-related regressive neurodevelopmental disorder-dystonia-seizures syndrome
MONDO:0035369 obsolete MTHFS-related developmental delay-microcephaly-short stature-epilepsy syndrome MTHFS-related developmental delay-microcephaly-short stature-epilepsy syndrome obsolete MTHFS-related developmental delay-microcephaly-short stature-epilepsy syndrome
MONDO:0054844 pontocerebellar hypoplasia, type 1D pontocerebellar hypoplasia, type 1d pontocerebellar hypoplasia, type 1D
MONDO:0100027 obsolete febrile seizures plus, genetic epilepsy with febrile seizures plus febrile seizures plus, genetic epilepsy with febrile seizures plus obsolete febrile seizures plus, genetic epilepsy with febrile seizures plus

Changed definition

Mondo ID Label Previous release New release
MONDO:0005550 infectious disease A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact. A disorder directly resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact.
MONDO:0005990 tracheitis An inflammatory process affecting the wall of the trachea. A tracheal disease which involves bacterial infection of the trachea often caused by Staphylococcus aureus and streptococci that follows a recent viral upper respiratory infection. The symptoms include barking croup cough, loud squeaking noise while breathing, scratchy feeling in the throat, high fever, and production of large amounts of pus-filled secretions.
MONDO:0017279 young-onset Parkinson disease Young-onset Parkinson disease (YOPD) is a form of Parkinson disease (PD), characterized by an age of onset between 21-45 years, rigidity, painful cramps followed by tremor, bradykinesia, dystonia, gait complaints and falls, and other non-motor symptoms. A slow disease progression and a more pronounced response to dopaminergic therapy are also observed in most YOPD forms. A form of Parkinson disease (PD) characterized by an age of onset between 21-45 years, rigidity, painful cramps followed by tremor, bradykinesia, dystonia, gait complaints and falls, and other non-motor symptoms. A slow disease progression and a more pronounced response to dopaminergic therapy are also observed in most YOPD forms.
MONDO:0019724 secondary glomerular disease Secondary glomerular diseases are conditions with glomerular pathology in which an underlying cause can be established Secondary glomerular diseases are conditions with glomerular pathology in which an underlying cause can be established.
MONDO:0009410 Addison disease Addison disease (AD) is a chronic and rare endocrine disorder due to autoimmune destruction of the adrenal cortex and resulting in a glucocorticoid and mineralocorticoid deficiency. Properly speaking AD designates autoimmune adrenalitis, but it is a term commonly used to describe any form of chronic primary adrenal insufficiency (CPAI). A chronic and rare endocrine disorder due to autoimmune destruction of the adrenal cortex and resulting in a glucocorticoid and mineralocorticoid deficiency. Properly speaking AD designates autoimmune adrenalitis, but it is a term commonly used to describe any form of chronic primary adrenal insufficiency (CPAI).
MONDO:0007489 dysplasia epiphysealis hemimelica Dysplasia epiphysealis hemimelica (DEH), or Trevor's disease, is a rarecondition that most commonly affects the epiphysis (the end) of long bones in children.Early diagnosis and treatment are necessary to prevent jointdysfunction and deformity and may be surgical or non-surgical depending on the location and the symptoms. Due to the progressive nature of this disorder and the chance of worsening deformity, patients should be followed until skeletal maturity.Thecause ofdysplasia epiphysealis hemimelica is not known. Dysplasia epiphysealis hemimelica (DEH), or Trevor's disease, is a rare condition that most commonly affects the epiphysis (the end) of long bones in children. Early diagnosis and treatment are necessary to prevent joint dysfunction and deformity and may be surgical or non-surgical depending on the location and the symptoms. Due to the progressive nature of this disorder and the chance of worsening deformity, patients should be followed until skeletal maturity. The cause of dysplasia epiphysealis hemimelica is not known.
MONDO:0019313 lymphatic malformation Milroy disease is a frequent form of primary lymphedema characterized generally by painless, chronic lower-limb lymphedema found at birth or developing in the early neonatal period. Primary lymphedema is caused by anatomic or functional defects in the lymphatic system, resulting in chronic swelling of body parts and lymphatic-system malformation.
MONDO:0007920 lymphatic malformation 5 Meige disease is a frequent form of late-onset, primary lymphedema characterized by lower limb lymphedema typically developing during puberty. A frequent form of late-onset, primary lymphedema characterized by lower limb lymphedema typically developing during puberty.
MONDO:0008145 Ollier disease Enchondromatosis is a rare primary bone dysplasia disorder characterized by the development of multiple mainly unilateral or asymmetrically distributed enchondromas throughout the metaphyses of the long bones. A rare primary bone dysplasia disorder characterized by the development of multiple mainly unilateral or asymmetrically distributed enchondromas throughout the metaphyses of the long bones.
MONDO:0008156 autosomal dominant osteopetrosis 2 Albers-Schoenberg osteopetrosis is a sclerosing disorder of the skeleton characterized by increased bone density that classically displays the radiographic sign of ''sandwich vertebrae'' (dense bands of sclerosis parallel to the vertebral endplates). A sclerosing disorder of the skeleton characterized by increased bone density that classically displays the radiographic sign of ''sandwich vertebrae'' (dense bands of sclerosis parallel to the vertebral endplates).
MONDO:0008199 late-onset Parkinson disease A Parkinson disease that begins after around the age of 50.
MONDO:0018466 hereditary late onset Parkinson disease Hereditary late-onset Parkinson disease (LOPD) is a form of Parkinson disease (PD), characterized by an age of onset of more than 50 years, tremor at rest, gait complaints and falls, bradykinesia, rigidity and painful cramps. Patients usually present a low risk of developing non motor symptoms, dystonia, dyskinesia and levodopa-induced dyskinesia (LID). A form of Parkinson disease (PD) characterized by an age of onset of more than 50 years, tremor at rest, gait complaints and falls, bradykinesia, rigidity and painful cramps. Patients usually present a low risk of developing non motor symptoms, dystonia, dyskinesia and levodopa-induced dyskinesia (LID).
MONDO:0008771 amelogenesis imperfecta type 1G Amelogenesis imperfecta-nephrocalcinosis, also called enamel-renal syndrome, is an extremely rare syndrome which is characterized by hypoplastic amelogenesis imperfecta (hypoplastic dental enamel) and nephrocalcinosis (precipitation of calcium salts in renal tissue). Oral manifestations include yellow and misshaped teeth, delayed tooth eruption, and intrapulpal calcifications. Nephrocalcinosis is often asymptomatic but can progress during late childhood or early adulthood to impaired renal function (e.g. recurrent urinary infections and renal tubular acidosis), and rarely to end-stage renal failure. An extremely rare syndrome which is characterized by hypoplastic amelogenesis imperfecta (hypoplastic dental enamel) and nephrocalcinosis (precipitation of calcium salts in renal tissue). Oral manifestations include yellow and misshaped teeth, delayed tooth eruption, and intrapulpal calcifications. Nephrocalcinosis is often asymptomatic but can progress during late childhood or early adulthood to impaired renal function (e.g. recurrent urinary infections and renal tubular acidosis), and rarely to end-stage renal failure.
MONDO:0009303 anti-glomerular basement membrane disease Goodpasture syndrome is an autoimmune disease that affects the lungs and kidneys and is characterized by pulmonary alveolar hemorrhage (bleeding in the lungs) and a kidney disease known as glomerulonephritis. Some use the term 'Goodpasture syndrome' for the findings of glomerulonephritis and pulmonary hemorrhage and the term 'Goodpasture disease' for those patients with glomerulonephritis, pulmonary hemorrhage, and anti-GBM antibodies. Currently, the preferred term for both conditions is “ anti-GBM antibody disease ”. Circulating antibodies are directed against the collagen of the part of the kidney known as the glomerular basement membrane (GBM), resulting in acute or rapidly progressive glomerulonephritis. Antibodies also attack the collagen of the air sacs of the lung (alveoli) resulting in bleeding of the lung (pulmonary hemorrhage). Symptoms may include general body discomfort or pain, bleeding from the nose and/or blood in the urine, respiratory problems, anemia, chest pain, and kidney failure. Anti-GBM disease is thought to result from an environmental insult (smoking, infections, exposure to certain drugs) in a person with genetic susceptibility, such as a specific human leukocyte antigen (HLA) type. Diagnosis is confirmed with the presence of anti-GBM antibody in the blood or in the kidney. The treatment of choice is plasmapheresis in conjunction with prednisone and cyclophosphamide. An autoimmune disease that affects the lungs and kidneys and is characterized by pulmonary alveolar hemorrhage (bleeding in the lungs) and a kidney disease known as glomerulonephritis. Some use the term 'Goodpasture syndrome' for the findings of glomerulonephritis and pulmonary hemorrhage and the term 'Goodpasture disease' for those patients with glomerulonephritis, pulmonary hemorrhage, and anti-GBM antibodies. Currently, the preferred term for both conditions is “ anti-GBM antibody disease ”. Circulating antibodies are directed against the collagen of the part of the kidney known as the glomerular basement membrane (GBM), resulting in acute or rapidly progressive glomerulonephritis. Antibodies also attack the collagen of the air sacs of the lung (alveoli) resulting in bleeding of the lung (pulmonary hemorrhage). Symptoms may include general body discomfort or pain, bleeding from the nose and/or blood in the urine, respiratory problems, anemia, chest pain, and kidney failure. Anti-GBM disease is thought to result from an environmental insult (smoking, infections, exposure to certain drugs) in a person with genetic susceptibility, such as a specific human leukocyte antigen (HLA) type. Diagnosis is confirmed with the presence of anti-GBM antibody in the blood or in the kidney. The treatment of choice is plasmapheresis in conjunction with prednisone and cyclophosphamide.
MONDO:0009774 cloacal exstrophy Cloacal exstrophy (EC) is a major birth defect representing the severe end of the spectrum of the exstrophy-epispadias complex (EEC) characterized by omphalocele, exstrophy, imperforate anus and spinal defects (also referred to as the OEIS complex), often associated with other malformations. A major birth defect representing the severe end of the spectrum of the exstrophy-epispadias complex (EEC) characterized by omphalocele, exstrophy, imperforate anus and spinal defects (also referred to as the OEIS complex), often associated with other malformations.
MONDO:0017919 bladder exstrophy-epispadias-cloacal exstrophy complex Exstrophy-Epispadias Complex (EEC) represents a spectrum of genitourinary malformations ranging in severity from epispadias (E) and classical bladder exstrophy (CEB) to exstrophy of the cloaca (EC) as the most severe form. Depending on severity, the EEC may involve the urinary system, the musculoskeletal system, the pelvis, the pelvic floor, the abdominal wall, the genitalia and sometimes the spine and the anus. A spectrum of genitourinary malformations ranging in severity from epispadias (E) and classical bladder exstrophy (CEB) to exstrophy of the cloaca (EC) as the most severe form. Depending on severity, the EEC may involve the urinary system, the musculoskeletal system, the pelvis, the pelvic floor, the abdominal wall, the genitalia and sometimes the spine and the anus.
MONDO:0010079 Canavan disease Canavan disease (CD) is a neurodegenerative disorder; its spectrum varies between severe forms with leukodystrophy, macrocephaly and severe developmental delay, and a very rare mild/juvenile form characterized by mild developmental delay. A neurodegenerative disorder; its spectrum varies between severe forms with leukodystrophy, macrocephaly and severe developmental delay, and a very rare mild/juvenile form characterized by mild developmental delay.
MONDO:0010080 familial infantile bilateral striatal necrosis Familial infantile bilateral striatal necrosis is the familial form of infantile bilateral striatal necrosis (IBSN), a syndrome of bilateral symmetric spongy degeneration of the caudate nucleus, putamen and globus pallidus characterized by developmental regression, choreoathetosis and dystonia progressing to spastic quadriparesis. The familial form of infantile bilateral striatal necrosis (IBSN), a syndrome of bilateral symmetric spongy degeneration of the caudate nucleus, putamen and globus pallidus characterized by developmental regression, choreoathetosis and dystonia progressing to spastic quadriparesis.
MONDO:0015518 infantile bilateral striatal necrosis Infantile bilateral striatal necrosis (IBSN) comprises several syndromes of bilateral symmetric spongy degeneration of the caudate nucleaus, putamen and globus pallidus characterized by developmental regression, choreoathetosis and dystonia progressing to spastic quadriparesis. IBSN can be familial or sporadic. Several syndromes of bilateral symmetric spongy degeneration of the caudate nucleaus, putamen and globus pallidus characterized by developmental regression, choreoathetosis and dystonia progressing to spastic quadriparesis. IBSN can be familial or sporadic.
MONDO:0010371 Aland island eye disease Aland Island Eye Disease (AIED) is an X-linked recessive retinal disease characterized by fundus hypopigmentation, decrased visual acuity, nystagmus, astigmatism, progressive axial myopia, defective dark adaptation and protanopia. An X-linked recessive retinal disease characterized by fundus hypopigmentation, decrased visual acuity, nystagmus, astigmatism, progressive axial myopia, defective dark adaptation and protanopia.
MONDO:0011669 hypotonia-cystinuria syndrome Hypotonia-Cystinuria syndrome (HCS) is a rare syndrome including neonatal and infantile hypotonia and failure to thrive, cystinuria type 1 and nephrolithiasis, growth retardation due to growth hormone deficiency, and minor facial dysmorphism. A rare syndrome including neonatal and infantile hypotonia and failure to thrive, cystinuria type 1 and nephrolithiasis, growth retardation due to growth hormone deficiency, and minor facial dysmorphism.
MONDO:0015999 primary pigmented nodular adrenocortical disease Primary pigmented nodular adrenocortical disease (PPNAD) is a form of bilateral adrenocortical hyperplasia that is often associated with adrenocorticotrophin hormone (ACTH) independent Cushing syndrome and is characterized by small to normal sized adrenal glands containing multiple small cortical pigmented nodules (less than 1 cm in diameter). A form of bilateral adrenocortical hyperplasia that is often associated with adrenocorticotrophin hormone (ACTH) independent Cushing syndrome and is characterized by small to normal sized adrenal glands containing multiple small cortical pigmented nodules (less than 1 cm in diameter).
MONDO:0012608 autosomal recessive lower motor neuron disease with childhood onset Autosomal recessive lower motor neuron disease with childhood onset is a rare, genetic, neuromuscular disease characterized by proximal muscle weakness with an early involvement of foot and hand muscles following normal motor development in early childhood, a rapidly progressive disease course leading to generalized areflexic tetraplegia with contractures, severe scoliosis, hyperlordosis, and progressive respiratory insufficiency leading to assisted ventilation. Cranial nerve functions are normal and tongue wasting and fasciculations are absent. Milder phenotype with a moderate generalized weakness and slower disease progress was reported. A rare, genetic, neuromuscular disease characterized by proximal muscle weakness with an early involvement of foot and hand muscles following normal motor development in early childhood, a rapidly progressive disease course leading to generalized areflexic tetraplegia with contractures, severe scoliosis, hyperlordosis, and progressive respiratory insufficiency leading to assisted ventilation. Cranial nerve functions are normal and tongue wasting and fasciculations are absent. Milder phenotype with a moderate generalized weakness and slower disease progress was reported.
MONDO:0012892 bone fragility with contractures, arterial rupture, and deafness Connective tissue disorder due to lysyl hydroxylase-3 deficiency is a rare, genetic disease, caused by lack of lysyl hydrohylase 3 (LH3) activity, characterized by multiple tissue and organ involvement, including skeletal abnormalities (club foot, progressive scoliosis, osteopenia, pathologic fractures), ocular involvement (flat retinae, myopia, cataracts) and hair, nail and skin anomalies (coarse, abnormally distributed hair, skin blistering, reduced palmar creases, hypoplastic nails). Patients also present intrauterine growth retardation, facial dysmorphism (flat facial profile, low-set ears, shallow orbits, short and upturned nose, downturned corners of mouth) and joint flexion contractures. Growth and developmental delay, bilateral sensorineural deafness, friable diaphragm and later-onset spontaneous vascular ruptures are additional reported features. A rare, genetic disease, caused by lack of lysyl hydrohylase 3 (LH3) activity, characterized by multiple tissue and organ involvement, including skeletal abnormalities (club foot, progressive scoliosis, osteopenia, pathologic fractures), ocular involvement (flat retinae, myopia, cataracts) and hair, nail and skin anomalies (coarse, abnormally distributed hair, skin blistering, reduced palmar creases, hypoplastic nails). Patients also present intrauterine growth retardation, facial dysmorphism (flat facial profile, low-set ears, shallow orbits, short and upturned nose, downturned corners of mouth) and joint flexion contractures. Growth and developmental delay, bilateral sensorineural deafness, friable diaphragm and later-onset spontaneous vascular ruptures are additional reported features.
MONDO:0013060 autosomal recessive Parkinson disease 14 Adult-onset dystonia-parkinsonism is a rare neurodegenerative disease usually presenting before the age of 30 and which is characterized by dystonia, L-dopa-responsive parkinsonism, pyramidal signs and rapid cognitive decline. A rare neurodegenerative disease usually presenting before the age of 30 and which is characterized by dystonia, L-dopa-responsive parkinsonism, pyramidal signs and rapid cognitive decline.
MONDO:0016536 autosomal recessive lymphoproliferative disease Autosomal recessive lymphoproliferative disease is a rare combined T and B cell immunodeficiency with a predisposition to lymphoproliferative syndrome. It is characterized by persistent symptomatic EBV-viremia and hypogammaglobulinemia variably presenting with fever, lymphadenopathy and systemic inflammatory conditions including hepatitis, pneumonia and sepsis. It may be associated with lymphoma, hemophagocytic lymphohistiocytosis, and aplastic anemia. A rare combined T and B cell immunodeficiency with a predisposition to lymphoproliferative syndrome. It is characterized by persistent symptomatic EBV-viremia and hypogammaglobulinemia variably presenting with fever, lymphadenopathy and systemic inflammatory conditions including hepatitis, pneumonia and sepsis. It may be associated with lymphoma, hemophagocytic lymphohistiocytosis, and aplastic anemia.
MONDO:0013172 polymicrogyria with optic nerve hypoplasia Polymicrogyria with optic nerve hypoplasia is a rare genetic syndrome with central nervous system malformations characterized by severe developmental delay, neonatal hypotonia, seizures, optic nerve hypoplasia and distinct central nervous system malformations including extensive bilateral polymicrogyria, dysplastic or absent corpus callosum and malformed brainstem with loss of demarcation of the pontomedullary junction. A rare genetic syndrome with central nervous system malformations characterized by severe developmental delay, neonatal hypotonia, seizures, optic nerve hypoplasia and distinct central nervous system malformations including extensive bilateral polymicrogyria, dysplastic or absent corpus callosum and malformed brainstem with loss of demarcation of the pontomedullary junction.
MONDO:0013759 melanoma, cutaneous malignant, susceptibility to, 8 MITF-related melanoma and renal cell carcinoma predisposition syndrome is an inherited cancer-predisposing syndrome due to a gain-of-function germline mutation in the MITF gene, associated with a higher incidence of amelanotic and nodular melanoma, multiple primary melanomas and increase in nevus number and size. It may also predispose to co-occurring melanoma and renal cell carcinoma and to pancreatic cancer. An inherited cancer-predisposing syndrome due to a gain-of-function germline mutation in the MITF gene, associated with a higher incidence of amelanotic and nodular melanoma, multiple primary melanomas and increase in nevus number and size. It may also predispose to co-occurring melanoma and renal cell carcinoma and to pancreatic cancer.
MONDO:0014061 Steel syndrome A rare genetic bone disease characterized by short stature, bilateral congenital hip dislocation, radial head dislocation, carpal coalition, scoliosis, pes cavus, and atlantoaxial subluxation. Dysmorphic facial features include broad forehead, broad nasal bridge, hypertelorism, and mild midface hypoplasia. Association with bilateral sensorineural hearing loss has also been described.
MONDO:0014500 atrial conduction disease Atrial conduction disorder is a form of heart disease in which the conduction of the cardiac atrium is disrupted Atrial conduction disorder is a form of heart disease in which the conduction of the cardiac atrium is disrupted.
MONDO:0014629 autoimmune interstitial lung disease-arthritis syndrome A respiratory disease characterized by interstitial lung disease (often with pulmonary hemorrhage) and inflammatory arthritis, associated with high-titer autoantibodies (including anti-nuclear and anti-neutrophil cytoplasmic antibodies, and rheumatoid factor). Patients present from infancy to adolescence with tachypnea, cough, hemoptysis, and/or joint pain. Some patients may also develop glomerular disease.
MONDO:0015583 2p21 microdeletion syndrome The 2p21 microdeletion syndrome consists of cystinuria, neonatal seizures, hypotonia, severe growthand developmental delay, facial dysmorphism, and lactic acidemia. The 2p21 microdeletion syndrome consists of cystinuria, neonatal seizures, hypotonia, severe growth and developmental delay, facial dysmorphism, and lactic acidemia.
MONDO:0015633 obsolete Bazex syndrome Bazex syndrome is a rare paraneoplastic syndrome characterized by acral psoriasiform lesions.
MONDO:0015750 obsolete amelogenesis imperfecta-gingival hyperplasia syndrome This syndrome associates gingival fibromatosis with dental abnormalities including generalized thin hypoplastic amelogenesis imperfecta, intrapulpal calcifications, and delay of tooth eruption.
MONDO:0015938 obsolete systemic disease A systemic disease is one that affects a number of organs and tissues, or affects the body as a whole.
MONDO:0016822 myalgia-eosinophilia syndrome associated with tryptophan Myalgia-eosinophilia syndrome associated with tryptophan is a rare systemic disease characterized by severe myalgia and peripheral eosinophilia associated with tryptophan dietary supplementation. The symptoms do not subside after tryptophan discontinuation. Clinical presentation includes muscle tenderness and cramps, fatigue, weakness, paresthesia, peripheral edema, arthralgia, dyspnea, skin rash, dry mouth, and development of scleroderma-like skin abnormalities. A rare systemic disease characterized by severe myalgia and peripheral eosinophilia associated with tryptophan dietary supplementation. The symptoms do not subside after tryptophan discontinuation. Clinical presentation includes muscle tenderness and cramps, fatigue, weakness, paresthesia, peripheral edema, arthralgia, dyspnea, skin rash, dry mouth, and development of scleroderma-like skin abnormalities.
MONDO:0017133 obsolete genetic systemic or rheumatologic disease An instance of systemic or rheumatic disease that is caused by a modification of the individual's genome.
MONDO:0017213 postorgasmic illness syndrome Postorgasmic illness syndrome (POIS) is a rare condition in which a man develops flu-like symptoms after ejaculation (when semen is released from the penis). Specific symptoms can include extreme fatigue, weakness, feverishness or sweating, mood changes or irritability, memory or concentration problems, and/or a stuffy nose or itching eyes. Symptoms may occur within seconds, minutes, or a few hours after ejaculation. Most symptoms last for 2 to 7 days and go away on their own. The underlying cause of POIS is poorly understood. Some scientists believe it may be due to a semen allergy that causes an immediate hypersensitivity reaction. There is no standard treatment for POIS, but some men have been treated with SSRIs, antihistamines, and/or benzodiazepines. Hyposensitization therapy (decreasing the immune response by exposure to semen) reportedly improved symptoms in two men with POIS. A rare condition in which a man develops flu-like symptoms after ejaculation (when semen is released from the penis). Specific symptoms can include extreme fatigue, weakness, feverishness or sweating, mood changes or irritability, memory or concentration problems, and/or a stuffy nose or itching eyes. Symptoms may occur within seconds, minutes, or a few hours after ejaculation. Most symptoms last for 2 to 7 days and go away on their own. The underlying cause of POIS is poorly understood. Some scientists believe it may be due to a semen allergy that causes an immediate hypersensitivity reaction. There is no standard treatment for POIS, but some men have been treated with SSRIs, antihistamines, and/or benzodiazepines. Hyposensitization therapy (decreasing the immune response by exposure to semen) reportedly improved symptoms in two men with POIS.
MONDO:0019355 adult-onset Still disease Adult-onset Still disease (AOSD) is a rare inflammatory multisystem disorder characterized clinically by fever of unknown origin, arthralgia or arthritis, hyperleucocytosis, and typical skin rash. A rare inflammatory multisystem disorder characterized clinically by fever of unknown origin, arthralgia or arthritis, hyperleucocytosis, and typical skin rash.
MONDO:0100027 obsolete febrile seizures plus, genetic epilepsy with febrile seizures plus These epilepsy syndromes are characterized by the presence of febrile seizures in an individual that may continue past the usual age where these are expected to resolve and/or be accompanied by afebrile seizures that may be generalized seizures (tonic-clonic, atonic, myoclonic, myoclonic-atonic or absence) or focal seizures. Febrile seizures plus and genetic epilepsy with febrile seizures plus are distinguished on the basis of family history. A number of dominantly inherited genes have been linked to these syndromes, with implications for specific genetic counseling, due to the variable severity of the resulting epilepsy in different family members.
MONDO:0100318 SARS-CoV-2-related disease A related disease caused by infection with severe acute respiratory syndrome coronavirus 2 or the associated aftereffects of the disease. A viral disease or post-viral disorder caused by infection with severe acute respiratory syndrome coronavirus 2 or the associated aftereffects of the disease.

Obsoletion candidates

New obsoletion candidates:

Mondo ID Label
MONDO:0019708 primary bone dysplasia with disorganized development of skeletal components
MONDO:0000881 myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB, and FGFR1
MONDO:0000882 myeloid and lymphoid neoplasms associated with PDGFRA rearrangement
MONDO:0000883 myeloid neoplasms associated with PDGFRB rearrangement
MONDO:0006475 unclassified renal cell carcinoma
MONDO:0006728 discitis
MONDO:0018232 primary bone dysplasia with micromelia
MONDO:0019700 primary bone dysplasia with multiple joint dislocations
MONDO:0017957 unclassified autoinflammatory syndrome
MONDO:0019703 primary bone dysplasia with increased bone density
MONDO:0019704 primary bone dysplasia with decreased bone density
MONDO:0017608 dystrophic epidermolysis bullosa
MONDO:0019299 unclassified genetic skin disorder
MONDO:0007600 primary Fanconi syndrome
MONDO:0018231 primary bone dysplasia with progressive ossification of skin, skeletal muscle, fascia, tendons and ligaments
MONDO:0020244 unclassified primitive or secondary maculopathy
MONDO:0007684 granulomatous disease, chronic, autosomal dominant type
MONDO:0007749 autosomal recessive infantile hypercalcemia
MONDO:0007815 immunodeficiency with defective leukocyte and lymphocyte function and with response to histamine-1 antagonist
MONDO:0008091 abnormal neutrophil chemotactic response
MONDO:0008122 olivopontocerebellar atrophy 5
MONDO:0009799 pachydermoperiostosis
MONDO:0018466 hereditary late onset Parkinson disease
MONDO:0008956 congenital neuronal ceroid lipofuscinosis
MONDO:0009004 combined inflammatory and immunologic defect
MONDO:0019705 primary bone dysplasia with defective bone mineralization
MONDO:0009494 Ketoadipicaciduria
MONDO:0009535 lymphedema, congenital recessive
MONDO:0009654 mucopolysaccharidoses, unclassified types
MONDO:0020241 unclassified familial retinal dystrophy
MONDO:0010527 microphthalmia-ankyloblepharon-intellectual disability syndrome
MONDO:0019302 mucopolysaccharidosis with skin involvement
MONDO:0011329 cerebral palsy, spastic quadriplegic, 1
MONDO:0016538 hypotonia-cystinuria syndrome type 1
MONDO:0015192 unclassified intestinal pseudoobstruction
MONDO:0016665 unclassified vasculitis
MONDO:0018139 scleredema
MONDO:0018348 polyglucosan body myopathy type 1
MONDO:0020313 unclassified myelodysplastic/myeloproliferative disease
MONDO:0020315 unclassified myelodysplastic syndrome
MONDO:0035398 hypomyelination of early myelinating structures

Terms that were previously candidate for obsoletion and are now not anymore:

No changes.

Obsoletions

Mondo ID Label
MONDO:0010301 obsolete thrombocythemia, X-linked
MONDO:0011293 obsolete Homocysteinemia
MONDO:0015318 obsolete Pierre Robin syndrome associated with collagen disease
MONDO:0015320 obsolete Pierre Robin syndrome associated with a chromosomal anomaly
MONDO:0015321 obsolete Pierre Robin syndrome associated with branchial archs anomalies
MONDO:0015322 obsolete Pierre Robin syndrome associated with bone disease
MONDO:0015543 obsolete hemophagocytic syndrome associated with an infection
MONDO:0015633 obsolete Bazex syndrome
MONDO:0015750 obsolete amelogenesis imperfecta-gingival hyperplasia syndrome
MONDO:0015938 obsolete systemic disease
MONDO:0016148 obsolete qualitative or quantitative defects of collagen 6
MONDO:0016329 obsolete familial syndrome associated with hypertrophic cardiomyopathy
MONDO:0017133 obsolete genetic systemic or rheumatologic disease
MONDO:0017274 obsolete autosomal ichthyosis syndrome with other associated signs
MONDO:0019687 obsolete type 11 collagen-related bone disorder
MONDO:0020012 obsolete systemic or rheumatic disease
MONDO:0020272 obsolete connective tissue disease with eye involvement
MONDO:0020277 obsolete ectodermal malformation syndrome associated with ocular features
MONDO:0035354 obsolete IgG4-related systemic disease
MONDO:0035363 obsolete IRF2BPL-related regressive neurodevelopmental disorder-dystonia-seizures syndrome
MONDO:0035369 obsolete MTHFS-related developmental delay-microcephaly-short stature-epilepsy syndrome
MONDO:0100027 obsolete febrile seizures plus, genetic epilepsy with febrile seizures plus
matentzn commented 2 years ago

I have committed this to master already, so if you are happy with the output above, you can just close this @sabrinatoro

sabrinatoro commented 2 years ago

It looks good to me. And I don't think the "update the column titles to "Previous release definition" and "New release definition" " is a big deal (and I definitely don't think it is worth the extra effort. Thank you @matentzn! Closing.