nicolevasilevsky
commented
1 year ago Hi @jdesaphy
Orphanet:93444 Primary bone dysplasia with increased bone density is already an equivalent database cross reference on MONDO:0800084 primary bone dysplasia with increased bone density.
and Orphanet:93448 Lysosomal storage disease with skeletal involvement is an equivalent database cross reference on MONDO_0800088 lysosomal storage disease with skeletal involvement.
I will add EFO:0020005 pheochromocytoma-paraganglioma as an xref to MONDO:0035540 pheochromocytoma-paraganglioma.
We cannot merge the other terms together, as they are from different ontologies. For example, a term in HPO is intended to represent the phenotypic form of the term and Mondo represents the disease form.
On our FAQ page, we describe the difference between a disease and a phenotype:
There is a lot of overlap between diseases and phenotypes. Mondo and Human Phenotype Ontology (HPO) define a disease as an entity that has all four of the following features:
an etiology (whether identified or as yet unknown) a time course a set of phenotypic features if treatments exist, there is a characteristic response to them A phenotype (or a phenotypic feature) is a component of a disease, and HPO terms can be used to describe the set of phenotypic features that characterize a disease. There is a grey zone between diseases and phenotypic features. For instance, diabetes mellitus can be conceptualized as a disease, but it is also a feature of other diseases such as Bardet Biedl syndrome. In some cases like this, Mondo may label the disease entity with (disease) after the disease name, to distinguish it from the HPO phenotype term (for example, MONDO:0005466 ‘hypersomnia (disease)’ and HP:0100786 Hypersomnia).
-- While these terms listed above have the same label, they do not necessarily have the same meaning. For example, MONDO:0002280 anemia is a disease and NCBITaxon:12939 Anemia is a plant.
Please let me know if you'd like to discuss further, otherwise I will close this ticket. Thanks!
Would it be possible to merge those pairs together please?
NCIT_C12664 | Abdomen | UBERON_0000916 | abdomen MONDO_0005227 | abscess | MPATH_608 | abscess HP_0001735 | Acute pancreatitis | MONDO_0006515 | acute pancreatitis HP_0010524 | Agnosia | MONDO_0005638 | agnosia HP_0012234 | Agranulocytosis | MONDO_0001609 | agranulocytosis HP_0001022 | Albinism | MONDO_0043209 | albinism HP_0001596 | Alopecia | MONDO_0004907 | alopecia HP_0000646 | Amblyopia | MONDO_0001020 | amblyopia CHEBI_16134 | ammonia | NCBITaxon_29189 | Ammonia HP_0007354 | Amyotrophic lateral sclerosis | MONDO_0004976 | amyotrophic lateral sclerosis CARO_0000000 | anatomical entity | UBERON_0001062 | anatomical entity MONDO_0002280 | anemia | NCBITaxon_12939 | Anemia HP_0001903 | Anemia | MONDO_0002280 | anemia HP_0001903 | Anemia | NCBITaxon_12939 | Anemia HP_0000970 | Anhidrosis | MONDO_0006527 | anhidrosis HP_0000526 | Aniridia | MONDO_0019172 | aniridia HP_0000458 | Anosmia | MONDO_0010528 | anosmia HP_0000739 | Anxiety | MONDO_0011918 | anxiety HP_0001650 | Aortic valve stenosis | MONDO_0042981 | aortic valve stenosis HP_0002186 | Apraxia | MONDO_0000665 | apraxia HP_0010527 | Astereognosia | MONDO_0000680 | astereognosia HP_0002099 | Asthma | MONDO_0004979 | asthma HP_0000717 | Autism | MONDO_0005260 | autism HP_0010885 | Avascular necrosis | MONDO_0018373 | avascular necrosis HP_0000027 | Azoospermia | MONDO_0100459 | azoospermia GO_0007610 | behavior | NCIT_C16326 | Behavior HP_0005912 | Biliary atresia | MONDO_0008867 | biliary atresia HP_0001156 | Brachydactyly | MONDO_0021004 | brachydactyly HP_0002110 | Bronchiectasis | MONDO_0004822 | bronchiectasis HP_0001638 | Cardiomyopathy | MONDO_0004994 | cardiomyopathy GO_0003824 | catalytic activity | PATO_0001414 | catalytic activity HP_0000518 | Cataract | MONDO_0005129 | cataract HP_0100658 | Cellulitis | MONDO_0005230 | cellulitis HP_0030724 | Central nervous system cyst | MONDO_0005262 | central nervous system cyst HP_0002438 | Cerebellar malformation | MONDO_0015915 | cerebellar malformation HP_0007313 | Cerebral degeneration | MONDO_0024238 | cerebral degeneration HP_0030159 | Cervical polyp | MONDO_0000751 | cervical polyp HP_0001396 | Cholestasis | MONDO_0001751 | cholestasis HP_0009797 | Cholesteatoma | MONDO_0006530 | cholesteatoma HP_0010762 | Chordoma | MONDO_0008978 | chordoma HP_0005558 | Chronic leukemia | MONDO_0001014 | chronic leukemia HP_0002257 | Chronic rhinitis | MONDO_0004514 | chronic rhinitis PATO_0000411 | circular | SO_0000988 | circular HP_0000175 | Cleft palate | MONDO_0016064 | cleft palate HP_0005387 | Combined immunodeficiency | MONDO_0015131 | combined immunodeficiency HP_0004431 | Complement deficiency | MONDO_0003832 | complement deficiency HP_0001635 | Congestive heart failure | MONDO_0005009 | congestive heart failure HP_0000509 | Conjunctivitis | MONDO_0003799 | conjunctivitis HP_0002812 | Coxa vara | MONDO_0007391 | coxa vara HP_0031258 | Delirium | MONDO_0045057 | delirium HP_0000726 | Dementia | MONDO_0001627 | dementia HP_0001651 | Dextrocardia | MONDO_0015661 | dextrocardia HP_0000819 | Diabetes mellitus | MONDO_0005015 | diabetes mellitus NCIT_C12378 | Digestive System | UBERON_0001007 | digestive system HP_0001644 | Dilated cardiomyopathy | MONDO_0005021 | dilated cardiomyopathy HP_0010522 | Dyslexia | MONDO_0005489 | dyslexia ENVO_00000176 | elevation | PATO_0001687 | elevation HP_0002383 | Encephalitis | MONDO_0019956 | encephalitis HP_0100584 | Endocarditis | MONDO_0005025 | endocarditis MFOMD_0000105 | enuresis | MONDO_0024290 | enuresis HP_0000031 | Epididymitis | MONDO_0004779 | epididymitis HP_0100639 | Erectile dysfunction | MONDO_0005362 | erectile dysfunction HP_0010525 | Finger agnosia | MONDO_0000671 | finger agnosia CHEBI_64047 | food additive | FOODON_03412972 | food additive HP_0002145 | Frontotemporal dementia | MONDO_0017276 | frontotemporal dementia HP_0009064 | Generalized lipodystrophy | MONDO_0027766 | generalized lipodystrophy HP_0000230 | Gingivitis | MONDO_0002508 | gingivitis HP_0000501 | Glaucoma | MONDO_0005041 | glaucoma HP_0000099 | Glomerulonephritis | MONDO_0002462 | glomerulonephritis HP_0001952 | Glucose intolerance | MONDO_0001076 | glucose intolerance HP_0000853 | Goiter | MONDO_0005397 | goiter HP_0000133 | Gonadal dysgenesis | MONDO_0001967 | gonadal dysgenesis HP_0001997 | Gout | MONDO_0005393 | gout HP_0010566 | Hamartoma | MONDO_0006499 | hamartoma HP_0001878 | Hemolytic anemia | MONDO_0003664 | hemolytic anemia HP_0012115 | Hepatitis | MONDO_0002251 | hepatitis HP_0002156 | Homocystinuria | MONDO_0004737 | homocystinuria HP_0010606 | Hordeolum | MONDO_0005800 | hordeolum HP_0000238 | Hydrocephalus | MONDO_0001150 | hydrocephalus HP_0001789 | Hydrops fetalis | MONDO_0015193 | hydrops fetalis HP_0000859 | Hyperaldosteronism | MONDO_0003009 | hyperaldosteronism HP_0002904 | Hyperbilirubinemia | MONDO_0024288 | hyperbilirubinemia HP_0003074 | Hyperglycemia | MONDO_0002909 | hyperglycemia HP_0003077 | Hyperlipidemia | MONDO_0021187 | hyperlipidemia HP_0010980 | Hyperlipoproteinemia | MONDO_0037748 | hyperlipoproteinemia HP_0100774 | Hyperostosis | MONDO_0002185 | hyperostosis HP_0000843 | Hyperparathyroidism | MONDO_0001741 | hyperparathyroidism HP_0002905 | Hyperphosphatemia | MONDO_0000328 | hyperphosphatemia HP_0000953 | Hyperpigmentation of the skin | MONDO_0019289 | hyperpigmentation of the skin HP_0010514 | Hyperpituitarism | MONDO_0006793 | hyperpituitarism HP_0100786 | Hypersomnia | MONDO_0005466 | hypersomnia HP_0000998 | Hypertrichosis | MONDO_0019280 | hypertrichosis HP_0001931 | Hypochromic anemia | MONDO_0001357 | hypochromic anemia HP_0001943 | Hypoglycemia | MONDO_0004946 | hypoglycemia HP_0000135 | Hypogonadism | MONDO_0002146 | hypogonadism HP_0000044 | Hypogonadotropic hypogonadism | MONDO_0018555 | hypogonadotropic hypogonadism HP_0000966 | Hypohidrosis | MONDO_0006560 | hypohidrosis HP_0000829 | Hypoparathyroidism | MONDO_0001220 | hypoparathyroidism HP_0002148 | Hypophosphatemia | MONDO_0000313 | hypophosphatemia HP_0001010 | Hypopigmentation of the skin | MONDO_0019290 | hypopigmentation of the skin HP_0040075 | Hypopituitarism | MONDO_0005152 | hypopituitarism CARO_0000007 | immaterial anatomical entity | UBERON_0000466 | immaterial anatomical entity HP_0001249 | Intellectual disability | MONDO_0001071 | intellectual disability NCIT_C12736 | Intestine | UBERON_0000160 | intestine HP_0000491 | Keratitis | MONDO_0003085 | keratitis HP_0001096 | Keratoconjunctivitis | MONDO_0004768 | keratoconjunctivitis HP_0003128 | Lactic acidosis | MONDO_0006040 | lactic acidosis HP_0004789 | Lactose intolerance | MONDO_0100345 | lactose intolerance HP_0030682 | Left ventricular noncompaction | MONDO_0018901 | left ventricular noncompaction HP_0001909 | Leukemia | MONDO_0005059 | leukemia HP_0001882 | Leukopenia | MONDO_0003785 | leukopenia HP_0009125 | Lipodystrophy | MONDO_0006573 | lipodystrophy HP_0002840 | Lymphadenitis | MONDO_0002052 | lymphadenitis HP_0001004 | Lymphedema | MONDO_0019297 | lymphedema HP_0001888 | Lymphopenia | MONDO_0003783 | lymphopenia Orphanet_93448 | Lysosomal storage disease with skeletal involvement | MONDO_0800088 | lysosomal storage disease with skeletal involvement HP_0001972 | Macrocytic anemia | MONDO_0002281 | macrocytic anemia HP_0000608 | Macular degeneration | MONDO_0003004 | macular degeneration CARO_0000006 | material anatomical entity | UBERON_0000465 | material anatomical entity HP_0001889 | Megaloblastic anemia | MONDO_0001700 | megaloblastic anemia HP_0001287 | Meningitis | MONDO_0021108 | meningitis HP_0002435 | Meningocele | MONDO_0001147 | meningocele MFOMD_0000004 | mental disorder | MONDO_0005084 | mental disorder HP_0001942 | Metabolic acidosis | MONDO_0000440 | metabolic acidosis HP_0002912 | Methylmalonic acidemia | MONDO_0002012 | methylmalonic acidemia HP_0000252 | Microcephaly | MONDO_0001149 | microcephaly HP_0001935 | Microcytic anemia | MONDO_0001245 | microcytic anemia HP_0000568 | Microphthalmia | MONDO_0021129 | microphthalmia CARO_0010000 | multicellular anatomical structure | UBERON_0010000 | multicellular anatomical structure HP_0003560 | Muscular dystrophy | MONDO_0020121 | muscular dystrophy HP_0002300 | Mutism | MONDO_0002905 | mutism HP_0011974 | Myelofibrosis | MONDO_0044903 | myelofibrosis HP_0002475 | Myelomeningocele | MONDO_0019773 | myelomeningocele HP_0003198 | Myopathy | MONDO_0005336 | myopathy HP_0030050 | Narcolepsy | MONDO_0021107 | narcolepsy HP_0002664 | Neoplasm | MONDO_0005070 | neoplasm HP_0000123 | Nephritis | MONDO_0001166 | nephritis HP_0000090 | Nephronophthisis | MONDO_0019005 | nephronophthisis HP_0045005 | Neural tube defect | MONDO_0018075 | neural tube defect CARO_0001001 | neuron projection bundle | UBERON_0000122 | neuron projection bundle HP_0000648 | Optic atrophy | MONDO_0003608 | optic atrophy NCIT_C13018 | Organ | UBERON_0000062 | organ HP_0002754 | Osteomyelitis | MONDO_0005246 | osteomyelitis HP_0011002 | Osteopetrosis | MONDO_0017198 | osteopetrosis HP_0000939 | Osteoporosis | MONDO_0005298 | osteoporosis HP_0001733 | Pancreatitis | MONDO_0004982 | pancreatitis HP_0001876 | Pancytopenia | MONDO_0001529 | pancytopenia HP_0010550 | Paraplegia | MONDO_0003757 | paraplegia HP_0001698 | Pericardial effusion | MONDO_0001370 | pericardial effusion HP_0009830 | Peripheral neuropathy | MONDO_0005244 | peripheral neuropathy EFO_0020005 | pheochromocytoma-paraganglioma | MONDO_0035540 | pheochromocytoma-paraganglioma HP_0002090 | Pneumonia | MONDO_0005249 | pneumonia HP_0010442 | Polydactyly | MONDO_0021003 | polydactyly HP_0000826 | Precocious puberty | MONDO_0000088 | precocious puberty HP_0008207 | Primary adrenal insufficiency | MONDO_0015128 | primary adrenal insufficiency Orphanet_93444 | Primary bone dysplasia with increased bone density | MONDO_0800084 | primary bone dysplasia with increased bone density PO_0025127 | primordium | UBERON_0001048 | primordium HP_0010528 | Prosopagnosia | MONDO_0003227 | prosopagnosia HP_0000093 | Proteinuria | MONDO_0003634 | proteinuria HP_0000508 | Ptosis | MONDO_0000728 | ptosis HP_0100598 | Pulmonary edema | MONDO_0006932 | pulmonary edema HP_0002204 | Pulmonary embolism | MONDO_0005279 | pulmonary embolism HP_0000979 | Purpura | MONDO_0002610 | purpura HP_0000999 | Pyoderma | MONDO_0002922 | pyoderma BFO_0000019 | quality | PATO_0000001 | quality HP_0002035 | Rectal prolapse | MONDO_0004754 | rectal prolapse GO_0050795 | regulation of behavior | NBO_0001786 | regulation of behavior GO_0019098 | reproductive behavior | NBO_0000010 | reproductive behavior HP_0000546 | Retinal degeneration | MONDO_0004580 | retinal degeneration HP_0001370 | Rheumatoid arthritis | MONDO_0008383 | rheumatoid arthritis HP_0012384 | Rhinitis | MONDO_0003014 | rhinitis HP_0002748 | Rickets | MONDO_0005520 | rickets BFO_0000023 | role | CHEBI_50906 | role HP_0100324 | Scleroderma | MONDO_0019340 | scleroderma HP_0001051 | Seborrheic dermatitis | MONDO_0006608 | seborrheic dermatitis HP_0001153 | Septate vagina | MONDO_0015848 | septate vagina HP_0004430 | Severe combined immunodeficiency | MONDO_0015974 | severe combined immunodeficiency HP_0001924 | Sideroblastic anemia | MONDO_0015194 | sideroblastic anemia HP_0002652 | Skeletal dysplasia | MONDO_0018230 | skeletal dysplasia GO_0035176 | social behavior | NBO_0000011 | social behavior HP_0001328 | Specific learning disability | MONDO_0016225 | specific learning disability HP_0002414 | Spina bifida | MONDO_0008449 | spina bifida 11359 | STAR | ENVO_01000801 | star HP_0010280 | Stomatitis | MONDO_0004842 | stomatitis HP_0000486 | Strabismus | MONDO_0003432 | strabismus HP_0004381 | Supravalvular aortic stenosis | MONDO_0008504 | supravalvular aortic stenosis HP_0001159 | Syndactyly | MONDO_0021002 | syndactyly HP_0002725 | Systemic lupus erythematosus | MONDO_0007915 | systemic lupus erythematosus HP_0001873 | Thrombocytopenia | MONDO_0002049 | thrombocytopenia HP_0009804 | Tooth agenesis | MONDO_0005486 | tooth agenesis HP_0100603 | Toxemia of pregnancy | MONDO_0045048 | toxemia of pregnancy HP_0001669 | Transposition of the great arteries | MONDO_0000153 | transposition of the great arteries HP_0000243 | Trigonocephaly | MONDO_0000156 | trigonocephaly HP_0001660 | Truncus arteriosus | UBERON_0002061 | truncus arteriosus HP_0006000 | Ureteral obstruction | MONDO_0003329 | ureteral obstruction HP_0001025 | Urticaria | MONDO_0005492 | urticaria HP_0000554 | Uveitis | MONDO_0020283 | uveitis HP_0002633 | Vasculitis | MONDO_0018882 | vasculitis HP_0005293 | Venous insufficiency | MONDO_0000945 | venous insufficiency HP_0001663 | Ventricular fibrillation | MONDO_0000190 | ventricular fibrillation HP_0006562 | Viral hepatitis | MONDO_0006011 | viral hepatitis HP_0030222 | Visual agnosia | MONDO_0000685 | visual agnosia HP_0100502 | Vitamin B12 deficiency | MONDO_0020696 | vitamin B12 deficiency HP_0000991 | Xanthomatosis | MONDO_0002615 | xanthomatosis