Fix robot report errors

category	error	class	property	value
ERROR	duplicate_definition	Usher syndrome type 1C [MONDO:0010171]	definition [IAO:0000115]	Usher syndrome is a genetic disorder characterized by sensorineural hearing loss or deafness and progressive vision loss due to retinitis pigmentosa . Sensorineural hearing means it is caused by abnormalities of the inner ear . Retinitis pigmentosa is an eye disease that affects the layer of light-sensitive tissue at the back of the eye ( the retina ). Vision loss occurs as the light-sensing cells of the retina gradually deteriorate. Night vision loss begins first, followed by blind spots that develop in the side (peripheral) vision, that can enlarge and merge to produce tunnel vision (loss of all peripheral vision). In some cases, vision is further impaired by clouding of the lens of the eye ( cataracts ). Three major types of Usher syndrome have been described - types I , II , and III . The different typesare distinguished by their severity and the age when signs and symptoms appear. All three types are inherited in an autosomal recessive manner . Treatment for the hearing loss may include hearing aids or surgery for a cochlear implant . Vitamin A palmitate is useful for treating the vision loss in people with Usher syndrome type II.
ERROR	duplicate_definition	Usher syndrome type 1D [MONDO:0010984]	definition [IAO:0000115]	Usher syndrome is a genetic disorder characterized by sensorineural hearing loss or deafness and progressive vision loss due to retinitis pigmentosa . Sensorineural hearing means it is caused by abnormalities of the inner ear . Retinitis pigmentosa is an eye disease that affects the layer of light-sensitive tissue at the back of the eye ( the retina ). Vision loss occurs as the light-sensing cells of the retina gradually deteriorate. Night vision loss begins first, followed by blind spots that develop in the side (peripheral) vision, that can enlarge and merge to produce tunnel vision (loss of all peripheral vision). In some cases, vision is further impaired by clouding of the lens of the eye ( cataracts ). Three major types of Usher syndrome have been described - types I , II , and III . The different typesare distinguished by their severity and the age when signs and symptoms appear. All three types are inherited in an autosomal recessive manner . Treatment for the hearing loss may include hearing aids or surgery for a cochlear implant . Vitamin A palmitate is useful for treating the vision loss in people with Usher syndrome type II.
ERROR	duplicate_definition	Usher syndrome type 1F [MONDO:0011186]	definition [IAO:0000115]	Usher syndrome is a genetic disorder characterized by sensorineural hearing loss or deafness and progressive vision loss due to retinitis pigmentosa . Sensorineural hearing means it is caused by abnormalities of the inner ear . Retinitis pigmentosa is an eye disease that affects the layer of light-sensitive tissue at the back of the eye ( the retina ). Vision loss occurs as the light-sensing cells of the retina gradually deteriorate. Night vision loss begins first, followed by blind spots that develop in the side (peripheral) vision, that can enlarge and merge to produce tunnel vision (loss of all peripheral vision). In some cases, vision is further impaired by clouding of the lens of the eye ( cataracts ). Three major types of Usher syndrome have been described - types I , II , and III . The different typesare distinguished by their severity and the age when signs and symptoms appear. All three types are inherited in an autosomal recessive manner . Treatment for the hearing loss may include hearing aids or surgery for a cochlear implant . Vitamin A palmitate is useful for treating the vision loss in people with Usher syndrome type II.
ERROR	duplicate_definition	Usher syndrome type 1E [MONDO:0011195]	definition [IAO:0000115]	Usher syndrome is a genetic disorder characterized by sensorineural hearing loss or deafness and progressive vision loss due to retinitis pigmentosa . Sensorineural hearing means it is caused by abnormalities of the inner ear . Retinitis pigmentosa is an eye disease that affects the layer of light-sensitive tissue at the back of the eye ( the retina ). Vision loss occurs as the light-sensing cells of the retina gradually deteriorate. Night vision loss begins first, followed by blind spots that develop in the side (peripheral) vision, that can enlarge and merge to produce tunnel vision (loss of all peripheral vision). In some cases, vision is further impaired by clouding of the lens of the eye ( cataracts ). Three major types of Usher syndrome have been described - types I , II , and III . The different typesare distinguished by their severity and the age when signs and symptoms appear. All three types are inherited in an autosomal recessive manner . Treatment for the hearing loss may include hearing aids or surgery for a cochlear implant . Vitamin A palmitate is useful for treating the vision loss in people with Usher syndrome type II.
ERROR	duplicate_definition	Usher syndrome type 2C [MONDO:0011558]	definition [IAO:0000115]	Usher syndrome is a genetic disorder characterized by sensorineural hearing loss or deafness and progressive vision loss due to retinitis pigmentosa . Sensorineural hearing means it is caused by abnormalities of the inner ear . Retinitis pigmentosa is an eye disease that affects the layer of light-sensitive tissue at the back of the eye ( the retina ). Vision loss occurs as the light-sensing cells of the retina gradually deteriorate. Night vision loss begins first, followed by blind spots that develop in the side (peripheral) vision, that can enlarge and merge to produce tunnel vision (loss of all peripheral vision). In some cases, vision is further impaired by clouding of the lens of the eye ( cataracts ). Three major types of Usher syndrome have been described - types I , II , and III . The different typesare distinguished by their severity and the age when signs and symptoms appear. All three types are inherited in an autosomal recessive manner . Treatment for the hearing loss may include hearing aids or surgery for a cochlear implant . Vitamin A palmitate is useful for treating the vision loss in people with Usher syndrome type II.
ERROR	duplicate_definition	methylmalonic aciduria and homocystinuria type cblF [MONDO:0010183]	definition [IAO:0000115]	type methylmalonic acidemia with homocystinuria is a form of methylmalonic acidemia with homocystinuria (see this term), an inborn error of vitamin B12 (cobalamin) metabolism characterized by megaloblastic anemia, lethargy, failure to thrive, developmental delay, intellectual deficit and seizures.
ERROR	duplicate_definition	methylmalonic aciduria and homocystinuria type cblC [MONDO:0010184]	definition [IAO:0000115]	type methylmalonic acidemia with homocystinuria is a form of methylmalonic acidemia with homocystinuria (see this term), an inborn error of vitamin B12 (cobalamin) metabolism characterized by megaloblastic anemia, lethargy, failure to thrive, developmental delay, intellectual deficit and seizures.
ERROR	duplicate_definition	angle-closure glaucoma [MONDO:0001744]	definition [IAO:0000115]	The sudden increase of intraocular pressure, resulting in pain and an abrupt decrease in visual acuity.
ERROR	duplicate_definition	primary angle-closure glaucoma [MONDO:0001868]	definition [IAO:0000115]	The sudden increase of intraocular pressure, resulting in pain and an abrupt decrease in visual acuity.
ERROR	duplicate_definition	bacterial arthritis [MONDO:0004471]	definition [IAO:0000115]	The inflammation of one or more joints caused by any infectious pathogen within the joint space. Symptoms include pain, stiffness, and decreased range of motion in the affected joint.
ERROR	duplicate_definition	infective arthritis [MONDO:0042485]	definition [IAO:0000115]	The inflammation of one or more joints caused by any infectious pathogen within the joint space. Symptoms include pain, stiffness, and decreased range of motion in the affected joint.
ERROR	duplicate_definition	Stickler syndrome type 3 [MONDO:0008490]	definition [IAO:0000115]	Stickler syndrome is a group of hereditary connective tissue disorders characterized by distinctive facial features, eye abnormalities, hearing loss, and joint problems. The features vary widely among affected people. Stickler syndrome type 1 may be divided into 2 subgroups: the membranous vitreous type and a predominantly ocular type. Both arecaused by mutations in the COL2A1 gene. Stickler syndrome type II , sometimes called the beaded vitreous type, is caused by mutations in the COL11A1 gene. Stickler syndrome type III , sometimes called the nonocular form, is caused by mutations in the COL11A2 gene. These forms of Stickler syndrome are inherited in an autosomal dominant manner. Stickler syndrome type IV is caused by mutations in the COL9A1 gene, and Stickler syndrome type V is caused by mutations in the COL9A2 gene. These types of Stickler syndrome are inherited in an autosomal recessive manner.
ERROR	duplicate_definition	Stickler syndrome type 2 [MONDO:0011493]	definition [IAO:0000115]	Stickler syndrome is a group of hereditary connective tissue disorders characterized by distinctive facial features, eye abnormalities, hearing loss, and joint problems. The features vary widely among affected people. Stickler syndrome type 1 may be divided into 2 subgroups: the membranous vitreous type and a predominantly ocular type. Both arecaused by mutations in the COL2A1 gene. Stickler syndrome type II , sometimes called the beaded vitreous type, is caused by mutations in the COL11A1 gene. Stickler syndrome type III , sometimes called the nonocular form, is caused by mutations in the COL11A2 gene. These forms of Stickler syndrome are inherited in an autosomal dominant manner. Stickler syndrome type IV is caused by mutations in the COL9A1 gene, and Stickler syndrome type V is caused by mutations in the COL9A2 gene. These types of Stickler syndrome are inherited in an autosomal recessive manner.
ERROR	duplicate_definition	subcorneal pustular dermatosis [MONDO:0006614]	definition [IAO:0000115]	Skin diseases characterized by local or general distributions of blisters. They are classified according to the site and mode of blister formation. Lesions can appear spontaneously or be precipitated by infection, trauma, or sunlight. Etiologies include immunologic and genetic factors. (From Scientific American Medicine, 1990)
ERROR	duplicate_definition	vesiculobullous skin disease [MONDO:0006617]	definition [IAO:0000115]	Skin diseases characterized by local or general distributions of blisters. They are classified according to the site and mode of blister formation. Lesions can appear spontaneously or be precipitated by infection, trauma, or sunlight. Etiologies include immunologic and genetic factors. (From Scientific American Medicine, 1990)
ERROR	duplicate_definition	bulimia nervosa [MONDO:0005452]	definition [IAO:0000115]	Recurrent episodes of over-eating.
ERROR	duplicate_definition	binge eating disorder [MONDO:0005582]	definition [IAO:0000115]	Recurrent episodes of over-eating.
ERROR	duplicate_definition	rheumatic myocarditis [MONDO:0004582]	definition [IAO:0000115]	Pancarditis, involving inflammation of the endocardium, myocardium, and epicardium. It results from an autoimmune reaction following an infection with Streptococcus pyogenes (Group A Streptococci).
ERROR	duplicate_definition	acute rheumatic heart disease [MONDO:0021777]	definition [IAO:0000115]	Pancarditis, involving inflammation of the endocardium, myocardium, and epicardium. It results from an autoimmune reaction following an infection with Streptococcus pyogenes (Group A Streptococci).
ERROR	duplicate_definition	autosomal recessive osteopetrosis 1 [MONDO:0009815]	definition [IAO:0000115]	Osteopetrosis refers to a group of rare, inherited skeletal disorders characterized by increased bone density and abnormal bone growth. Symptoms and severity can vary greatly,ranging from neonatal onset with life-threatening complications (such as bone marrow failure) to the incidental finding of osteopetrosis on X-ray. Depending on severity and age of onset, features may includefractures, short stature, compressive neuropathies (pressure on the nerves), hypocalcemia with attendant tetanic seizures ,and life-threatening pancytopenia . In rare cases, there may be neurological impairment or involvement of other body systems. Osteopetrosis may be caused by mutations in at least 10 genes . Inheritance can be autosomal recessive , autosomal dominant , or X-linked recessive with the most severe forms being autosomal recessive. Management depends on the specific symptoms and severity and may include vitamin D supplements, various medications, and/or surgery. adult osteopetrosis requires no treatment by itself, but complications may require intervention.
ERROR	duplicate_definition	autosomal recessive osteopetrosis 2 [MONDO:0009816]	definition [IAO:0000115]	Osteopetrosis refers to a group of rare, inherited skeletal disorders characterized by increased bone density and abnormal bone growth. Symptoms and severity can vary greatly,ranging from neonatal onset with life-threatening complications (such as bone marrow failure) to the incidental finding of osteopetrosis on X-ray. Depending on severity and age of onset, features may includefractures, short stature, compressive neuropathies (pressure on the nerves), hypocalcemia with attendant tetanic seizures ,and life-threatening pancytopenia . In rare cases, there may be neurological impairment or involvement of other body systems. Osteopetrosis may be caused by mutations in at least 10 genes . Inheritance can be autosomal recessive , autosomal dominant , or X-linked recessive with the most severe forms being autosomal recessive. Management depends on the specific symptoms and severity and may include vitamin D supplements, various medications, and/or surgery. adult osteopetrosis requires no treatment by itself, but complications may require intervention.
ERROR	duplicate_definition	autosomal recessive osteopetrosis 5 [MONDO:0009817]	definition [IAO:0000115]	Osteopetrosis refers to a group of rare, inherited skeletal disorders characterized by increased bone density and abnormal bone growth. Symptoms and severity can vary greatly,ranging from neonatal onset with life-threatening complications (such as bone marrow failure) to the incidental finding of osteopetrosis on X-ray. Depending on severity and age of onset, features may includefractures, short stature, compressive neuropathies (pressure on the nerves), hypocalcemia with attendant tetanic seizures ,and life-threatening pancytopenia . In rare cases, there may be neurological impairment or involvement of other body systems. Osteopetrosis may be caused by mutations in at least 10 genes . Inheritance can be autosomal recessive , autosomal dominant , or X-linked recessive with the most severe forms being autosomal recessive. Management depends on the specific symptoms and severity and may include vitamin D supplements, various medications, and/or surgery. adult osteopetrosis requires no treatment by itself, but complications may require intervention.
ERROR	duplicate_definition	autosomal recessive osteopetrosis 4 [MONDO:0012676]	definition [IAO:0000115]	Osteopetrosis refers to a group of rare, inherited skeletal disorders characterized by increased bone density and abnormal bone growth. Symptoms and severity can vary greatly,ranging from neonatal onset with life-threatening complications (such as bone marrow failure) to the incidental finding of osteopetrosis on X-ray. Depending on severity and age of onset, features may includefractures, short stature, compressive neuropathies (pressure on the nerves), hypocalcemia with attendant tetanic seizures ,and life-threatening pancytopenia . In rare cases, there may be neurological impairment or involvement of other body systems. Osteopetrosis may be caused by mutations in at least 10 genes . Inheritance can be autosomal recessive , autosomal dominant , or X-linked recessive with the most severe forms being autosomal recessive. Management depends on the specific symptoms and severity and may include vitamin D supplements, various medications, and/or surgery. adult osteopetrosis requires no treatment by itself, but complications may require intervention.
ERROR	duplicate_definition	autosomal recessive osteopetrosis 6 [MONDO:0012679]	definition [IAO:0000115]	Osteopetrosis refers to a group of rare, inherited skeletal disorders characterized by increased bone density and abnormal bone growth. Symptoms and severity can vary greatly,ranging from neonatal onset with life-threatening complications (such as bone marrow failure) to the incidental finding of osteopetrosis on X-ray. Depending on severity and age of onset, features may includefractures, short stature, compressive neuropathies (pressure on the nerves), hypocalcemia with attendant tetanic seizures ,and life-threatening pancytopenia . In rare cases, there may be neurological impairment or involvement of other body systems. Osteopetrosis may be caused by mutations in at least 10 genes . Inheritance can be autosomal recessive , autosomal dominant , or X-linked recessive with the most severe forms being autosomal recessive. Management depends on the specific symptoms and severity and may include vitamin D supplements, various medications, and/or surgery. adult osteopetrosis requires no treatment by itself, but complications may require intervention.
ERROR	duplicate_definition	autosomal recessive osteopetrosis 7 [MONDO:0012859]	definition [IAO:0000115]	Osteopetrosis refers to a group of rare, inherited skeletal disorders characterized by increased bone density and abnormal bone growth. Symptoms and severity can vary greatly,ranging from neonatal onset with life-threatening complications (such as bone marrow failure) to the incidental finding of osteopetrosis on X-ray. Depending on severity and age of onset, features may includefractures, short stature, compressive neuropathies (pressure on the nerves), hypocalcemia with attendant tetanic seizures ,and life-threatening pancytopenia . In rare cases, there may be neurological impairment or involvement of other body systems. Osteopetrosis may be caused by mutations in at least 10 genes . Inheritance can be autosomal recessive , autosomal dominant , or X-linked recessive with the most severe forms being autosomal recessive. Management depends on the specific symptoms and severity and may include vitamin D supplements, various medications, and/or surgery. adult osteopetrosis requires no treatment by itself, but complications may require intervention.
ERROR	duplicate_definition	pseudo-Hurler polydystrophy [MONDO:0009651]	definition [IAO:0000115]	Mucolipidosis III alpha/beta (MLIII alpha/beta) is a lysosomal disorder characterized by progressive slowing of the growth rate from early childhood, stiffness and pain in joints, gradual coarsening of facial features, moderate developmental delay and mild intellectual disability in most patients.
ERROR	duplicate_definition	mucolipidosis type III [MONDO:0018931]	definition [IAO:0000115]	Mucolipidosis III alpha/beta (MLIII alpha/beta) is a lysosomal disorder characterized by progressive slowing of the growth rate from early childhood, stiffness and pain in joints, gradual coarsening of facial features, moderate developmental delay and mild intellectual disability in most patients.
ERROR	duplicate_definition	mitochondrial myopathy with lactic acidosis [MONDO:0009639]	definition [IAO:0000115]	Mitochondrial myopathy-lactic acidosis-deafness is a type of metabolic myopathy described only in two sisters to date, presenting during childhood, and characterized clinically by growth failure, severe muscle weakness, and moderate sensorineural deafness and biochemically by metabolic acidosis, elevated serum pyruvate concentration, hyperalaninemia and hyperalaninuria. There have been no further descriptions in the literature since 1973.
ERROR	duplicate_definition	mitochondrial myopathy-lactic acidosis-deafness syndrome [MONDO:0016825]	definition [IAO:0000115]	Mitochondrial myopathy-lactic acidosis-deafness is a type of metabolic myopathy described only in two sisters to date, presenting during childhood, and characterized clinically by growth failure, severe muscle weakness, and moderate sensorineural deafness and biochemically by metabolic acidosis, elevated serum pyruvate concentration, hyperalaninemia and hyperalaninuria. There have been no further descriptions in the literature since 1973.
ERROR	duplicate_definition	allergic cutaneous vasculitis [MONDO:0001290]	definition [IAO:0000115]	Inflammation of the small vessels of the skin that is mediated by the immune system.
ERROR	duplicate_definition	hypersensitivity vasculitis [MONDO:0006794]	definition [IAO:0000115]	Inflammation of the small vessels of the skin that is mediated by the immune system.
ERROR	duplicate_definition	acute proliferative glomerulonephritis [MONDO:0001644]	definition [IAO:0000115]	Inflammation of the glomeruli status post infection with nephritogenic streptococci, most often group A beta hemolytic streptococcus.
ERROR	duplicate_definition	acute poststreptococcal glomerulonephritis [MONDO:0001870]	definition [IAO:0000115]	Inflammation of the glomeruli status post infection with nephritogenic streptococci, most often group A beta hemolytic streptococcus.
ERROR	duplicate_definition	staphylococcus aureus infection [MONDO:0005545]	definition [IAO:0000115]	infection by Staphylococcus.
ERROR	duplicate_definition	staphylococcal infection [MONDO:0024313]	definition [IAO:0000115]	infection by Staphylococcus.
ERROR	duplicate_definition	congestive heart failure [MONDO:0005009]	definition [IAO:0000115]	Inability of the heart to pump blood at an adequate rate to meet tissue metabolic requirements. Clinical symptoms of heart failure include: unusual dyspnea on light exertion, recurrent dyspnea occurring in the supine position, fluid retention or rales, jugular venous distension, pulmonary edema on physical exam, or pulmonary edema on chest x-ray presumed to be cardiac dysfunction.
ERROR	duplicate_definition	heart failure [MONDO:0005252]	definition [IAO:0000115]	Inability of the heart to pump blood at an adequate rate to meet tissue metabolic requirements. Clinical symptoms of heart failure include: unusual dyspnea on light exertion, recurrent dyspnea occurring in the supine position, fluid retention or rales, jugular venous distension, pulmonary edema on physical exam, or pulmonary edema on chest x-ray presumed to be cardiac dysfunction.
ERROR	duplicate_definition	prostate carcinoma in situ [MONDO:0004623]	definition [IAO:0000115]	High grade prostatic intraepithelial neoplasia characterized by the presence of severe architectural and cytologic abnormalities.
ERROR	duplicate_definition	grade III prostatic intraepithelial neoplasia [MONDO:0006234]	definition [IAO:0000115]	High grade prostatic intraepithelial neoplasia characterized by the presence of severe architectural and cytologic abnormalities.
ERROR	duplicate_definition	malignant histiocytic disease [MONDO:0002346]	definition [IAO:0000115]	Distinctive neoplastic disorders of histiocytes. Included are malignant neoplasms of macrophages and dendritic cells.
ERROR	duplicate_definition	malignant histiocytosis [MONDO:0004612]	definition [IAO:0000115]	Distinctive neoplastic disorders of histiocytes. Included are malignant neoplasms of macrophages and dendritic cells.
ERROR	duplicate_definition	uterine corpus leiomyomatosis [MONDO:0003703]	definition [IAO:0000115]	An unusual condition characterized by the presence of numerous small benign smooth muscle neoplasms located throughout the body of the uterus.
ERROR	duplicate_definition	uterine corpus diffuse leiomyomatosis [MONDO:0003704]	definition [IAO:0000115]	An unusual condition characterized by the presence of numerous small benign smooth muscle neoplasms located throughout the body of the uterus.
ERROR	duplicate_definition	phaeohyphomycosis [MONDO:0001867]	definition [IAO:0000115]	An opportunistic fungal infection caused by any of a variety of normally saprophytic fungi with hyaline hyphal elements. For example, Fusarium spp. infect neutropenic patients to cause pneumonia, fungemia, and disseminated infection with cutaneous lesions.
ERROR	duplicate_definition	hyalohyphomycosis [MONDO:0045037]	definition [IAO:0000115]	An opportunistic fungal infection caused by any of a variety of normally saprophytic fungi with hyaline hyphal elements. For example, Fusarium spp. infect neutropenic patients to cause pneumonia, fungemia, and disseminated infection with cutaneous lesions.
ERROR	duplicate_definition	motor peripheral neuropathy [MONDO:0002316]	definition [IAO:0000115]	An inherited degenerative disorder involving the peripheral nerves. It is caused by mutations in the genes that are responsible for the production of proteins necessary for the function and structure of the peripheral nerves. It is characterized by muscle atrophy and weakness in the feet, legs, hands, and arms and loss of sensation in the limbs.
ERROR	duplicate_definition	Charcot-Marie-Tooth disease [MONDO:0015626]	definition [IAO:0000115]	An inherited degenerative disorder involving the peripheral nerves. It is caused by mutations in the genes that are responsible for the production of proteins necessary for the function and structure of the peripheral nerves. It is characterized by muscle atrophy and weakness in the feet, legs, hands, and arms and loss of sensation in the limbs.
ERROR	duplicate_definition	intestinal schistosomiasis [MONDO:0008412]	definition [IAO:0000115]	An infection that is caused by Schistosoma japonicum.
ERROR	duplicate_definition	Schistosoma japonicum infectious disease [MONDO:0044344]	definition [IAO:0000115]	An infection that is caused by Schistosoma japonicum.
ERROR	duplicate_definition	acute stress disorder [MONDO:0003763]	definition [IAO:0000115]	An anxiety disorder precipitated by an experience of intense fear or horror while exposed to a traumatic (especially life-threatening) event. The disorder is characterized by dissociative symptoms; vivid recollections of the traumatic event; avoidance of stimuli associated with the traumatic event; and a constant state of hyperarousal for no more than one month.
ERROR	duplicate_definition	acute stress reaction [MONDO:0005457]	definition [IAO:0000115]	An anxiety disorder precipitated by an experience of intense fear or horror while exposed to a traumatic (especially life-threatening) event. The disorder is characterized by dissociative symptoms; vivid recollections of the traumatic event; avoidance of stimuli associated with the traumatic event; and a constant state of hyperarousal for no more than one month.
ERROR	duplicate_definition	acute erythroleukemia, familial [MONDO:0007573]	definition [IAO:0000115]	An acute myeloid leukemia characterized by a predominant immature erythroid population. There are two subtypes recognized: erythroleukemia and pure erythroid leukemia. (WHO, 2001)
ERROR	duplicate_definition	acute erythroid leukemia [MONDO:0017858]	definition [IAO:0000115]	An acute myeloid leukemia characterized by a predominant immature erythroid population. There are two subtypes recognized: erythroleukemia and pure erythroid leukemia. (WHO, 2001)
ERROR	duplicate_definition	b- and T-cell mixed leukemia [MONDO:0006667]	definition [IAO:0000115]	An acute leukemia of ambiguous lineage characterized by blasts which coexpress myeloid and T or B lineage antigens or concurrent B and T lineage antigens. (WHO, 2001)
ERROR	duplicate_definition	acute biphenotypic leukemia [MONDO:0020322]	definition [IAO:0000115]	An acute leukemia of ambiguous lineage characterized by blasts which coexpress myeloid and T or B lineage antigens or concurrent B and T lineage antigens. (WHO, 2001)
ERROR	duplicate_definition	benign ependymoma [MONDO:0003161]	definition [IAO:0000115]	A WHO grade II, slow growing tumor of children and young adults, usually located intraventricularly. It is the most common ependymal neoplasm. It often causes clinical symptoms by blocking cerebrospinal fluid pathways. Key histological features include perivascular pseudorosettes and ependymal rosettes. (WHO)
ERROR	duplicate_definition	ependymoma [MONDO:0016698]	definition [IAO:0000115]	A WHO grade II, slow growing tumor of children and young adults, usually located intraventricularly. It is the most common ependymal neoplasm. It often causes clinical symptoms by blocking cerebrospinal fluid pathways. Key histological features include perivascular pseudorosettes and ependymal rosettes. (WHO)
ERROR	duplicate_definition	benign mesothelioma [MONDO:0002373]	definition [IAO:0000115]	A usually malignant and aggressive neoplasm of the mesothelium which is often associated with exposure to asbestos.
ERROR	duplicate_definition	mesothelioma [MONDO:0005065]	definition [IAO:0000115]	A usually malignant and aggressive neoplasm of the mesothelium which is often associated with exposure to asbestos.
ERROR	duplicate_definition	autosomal dominant polycystic kidney disease [MONDO:0004691]	definition [IAO:0000115]	A usually autosomal dominant and less frequently autosomal recessive genetic disorder characterized by the presence of numerous cysts in the kidneys leading to end-stage renal failure. The autosomal dominant trait is associated with abnormalities on the short arm of chromosome 16. Symptoms in patients with the autosomal dominant trait usually appear at middle age and include abdominal pain, hematuria, and high blood pressure. Patients may develop brain aneurysms and liver cysts. Patients with the autosomal recessive trait present with progressive renal failure early in life and symptoms resulting from hepatic fibrosis. The autosomal recessive trait is associated with abnormalities of chromosome 6. Polycystic kidney disease may also result as a side effect in patients on renal dialysis.
ERROR	duplicate_definition	polycystic kidney disease [MONDO:0020642]	definition [IAO:0000115]	A usually autosomal dominant and less frequently autosomal recessive genetic disorder characterized by the presence of numerous cysts in the kidneys leading to end-stage renal failure. The autosomal dominant trait is associated with abnormalities on the short arm of chromosome 16. Symptoms in patients with the autosomal dominant trait usually appear at middle age and include abdominal pain, hematuria, and high blood pressure. Patients may develop brain aneurysms and liver cysts. Patients with the autosomal recessive trait present with progressive renal failure early in life and symptoms resulting from hepatic fibrosis. The autosomal recessive trait is associated with abnormalities of chromosome 6. Polycystic kidney disease may also result as a side effect in patients on renal dialysis.
ERROR	duplicate_definition	pulmonary large cell neuroendocrine carcinoma [MONDO:0003960]	definition [IAO:0000115]	A usually aggressive carcinoma composed of large malignant cells which display neuroendocrine characteristics. It is characterized by the presence of high mitotic activity and necrotic changes. The vast majority of cases are positive for neuron-specific enolase. Representative examples include lung, breast, cervical, and thymic neuroendocrine carcinomas.
ERROR	duplicate_definition	large cell neuroendocrine carcinoma [MONDO:0005057]	definition [IAO:0000115]	A usually aggressive carcinoma composed of large malignant cells which display neuroendocrine characteristics. It is characterized by the presence of high mitotic activity and necrotic changes. The vast majority of cases are positive for neuron-specific enolase. Representative examples include lung, breast, cervical, and thymic neuroendocrine carcinomas.
ERROR	duplicate_definition	hyperinsulinemic hypoglycemia (disease) [MONDO:0005803]	definition [IAO:0000115]	A sporadic or inherited disorder characterized by the focal or diffuse proliferation of the cells of the islets of Langerhans in the pancreas. It results in hyperinsulinemia and hypoglycemia.
ERROR	duplicate_definition	islet cell adenomatosis [MONDO:0007834]	definition [IAO:0000115]	A sporadic or inherited disorder characterized by the focal or diffuse proliferation of the cells of the islets of Langerhans in the pancreas. It results in hyperinsulinemia and hypoglycemia.
ERROR	duplicate_definition	verrucous keratotic hemangioma [MONDO:0003106]	definition [IAO:0000115]	A skin hemangioma characterized by the presence of epidermal hyperplasia.
ERROR	duplicate_definition	verrucous hemangioma [MONDO:0018734]	definition [IAO:0000115]	A skin hemangioma characterized by the presence of epidermal hyperplasia.
ERROR	duplicate_definition	neonatal systemic lupus erthematosus [MONDO:0005403]	definition [IAO:0000115]	A self-limited skin rash that appears in the neonatal period and usually resolves in four to six months after birth. It is caused by placental transfer of maternal autoantibodies, usually anti-Ro antibody. In a minority of cases, it is associated with congenital heart block, hepatitis, or thrombocytopenia. The mothers of the affected babies may be asymptomatic or suffer from systemic lupus erythematosus, Sjogren's syndrome, or rheumatoid arthritis.
ERROR	duplicate_definition	neonatal lupus erythematosus [MONDO:0018360]	definition [IAO:0000115]	A self-limited skin rash that appears in the neonatal period and usually resolves in four to six months after birth. It is caused by placental transfer of maternal autoantibodies, usually anti-Ro antibody. In a minority of cases, it is associated with congenital heart block, hepatitis, or thrombocytopenia. The mothers of the affected babies may be asymptomatic or suffer from systemic lupus erythematosus, Sjogren's syndrome, or rheumatoid arthritis.
ERROR	duplicate_definition	aphthous stomatitis [MONDO:0004845]	definition [IAO:0000115]	A recurrent disease of the oral mucosa of unknown etiology. It is characterized by small white ulcerative lesions, single or multiple, round or oval, lasting for 7-14 days and healing without scarring.
ERROR	duplicate_definition	canker sore [MONDO:0005318]	definition [IAO:0000115]	A recurrent disease of the oral mucosa of unknown etiology. It is characterized by small white ulcerative lesions, single or multiple, round or oval, lasting for 7-14 days and healing without scarring.
ERROR	duplicate_definition	peritoneal serous adenocarcinoma [MONDO:0003195]	definition [IAO:0000115]	A rare, serous adenocarcinoma that arises from the lining of the peritoneum. It affects females. The clinical behavior and pathologic characteristics are similar to the serous adenocarcinoma that arises from the ovary.
ERROR	duplicate_definition	primary peritoneal serous adenocarcinoma [MONDO:0006386]	definition [IAO:0000115]	A rare, serous adenocarcinoma that arises from the lining of the peritoneum. It affects females. The clinical behavior and pathologic characteristics are similar to the serous adenocarcinoma that arises from the ovary.
ERROR	duplicate_definition	erythropoietic protoporphyria [MONDO:0001676]	definition [IAO:0000115]	A rare congenital metabolic disorder characterized by an inborn error of porphyrin-heme biosynthesis. It is caused by deficiency of the enzyme ferrochelatase. Signs and symptoms include painful cutaneous photosensitivity leading to blistering and scarring of the exposed skin areas, erythrodontia, red discoloration of urine, hemolytic anemia, and splenomegaly.
ERROR	duplicate_definition	protoporphyria, erythropoietic [MONDO:0008319]	definition [IAO:0000115]	A rare congenital metabolic disorder characterized by an inborn error of porphyrin-heme biosynthesis. It is caused by deficiency of the enzyme ferrochelatase. Signs and symptoms include painful cutaneous photosensitivity leading to blistering and scarring of the exposed skin areas, erythrodontia, red discoloration of urine, hemolytic anemia, and splenomegaly.
ERROR	duplicate_definition	TSH producing pituitary tumor [MONDO:0003837]	definition [IAO:0000115]	A rare adenoma of the anterior lobe of the pituitary gland that produces thyrotropin. It is usually associated with goiter and hyperthyroidism.
ERROR	duplicate_definition	TSH-secreting pituitary adenoma [MONDO:0019611]	definition [IAO:0000115]	A rare adenoma of the anterior lobe of the pituitary gland that produces thyrotropin. It is usually associated with goiter and hyperthyroidism.
ERROR	duplicate_definition	sarcomatoid squamous cell skin carcinoma [MONDO:0003499]	definition [IAO:0000115]	A poorly differentiated squamous cell carcinoma characterized by the presence of malignant cells with spindle cell features.
ERROR	duplicate_definition	sarcomatoid squamous cell carcinoma [MONDO:0021663]	definition [IAO:0000115]	A poorly differentiated squamous cell carcinoma characterized by the presence of malignant cells with spindle cell features.
ERROR	duplicate_definition	pharyngitis [MONDO:0002258]	definition [IAO:0000115]	A non-neoplastic or neoplastic disorder that affects the pharynx. Representative examples include pharyngitis and carcinoma.
ERROR	duplicate_definition	disease of pharynx [MONDO:0020592]	definition [IAO:0000115]	A non-neoplastic or neoplastic disorder that affects the pharynx. Representative examples include pharyngitis and carcinoma.
ERROR	duplicate_definition	abducens nerve palsy [MONDO:0007033]	definition [IAO:0000115]	A non-neoplastic or neoplastic disorder affecting the abducens nerve (sixth cranial nerve).
ERROR	duplicate_definition	abducens nerve disease [MONDO:0020594]	definition [IAO:0000115]	A non-neoplastic or neoplastic disorder affecting the abducens nerve (sixth cranial nerve).
ERROR	duplicate_definition	papillary transitional carcinoma [MONDO:0002835]	definition [IAO:0000115]	A non-invasive or invasive transitional cell carcinoma characterized by a papillary growth pattern. It may occur in the bladder or the renal pelvis.
ERROR	duplicate_definition	papillary transitional cell carcinoma [MONDO:0006350]	definition [IAO:0000115]	A non-invasive or invasive transitional cell carcinoma characterized by a papillary growth pattern. It may occur in the bladder or the renal pelvis.
ERROR	duplicate_definition	precursor T-lymphoblastic lymphoma/leukemia [MONDO:0003537]	definition [IAO:0000115]	A neoplasm of lymphoblasts committed to the T-cell lineage, typically composed of small to medium-sized blast cells. When the neoplasm involves predominantly the bone marrow and the peripheral blood, it is called T acute lymphoblastic leukemia. When it involves nodal or extranodal sites it is called T lymphoblastic lymphoma. (WHO, 2001)
ERROR	duplicate_definition	T-cell leukemia [MONDO:0005525]	definition [IAO:0000115]	A neoplasm of lymphoblasts committed to the T-cell lineage, typically composed of small to medium-sized blast cells. When the neoplasm involves predominantly the bone marrow and the peripheral blood, it is called T acute lymphoblastic leukemia. When it involves nodal or extranodal sites it is called T lymphoblastic lymphoma. (WHO, 2001)
ERROR	duplicate_definition	parasagittal meningioma [MONDO:0004022]	definition [IAO:0000115]	A meningioma that affects the falx cerebri.
ERROR	duplicate_definition	cerebral falx meningioma [MONDO:0004422]	definition [IAO:0000115]	A meningioma that affects the falx cerebri.
ERROR	duplicate_definition	cutaneous Paget disease [MONDO:0002655]	definition [IAO:0000115]	A malignant neoplasm in which there is infiltration of the skin by neoplastic large cells with abundant pale cytoplasm and large nuclei with prominent nucleoli (Paget cells). It may affect the anus, penis, scrotum, and vulva.
ERROR	duplicate_definition	extramammary Paget disease [MONDO:0008177]	definition [IAO:0000115]	A malignant neoplasm in which there is infiltration of the skin by neoplastic large cells with abundant pale cytoplasm and large nuclei with prominent nucleoli (Paget cells). It may affect the anus, penis, scrotum, and vulva.
ERROR	duplicate_definition	capillary lymphangioma [MONDO:0002262]	definition [IAO:0000115]	A lymphangioma arising from the skin.
ERROR	duplicate_definition	skin lymphangioma [MONDO:0024673]	definition [IAO:0000115]	A lymphangioma arising from the skin.
ERROR	duplicate_definition	uterine corpus serous adenocarcinoma [MONDO:0003629]	definition [IAO:0000115]	A high grade, aggressive adenocarcinoma arising from the endometrium. It is characterized by the presence of complex papillary patterns with cellular budding. Atypical mitoses, necrosis, and psammoma bodies may be present. It is classified as type II endometrial carcinoma and it is not associated with endometrial hyperplasia. It tends to invade deeply into the myometrium and spreads into the lymphatic vessels. Patients frequently present with spread of the tumor beyond the uterus at the time of diagnosis. The prognosis is usually poor.
ERROR	duplicate_definition	endometrial serous adenocarcinoma [MONDO:0006196]	definition [IAO:0000115]	A high grade, aggressive adenocarcinoma arising from the endometrium. It is characterized by the presence of complex papillary patterns with cellular budding. Atypical mitoses, necrosis, and psammoma bodies may be present. It is classified as type II endometrial carcinoma and it is not associated with endometrial hyperplasia. It tends to invade deeply into the myometrium and spreads into the lymphatic vessels. Patients frequently present with spread of the tumor beyond the uterus at the time of diagnosis. The prognosis is usually poor.
ERROR	duplicate_definition	conventional osteosarcoma [MONDO:0002631]	definition [IAO:0000115]	A high grade malignant bone-forming mesenchymal neoplasm producing osteoid. The tumor arises from the medullary portion of the bone. It affects the long bones and most commonly, the distal femur, proximal tibia, and proximal humerus. Pain with or without a palpable mass is the most common clinical presentation. It usually has an aggressive growth and may metastasize through the hematogenous route. The lung is the most frequent site of metastasis.
ERROR	duplicate_definition	intracortical osteogenic sarcoma [MONDO:0004300]	definition [IAO:0000115]	A high grade malignant bone-forming mesenchymal neoplasm producing osteoid. The tumor arises from the medullary portion of the bone. It affects the long bones and most commonly, the distal femur, proximal tibia, and proximal humerus. Pain with or without a palpable mass is the most common clinical presentation. It usually has an aggressive growth and may metastasize through the hematogenous route. The lung is the most frequent site of metastasis.
ERROR	duplicate_definition	histiocytoid hemangioma [MONDO:0003119]	definition [IAO:0000115]	A hemangioma characterized by the presence of epithelioid endothelial cells.
ERROR	duplicate_definition	epithelioid hemangioma [MONDO:0021169]	definition [IAO:0000115]	A hemangioma characterized by the presence of epithelioid endothelial cells.
ERROR	duplicate_definition	SM-AHNMD [MONDO:0003148]	definition [IAO:0000115]	A disorder characterized by systemic infiltration of internal organs by aggregates of neoplastic mast cells and the presence of a clonal non-mast cell hematologic neoplasm (e.g., myelodysplastic syndrome, chronic myeloproliferative disorder, acute myeloid leukemia, and lymphoma).
ERROR	duplicate_definition	systemic mastocytosis with associated clonal hematological non-mast-cell lineage disease [MONDO:0006440]	definition [IAO:0000115]	A disorder characterized by systemic infiltration of internal organs by aggregates of neoplastic mast cells and the presence of a clonal non-mast cell hematologic neoplasm (e.g., myelodysplastic syndrome, chronic myeloproliferative disorder, acute myeloid leukemia, and lymphoma).
ERROR	duplicate_definition	Brucella abortus brucellosis [MONDO:0001973]	definition [IAO:0000115]	A disease of cattle caused by bacteria of the genus brucella leading to abortion in late pregnancy. brucella abortus is the primary infective agent.
ERROR	duplicate_definition	brucellosis, bovine [MONDO:0025389]	definition [IAO:0000115]	A disease of cattle caused by bacteria of the genus brucella leading to abortion in late pregnancy. brucella abortus is the primary infective agent.
ERROR	duplicate_definition	ampulla of vater squamous cell carcinoma [MONDO:0003490]	definition [IAO:0000115]	A carcinoma with glandular and squamous differentiation arising from the ampulla of Vater. Signs and symptoms include jaundice, abdominal pain, anorexia, nausea, vomiting, and weight loss.
ERROR	duplicate_definition	ampulla of vater adenosquamous carcinoma [MONDO:0003553]	definition [IAO:0000115]	A carcinoma with glandular and squamous differentiation arising from the ampulla of Vater. Signs and symptoms include jaundice, abdominal pain, anorexia, nausea, vomiting, and weight loss.
ERROR	duplicate_definition	squamous cell bile duct carcinoma [MONDO:0003500]	definition [IAO:0000115]	A carcinoma that arises from the extrahepatic bile ducts. It is composed entirely by malignant squamous epithelial cells.
ERROR	duplicate_definition	extrahepatic bile duct squamous cell carcinoma [MONDO:0006203]	definition [IAO:0000115]	A carcinoma that arises from the extrahepatic bile ducts. It is composed entirely by malignant squamous epithelial cells.
ERROR	duplicate_definition	adenosquamous bile duct carcinoma [MONDO:0003549]	definition [IAO:0000115]	A carcinoma that arises from the extrahepatic bile ducts. It is characterized by the presence of glandular and squamous malignant epithelial components.
ERROR	duplicate_definition	extrahepatic bile duct adenosquamous carcinoma [MONDO:0006202]	definition [IAO:0000115]	A carcinoma that arises from the extrahepatic bile ducts. It is characterized by the presence of glandular and squamous malignant epithelial components.
ERROR	duplicate_definition	nasopharyngeal squamous cell carcinoma [MONDO:0006060]	definition [IAO:0000115]	A carcinoma arising from the nasopharyngeal epithelium. It includes the following types: keratinizing squamous cell carcinoma, nonkeratinizing carcinoma (differentiated and undifferentiated), basaloid squamous cell carcinoma, and papillary adenocarcinoma.
ERROR	duplicate_definition	nasopharyngeal carcinoma [MONDO:0015459]	definition [IAO:0000115]	A carcinoma arising from the nasopharyngeal epithelium. It includes the following types: keratinizing squamous cell carcinoma, nonkeratinizing carcinoma (differentiated and undifferentiated), basaloid squamous cell carcinoma, and papillary adenocarcinoma.
ERROR	duplicate_definition	Ritter disease [MONDO:0005948]	definition [IAO:0000115]	A blistering skin disorder caused by exfoliative toxins produced by Staphylococcus aureus infection. The toxins cause the formation of bullae and diffuse skin desquamation. The lesions may be localized or generalized, far away from the initial site of infection.
ERROR	duplicate_definition	staphylococcal scalded skin syndrome [MONDO:0018181]	definition [IAO:0000115]	A blistering skin disorder caused by exfoliative toxins produced by Staphylococcus aureus infection. The toxins cause the formation of bullae and diffuse skin desquamation. The lesions may be localized or generalized, far away from the initial site of infection.
ERROR	duplicate_definition	breast tumor luminal A or B [MONDO:0004990]	definition [IAO:0000115]	A biologic subset of breast carcinoma defined by low to moderate expression of genes characteristic of luminal epithelial cells including estrogen receptor (ER), and high expression of GGH, LAPTM4B, and CCNE1. This subtype of breast cancer is associated with a good prognosis, although not as favorable as the luminal A subtype.
ERROR	duplicate_definition	luminal B breast carcinoma [MONDO:0021115]	definition [IAO:0000115]	A biologic subset of breast carcinoma defined by low to moderate expression of genes characteristic of luminal epithelial cells including estrogen receptor (ER), and high expression of GGH, LAPTM4B, and CCNE1. This subtype of breast cancer is associated with a good prognosis, although not as favorable as the luminal A subtype.
ERROR	duplicate_definition	fibrosarcoma (disease) [MONDO:0005164]	definition [IAO:0000115]	A benign, intermediate, or malignant mesenchymal neoplasm characterized by the presence of neoplastic fibroblasts.
ERROR	duplicate_definition	fibroblastic neoplasm [MONDO:0006209]	definition [IAO:0000115]	A benign, intermediate, or malignant mesenchymal neoplasm characterized by the presence of neoplastic fibroblasts.
ERROR	duplicate_definition	biliary tract neoplasm (disease) [MONDO:0005304]	definition [IAO:0000115]	A benign or malignant neoplasm that affects the extrahepatic bile ducts. Representative examples include adenoma and adenocarcinoma.
ERROR	duplicate_definition	extrahepatic bile duct neoplasm [MONDO:0021385]	definition [IAO:0000115]	A benign or malignant neoplasm that affects the extrahepatic bile ducts. Representative examples include adenoma and adenocarcinoma.
ERROR	duplicate_definition	Bartholin gland benign neoplasm [MONDO:0002193]	definition [IAO:0000115]	A benign or malignant neoplasm that affects the Bartholin gland. Representative examples include adenoma, adenomyoma, adenocarcinoma, and squamous cell carcinoma.
ERROR	duplicate_definition	Bartholin gland neoplasm [MONDO:0021114]	definition [IAO:0000115]	A benign or malignant neoplasm that affects the Bartholin gland. Representative examples include adenoma, adenomyoma, adenocarcinoma, and squamous cell carcinoma.
ERROR	duplicate_definition	benign peritoneal mesothelioma [MONDO:0002112]	definition [IAO:0000115]	A benign or malignant mesothelial neoplasm that arises from the peritoneum.
ERROR	duplicate_definition	peritoneal mesothelioma (disease) [MONDO:0006362]	definition [IAO:0000115]	A benign or malignant mesothelial neoplasm that arises from the peritoneum.
ERROR	duplicate_definition	ovarian serous cystadenofibroma [MONDO:0004185]	definition [IAO:0000115]	A benign neoplasm of the ovary characterized by the presence of cystic structures lined by serous epithelial cells in a fibrotic stroma.
ERROR	duplicate_definition	serous cystadenofibroma [MONDO:0005182]	definition [IAO:0000115]	A benign neoplasm of the ovary characterized by the presence of cystic structures lined by serous epithelial cells in a fibrotic stroma.
ERROR	duplicate_definition	cystic lymphangioma [MONDO:0006719]	definition [IAO:0000115]	A benign lymphatic neoplasm usually arising from the neck and characterized by cystic dilation of the lymphatic vessels.
ERROR	duplicate_definition	cystic hygroma [MONDO:0009761]	definition [IAO:0000115]	A benign lymphatic neoplasm usually arising from the neck and characterized by cystic dilation of the lymphatic vessels.
ERROR	duplicate_definition	DPAGT1-CDG [MONDO:0011964]	definition [IAO:0000115]	(11q23.3).
ERROR	duplicate_definition	STT3A-CDG [MONDO:0014270]	definition [IAO:0000115]	(11q23.3).
ERROR	missing_label	MONDO_0003750 [MONDO:0003750]	label [rdfs:label]
ERROR	deprecated_class_reference	MONDO_0024253 [MONDO:0024253]	rdfs:subClassOf	intellectual disability, autosomal recessive 53 [MONDO:0014832]
ERROR	missing_ontology_description	mondo.owl	dc11:description

I am keeping track of these errors and revised defs in this spreadsheet

how are we getting on with this? @wdduncan can you help?

according to my spreadsheet, 15 of these have been addressed. There are a couple open tickets, I can prioritize those.

There are 132 terms that need to be reviewed, so there is still a lot of work left to do. It would be great to have some help! :)

I just ran robot report, we have 1660 duplicate_exact_synonym lines, can we prioritize these? I think most of these are very obvious, but it may be v inefficient to fix in Protege, I could do these in emacs in 15 mins but not sure when I have the time...

Sorry ... I'm a bit confused. I manually checked the mondo-edit.obo for 5 classes noted in the spreadsheet. I am not seeing duplicates. Is there a problem with robot report?

Classes checked:

[Term]
id: MONDO:0002631
name: conventional osteosarcoma
def: "A high grade malignant bone-forming mesenchymal neoplasm producing osteoid. The tumor arises from the medullary portion of the bone. It affects the long bones and most commonly, the distal femur, proximal tibia, and proximal humerus. Pain with or without a palpable mass is the most common clinical presentation. It usually has an aggressive growth and may metastasize through the hematogenous route. The lung is the most frequent site of metastasis." [NCIT:C35870]
synonym: "central osteosarcoma" EXACT [NCIT:C35870]
synonym: "conventional central osteosarcoma" EXACT [DOID:3378, NCIT:C35870]
synonym: "conventional osteosarcoma" EXACT [NCIT:C35870]
synonym: "intracortical osteogenic sarcoma" EXACT [NCIT:C35870]
synonym: "intracortical osteosarcoma" EXACT [NCIT:C35870]
synonym: "medullary osteosarcoma" EXACT [NCIT:C35870]
xref: DOID:3378 {source="MONDO:equivalentTo"}
xref: ICDO:9186/3 {source="NCIT:C35870"}
xref: ICDO:9195/3 {source="NCIT:C35870"}
xref: NCIT:C35870 {source="MONDO:equivalentTo"}
xref: UMLS:C1266166 {source="NCIT:C35870", source="MONDO:superClassOf"}
is_a: MONDO:0002629 {source="DOID:3378", source="NCIT:C35870/inferred"} ! bone osteosarcoma
relationship: disease_arises_from_structure UBERON:0007195 ! stroma of bone marrow

[Term]
id: MONDO:0003500
name: squamous cell bile duct carcinoma
def: "A carcinoma that arises from the extrahepatic bile ducts. It is composed entirely by malignant squamous epithelial cells." [NCIT:P378]
synonym: "bile duct squamous cell carcinoma" EXACT [DOID:5537, MONDO:patterns/location, NCIT:C5777]
xref: DOID:5537 {source="MONDO:equivalentTo"}
xref: NCIT:C5777 {source="DOID:5537", source="MONDO:directSiblingOf"}
xref: UMLS:C0861861 {source="DOID:5537", source="MONDO:equivalentTo"}
is_a: MONDO:0005096 {source="DOID:5537", source="MONDO:Entailed", source="indirect"} ! squamous cell carcinoma
is_a: MONDO:0005496 {source="DOID:5537", source="MONDO:Redundant", source="MONDOLEX:0003500"} ! bile duct carcinoma
intersection_of: MONDO:0005096 ! squamous cell carcinoma
intersection_of: disease_has_location UBERON:0002394 ! bile duct

[Term]
id: MONDO:0021114
name: Bartholin gland neoplasm
def: "A benign or malignant neoplasm that affects the Bartholin gland. Representative examples include adenoma, adenomyoma, adenocarcinoma, and squamous cell carcinoma." [NCIT:C6434]
synonym: "Bartholin gland neoplasm" EXACT [NCIT:C6434]
synonym: "Bartholin's gland neoplasm" EXACT [NCIT:C6434]
synonym: "Bartholin's gland tumor" EXACT [NCIT:C6434]
synonym: "major vestibular gland neoplasm" EXACT []
synonym: "major vestibular gland neoplasm (disease)" EXACT [MONDO:patterns/location]
synonym: "major vestibular gland tumor" EXACT [MONDO:patterns/neoplasm]
synonym: "neoplasm of Bartholin's gland" EXACT [NCIT:C6434]
synonym: "neoplasm of major vestibular gland" EXACT [MONDO:patterns/neoplasm]
synonym: "neoplasm of the Bartholin's gland" EXACT [NCIT:C6434]
synonym: "tumor of Bartholin's gland" EXACT [NCIT:C6434]
synonym: "tumor of major vestibular gland" EXACT [MONDO:patterns/neoplasm]
synonym: "tumor of the Bartholin's gland" EXACT [NCIT:C6434]
xref: NCIT:C6434 {source="MONDO:equivalentTo"}
xref: UMLS:C0220616 {source="NCIT:C6434", source="MONDO:notFoundInDiseaseSubset"}
is_a: MONDO:0021049 {source="MONDO:Redundant", source="NCIT:C6434"} ! vulvar neoplasm
intersection_of: MONDO:0005070 ! neoplasm (disease)
intersection_of: disease_has_location UBERON:0000460 ! major vestibular gland

[Term]
id: MONDO:0021115
name: luminal B breast carcinoma
def: "A biologic subset of breast carcinoma defined by low to moderate expression of genes characteristic of luminal epithelial cells including estrogen receptor (ER), and high expression of GGH, LAPTM4B, and CCNE1. This subtype of breast cancer is associated with a good prognosis, although not as favorable as the luminal A subtype." [NCIT:C53555]
synonym: "Luminal B" EXACT [NCIT:C53555]
synonym: "Luminal B breast cancer" EXACT [NCIT:C53555]
synonym: "Luminal B breast carcinoma" EXACT [NCIT:C53555]
synonym: "Luminal B estrogen receptor positive subtype of breast carcinoma" EXACT [NCIT:C53555]
synonym: "Luminal B subtype of breast carcinoma" EXACT [NCIT:C53555]
xref: NCIT:C53555 {source="MONDO:equivalentTo"}
xref: UMLS:C3642346 {source="MONDO:equivalentTo", source="NCIT:C53555"}
is_a: MONDO:0004990 ! breast tumor luminal A or B
is_a: MONDO:0006116 {source="MONDO:Redundant", source="NCIT:C53555", source="indirect"} ! breast carcinoma by gene expression profile

[Term]
id: MONDO:0009761
name: cystic hygroma
def: "A benign lymphatic neoplasm usually arising from the neck and characterized by cystic dilation of the lymphatic vessels." [NCIT:C3724]
subset: gard_rare
subset: ordo_clinical_subtype {source="Orphanet:79486"}
synonym: "cystic hygroma" EXACT [NCIT:C3724]
synonym: "cystic hygroma, fetal" RELATED [OMIM:257350]
synonym: "cystic lymphangioma" EXACT [GARD:0006234, NCIT:C3724]
synonym: "hygroma" EXACT [NCIT:C3724]
synonym: "macrocystic lymphatic malformation" RELATED [GARD:0006234]
synonym: "nuchal bleb, familial" RELATED [OMIM:257350]
xref: GARD:0006234 {source="MONDO:equivalentTo"}
xref: ICD10:D18.1 {source="ORDO:79486/ntbt", source="Orphanet:79486"}
xref: ICDO:9173/0 {source="NCIT:C3724"}
xref: NCIT:C3724 {source="kboom:pr0.78-conf7.23", source="MONDO:equivalentTo"}
xref: OMIM:257350 {source="MONDO:equivalentTo", source="ORDO:79486/e", source="Orphanet:79486", source="GARD:0006234"}
xref: Orphanet:137923 {source="OMIM:257350"}
xref: Orphanet:79486 {source="OMIM:257350", source="MONDO:equivalentTo"}
xref: SCTID:399882002 {source="MONDO:kboom-pr-0.89/0.77/0.05", source="MONDO:equivalentTo"}
xref: UMLS:C0206620 {source="MONDO:notFoundInDiseaseSubset", source="Orphanet:79486", source="GARD:0006234", source="NCIT:C3724"}
xref: UMLS:C0948242 {source="OMIM:257350", source="NCBI:mim2gene_medline", source="MONDO:notFoundInDiseaseSubset"}
is_a: MONDO:0002013 {source="NCIT:C3724", source="linkedlifedata"} ! lymphangioma
is_a: MONDO:0018720 {source="Orphanet:79486"} ! common cystic lymphatic malformation
property_value: confidence "8.333333333333334" xsd:double

@wdduncan I think it's that the exact synonym is the same as the label.

@balhoff Yes. I see the exact synonyms. Do you know why the error report says duplicate definition?

I ran a report on my local machine on mondo-edit.obo. Report results were:

Violations: 16333
-----------------
ERROR:      169
WARN:       9890
INFO:       6274

I also find 1660 duplicate_exact_synonym warnings.

I checked 5 random classes in mondo-edit.obo. I did not find two lines of exact synonym labels that completely matched. What I did find were cases where:

The name and the exact synonym matched (e.g, hereditary xanthinuria)
The name was contained in an exact synonym (e.g, vulva cancer)
Exact synonyms that contained parts of each other (e.g., poikiloderma with neutropenia)

However, what I did find was cases where the ID of the exact synonym appeared multiple times (e.g, Orphanet:3467, DOID:1245, NCIT:C9423).

So the question is what do you want to mean by "exact"? The label or the ID.

Classes checked:

[Term]
id: MONDO:0018106
name: hereditary xanthinuria
def: "Hereditary xanthinuria is a purine metabolism disorder due to inherited deficiency of the xanthine dehydrogenase/oxidase enzyme and is characterized by very low (or undetectable) concentrations of uric acid in blood and urine and very high concentration of xanthine in urine, leading to urolithiasis." [Orphanet:3467]
subset: ordo_disease {source="Orphanet:3467"}
synonym: "classic xanthinuria" EXACT [Orphanet:3467]
synonym: "hereditary xanthinuria" EXACT [MONDO:patterns/hereditary]
synonym: "xanthic urolithiasis" EXACT [Orphanet:3467]
synonym: "xanthine dehydrogenase deficiency" EXACT [DOID:0060236]
synonym: "xanthine oxidase deficiency" EXACT [DOID:0060236]
synonym: "xanthine stone disease" EXACT [Orphanet:3467]
synonym: "xanthinuria" RELATED [DOID:0060236]
xref: DOID:0060236 {source="MONDO:equivalentTo"}
xref: HP:0010934 {source="MONDO:otherHierarchy", source="DOID:0060236"}
xref: ICD10:E79.8 {source="Orphanet:3467", source="ORDO:3467/ntbt", source="ORDO:3467/inclusion"}
xref: ICD9:277.2 {source="MONDO:relatedTo", source="i2s"}
xref: MESH:C562584 {source="DOID:0060236", source="MONDO:superClassOf"}
xref: MESH:C566358 {source="DOID:0060236", source="MONDO:superClassOf"}
xref: OMIM:278300 {source="Orphanet:3467", source="DOID:0060236", source="MONDO:superClassOf", source="ORDO:3467/btnt"}
xref: OMIM:603592 {source="Orphanet:3467", source="DOID:0060236", source="MONDO:superClassOf", source="ORDO:3467/btnt"}
xref: Orphanet:3467 {source="MONDO:equivalentTo", source="DOID:0060236", source="MONDO:superClassOf"}
xref: SCTID:124147007 {source="DOID:0060236"}
xref: SCTID:54627004 {source="MONDO:kboom-pr-0.93/0.85/0.06", source="MONDO:equivalentTo"}
xref: SCTID:72682008 {source="DOID:0060236", source="MONDO:superClassOf"}
xref: UMLS:C0268118 {source="DOID:0060236", source="MONDO:notFoundInDiseaseSubset"}
xref: UMLS:C1863688 {source="DOID:0060236", source="MONDO:superClassOf"}
is_a: MONDO:0000721 {source="MONDO:Redundant", source="MONDO:cjm"} ! xanthinuria
is_a: MONDO:0019236 {source="Orphanet:3467"} ! inborn disorder of purine metabolism
is_a: MONDO:0019743 {source="Orphanet:3467"} ! nephropathy secondary to a storage or other metabolic disease
intersection_of: MONDO:0000721 ! xanthinuria
intersection_of: has_modifier MONDO:0021152 ! inherited
property_value: confidence "19.999999999999982" xsd:double

[Term]
id: MONDO:0001528
name: vulva cancer
def: "A primary or metastatic malignant neoplasm involving the vulva." [NCIT:C7502]
synonym: "Ca vulva" EXACT [DOID:1245]
synonym: "cancer of mammalian vulva" EXACT [MONDO:patterns/cancer]
synonym: "malignant mammalian vulva neoplasm" EXACT [MONDO:patterns/cancer]
synonym: "malignant neoplasm of mammalian vulva" EXACT [MONDO:patterns/cancer]
synonym: "malignant neoplasm of the vulva" EXACT [NCIT:C7502]
synonym: "malignant neoplasm of vulva" EXACT [NCIT:C7502]
synonym: "malignant neoplasm of vulva unspecified" EXACT [DOID:1245]
synonym: "malignant neoplasm of vulva, NOS" RELATED EXCLUDE [DOID:1245]
synonym: "malignant neoplasm of vulva, unspecified" EXACT [DOID:1245, ICD9CM_2006:184.4]
synonym: "malignant tumor of the vulva" EXACT [NCIT:C7502]
synonym: "malignant tumor of vulva" EXACT [NCIT:C7502]
synonym: "malignant vulva neoplasm" EXACT [NCIT:C7502]
synonym: "malignant vulva tumor" EXACT [NCIT:C7502]
synonym: "malignant vulvar neoplasm" EXACT [NCIT:C7502]
synonym: "malignant vulvar tumor" EXACT [DOID:1245, NCIT:C7502]
synonym: "mammalian vulva cancer" EXACT [MONDO:patterns/location]
synonym: "neoplasm of vulva" EXACT [DOID:1245]
synonym: "vulval cancer" EXACT [CSP2005:2016-2183, DOID:1245]
synonym: "vulval neoplasm" EXACT [DOID:1245]
synonym: "vulvar cancer" EXACT [MONDO:patterns/location]
synonym: "vulvar neoplasm" EXACT [DOID:1245]
synonym: "vulvar tumor" EXACT [DOID:1245]
xref: DOID:1245 {source="MONDO:equivalentTo"}
xref: GARD:0009349 {source="MONDO:equivalentTo"}
xref: ICD10:C51 {source="DOID:1245"}
xref: ICD10:C51.9 {source="DOID:1245"}
xref: ICD9:184.4 {source="DOID:1245", source="MONDO:equivalentTo", source="i2s"}
xref: MESH:D014846 {source="DOID:1245", source="MONDO:equivalentTo", source="MONDO:ontobio"}
xref: NCIT:C7502 {source="DOID:1245", source="MONDO:equivalentTo"}
xref: SCTID:126922007 {source="MONDO:subClassOf", source="DOID:1245"}
xref: SCTID:154535008 {source="DOID:1245"}
xref: SCTID:188214009 {source="DOID:1245"}
xref: SCTID:269471005 {source="DOID:1245"}
xref: SCTID:269604005 {source="DOID:1245"}
xref: SCTID:363367000 {source="DOID:1245", source="MONDO:equivalentTo", source="MONDO:kboom-pr-1.00/0.92/9.67"}
xref: SCTID:94143002 {source="DOID:1245"}

[Term]
id: MONDO:0004100
name: lung mixed small cell and squamous cell carcinoma
def: "A lung carcinoma characterized by a combination of small cell carcinoma and squamous cell carcinoma." [NCIT:P378]
synonym: "combined small and large cell lung cancer" EXACT [DOID:7081]
synonym: "combined small cell and squamous cell lung carcinoma" EXACT [NCIT:C9423]
synonym: "mixed small cell and squamous cell carcinoma of lung" RELATED [DOID:7081]
synonym: "mixed small cell and squamous cell carcinoma of the lung" EXACT [NCIT:C9423]
synonym: "small cell and large cell carcinoma of the lung" EXACT [DOID:7081, NCIT:C9424]
synonym: "small cell and squamous cell carcinoma of lung" EXACT [NCIT:C9423]
synonym: "small cell and squamous cell carcinoma of the lung" EXACT [DOID:7081, NCIT:C9423]
synonym: "small cell and squamous cell lung carcinoma" EXACT [NCIT:C9423]
xref: DOID:7081 {source="MONDO:equivalentTo"}
xref: NCIT:C9423 {source="DOID:7081", source="MONDO:equivalentTo", source="MONDO:kboom-pr-0.92/0.77/1.05"}
xref: UMLS:C1334788 {source="DOID:7081", source="NCIT:C9423", source="MONDO:equivalentTo"}
is_a: MONDO:0005454 {source="DOID:7081", source="NCIT:C9423/inferred"} ! lung neuroendocrine neoplasm

[Term]
id: MONDO:0011405
name: poikiloderma with neutropenia
def: "A skin disease characterized by poikiloderma, hyperkeratotic nails, generalized hyperkeratosis on palms and soles, neutropenia, short stature, and recurrent pulmonary infections. It has material basis in mutation in the C16ORF57 gene on chromosome 16q13." [DOID:0060551, PMID:20734427]
subset: ordo_disease {source="Orphanet:221046"}
synonym: "Clericuzio type poikiloderma with neutropenia" RELATED [GARD:0004085]
synonym: "PN" RELATED [MONDO:Lexical, OMIM:604173]
synonym: "poikiloderma with neutropenia" EXACT [MONDO:Lexical, OMIM:604173]
synonym: "poikiloderma with neutropenia Clericuzio type" RELATED [GARD:0004085]
synonym: "poikiloderma with neutropenia, Clericuzio type" EXACT [Orphanet:221046]
synonym: "poikiloderma with neutropenia, Clericuzio-type" RELATED [OMIM:604173]
synonym: "poikiloderma with neutropenia; PN" RELATED [OMIM:604173]
xref: DOID:0060551 {source="MONDO:equivalentTo"}
xref: GARD:0004085 {source="MONDO:equivalentTo", source="Orphanet-shared", source="OMIM-shared"}
xref: ICD10:D82.8 {source="Orphanet:221046", source="DOID:0060551", source="ORDO:221046/attributed", source="ORDO:221046/ntbt"}
xref: OMIM:604173 {source="Orphanet:221046", source="DOID:0060551", source="ORDO:221046/e", source="MONDO:equivalentTo"}
xref: Orphanet:221046 {source="DOID:0060551", source="MONDO:equivalentTo", source="OMIM:604173"}
xref: UMLS:C1858723 {source="Orphanet:221046", source="NCBI:mim2gene_medline", source="MONDO:notFoundInDiseaseSubset", source="OMIM:604173"}
is_a: MONDO:0016382 {source="Orphanet:221046"} ! hereditary poikiloderma
is_a: MONDO:0018032 {source="Orphanet:221046"} ! constitutional neutropenia with extra-hematopoietic manifestations
relationship: disease_has_basis_in_dysfunction_of http://identifiers.org/hgnc/25792 {source="mim2gene_medgen"} ! USB1
relationship: disease_has_feature MONDO:0001475 {source="Wikidata"} ! neutropenia
property_value: confidence "30.666666666666668" xsd:double

Term]
id: MONDO:0021227
name: adrenal gland neoplasm
def: "A neoplasm (disease) that involves the adrenal gland." [MONDO:patterns/location]
synonym: "adrenal gland neoplasm (disease)" EXACT [MONDO:patterns/location]
synonym: "adrenal gland tumor" EXACT [MONDO:patterns/neoplasm, NCIT:C2859]
synonym: "adrenal neoplasm" EXACT [NCIT:C2859]
synonym: "adrenal neoplasms" EXACT [NCIT:C2859]
synonym: "adrenal tumor" EXACT [NCIT:C2859]
synonym: "ADRENALGLAND" RELATED [ONCOTREE:ADRENALGLAND]
synonym: "neoplasm of adrenal gland" EXACT [MONDO:patterns/neoplasm, NCIT:C2859]
synonym: "neoplasm of the adrenal gland" EXACT [NCIT:C2859]
synonym: "tumor of adrenal gland" EXACT [MONDO:patterns/neoplasm, NCIT:C2859]
synonym: "tumor of the adrenal gland" EXACT [NCIT:C2859]
xref: EFO:0003850 {source="MONDO:equivalentTo"}
xref: NCIT:C12666 {source="ONCOTREE:ADRENALGLAND"}
xref: NCIT:C2859 {source="MONDO:equivalentTo"}
xref: ONCOTREE:ADRENALGLAND {source="MONDO:equivalentTo"}
xref: UMLS:C0001624 {source="NCIT:C2859", source="MONDO:notFoundInDiseaseSubset"}
xref: UMLS:C0001625 {source="MONDO:notFoundInDiseaseSubset", source="ONCOTREE:ADRENALGLAND"}
is_a: MONDO:0005495 {source="MONDO:Redundant", source="NCIT:C2859"} ! adrenal gland disease
intersection_of: MONDO:0005070 ! neoplasm (disease)
intersection_of: disease_has_location UBERON:0002369 ! adrenal gland

@cmungall and @wdduncan how should we address these? I can fix them manually but it will take me more than 15 minutes. :)

If you'd like me to fix them manually, could one of you share a spreadsheet with a list of the terms that need to be addressed?

thanks!

The name and the exact synonym matched (e.g, hereditary xanthinuria)

true positives (maybe the name of the check should change)

The name was contained in an exact synonym (e.g, vulva cancer)

false positive

Exact synonyms that contained parts of each other (e.g., poikiloderma with neutropenia)

false positive

If you can confirm this then it should be easy for you to fix the robot sparql to use = vs substr

On Thu, Nov 14, 2019 at 1:07 PM Bill Duncan notifications@github.com wrote:

I ran a report on my local machine on mondo-edit.obo. Report results were:

Violations: 16333

ERROR: 169 WARN: 9890 INFO: 6274

I also find 1660 duplicate_exact_synonym warnings.

I checked 5 random classes in mondo-edit.obo. I did not find two lines of exact synonym labels that completely matched. What I did find were cases where:

The name and the exact synonym matched (e.g, hereditary xanthinuria)

The name was contained in an exact synonym (e.g, vulva cancer)

Exact synonyms that contained parts of each other (e.g., poikiloderma with neutropenia)

However, what I did find was cases where the ID of the exact synonym appeared multiple times (e.g, Orphanet:3467, DOID:1245, NCIT:C9423).

So the question is what do you want to mean by "exact"? The label or the ID.

Classes checked:

[Term] id: MONDO:0018106 name: hereditary xanthinuria def: "Hereditary xanthinuria is a purine metabolism disorder due to inherited deficiency of the xanthine dehydrogenase/oxidase enzyme and is characterized by very low (or undetectable) concentrations of uric acid in blood and urine and very high concentration of xanthine in urine, leading to urolithiasis." [Orphanet:3467] subset: ordo_disease {source="Orphanet:3467"} synonym: "classic xanthinuria" EXACT [Orphanet:3467] synonym: "hereditary xanthinuria" EXACT [MONDO:patterns/hereditary] synonym: "xanthic urolithiasis" EXACT [Orphanet:3467] synonym: "xanthine dehydrogenase deficiency" EXACT [DOID:0060236] synonym: "xanthine oxidase deficiency" EXACT [DOID:0060236] synonym: "xanthine stone disease" EXACT [Orphanet:3467] synonym: "xanthinuria" RELATED [DOID:0060236] xref: DOID:0060236 {source="MONDO:equivalentTo"} xref: HP:0010934 {source="MONDO:otherHierarchy", source="DOID:0060236"} xref: ICD10:E79.8 {source="Orphanet:3467", source="ORDO:3467/ntbt", source="ORDO:3467/inclusion"} xref: ICD9:277.2 {source="MONDO:relatedTo", source="i2s"} xref: MESH:C562584 {source="DOID:0060236", source="MONDO:superClassOf"} xref: MESH:C566358 {source="DOID:0060236", source="MONDO:superClassOf"} xref: OMIM:278300 {source="Orphanet:3467", source="DOID:0060236", source="MONDO:superClassOf", source="ORDO:3467/btnt"} xref: OMIM:603592 {source="Orphanet:3467", source="DOID:0060236", source="MONDO:superClassOf", source="ORDO:3467/btnt"} xref: Orphanet:3467 {source="MONDO:equivalentTo", source="DOID:0060236", source="MONDO:superClassOf"} xref: SCTID:124147007 {source="DOID:0060236"} xref: SCTID:54627004 {source="MONDO:kboom-pr-0.93/0.85/0.06", source="MONDO:equivalentTo"} xref: SCTID:72682008 {source="DOID:0060236", source="MONDO:superClassOf"} xref: UMLS:C0268118 {source="DOID:0060236", source="MONDO:notFoundInDiseaseSubset"} xref: UMLS:C1863688 {source="DOID:0060236", source="MONDO:superClassOf"} is_a: MONDO:0000721 {source="MONDO:Redundant", source="MONDO:cjm"} ! xanthinuria is_a: MONDO:0019236 {source="Orphanet:3467"} ! inborn disorder of purine metabolism is_a: MONDO:0019743 {source="Orphanet:3467"} ! nephropathy secondary to a storage or other metabolic disease intersection_of: MONDO:0000721 ! xanthinuria intersection_of: has_modifier MONDO:0021152 ! inherited property_value: confidence "19.999999999999982" xsd:double

[Term] id: MONDO:0001528 name: vulva cancer def: "A primary or metastatic malignant neoplasm involving the vulva." [NCIT:C7502] synonym: "Ca vulva" EXACT [DOID:1245] synonym: "cancer of mammalian vulva" EXACT [MONDO:patterns/cancer] synonym: "malignant mammalian vulva neoplasm" EXACT [MONDO:patterns/cancer] synonym: "malignant neoplasm of mammalian vulva" EXACT [MONDO:patterns/cancer] synonym: "malignant neoplasm of the vulva" EXACT [NCIT:C7502] synonym: "malignant neoplasm of vulva" EXACT [NCIT:C7502] synonym: "malignant neoplasm of vulva unspecified" EXACT [DOID:1245] synonym: "malignant neoplasm of vulva, NOS" RELATED EXCLUDE [DOID:1245] synonym: "malignant neoplasm of vulva, unspecified" EXACT [DOID:1245, ICD9CM_2006:184.4] synonym: "malignant tumor of the vulva" EXACT [NCIT:C7502] synonym: "malignant tumor of vulva" EXACT [NCIT:C7502] synonym: "malignant vulva neoplasm" EXACT [NCIT:C7502] synonym: "malignant vulva tumor" EXACT [NCIT:C7502] synonym: "malignant vulvar neoplasm" EXACT [NCIT:C7502] synonym: "malignant vulvar tumor" EXACT [DOID:1245, NCIT:C7502] synonym: "mammalian vulva cancer" EXACT [MONDO:patterns/location] synonym: "neoplasm of vulva" EXACT [DOID:1245] synonym: "vulval cancer" EXACT [CSP2005:2016-2183, DOID:1245] synonym: "vulval neoplasm" EXACT [DOID:1245] synonym: "vulvar cancer" EXACT [MONDO:patterns/location] synonym: "vulvar neoplasm" EXACT [DOID:1245] synonym: "vulvar tumor" EXACT [DOID:1245] xref: DOID:1245 {source="MONDO:equivalentTo"} xref: GARD:0009349 {source="MONDO:equivalentTo"} xref: ICD10:C51 {source="DOID:1245"} xref: ICD10:C51.9 {source="DOID:1245"} xref: ICD9:184.4 {source="DOID:1245", source="MONDO:equivalentTo", source="i2s"} xref: MESH:D014846 {source="DOID:1245", source="MONDO:equivalentTo", source="MONDO:ontobio"} xref: NCIT:C7502 {source="DOID:1245", source="MONDO:equivalentTo"} xref: SCTID:126922007 {source="MONDO:subClassOf", source="DOID:1245"} xref: SCTID:154535008 {source="DOID:1245"} xref: SCTID:188214009 {source="DOID:1245"} xref: SCTID:269471005 {source="DOID:1245"} xref: SCTID:269604005 {source="DOID:1245"} xref: SCTID:363367000 {source="DOID:1245", source="MONDO:equivalentTo", source="MONDO:kboom-pr-1.00/0.92/9.67"} xref: SCTID:94143002 {source="DOID:1245"}

[Term] id: MONDO:0004100 name: lung mixed small cell and squamous cell carcinoma def: "A lung carcinoma characterized by a combination of small cell carcinoma and squamous cell carcinoma." [NCIT:P378] synonym: "combined small and large cell lung cancer" EXACT [DOID:7081] synonym: "combined small cell and squamous cell lung carcinoma" EXACT [NCIT:C9423] synonym: "mixed small cell and squamous cell carcinoma of lung" RELATED [DOID:7081] synonym: "mixed small cell and squamous cell carcinoma of the lung" EXACT [NCIT:C9423] synonym: "small cell and large cell carcinoma of the lung" EXACT [DOID:7081, NCIT:C9424] synonym: "small cell and squamous cell carcinoma of lung" EXACT [NCIT:C9423] synonym: "small cell and squamous cell carcinoma of the lung" EXACT [DOID:7081, NCIT:C9423] synonym: "small cell and squamous cell lung carcinoma" EXACT [NCIT:C9423] xref: DOID:7081 {source="MONDO:equivalentTo"} xref: NCIT:C9423 {source="DOID:7081", source="MONDO:equivalentTo", source="MONDO:kboom-pr-0.92/0.77/1.05"} xref: UMLS:C1334788 {source="DOID:7081", source="NCIT:C9423", source="MONDO:equivalentTo"} is_a: MONDO:0005454 {source="DOID:7081", source="NCIT:C9423/inferred"} ! lung neuroendocrine neoplasm

[Term] id: MONDO:0011405 name: poikiloderma with neutropenia def: "A skin disease characterized by poikiloderma, hyperkeratotic nails, generalized hyperkeratosis on palms and soles, neutropenia, short stature, and recurrent pulmonary infections. It has material basis in mutation in the C16ORF57 gene on chromosome 16q13." [DOID:0060551, PMID:20734427] subset: ordo_disease {source="Orphanet:221046"} synonym: "Clericuzio type poikiloderma with neutropenia" RELATED [GARD:0004085] synonym: "PN" RELATED [MONDO:Lexical, OMIM:604173] synonym: "poikiloderma with neutropenia" EXACT [MONDO:Lexical, OMIM:604173] synonym: "poikiloderma with neutropenia Clericuzio type" RELATED [GARD:0004085] synonym: "poikiloderma with neutropenia, Clericuzio type" EXACT [Orphanet:221046] synonym: "poikiloderma with neutropenia, Clericuzio-type" RELATED [OMIM:604173] synonym: "poikiloderma with neutropenia; PN" RELATED [OMIM:604173] xref: DOID:0060551 {source="MONDO:equivalentTo"} xref: GARD:0004085 {source="MONDO:equivalentTo", source="Orphanet-shared", source="OMIM-shared"} xref: ICD10:D82.8 {source="Orphanet:221046", source="DOID:0060551", source="ORDO:221046/attributed", source="ORDO:221046/ntbt"} xref: OMIM:604173 {source="Orphanet:221046", source="DOID:0060551", source="ORDO:221046/e", source="MONDO:equivalentTo"} xref: Orphanet:221046 {source="DOID:0060551", source="MONDO:equivalentTo", source="OMIM:604173"} xref: UMLS:C1858723 {source="Orphanet:221046", source="NCBI:mim2gene_medline", source="MONDO:notFoundInDiseaseSubset", source="OMIM:604173"} is_a: MONDO:0016382 {source="Orphanet:221046"} ! hereditary poikiloderma is_a: MONDO:0018032 {source="Orphanet:221046"} ! constitutional neutropenia with extra-hematopoietic manifestations relationship: disease_has_basis_in_dysfunction_of http://identifiers.org/hgnc/25792 {source="mim2gene_medgen"} ! USB1 relationship: disease_has_feature MONDO:0001475 {source="Wikidata"} ! neutropenia property_value: confidence "30.666666666666668" xsd:double

Term] id: MONDO:0021227 name: adrenal gland neoplasm def: "A neoplasm (disease) that involves the adrenal gland." [MONDO:patterns/location] synonym: "adrenal gland neoplasm (disease)" EXACT [MONDO:patterns/location] synonym: "adrenal gland tumor" EXACT [MONDO:patterns/neoplasm, NCIT:C2859] synonym: "adrenal neoplasm" EXACT [NCIT:C2859] synonym: "adrenal neoplasms" EXACT [NCIT:C2859] synonym: "adrenal tumor" EXACT [NCIT:C2859] synonym: "ADRENALGLAND" RELATED [ONCOTREE:ADRENALGLAND] synonym: "neoplasm of adrenal gland" EXACT [MONDO:patterns/neoplasm, NCIT:C2859] synonym: "neoplasm of the adrenal gland" EXACT [NCIT:C2859] synonym: "tumor of adrenal gland" EXACT [MONDO:patterns/neoplasm, NCIT:C2859] synonym: "tumor of the adrenal gland" EXACT [NCIT:C2859] xref: EFO:0003850 {source="MONDO:equivalentTo"} xref: NCIT:C12666 {source="ONCOTREE:ADRENALGLAND"} xref: NCIT:C2859 {source="MONDO:equivalentTo"} xref: ONCOTREE:ADRENALGLAND {source="MONDO:equivalentTo"} xref: UMLS:C0001624 {source="NCIT:C2859", source="MONDO:notFoundInDiseaseSubset"} xref: UMLS:C0001625 {source="MONDO:notFoundInDiseaseSubset", source="ONCOTREE:ADRENALGLAND"} is_a: MONDO:0005495 {source="MONDO:Redundant", source="NCIT:C2859"} ! adrenal gland disease intersection_of: MONDO:0005070 ! neoplasm (disease) intersection_of: disease_has_location UBERON:0002369 ! adrenal gland

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@cmungall @nicolevasilevsky Do you want to match on strings or IRIs?

I think you'd just want to match on the strings for the name and synonym

yes, I don't think I understand the question... we may have crossed lines here.

Can you give a specific example of a false positive?

On Thu, Nov 14, 2019 at 3:11 PM Nicole Vasilevsky notifications@github.com wrote:

I think you'd just want to match on the strings for the name and synonym

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is this a question for @wdduncan ?

I am confused now too! :)

it is

On Thu, Nov 14, 2019 at 3:23 PM Nicole Vasilevsky notifications@github.com wrote:

is this a question for @wdduncan https://github.com/wdduncan ?

I am confused now too! :)

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@cmungall The robot query (see below) seems to be looking for two entities that have a matching exact synonym or alternative term (IAO_0000118).

Focusing on MONDO:0004100 "lung mixed small cell and squamous cell carcinoma" I searched the mondo-edit.obo file for all occurrences of:

lung mixed small cell and squamous cell carcinoma; found 1 (MONDO:0004100)
combined small and large cell lung cancer; found 2 (MONDO:0004100, MONDO:0003438)
mixed small cell and squamous cell carcinoma of the lung; found 1 (MONDO:0004100)
small cell and large cell carcinoma of the lung; found 2 (MONDO:0004100 , MONDO:0003438)

So, yes, matching exact synonym labels are showing up across classes.

SPARQL query from duplicate_exact_synonym.rq file in robot repo.

PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?entity ?property ?value WHERE {
  VALUES ?property {
    obo:IAO_0000118
    oboInOwl:hasExactSynonym
  }
  ?entity ?property ?value.
  ?entity2 ?property ?value .
  FILTER NOT EXISTS { ?entity owl:deprecated true }
  FILTER NOT EXISTS { ?entity2 owl:deprecated true }
  FILTER (?entity != ?entity2)
}
ORDER BY DESC(UCASE(str(?value)))

The robot query is doing the correct thing, and this is a true positive and hence needs fixed in the ontology

On Thu, Nov 14, 2019 at 3:43 PM Bill Duncan notifications@github.com wrote:

@cmungall https://github.com/cmungall The robot query (see below) seems to be looking for two entities that have a matching exact synonym or alternative term (IAO_0000118).

Focusing on MONDO:0004100 "lung mixed small cell and squamous cell carcinoma" I searched the mondo-edit.obo file for all occurrences of:

lung mixed small cell and squamous cell carcinoma; found 1 (MONDO:0004100)

combined small and large cell lung cancer; found 2 (MONDO:0004100, MONDO:0003438)

mixed small cell and squamous cell carcinoma of the lung; found 1 (MONDO:0004100)

small cell and large cell carcinoma of the lung; found 2 (MONDO:0004100 , MONDO:0003438)

So, yes, matching exact synonym labels are showing up across classes.

SPARQL query from duplicate_exact_synonym.rq file in robot repo.

PREFIX obo: http://purl.obolibrary.org/obo/ PREFIX oboInOwl: http://www.geneontology.org/formats/oboInOwl# PREFIX owl: http://www.w3.org/2002/07/owl# PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema#

SELECT DISTINCT ?entity ?property ?value WHERE { VALUES ?property { obo:IAO_0000118 oboInOwl:hasExactSynonym } ?entity ?property ?value. ?entity2 ?property ?value . FILTER NOT EXISTS { ?entity owl:deprecated true } FILTER NOT EXISTS { ?entity2 owl:deprecated true } FILTER (?entity != ?entity2) } ORDER BY DESC(UCASE(str(?value)))

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I'm going to do a report to output the matching entities.

In the attached spreadsheet, I have the matching entity IRIs, labels, and the value of synonym.
We can delete programmatically, but how do we know which exact synonym should be deleted?

mondo_duplicate_exact_synonyms.xlsx

Query used for report:

PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?entity1 ?entity1_label ?entity2 ?entity2_label ?property ?value WHERE {
  VALUES ?property {
    obo:IAO_0000118
    oboInOwl:hasExactSynonym
  }
  ?entity1 ?property ?value; rdfs:label ?entity1_label .
  ?entity2 ?property ?value; rdfs:label ?entity2_label .
  FILTER NOT EXISTS { ?entity1 owl:deprecated true }
  FILTER NOT EXISTS { ?entity2 owl:deprecated true }
  FILTER (?entity1 != ?entity2)
}
ORDER BY DESC(UCASE(str(?value)))

I made a start removing the most egregious clashes. These were easy to spot as they came from DO and did not have backup from other sources, and are to do with systematic errors, such as confusing neoplasm/tumor with cancer.

This ticket has become too complex and I am covering it in more targeted tickets now.

monarch-initiative / mondo

Fix robot report errors #808

Violations: 16333