BFF-PXF-SIMULATOR¶
We have developed a tool for generating simulated (synthetic) data in either BFF or PXF formats.
The tool, bff-pxf-simulator, is included as an executable (if downloaded from CPAN) or found in the utils directory (if downloaded from GitHub or Docker).
Potential uses for synthetic data
The simulated data can be used to:
- Testing software and installations
- Benchmarking
- Sample classification
- Outlier identification
- ...
Default Ontologies used
Below are the default ontology terms utilized by the script. Please note that it is possible to use an external ontologies YAML file instead, by employing the --external-ontologies flag.
The word "ontology" is used broadly here, including terms from recognized ontologies (e.g., HPO and NCIt), as well as terminologies (e.g., (e.g., LOINC or RxNorm). While the latter do not meet the stringent criteria of ontologies, they fulfill analogous roles in facilitating data standardization.
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diseases:
- id: OMIM:101000
label: Neurofibromatosis, type 2
- id: OMIM:102578
label: Leukemia, acute promyelocytic, somatic
- id: OMIM:103050
label: Adenylosuccinase deficiency
- id: OMIM:103900
label: Aldosteronism, glucocorticoid-remediable
- id: OMIM:104200
label: Alport syndrome, autosomal dominant
- id: OMIM:104300
label: Alzheimer disease, susceptibility to
- id: OMIM:105120
label: Amyloidosis, Finnish type
- id: OMIM:105400
label: Amyotrophic lateral sclerosis 1
- id: OMIM:105800
label: Aneurysm, intracranial berry, 1
- id: OMIM:105830
label: Angelman syndrome
- id: OMIM:108725
label: Atherosclerosis, susceptibility to
- id: OMIM:108800
label: Atrial septal defect 1
- id: OMIM:109800
label: Bladder cancer, somatic
- id: OMIM:111200
label: Blood group, Auberger system
- id: OMIM:111200
label: Blood group, Lutheran system
- id: OMIM:111250
label: Blood group, Landsteiner-Wiener
- id: OMIM:111800
label: Blood group, Stoltzfus system
- id: OMIM:112100
label: Blood group, Yt system
- id: OMIM:113970
label: Burkitt lymphoma
- id: OMIM:114500
label: Colonic adenoma recurrence, reduced risk of
- id: OMIM:114500
label: Colorectal cancer, susceptibility to
- id: OMIM:114550
label: Hepatocellular carcinoma, somatic
- id: OMIM:115665
label: Cataract 8, multiple types
- id: OMIM:118450
label: Alagille syndrome 1
- id: OMIM:121400
label: Cornea plana 1, autosomal dominant
- id: OMIM:123320
label: Creatine phosphokinase, elevated serum
- id: OMIM:125264
label: Leukemia, acute nonlymphocytic
- id: OMIM:125853
label: Diabetes, type 2, susceptibility to
- id: OMIM:125853
label: Insulin resistance, susceptibility to
- id: OMIM:127300
label: Leri-Weill dyschondrosteosis
- id: OMIM:127750
label: Lewy body dementia, susceptibility to
- id: OMIM:130050
label: Ehlers-Danlos syndrome, type IV
- id: OMIM:130060
label: Ehlers-Danlos syndrome, type VIIB
- id: OMIM:130650
label: Beckwith-Wiedemann syndrome
- id: OMIM:131100
label: Multiple endocrine neoplasia 1
- id: OMIM:132100
label: Photoparoxysmal response 1
- id: OMIM:133700
label: Exostoses, multiple, type 1
- id: OMIM:134610
label: Familial Mediterranean fever, AD
- id: OMIM:136120
label: Fish-eye disease
- id: OMIM:137215
label: Gastric cancer risk after H. pylori infection
- id: OMIM:137550
label: Spitz nevus or nevus spilus, somatic
- id: OMIM:137580
label: Tourette syndrome
- id: OMIM:139300
label: Aromatase excess syndrome
- id: OMIM:140700
label: Heinz body anemias, beta-
- id: OMIM:141200
label: Hematuria, benign familial
- id: OMIM:141749
label: Delta-beta thalassemia
- id: OMIM:141749
label: Hereditary persistence of fetal hemoglobin
- id: OMIM:142335
label: Fetal hemoglobin QTL5
- id: OMIM:142945
label: Holoprosencephaly 3
- id: OMIM:143100
label: Huntington disease
- id: OMIM:143465
label: Attention deficit-hyperactivity disorder
- id: OMIM:143465
label: Attention deficit-hyperactivity disorder, susceptibility to
- id: OMIM:143890
label: Hypercholesterolemia, familial
- id: OMIM:143890
label: LDL cholesterol level QTL2
- id: OMIM:144650
label: Hyperchylomicronemia, late-onset
- id: OMIM:144700
label: Renal cell carcinoma
- id: OMIM:145750
label: Hypertriglyceridemia, susceptibility to
- id: OMIM:146200
label: Hypoparathyroidism, autosomal dominant
- id: OMIM:146200
label: Hypoparathyroidism, autosomal recessive
- id: OMIM:146510
label: Pallister-Hall syndrome
- id: OMIM:147050
label: Atopy, susceptibility to
- id: OMIM:147050
label: IgE, elevated level of
- id: OMIM:147250
label: Single median maxillary central incisor
- id: OMIM:147791
label: Jacobsen syndrome
- id: OMIM:150699
label: Leiomyoma, uterine, somatic
- id: OMIM:152700
label: Lupus nephritis, susceptibility to
- id: OMIM:154800
label: Mast cell disease
- id: OMIM:155240
label: Medullary thyroid carcinoma, familial
- id: OMIM:155600
label: Melanoma, cutaneous malignant, 1
- id: OMIM:157300
label: Migraine without aura, susceptibility to
- id: OMIM:159900
label: Dystonia-11, myoclonic
- id: OMIM:160900
label: Myotonic dystrophy 1
- id: OMIM:162091
label: Schwannomatosis
- id: OMIM:162900
label: Nevus sebaceous or woolly hair nevus, somatic
- id: OMIM:163200
label: Schimmelpenning-Feuerstein-Mims syndrome, somatic mosaic
- id: OMIM:166210
label: Osteogenesis imperfecta, type II
- id: OMIM:166220
label: Osteogenesis imperfecta, type IV
- id: OMIM:166710
label: Osteoporosis, postmenopausal
- id: OMIM:166710
label: Osteoporosis, postmenopausal, susceptibility
- id: OMIM:167210
label: Pachyonychia congenita 2
- id: OMIM:167800
label: Pancreatitis, hereditary
- id: OMIM:167800
label: Pancreatitis, idiopathic
- id: OMIM:168600
label: Parkinson disease, late-onset, susceptibility to
- id: OMIM:168600
label: Parkinson disease, susceptibility to
- id: OMIM:170100
label: Prolidase deficiency
- id: OMIM:171300
label: Pheochromocytoma, susceptibility to
- id: OMIM:172700
label: Pick disease
- id: OMIM:172800
label: Piebaldism
- id: OMIM:174000
label: Medullary cystic kidney disease 1
- id: OMIM:174200
label: Polydactyly, postaxial, types A1 and B
- id: OMIM:174700
label: Polydactyly, preaxial, type IV
- id: OMIM:175700
label: Greig cephalopolysyndactyly syndrome
- id: OMIM:176310
label: Leukemia, acute pre-B-cell
- id: OMIM:176807
label: Prostate cancer, hereditary
- id: OMIM:177700
label: Glaucoma 1, open angle, P
- id: OMIM:178500
label: Pulmonary fibrosis, idiopathic, susceptibility to
- id: OMIM:180105
label: Retinitis pigmentosa 10
- id: OMIM:180385
label: Leukemia, acute T-cell
- id: OMIM:180849
label: Rubinstein-Taybi syndrome
- id: OMIM:180860
label: Silver-Russell syndrome
ethnicity:
- id: NCIT:C42331
label: African
- id: NCIT:C67109
label: Multiracial
- id: NCIT:C16352
label: Black or African American
- id: NCIT:C41261
label: White
- id: NCIT:C41260
label: Asian
- id: NCIT:C17459
label: Hispanic or Latino
exposures:
- id: NCIT:C194
label: 4-Nitroquinoline-1-Oxide
- id: NCIT:C196
label: Benzo(a)pyrene-7,8-diol 9,10-Epoxide
- id: NCIT:C197
label: Dimethylbenzanthracene
- id: NCIT:C213
label: Aflatoxin
- id: NCIT:C251
label: Anthracene
- id: NCIT:C284
label: Asbestos
- id: NCIT:C294
label: Azoxymethane
- id: NCIT:C296
label: Bacterial Toxin
- id: NCIT:C297
label: Batrachotoxin
- id: NCIT:C302
label: Benzene
- id: NCIT:C349
label: Carmustine
- id: NCIT:C361
label: Chewing Tobacco
- id: NCIT:C368
label: Cholera Toxin
- id: NCIT:C442
label: Dioxin Compound
- id: NCIT:C470
label: Enterotoxin
- id: NCIT:C490
label: Ethylene Dibromide
- id: NCIT:C541
label: Herbicide
- id: NCIT:C645
label: Methylnitrosourea
- id: NCIT:C671
label: Bischloroethylsulfide
- id: NCIT:C674
label: Mycotoxin
- id: NCIT:C688
label: Neurotoxin
- id: NCIT:C690
label: Nickel
- id: NCIT:C736
label: Pertussis Toxin
- id: NCIT:C737
label: Pesticide
- id: NCIT:C742
label: Phorbol Ester
- id: NCIT:C760
label: Polychlorinated Biphenyl
- id: NCIT:C809
label: Ricin
- id: NCIT:C810
label: Ricin A Chain
- id: NCIT:C829
label: Tobacco Smoke
- id: NCIT:C859
label: Teratogen
- id: NCIT:C864
label: 2,3,7,8-Tetrachlorodibenzo-P-dioxin
- id: NCIT:C892
label: Smokeless Tobacco
- id: NCIT:C894
label: Toxin
- id: NCIT:C920
label: Urethane
- id: NCIT:C936
label: Vinyl Chloride
- id: NCIT:C951
label: Dibenzo[a,h]anthracene
- id: NCIT:C1068
label: Anguidine
- id: NCIT:C1069
label: Dibenzo (a,l) pyrene
- id: NCIT:C1072
label: 1,1-Dimethylhydrazine
- id: NCIT:C1107
label: Fumonisin B1
- id: NCIT:C1191
label: Phenol
- id: NCIT:C1225
label: Shiga Toxin
- id: NCIT:C1281
label: Biohazardous Substance
- id: NCIT:C1315
label: Aflatoxin B1
- id: NCIT:C1449
label: Thorium Dioxide
- id: NCIT:C1510
label: DNA Adduct
- id: NCIT:C1645
label: Dimethyl Ether
- id: NCIT:C1697
label: Fungicide
- id: NCIT:C1751
label: Pollutant
- id: NCIT:C2128
label: Sulfur Mustard Compound
- id: NCIT:C2434
label: Environmental Tobacco Smoke
- id: NCIT:C26451
label: Anthraquinone
- id: NCIT:C26563
label: Ethylnitrosourea
- id: NCIT:C28130
label: Acrylonitrile
- id: NCIT:C28131
label: Arsenic
- id: NCIT:C28140
label: Chlorine
- id: NCIT:C28171
label: narcotic
- id: NCIT:C28183
label: Radioactive Fallout
- id: NCIT:C28202
label: Nitric Acid
- id: NCIT:C29354
label: Permethrin
- id: NCIT:C29727
label: Pediculicide
- id: NCIT:C29744
label: Formaldehyde
- id: NCIT:C29768
label: 1-Aminobenzo[a]pyrene
- id: NCIT:C29779
label: 1-Nitrobenzo[a]pyrene
- id: NCIT:C29780
label: 1-Nitrobenzo[a]pyrene trans-7,8-Dihydrodiol
- id: NCIT:C29781
label: 1-Nitropyrene
- id: NCIT:C29787
label: 1,2-Dimethylhydrazine
- id: NCIT:C29788
label: 1,2-Dimethylhydrazine Dihydrochloride
- id: NCIT:C29789
label: 1,2,5,6-Dibenzanthracene
- id: NCIT:C29790
label: 1,3-Butadiene
- id: NCIT:C29791
label: 2-Acetylaminofluorene
- id: NCIT:C29792
label: 2-Amino-1-Methyl-6-Phenylimidazo[4,5-b]Pyridine
- id: NCIT:C29793
label: 2-Amino-3,4-Dimethylimidazole[4,5-f]quinoline
- id: NCIT:C29794
label: 2-Fluoroadenine
- id: NCIT:C29795
label: 20-Methylcholanthrene
- id: NCIT:C29797
label: 3-Aminobenzo[a]pyrene
- id: NCIT:C29798
label: 3-Nitrobenzo[a]pyrene
- id: NCIT:C29799
label: 3-Nitrobenzo[a]pyrene trans-7,8-Dihydrodiol
- id: NCIT:C29800
label: 3,4-Benzpyrene
- id: NCIT:C29801
label: 4-Methylnitrosamino-1,3-pyridyl-1-butanone
- id: NCIT:C29802
label: 4-Nitroquinoline N-oxide
- id: NCIT:C29803
label: 4-o-Tolylazo-o-Toluidine
- id: NCIT:C29804
label: 5-Methylchrysene
- id: NCIT:C29805
label: 6-Nitrochrysene
- id: NCIT:C29806
label: 9,10-Dimethyl-1,2-Benzanthracene
- id: NCIT:C29807
label: Acetone
- id: NCIT:C29808
label: Benzo[a]pyrene
- id: NCIT:C29809
label: Benzo[a]pyrene trans-7,8-Dihydrodiol
- id: NCIT:C29810
label: Benzo[b]fluoranthene
- id: NCIT:C29811
label: Benzotrichloride
- id: NCIT:C29813
label: Carbon Disulfide
- id: NCIT:C29814
label: Chlordane
- id: NCIT:C29815
label: Chloroform
- id: NCIT:C29816
label: Crocidolite Asbestos
- id: NCIT:C29817
label: Croton Oil
- id: NCIT:C29818
label: Cyclopenta[cd]pyrene
- id: NCIT:C29820
label: Ethyl Methanesulfonate
- id: NCIT:C29821
label: Ethylene Oxide
- id: NCIT:C29822
label: Ferric-Nitrilotriacetate
- id: NCIT:C29823
label: Hydroquinone
phenotypicFeatures:
- id: HP:0000020
label: Urinary incontinence
- id: HP:0000055
label: Abnormality of female external genitalia
- id: HP:0000141
label: Amenorrhea
- id: HP:0000553
label: Abnormal uvea morphology
- id: HP:0000630
label: Abnormal retinal artery morphology
- id: HP:0000632
label: Lacrimation abnormality
- id: HP:0000729
label: Autistic behavior
- id: HP:0000953
label: Hyperpigmentation of the skin
- id: HP:0001300
label: Parkinsonism
- id: HP:0001471
label: Aplasia/Hypoplasia of the musculature of the pelvis
- id: HP:0001473
label: Metatarsal osteolysis
- id: HP:0001609
label: Hoarse voice
- id: HP:0001629
label: Ventricular septal defect
- id: HP:0001730
label: Progressive hearing impairment
- id: HP:0001874
label: Abnormality of neutrophils
- id: HP:0002123
label: Generalized myoclonic seizure
- id: HP:0002418
label: Abnormal midbrain morphology
- id: HP:0002597
label: Abnormality of the vasculature
- id: HP:0002857
label: Genu valgum
- id: HP:0002863
label: Myelodysplasia
- id: HP:0002963
label: Abnormal delayed hypersensitivity skin test
- id: HP:0003174
label: Abnormality of the ischium
- id: HP:0003366
label: Abnormal femoral neck/head morphology
- id: HP:0003963
label: Lytic defects of the forearm bones
- id: HP:0004150
label: Abnormal 3rd finger morphology
- id: HP:0004362
label: Abnormality of enteric ganglion morphology
- id: HP:0004736
label: Crossed fused renal ectopia
- id: HP:0005035
label: Shortening of all phalanges of the toes
- id: HP:0005656
label: Positional foot deformity
- id: HP:0005830
label: Flexion contracture of toe
- id: HP:0006817
label: Aplasia/Hypoplasia of the cerebellar vermis
- id: HP:0007400
label: Irregular hyperpigmentation
- id: HP:0008066
label: Abnormal blistering of the skin
- id: HP:0008264
label: Neutrophil inclusion bodies
- id: HP:0009138
label: Synostosis involving bones of the lower limbs
- id: HP:0009404
label: Broad phalanges of the 4th finger
- id: HP:0009412
label: Cone-shaped epiphyses of the 3rd finger
- id: HP:0009421
label: Aplasia/Hypoplasia of the distal phalanx of the 3rd finger
- id: HP:0009489
label: Bracket epiphyses of the 2nd finger
- id: HP:0009500
label: Abnormality of the epiphysis of the middle phalanx of the 2nd finger
- id: HP:0009618
label: Abnormality of the proximal phalanx of the thumb
- id: HP:0009810
label: Abnormality of upper limb joint
- id: HP:0010160
label: Abnormal toe epiphysis morphology
- id: HP:0010178
label: Patchy sclerosis of toe phalanx
- id: HP:0010250
label: Fragmentation of the epiphyses of the distal phalanges of the hand
- id: HP:0010501
label: Limitation of knee mobility
- id: HP:0010514
label: Hyperpituitarism
- id: HP:0010784
label: Uterine neoplasm
- id: HP:0010841
label: Multifocal epileptiform discharges
- id: HP:0010930
label: Abnormal blood monovalent inorganic cation concentration
- id: HP:0010969
label: Abnormality of glycolipid metabolism
- id: HP:0011037
label: Decreased urine output
- id: HP:0011123
label: Inflammatory abnormality of the skin
- id: HP:0011176
label: EEG with constitutional variants
- id: HP:0011315
label: Unicoronal synostosis
- id: HP:0011488
label: Abnormal corneal endothelium morphology
- id: HP:0011636
label: Abnormal coronary artery origin
- id: HP:0012034
label: Liposarcoma
- id: HP:0012092
label: Abnormality of exocrine pancreas physiology
- id: HP:0012210
label: Abnormal renal morphology
- id: HP:0012310
label: Abnormal monocyte count
- id: HP:0012780
label: Neoplasm of the ear
- id: HP:0012836
label: Spatial pattern
- id: HP:0025429
label: Abnormal cry
- id: HP:0025487
label: Abnormality of bladder morphology
- id: HP:0025592
label: Superior oblique muscle weakness
- id: HP:0025646
label: Bilateral polymicrogyria
- id: HP:0030047
label: Abnormal lateral ventricle morphology
- id: HP:0030113
label: Abnormal muscle fiber dysferlin
- id: HP:0030119
label: Abnormal muscle fiber calpain-3
- id: HP:0030493
label: Abnormality of foveal pigmentation
- id: HP:0030604
label: Abnormal fundus fluorescein angiography
- id: HP:0030746
label: Intraventricular hemorrhage
- id: HP:0030828
label: Wheezing
- id: HP:0031607
label: Pelvic organ prolapse
- id: HP:0031704
label: Abnormal ear physiology
- id: HP:0031753
label: Medial rectus muscle weakness
- id: HP:0032011
label: Heterophoria
- id: HP:0032184
label: Increased proportion of memory T cells
- id: HP:0032422
label: Abnormal HDL2b concentration
- id: HP:0032900
label: Focal manual automatism seizure
- id: HP:0033095
label: Increased sulfur amino acid level in urine
- id: HP:0033823
label: Mediastinal mass
- id: HP:0034022
label: Anti-HLA-B antibody positivity
- id: HP:0040195
label: Decreased head circumference
- id: HP:0100569
label: Abnormally ossified vertebrae
- id: HP:0100612
label: Odontogenic neoplasm
- id: HP:0200040
label: Epidermoid cyst
- id: HP:0200042
label: Skin ulcer
- id: HP:0200065
label: Chorioretinal degeneration
- id: HP:0200114
label: Metabolic alkalosis
- id: HP:0200160
label: Agenesis of maxillary incisor
- id: HP:0410033
label: Unilateral alveolar cleft of maxilla
- id: HP:0500020
label: Abnormal cardiac biomarker test
- id: HP:0500073
label: Abnormal ocular alignment
- id: HP:0500093
label: Food allergy
- id: HP:0500155
label: Abnormal circulating asparagine concentration
- id: HP:0500158
label: Abnormal circulating aspartic acid concentration
- id: HP:5200018
label: Abnormal movements of the upper extremities
- id: HP:5200027
label: Abnormal social initiation
procedures:
- id: NCIT:C1447
label: Barium Enema Injection
- id: NCIT:C15189
label: Biopsy
- id: NCIT:C15190
label: Needle Biopsy
- id: NCIT:C15193
label: Bone Marrow Biopsy
- id: NCIT:C15220
label: Diagnosis
- id: NCIT:C15317
label: Second-Look Surgery
- id: NCIT:C15327
label: Lumbar Puncture
- id: NCIT:C15361
label: Fine-Needle Aspiration
- id: NCIT:C15385
label: Excisional Biopsy
- id: NCIT:C15386
label: Incisional Biopsy
- id: NCIT:C15387
label: Shave Biopsy
- id: NCIT:C15389
label: Endoscopic Biopsy
- id: NCIT:C15403
label: Endocervical Curettage
- id: NCIT:C15406
label: Cancer Screening
- id: NCIT:C15419
label: Disease Screening
- id: NCIT:C15427
label: Lymph Node Dissection
- id: NCIT:C15546
label: Breast Cancer Screening
- id: NCIT:C15547
label: Screening for Skin Cancer
- id: NCIT:C15548
label: Screening for Oral Cancer
- id: NCIT:C15549
label: Screening for Colorectal Cancer
- id: NCIT:C15550
label: Screening for Prostate Cancer
- id: NCIT:C15552
label: Screening for Testicular Cancer
- id: NCIT:C15567
label: Screening for Gastric Cancer
- id: NCIT:C15575
label: Screening for Lung Cancer
- id: NCIT:C15576
label: Screening for Ovarian Cancer
- id: NCIT:C15607
label: Clinical Diagnosis
- id: NCIT:C15608
label: Staging
- id: NCIT:C15638
label: Genetic Testing for Cancer Risk
- id: NCIT:C15641
label: Screening for Neuroblastoma
- id: NCIT:C15644
label: Bone Marrow Aspiration
- id: NCIT:C15652
label: Image Guided Biopsy
- id: NCIT:C15667
label: Sentinel Lymph Node Biopsy
- id: NCIT:C15671
label: Screening for Endometrial Cancer
- id: NCIT:C15680
label: Core Biopsy
- id: NCIT:C15703
label: Colposcopic Biopsy
- id: NCIT:C15741
label: Screening for Hepatocellular Cancer
- id: NCIT:C15775
label: Breast Cancer Detection Research
- id: NCIT:C15776
label: Cancer Detection
- id: NCIT:C15795
label: Detection of Measurable Residual Disease
- id: NCIT:C15842
label: Prevention, Early Detection of Premalignant Lesions
- id: NCIT:C15960
label: Blood Screening
- id: NCIT:C16094
label: Cardiac Function Study
- id: NCIT:C16107
label: Non-Invasive Cancer Detection
- id: NCIT:C16209
label: Early Detection
- id: NCIT:C16210
label: Detection
- id: NCIT:C16213
label: Cancer Diagnosis
- id: NCIT:C16291
label: Digital Subtraction Angiography
- id: NCIT:C16308
label: Arteriography
- id: NCIT:C16430
label: Endoscopic Retrograde Cholangiopancreatography
- id: NCIT:C16451
label: Colposcopy
- id: NCIT:C16502
label: Diagnostic Imaging
- id: NCIT:C16525
label: Echocardiography
- id: NCIT:C16546
label: Endoscopic Procedure
- id: NCIT:C16560
label: Esophagoscopy
- id: NCIT:C16587
label: Fluorophotometry
- id: NCIT:C16588
label: Fluoroscopy
- id: NCIT:C16781
label: Laryngoscopy
- id: NCIT:C16806
label: Lymphography
- id: NCIT:C16809
label: Magnetic Resonance Imaging
- id: NCIT:C16810
label: Magnetic Resonance Spectroscopy
- id: NCIT:C16811
label: Magnetoencephalography
- id: NCIT:C16818
label: Mammography
- id: NCIT:C16829
label: Mediastinoscopy
- id: NCIT:C16950
label: Palpation
- id: NCIT:C16969
label: Laparoscopy
- id: NCIT:C17007
label: Positron Emission Tomography
- id: NCIT:C17012
label: Proctoscopy
- id: NCIT:C17131
label: Sigmoidoscopy
- id: NCIT:C17137
label: Skin Test
- id: NCIT:C17194
label: Thermography
- id: NCIT:C17196
label: Thoracoscopy
- id: NCIT:C17203
label: Single Photon Emission Computed Tomography
- id: NCIT:C17204
label: Computed Tomography
- id: NCIT:C17261
label: Diagnostic Radiology
- id: NCIT:C17263
label: Xeroradiography
- id: NCIT:C17348
label: Pap Smear
- id: NCIT:C17369
label: Imaging Technique
- id: NCIT:C17436
label: Immunoscintigraphy
- id: NCIT:C17454
label: Diagnostic Test
- id: NCIT:C17558
label: Echo-Planar Imaging
- id: NCIT:C17631
label: Digital Rectal Examination
- id: NCIT:C17639
label: Upper Gastrointestinal Series
- id: NCIT:C17641
label: Percutaneous Transhepatic Cholangiography
- id: NCIT:C17644
label: Transvaginal Ultrasound
- id: NCIT:C17645
label: Radionuclide Scanning
- id: NCIT:C17646
label: Bone Scan
- id: NCIT:C17869
label: Assessment of Gonadal Function
- id: NCIT:C17958
label: Functional Magnetic Resonance Imaging
- id: NCIT:C18001
label: Digital X-Ray
- id: NCIT:C18020
label: Diagnostic Procedure
- id: NCIT:C18151
label: Diaphanography
- id: NCIT:C18190
label: Histopathologic Examination
- id: NCIT:C18210
label: Lymph Node Mapping
- id: NCIT:C18315
label: Transrectal Ultrasound
- id: NCIT:C18467
label: Digital Mammography
- id: NCIT:C18485
label: Three-Dimensional Imaging
- id: NCIT:C18869
label: Medical Imaging, Virtual Reality
- id: NCIT:C18980
label: Radiation Ionizing, Diagnostic Imaging
- id: NCIT:C18981
label: Radiation Non-Ionizing, Diagnostic Imaging
- id: NCIT:C19174
label: Lower GI Series
treatments:
- id: RxNorm:1000000
label: amlodipine 5 MG / hydrochlorothiazide 12.5 MG / olmesartan medoxomil 40 MG
Oral Tablet [Tribenzor]
- id: RxNorm:1000001
label: amlodipine 5 MG / hydrochlorothiazide 25 MG / olmesartan medoxomil 40 MG
Oral Tablet
- id: RxNorm:1000005
label: amlodipine 5 MG / hydrochlorothiazide 25 MG / olmesartan medoxomil 40 MG
Oral Tablet [Tribenzor]
- id: RxNorm:1000009
label: dimethicone 100 MG/ML / miconazole nitrate 20 MG/ML / zinc oxide 100 MG/ML
Topical Spray
- id: RxNorm:1000048
label: doxepin 10 MG Oral Capsule
- id: RxNorm:1000054
label: doxepin 10 MG/ML Oral Solution
- id: RxNorm:1000058
label: doxepin 100 MG Oral Capsule
- id: RxNorm:1000064
label: doxepin 150 MG Oral Capsule
- id: RxNorm:1000070
label: doxepin 25 MG Oral Capsule
- id: RxNorm:1000076
label: doxepin 50 MG Oral Capsule
- id: RxNorm:1000085
label: alcaftadine 2.5 MG/ML Ophthalmic Solution
- id: RxNorm:1000089
label: alcaftadine 2.5 MG/ML Ophthalmic Solution [Lastacaft]
- id: RxNorm:1000091
label: doxepin hydrochloride 50 MG/ML Topical Cream
- id: RxNorm:1000093
label: doxepin hydrochloride 50 MG/ML Topical Cream [Prudoxin]
- id: RxNorm:1000095
label: doxepin hydrochloride 50 MG/ML Topical Cream [Zonalon]
- id: RxNorm:1000097
label: doxepin 75 MG Oral Capsule
- id: RxNorm:1000107
label: incobotulinumtoxinA 200 UNT Injection
- id: RxNorm:1000114
label: medroxyprogesterone acetate 10 MG Oral Tablet
- id: RxNorm:1000124
label: medroxyprogesterone acetate 10 MG Oral Tablet [Provera]
- id: RxNorm:1000126
label: 1 ML medroxyprogesterone acetate 150 MG/ML Injection
- id: RxNorm:1000128
label: 1 ML medroxyprogesterone acetate 150 MG/ML Injection [Depo-Provera]
- id: RxNorm:1000131
label: medroxyprogesterone acetate 400 MG/ML Injectable Suspension
- id: RxNorm:1000133
label: medroxyprogesterone acetate 400 MG/ML Injectable Suspension [Depo-Provera]
- id: RxNorm:1000135
label: medroxyprogesterone acetate 2.5 MG Oral Tablet
- id: RxNorm:1000139
label: medroxyprogesterone acetate 2.5 MG Oral Tablet [Provera]
- id: RxNorm:1000141
label: medroxyprogesterone acetate 5 MG Oral Tablet
- id: RxNorm:1000145
label: medroxyprogesterone acetate 5 MG Oral Tablet [Provera]
- id: RxNorm:1000153
label: 1 ML medroxyprogesterone acetate 150 MG/ML Prefilled Syringe
- id: RxNorm:1000154
label: 1 ML medroxyprogesterone acetate 150 MG/ML Prefilled Syringe [Depo-Provera]
- id: RxNorm:1000156
label: 0.65 ML medroxyprogesterone acetate 160 MG/ML Prefilled Syringe
- id: RxNorm:1000158
label: 0.65 ML medroxyprogesterone acetate 160 MG/ML Prefilled Syringe [depo-subQ
provera]
- id: RxNorm:1000351
label: estrogens, conjugated (USP) 0.3 MG / medroxyprogesterone acetate 1.5 MG Oral
Tablet
- id: RxNorm:1000352
label: estrogens, conjugated (USP) 0.45 MG / medroxyprogesterone acetate 1.5 MG
Oral Tablet
- id: RxNorm:1000355
label: estrogens, conjugated (USP) 0.625 MG / medroxyprogesterone acetate 2.5 MG
Oral Tablet
- id: RxNorm:1000356
label: estrogens, conjugated (USP) 0.625 MG / medroxyprogesterone acetate 5 MG Oral
Tablet
- id: RxNorm:1000395
label: '{28 (estrogens, conjugated (USP) 0.625 MG / medroxyprogesterone acetate
2.5 MG Oral Tablet) } Pack'
- id: RxNorm:1000398
label: '{28 (estrogens, conjugated (USP) 0.625 MG / medroxyprogesterone acetate
5 MG Oral Tablet) } Pack'
- id: RxNorm:1000405
label: norethindrone acetate 5 MG Oral Tablet
- id: RxNorm:1000407
label: norethindrone acetate 5 MG Oral Tablet [Aygestin]
- id: RxNorm:1000479
label: '{1 (bisacodyl 5 MG Delayed Release Oral Tablet) / 1 (2000 ML) (polyethylene
glycol 3350 210000 MG / potassium chloride 740 MG / sodium bicarbonate 2860 MG
/ sodium chloride 5600 MG Powder for Oral Solution) } Pack'
- id: RxNorm:1000486
label: '{14 (estrogens, conjugated (USP) 0.625 MG / medroxyprogesterone acetate
5 MG Oral Tablet) / 14 (estrogens, conjugated (USP) 0.625 MG Oral Tablet) } Pack'
- id: RxNorm:1000487
label: '{14 (estrogens, conjugated (USP) 0.625 MG / medroxyprogesterone acetate
5 MG Oral Tablet) / 14 (estrogens, conjugated (USP) 0.625 MG Oral Tablet) } Pack
[Premphase 28 Day]'
- id: RxNorm:1000490
label: '{28 (estrogens, conjugated (USP) 0.3 MG / medroxyprogesterone acetate 1.5
MG Oral Tablet) } Pack'
- id: RxNorm:1000491
label: '{28 (estrogens, conjugated (USP) 0.3 MG / medroxyprogesterone acetate 1.5
MG Oral Tablet) } Pack [Prempro 0.3/1.5 28 Day]'
- id: RxNorm:1000495
label: resveratrol 250 MG Oral Capsule
- id: RxNorm:1000496
label: '{28 (estrogens, conjugated (USP) 0.45 MG / medroxyprogesterone acetate 1.5
MG Oral Tablet) } Pack'
- id: RxNorm:1000497
label: '{28 (estrogens, conjugated (USP) 0.45 MG / medroxyprogesterone acetate 1.5
MG Oral Tablet) } Pack [Prempro 0.45/1.5 28 Day]'
- id: RxNorm:1000499
label: '{28 (estrogens, conjugated (USP) 0.625 MG / medroxyprogesterone acetate
2.5 MG Oral Tablet) } Pack [Prempro 0.625/2.5 28 Day]'
- id: RxNorm:1000500
label: '{28 (estrogens, conjugated (USP) 0.625 MG / medroxyprogesterone acetate
5 MG Oral Tablet) } Pack [Prempro 0.625/5 28 Day]'
- id: RxNorm:1000502
label: dextromethorphan hydrobromide 6 MG/ML / guaifenesin 40 MG/ML / phenylephrine
hydrochloride 1.5 MG/ML Oral Solution
- id: RxNorm:1000556
label: fluorometholone 1 MG/ML / sulfacetamide sodium 100 MG/ML Ophthalmic Suspension
- id: RxNorm:1000558
label: fluorometholone 1 MG/ML / sulfacetamide sodium 100 MG/ML Ophthalmic Suspension
[FML-S]
- id: RxNorm:1000636
label: dimethicone 12.5 MG/ML Topical Lotion
- id: RxNorm:1000647
label: pilocarpine hydrochloride 10 MG/ML Ophthalmic Solution
- id: RxNorm:1000656
label: pilocarpine hydrochloride 10 MG/ML Ophthalmic Solution [Isoptocarpine]
- id: RxNorm:1000660
label: pilocarpine hydrochloride 10 MG/ML Ophthalmic Solution [Pilocar]
- id: RxNorm:1000673
label: sulfacetamide sodium 0.1 MG/MG Ophthalmic Ointment
- id: RxNorm:1000713
label: sulfacetamide sodium 0.1 MG/MG Topical Gel
- id: RxNorm:1000720
label: sulfacetamide sodium 100 MG/ML / sulfur 10 MG/ML Medicated Liquid Soap [BP
10-Wash]
- id: RxNorm:1000731
label: sulfacetamide sodium 100 MG/ML / sulfur 20 MG/ML Topical Cream
- id: RxNorm:1000736
label: sulfacetamide sodium 100 MG/ML / sulfur 20 MG/ML Topical Cream [Avar]
- id: RxNorm:1000859
label: sulfacetamide sodium 100 MG/ML / sulfur 40 MG/ML Medicated Liquid Soap
- id: RxNorm:1000861
label: sulfacetamide sodium 100 MG/ML / sulfur 40 MG/ML Medicated Liquid Soap [BP
Cleansing Wash]
- id: RxNorm:1000862
label: pilocarpine hydrochloride 20 MG/ML Ophthalmic Solution
- id: RxNorm:1000870
label: pilocarpine hydrochloride 20 MG/ML Ophthalmic Solution [Isoptocarpine]
- id: RxNorm:1000876
label: pilocarpine hydrochloride 20 MG/ML Ophthalmic Solution [Pilocar]
- id: RxNorm:1000895
label: sulfacetamide sodium 100 MG/ML / sulfur 20 MG/ML Medicated Liquid Soap
- id: RxNorm:1000897
label: pilocarpine hydrochloride 40 MG/ML Ophthalmic Solution
- id: RxNorm:1000903
label: pilocarpine hydrochloride 40 MG/ML Ophthalmic Solution [Isoptocarpine]
- id: RxNorm:1000907
label: pilocarpine hydrochloride 40 MG/ML Ophthalmic Solution [Pilocar]
- id: RxNorm:1000913
label: pilocarpine hydrochloride 5 MG Oral Tablet
- id: RxNorm:1000915
label: pilocarpine hydrochloride 5 MG Oral Tablet [Salagen]
- id: RxNorm:1000946
label: sulfacetamide sodium 100 MG/ML / sulfur 40 MG/ML Medicated Pad
- id: RxNorm:1000976
label: sulfacetamide sodium 100 MG/ML / sulfur 40 MG/ML Medicated Pad [Sumaxin]
- id: RxNorm:1000981
label: oxymetazoline hydrochloride 0.25 MG/ML Ophthalmic Solution
- id: RxNorm:1000990
label: oxymetazoline hydrochloride 0.5 MG/ML Nasal Spray
- id: RxNorm:1000992
label: oxymetazoline hydrochloride 0.5 MG/ML Nasal Spray [Afrin]
- id: RxNorm:1000994
label: oxymetazoline hydrochloride 0.5 MG/ML Nasal Spray [Allerest 12 Hour Nasal
Spray]
- id: RxNorm:1000996
label: oxymetazoline hydrochloride 0.5 MG/ML Nasal Spray [Dristan 12-Hour Nasal
Spray]
- id: RxNorm:1001002
label: oxymetazoline hydrochloride 0.5 MG/ML Nasal Spray [Duramist Plus]
- id: RxNorm:1001004
label: pilocarpine hydrochloride 7.5 MG Oral Tablet
- id: RxNorm:1001006
label: pilocarpine hydrochloride 7.5 MG Oral Tablet [Salagen]
- id: RxNorm:1001054
label: oxymetazoline hydrochloride 0.5 MG/ML Nasal Spray [Neo-Synephrine 12 Hour]
- id: RxNorm:1001058
label: oxymetazoline hydrochloride 0.5 MG/ML Nasal Spray [Nostrilla]
- id: RxNorm:1001066
label: oxymetazoline hydrochloride 0.5 MG/ML Nasal Spray [Sinex Long-Acting]
- id: RxNorm:1001084
label: oxymetazoline hydrochloride 0.5 MG/ML Nasal Spray [Zicam Sinus Relief]
- id: RxNorm:1001405
label: docetaxel 20 MG/ML Injectable Solution
- id: RxNorm:1001409
label: calcium carbonate 625 MG / ergocalciferol 125 UNT Oral Tablet
- id: RxNorm:1001433
label: 1.5 ML cabazitaxel 40 MG/ML Injection
- id: RxNorm:1001437
label: caffeine 50 MG / magnesium salicylate 162.5 MG Oral Tablet
- id: RxNorm:1001476
label: aspirin 325 MG Delayed Release Oral Tablet [Ecpirin]
- id: RxNorm:1001591
label: fibrinogen, human 337 MG / thrombin, human 123 UNT Medicated Patch
- id: RxNorm:1001593
label: fibrinogen, human 337 MG / thrombin, human 123 UNT Medicated Patch [TachoSil]
- id: RxNorm:1001679
label: calcium carbonate 400 MG / cholecalciferol 133 UNT / magnesium oxide 167
MG Oral Tablet
- id: RxNorm:1001689
label: '{2 (480 ML) (magnesium sulfate 0.0277 MEQ/ML / potassium sulfate 0.0374
MEQ/ML / sodium sulfate 0.257 MEQ/ML Oral Solution) } Pack'
- id: RxNorm:1001690
label: '{2 (480 ML) (magnesium sulfate 0.0277 MEQ/ML / potassium sulfate 0.0374
MEQ/ML / sodium sulfate 0.257 MEQ/ML Oral Solution) } Pack [Suprep Bowel Prep
Kit]'
- id: RxNorm:1001691
label: calcium carbonate 1250 MG / cholecalciferol 100 UNT / vitamin K1 0.04 MG
Chewable Tablet
- id: RxNorm:1001714
label: sulfacetamide sodium 90 MG/ML / sulfur 40 MG/ML Medicated Liquid Soap
- id: RxNorm:1001718
label: sulfacetamide sodium 90 MG/ML / sulfur 40 MG/ML Medicated Liquid Soap [Zencia
Wash]
- id: RxNorm:1001751
label: calcium citrate 250 MG / cholecalciferol 100 UNT Oral Tablet
NAME¶
bff-pxf-simulator: A script that creates a JSON array of simulated BFF/PXF
SYNOPSIS¶
bff-pxf-simulator [-options]
Options:
-f, --format <format> Format [bff|pxf]
-n, --number <number> Set the number of individuals to generate [100]
-o, --output <file> Output file [individuals.json]
--external-ontologies <file> Path to a YAML file containing ontology terms
--random-seed <seed> Initializes pseudorandom number sequences (seed must be an integer)
--diseases <number> Set the number of diseases per individual [1]
--exposures <number> Set the number of exposures per individual [1]
--phenotypicFeatures <number> Set the number of phenotypic features per individual [1]
--procedures <number> Set the number of procedures per individual [1]
--treatments <number> Set the number of treatments per individual [1]
--max-[term]-pool <size> Limit the selection to the first N elements of the term array
--max-ethnicity-pool <size> Restrict the ethnicity pool size; each individual will have only one ethnicity
Generic Options:
-debug <level> Print debugging (from 1 to 5, being 5 max)
-h, --help Brief help message
-man Full documentation
-v, --verbose Verbosity on
-V, --version Print version
DESCRIPTION¶
This script generates a JSON array of simulated BFF/PXF data. The files can be created based on pre-loaded ontologies or by utilizing an external YAML file.
SUMMARY¶
A script that creates a JSON array of simulated BFF/PXF.
Implemented array terms:
BFF: diseases, exposures, interventionsOrProcedures, phenotypicFeatures, treatments.
procedures = interventionsOrProcedures
PXF: interventionsOrProcedures, medicalActions.procedure, medicalActions.treatment, phenotypicFeatures.
procedures = medicalActions.procedure
treatments = medicalActions.treatment
INSTALLATION¶
(only needed if you did not install Pheno-Ranker)
$ cpanm --sudo --installdeps .
System requirements¶
* Ideally a Debian-based distribution (Ubuntu or Mint), but any other (e.g., CentOs, OpenSuse) should do as well.
* Perl 5 (>= 5.10 core; installed by default in most Linux distributions). Check the version with "perl -v"
* 1GB of RAM.
* 1 core (it only uses one core per job).
* At least 1GB HDD.
HOW TO RUN BFF-PXF-SIMULATOR¶
When run without any arguments, the software will use default settings. To modify any parameters, please refer to the synopsis for guidance.
If you prefer not to include a specific term in the analysis, set its value to zero. For example:
--treatments 0
Examples:
$ ./bff-pxf-simulator -f pxf # BFF with 100 samples
$ ./bff-pxf-simulator -f pxf -n 1000 -o pxf.json # PXF with 1K samples and saved to pxf.json
$ ./bff-pxf-simulator -phenotypicFeatures 10 # BFF with 100 samples and 10 pF each
$ ./bff-pxf-simulator -diseases 0 -exposures 0 -procedures 0 -phenotypicFeatures 0 -treatments 0 # Only sex and ethnicity
COMMON ERRORS AND SOLUTIONS¶
* Error message: Foo
Solution: Bar
* Error message: Foo
Solution: Bar
AUTHOR¶
Written by Manuel Rueda, PhD. Info about CNAG can be found at https://www.cnag.eu.
COPYRIGHT AND LICENSE¶
This PERL file is copyrighted. See the LICENSE file included in this distribution.