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feat: ema update (#2745)
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* ontology and datamodel edits

* ema datamodel to separate folder for now

* Publications back to format of >=3.7
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@BrendaHijmans
BrendaHijmans authored Jan 10, 2024
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6,979 changes: 6,979 additions & 0 deletions data/datacatalogue/CatalogueOntologies/ATC.csv
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369 changes: 188 additions & 181 deletions data/datacatalogue/CatalogueOntologies/Areas of information ds.csv
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501 changes: 251 additions & 250 deletions data/datacatalogue/CatalogueOntologies/Countries.csv
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2 changes: 1 addition & 1 deletion data/datacatalogue/CatalogueOntologies/Datasource types.csv
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order,name,code,parent,definition,ontologyTermURI
1,Hospital discharge records,,,,https://spor.ema.europa.eu/rmswi/#/lists/200000030015/terms/200000030038
2,Primary care medical records,,,,https://spor.ema.europa.eu/rmswi/#/lists/200000030015/terms/200000030039
3,Pharmacy dispensation records,,,,https://spor.ema.europa.eu/rmswi/#/lists/200000030015/terms/200000030040
3,Pharmacy dispensing records,,,,https://spor.ema.europa.eu/rmswi/#/lists/200000030015/terms/200000030040
4,Birth registry,,,,https://spor.ema.europa.eu/rmswi/#/lists/200000030015/terms/200000030041
5,Induced terminations registry,,,,https://spor.ema.europa.eu/rmswi/#/lists/200000030015/terms/200000030042
6,Congenital anomaly registry,,,,https://spor.ema.europa.eu/rmswi/#/lists/200000030015/terms/200000030043
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21 changes: 16 additions & 5 deletions data/datacatalogue/CatalogueOntologies/Diseases.csv
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Expand Up @@ -5559,9 +5559,9 @@ M34.2 Systemic sclerosis induced by drugs and chemicals,5557,M34.2,M30-M36 Syste
M34.8 Other forms of systemic sclerosis,5558,M34.8,M30-M36 Systemic connective tissue disorders,http://identifiers.org/icd/M34.8,ORPHAcode: 352763 Scleredema
"M34.9 Systemic sclerosis, unspecified",5559,M34.9,M30-M36 Systemic connective tissue disorders,http://identifiers.org/icd/M34.9,
M35 Other systemic involvement of connective tissue,5560,M35,M30-M36 Systemic connective tissue disorders,http://identifiers.org/icd/M35,
M35.0 Sicca syndrome [Sjögren,5561,M35.0,M30-M36 Systemic connective tissue disorders,http://identifiers.org/icd/M35.0,ORPHAcode: 289390 Primary Sj gren sy
M35.0 Other systemic involvement of connective tissue - Sicca syndrome [Sjögren],5561,M35.0,M30-M36 Systemic connective tissue disorders,http://identifiers.org/icd/M35.0,ORPHAcode: 289390 Primary Sjögren syndrome
M35.1 Other overlap syndromes,5562,M35.1,M30-M36 Systemic connective tissue disorders,http://identifiers.org/icd/M35.1,ORPHAcode: 809 Mixed connective tissue disease
M35.2 Behçet diseas,5563,M35.2,M30-M36 Systemic connective tissue disorders,http://identifiers.org/icd/M35.2,ORPHAcode: 117 Beh et d
M35.2 Other systemic involvement of connective tissue - Behçet disease,5563,M35.2,M30-M36 Systemic connective tissue disorders,http://identifiers.org/icd/M35.2,ORPHAcode: 117 Beh et d
M35.3 Other systemic involvement of connective tissue - Polymyalgia rheumatica,5564,M35.3,M30-M36 Systemic connective tissue disorders,http://identifiers.org/icd/M35.3,ORPHAcode: 93569 Polymyalgia rheumatica
M35.4 Other systemic involvement of connective tissue - Diffuse (eosinophilic) fasciitis,5565,M35.4,M30-M36 Systemic connective tissue disorders,http://identifiers.org/icd/M35.4,ORPHAcode: 3165 Eosinophilic fasciitis
M35.5 Other systemic involvement of connective tissue - Multifocal fibrosclerosis,5566,M35.5,M30-M36 Systemic connective tissue disorders,http://identifiers.org/icd/M35.5,
Expand Down Expand Up @@ -5973,9 +5973,12 @@ N00-N08 Glomerular diseases,5971,,XIV Diseases of the genitourinary system,,
N00 Acute nephritic syndrome,5972,N00,N00-N08 Glomerular diseases,http://identifiers.org/icd/N00,
N01 Rapidly progressive nephritic syndrome,5973,N01,N00-N08 Glomerular diseases,http://identifiers.org/icd/N01,
N02 Recurrent and persistent haematuria,5974,N02,N00-N08 Glomerular diseases,http://identifiers.org/icd/N02,
N02.8 Recurrent and persistent haematuria - Recurrent and persistent haematuria: Other,,N02.8,N00-N08 Glomerular diseases,http://identifiers.org/icd/N02.8,
N03 Chronic nephritic syndrome,5975,N03,N00-N08 Glomerular diseases,http://identifiers.org/icd/N03,
N04 Nephrotic syndrome,5976,N04,N00-N08 Glomerular diseases,http://identifiers.org/icd/N04,
N04.5 Nephrotic syndrome - Nephrotic syndrome: Diffuse mesangiocapillary glomerulonephritis,,N04.5,N00-N08 Glomerular diseases,http://identifiers.org/icd/N04.5,
N05 Unspecified nephritic syndrome,5977,N05,N00-N08 Glomerular diseases,http://identifiers.org/icd/N05,ORPHAcode: 567544 Idiopathic non-lupus full-house nephropathy
N05.5 Unspecified nephritic syndrome - Unspecified nephritic syndrome: Diffuse mesangiocapillary glomerulonephritis,,N05.5,N00-N08 Glomerular diseases,http://identifiers.org/icd/N05.5,
N06 Isolated proteinuria with specified morphological lesion,5978,N06,N00-N08 Glomerular diseases,http://identifiers.org/icd/N06,
"N07 Hereditary nephropathy, not elsewhere classified",5979,N07,N00-N08 Glomerular diseases,http://identifiers.org/icd/N07,
N08 Glomerular disorders in diseases classified elsewhere,5980,N08,N00-N08 Glomerular diseases,http://identifiers.org/icd/N08,
Expand Down Expand Up @@ -6056,6 +6059,7 @@ N25.1 Disorders resulting from impaired renal tubular function - Nephrogenic dia
N25.8 Other disorders resulting from impaired renal tubular function,6055,N25.8,N25-N29 Other disorders of kidney and ureter,http://identifiers.org/icd/N25.8,ORPHAcode: 18 Distal renal tubular acidosis
"N25.9 Disorder resulting from impaired renal tubular function, unspecified",6056,N25.9,N25-N29 Other disorders of kidney and ureter,http://identifiers.org/icd/N25.9,
N26 Unspecified contracted kidney,6057,N26,N25-N29 Other disorders of kidney and ureter,http://identifiers.org/icd/N26,
N26.9 DMS,,N26.9,N25-N29 Other disorders of kidney and ureter,http://identifiers.org/icd/N26.9,
N27 Small kidney of unknown cause,6058,N27,N25-N29 Other disorders of kidney and ureter,http://identifiers.org/icd/N27,
"N27.0 Small kidney, unilateral",6059,N27.0,N25-N29 Other disorders of kidney and ureter,http://identifiers.org/icd/N27.0,
"N27.1 Small kidney, bilateral",6060,N27.1,N25-N29 Other disorders of kidney and ureter,http://identifiers.org/icd/N27.1,
Expand Down Expand Up @@ -6177,6 +6181,7 @@ N51.0 Disorders of prostate in diseases classified elsewhere,6175,N51.0,N40-N51
N51.1 Disorders of testis and epididymis in diseases classified elsewhere,6176,N51.1,N40-N51 Diseases of male genital organs,http://identifiers.org/icd/N51.1,
N51.2 Balanitis in diseases classified elsewhere,6177,N51.2,N40-N51 Diseases of male genital organs,http://identifiers.org/icd/N51.2,
N51.8 Other disorders of male genital organs in diseases classified elsewhere,6178,N51.8,N40-N51 Diseases of male genital organs,http://identifiers.org/icd/N51.8,
N60 Benign mammary dysplasia,,N60,N60-N64 Disorders of breast,http://identifiers.org/icd/N60,
N60.0 Benign mammary dysplasia - Solitary cyst of breast,6179,N60.0,N60-N64 Disorders of breast,http://identifiers.org/icd/N60.0,
N60.1 Benign mammary dysplasia - Diffuse cystic mastopathy,6180,N60.1,N60-N64 Disorders of breast,http://identifiers.org/icd/N60.1,
N60.2 Benign mammary dysplasia - Fibroadenosis of breast,6181,N60.2,N60-N64 Disorders of breast,http://identifiers.org/icd/N60.2,
Expand Down Expand Up @@ -8068,7 +8073,7 @@ R19.6 Other symptoms and signs involving the digestive system and abdomen - Hali
R23.2 Other skin changes - Flushing,8067,R23.2,R20 Disturbances of skin sensation,http://identifiers.org/icd/R23.2,
R19.8 Other specified symptoms and signs involving the digestive system and abdomen,8068,R19.8,R10-R19 Symptoms and signs involving the digestive system and abdomen,http://identifiers.org/icd/R19.8,
R20-R23 Symptoms and signs involving the skin and subcutaneous tissue,8069,,"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified",,
R20 Disturbances of skin sensation,8070,R20,R20 Disturbances of skin sensation,http://identifiers.org/icd/R20,
R20 Disturbances of skin sensation,8070,R20,R20-R23 Symptoms and signs involving the skin and subcutaneous tissue,http://identifiers.org/icd/R20,
R20.0 Anaesthesia of skin,8071,R20.0,R20 Disturbances of skin sensation,http://identifiers.org/icd/R20.0,
R20.1 Hypoaesthesia of skin,8072,R20.1,R20 Disturbances of skin sensation,http://identifiers.org/icd/R20.1,
R20.2 Paraesthesia of skin,8073,R20.2,R20 Disturbances of skin sensation,http://identifiers.org/icd/R20.2,
Expand Down Expand Up @@ -10262,6 +10267,7 @@ X46 Accidental poisoning by and exposure to organic solvents and halogenated hyd
X47 Accidental poisoning by and exposure to other gases and vapours,10261,X47,X40-X49 Accidental poisoning by and exposure to noxious substances,http://identifiers.org/icd/X47,
X48 Accidental poisoning by and exposure to pesticides,10262,X48,X40-X49 Accidental poisoning by and exposure to noxious substances,http://identifiers.org/icd/X48,
X49 Accidental poisoning by and exposure to other and unspecified chemicals and noxious substances,10263,X49,X40-X49 Accidental poisoning by and exposure to noxious substances,http://identifiers.org/icd/X49,
X49.9 Toxic Oil Syndrome,,X49.9,X40-X49 Accidental poisoning by and exposure to noxious substances,http://identifiers.org/icd/X49.9,
"X50-X57 Overexertion, travel and privation",10264,X50-X57,W00-X59 Other external causes of accidental injury,,
X50 Overexertion and strenuous or repetitive movements,10265,X50,"X50-X57 Overexertion, travel and privation",http://identifiers.org/icd/X50,
X51 Travel and motion,10266,X51,"X50-X57 Overexertion, travel and privation",http://identifiers.org/icd/X51,
Expand Down Expand Up @@ -11253,7 +11259,6 @@ Z80.4 Family history of malignant neoplasm of genital organs,11251,Z80.4,Z80-Z99
Z80.5 Family history of malignant neoplasm of urinary tract,11252,Z80.5,Z80-Z99 Persons with potential health hazards related to family and personal history and certain conditions influencing health status,http://identifiers.org/icd/Z80.5,
Z80.6 Family history of leukaemia,11253,Z80.6,Z80-Z99 Persons with potential health hazards related to family and personal history and certain conditions influencing health status,http://identifiers.org/icd/Z80.6,
Z82.2 Family history of deafness and hearing loss,11254,Z82.2,Z80-Z99 Persons with potential health hazards related to family and personal history and certain conditions influencing health status,http://identifiers.org/icd/Z82.2,
U07.4 Emergency use of U07.4,11255,U07.4,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U07.4,
"Z80.7 Family history of other malignant neoplasms of lymphoid, haematopoietic and related tissues",11256,Z80.7,Z80-Z99 Persons with potential health hazards related to family and personal history and certain conditions influencing health status,http://identifiers.org/icd/Z80.7,
Z80.8 Family history of malignant neoplasm of other organs or systems,11257,Z80.8,Z80-Z99 Persons with potential health hazards related to family and personal history and certain conditions influencing health status,http://identifiers.org/icd/Z80.8,
"Z80.9 Family history of malignant neoplasm, unspecified",11258,Z80.9,Z80-Z99 Persons with potential health hazards related to family and personal history and certain conditions influencing health status,http://identifiers.org/icd/Z80.9,
Expand Down Expand Up @@ -11453,11 +11458,14 @@ U07.0 Emergency use of U07.0,11451,U07.0,U00-U49 Provisional assignment of new d
U07.1 Laboratory-confirmed COVID-19 diagnosis,11452,U07.1,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U07.1,
U07.2 suspect or probable COVID-19 diagnosis,11453,U07.2,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U07.2,
U07.3 Emergency use of U07.3,11454,U07.3,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U07.3,
U07.4 Emergency use of U07.4,,U07.4,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U07.4,
U07.5 Emergency use of U07.5,11455,U07.5,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U07.5,
U07.6 Emergency use of U07.6,11456,U07.6,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U07.6,
U07.7 Emergency use of U07.7,11457,U07.7,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U07.7,
U07.8 Emergency use of U07.8,11458,U07.8,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U07.8,
U07.9 Emergency use of U07.9,11459,U07.9,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U07.9,
U09 Post COVID-19 condition - Post COVID-19 condition,,U09,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U09,
"U09.9 Post COVID-19 condition - Post COVID-19 condition, unspecified",,U09.9,U00-U49 Provisional assignment of new diseases of uncertain etiology or emergency use,http://identifiers.org/icd/U09.9,
U82-U85 Resistance to antimicrobial and antineoplastic drugs,11460,,XXII Codes for special purposes,,
U82 Resistance to betalactam antibiotics,11461,U82,U82-U85 Resistance to antimicrobial and antineoplastic drugs,http://identifiers.org/icd/U82,
U82.0 Resistance to penicillin,11462,U82.0,U82-U85 Resistance to antimicrobial and antineoplastic drugs,http://identifiers.org/icd/U82.0,
Expand All @@ -11482,6 +11490,7 @@ U85 Resistance to antineoplastic drugs,11480,U85,U82-U85 Resistance to antimicro
ORPHAcodes,11481,,,,
"48,XXYY syndrome",11482,10,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_10,
Ataxia-telangiectasia,11483,100,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_100,Column6
OBSOLETE: Genetic optic atrophy,,103,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_103,
Ocular albinism with late-onset sensorineural deafness,11484,1000,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_1000,
Reticular perineurioma,11485,100000,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_100000,
Sclerosing perineurioma,11486,100001,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_100001,
Expand Down Expand Up @@ -18495,7 +18504,7 @@ Marfan syndrome,18493,558,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_558,
Idiopathic gastroparesis,18494,558411,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_558411,
Chondrosarcoma,18495,55880,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_55880,
Adamantinoma,18496,55881,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_55881,
Marinesco-Sjögren syndrom,18497,559,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_559,
Marinesco-Sjögren syndrome,18497,559,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_559,
Alkaptonuria,18498,56,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_56,
Marshall syndrome,18499,560,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_560,
Carcinoma of gallbladder and extrahepatic biliary tract,18500,56044,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_56044,
Expand Down Expand Up @@ -20239,7 +20248,9 @@ Hamel cerebro-palato-cardiac syndrome,20236,93946,ORPHAcodes,http://www.orpha.ne
"X-linked intellectual disability, Sutherland-Haan type",20238,93950,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_93950,
"X-linked intellectual disability, Hedera type",20239,93952,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_93952,
Familial thyroglossal duct cyst,20240,93953,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_93953,
OBSOLETE: Truncal dystonia,,93956,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_93956,
Oromandibular dystonia,20241,93958,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_93958,
OBSOLETE: Cervical dystonia,,93962,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_93962,
Blepharospasm-oromandibular dystonia syndrome,20242,93964,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_93964,
Meningocele,20243,93968,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_93968,
Myelomeningocele,20244,93969,ORPHAcodes,http://www.orpha.net/ORDO/Orphanet_93969,
Expand Down
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