From fd20d214076fa1dbdc09858ef2f25027e7093c59 Mon Sep 17 00:00:00 2001 From: Manuel Rueda Date: Wed, 18 Dec 2024 15:12:20 +0100 Subject: [PATCH] Update t --- t/omop2bff/out/individuals_csv.json.gz | Bin 43283 -> 43283 bytes .../out/individuals_drug_exposure.json.gz | Bin 231672 -> 231672 bytes t/omop2pxf/out/pxf.json | 158 +++++++-------- t/pxf2bff/out/individuals.json | 160 ++++++++-------- t/pxf2bff/out/individuals.yaml | 180 +++++++++--------- 5 files changed, 249 insertions(+), 249 deletions(-) diff --git a/t/omop2bff/out/individuals_csv.json.gz b/t/omop2bff/out/individuals_csv.json.gz index d3f6d33c2302927b9abf0076d532c1b9ee8abc66..cb7db2f8d4710784cc1953caaf83122b48fd9e8b 100644 GIT binary patch delta 18 acmbPyiD~jBCU*I54hGR1NgLUDRssM&GX_Ke delta 18 acmbPyiD~jBCU*I54u(%0dK=k!RssM&S_T~e diff --git a/t/omop2bff/out/individuals_drug_exposure.json.gz b/t/omop2bff/out/individuals_drug_exposure.json.gz index c70284f39f315a913b6eab34597221aaf1f51c20..b2d8c58c2aec6e6258587ad1a2df2c3d875b1d8e 100644 GIT binary patch delta 27 jcmew{k?+SuK6d$T4hE4MNsa8S?2N7KOk3HRKXw2Bh+YX1 delta 27 jcmew{k?+SuK6d$T4u+2$dX4O@?2N7KOk3HRKXw2Bhb9Q> diff --git a/t/omop2pxf/out/pxf.json b/t/omop2pxf/out/pxf.json index 0c1ef9e0..ba2d7175 100644 --- a/t/omop2pxf/out/pxf.json +++ b/t/omop2pxf/out/pxf.json @@ -244,7 +244,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -333,7 +333,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:703151001", "label" : "History of single seizure" @@ -1461,7 +1461,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -1586,7 +1586,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -2634,7 +2634,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:399211009", "label" : "History of myocardial infarction" @@ -2888,7 +2888,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:399211009", "label" : "History of myocardial infarction" @@ -4163,7 +4163,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:703151001", "label" : "History of single seizure" @@ -4909,7 +4909,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -5666,7 +5666,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -5740,7 +5740,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:703151001", "label" : "History of single seizure" @@ -5867,7 +5867,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:703151001", "label" : "History of single seizure" @@ -6142,7 +6142,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -6164,7 +6164,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:703151001", "label" : "History of single seizure" @@ -6199,7 +6199,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:399211009", "label" : "History of myocardial infarction" @@ -7610,7 +7610,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -9054,28 +9054,28 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:419263009", "label" : "Allergy to tree pollen" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:419474003", "label" : "Allergy to mold" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:418689008", "label" : "Allergy to grass pollen" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:232350006", "label" : "Allergy to house dust mite" @@ -9238,7 +9238,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -9378,14 +9378,14 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:91930004", "label" : "Allergy to eggs" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -9749,7 +9749,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:419474003", "label" : "Allergy to mold" @@ -9871,7 +9871,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -10218,7 +10218,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:703151001", "label" : "History of single seizure" @@ -10369,7 +10369,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:399211009", "label" : "History of myocardial infarction" @@ -10539,21 +10539,21 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:232350006", "label" : "Allergy to house dust mite" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:418689008", "label" : "Allergy to grass pollen" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:419474003", "label" : "Allergy to mold" @@ -11496,7 +11496,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -12046,7 +12046,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:703151001", "label" : "History of single seizure" @@ -12157,7 +12157,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -12398,7 +12398,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -13072,7 +13072,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -14315,7 +14315,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -15042,7 +15042,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -15314,21 +15314,21 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:399211009", "label" : "History of myocardial infarction" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:703151001", "label" : "History of single seizure" @@ -15350,7 +15350,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:417532002", "label" : "Allergy to fish" @@ -15877,7 +15877,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:419474003", "label" : "Allergy to mold" @@ -16343,49 +16343,49 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:300913006", "label" : "Shellfish allergy" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:419263009", "label" : "Allergy to tree pollen" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:91934008", "label" : "Allergy to nut" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:300916003", "label" : "Latex allergy" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:91935009", "label" : "Allergy to peanuts" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:419474003", "label" : "Allergy to mold" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:232347008", "label" : "Allergy to animal dander" @@ -17273,7 +17273,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -17816,7 +17816,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -18407,7 +18407,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -18467,7 +18467,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -19066,7 +19066,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -19931,7 +19931,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -20907,7 +20907,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -21356,7 +21356,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -21820,7 +21820,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -22582,7 +22582,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -22717,14 +22717,14 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:420174000", "label" : "Allergy to wheat" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:232347008", "label" : "Allergy to animal dander" @@ -23364,7 +23364,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -23386,14 +23386,14 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:399211009", "label" : "History of myocardial infarction" @@ -23606,14 +23606,14 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:703151001", "label" : "History of single seizure" @@ -24281,7 +24281,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:703151001", "label" : "History of single seizure" @@ -24860,7 +24860,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" @@ -25066,14 +25066,14 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:429007001", "label" : "History of cardiac arrest" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:399211009", "label" : "History of myocardial infarction" @@ -25175,49 +25175,49 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:232350006", "label" : "Allergy to house dust mite" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:91930004", "label" : "Allergy to eggs" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:232347008", "label" : "Allergy to animal dander" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:419474003", "label" : "Allergy to mold" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:417532002", "label" : "Allergy to fish" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:419263009", "label" : "Allergy to tree pollen" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:300913006", "label" : "Shellfish allergy" @@ -25317,7 +25317,7 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:428251008", "label" : "History of appendectomy" @@ -25404,14 +25404,14 @@ "metaData" : null, "phenotypicFeatures" : [ { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:419474003", "label" : "Allergy to mold" } }, { - "excluded" : null, + "excluded" : false, "type" : { "id" : "SNOMED:714035009", "label" : "Allergy to soy" diff --git a/t/pxf2bff/out/individuals.json b/t/pxf2bff/out/individuals.json index e39c3417..e6a1aa4c 100644 --- a/t/pxf2bff/out/individuals.json +++ b/t/pxf2bff/out/individuals.json @@ -12,7 +12,7 @@ "id" : "MONDO:0100308", "label" : "atactic disorder" }, - "excluded" : true + "excluded" : false } ], "id" : "16-year-old boy", @@ -323,7 +323,7 @@ ], "phenotypicFeatures" : [ { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001288", "label" : "Gait disturbance" @@ -335,7 +335,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001324", "label" : "Muscle weakness" @@ -353,7 +353,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0002066", "label" : "Gait ataxia" @@ -365,7 +365,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001308", "label" : "Tongue fasciculations" @@ -377,7 +377,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0002080", "label" : "Intention tremor" @@ -389,7 +389,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0002075", "label" : "Dysdiadochokinesis" @@ -401,7 +401,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001251", "label" : "Ataxia" @@ -413,7 +413,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001284", "label" : "Areflexia" @@ -425,7 +425,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0011448", "label" : "Ankle clonus" @@ -437,7 +437,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0003690", "label" : "Limb muscle weakness" @@ -616,7 +616,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001629", "label" : "Ventricular septal defect" @@ -641,7 +641,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000280", "label" : "Coarse facial features" @@ -660,7 +660,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0008689", "label" : "Bilateral cryptorchidism" @@ -685,7 +685,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001561", "label" : "Polyhydramnios" @@ -710,7 +710,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000054", "label" : "Micropenis" @@ -735,7 +735,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001798", "label" : "Anonychia" @@ -760,7 +760,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001320", "label" : "Cerebellar vermis hypoplasia" @@ -779,7 +779,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000518", "label" : "Cataract" @@ -804,7 +804,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0002198", "label" : "Dilated fourth ventricle" @@ -823,7 +823,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0100333", "label" : "Unilateral cleft lip" @@ -855,7 +855,7 @@ "id" : "MONDO:0004994", "label" : "cardiomyopathy" }, - "excluded" : true + "excluded" : false }, { "ageOfOnset" : { @@ -865,7 +865,7 @@ "id" : "MONDO:0100096", "label" : "COVID-19" }, - "excluded" : true + "excluded" : false } ], "id" : "P123542", @@ -1016,7 +1016,7 @@ ], "phenotypicFeatures" : [ { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001945", "label" : "Fever " @@ -1026,7 +1026,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0030157", "label" : "Flank pain" @@ -1036,7 +1036,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000790", "label" : "Hematuria" @@ -1046,7 +1046,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0012625", "label" : "Stage 3 chronic kidney disease" @@ -1056,7 +1056,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0003326", "label" : "Myalgia" @@ -1069,7 +1069,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0002014", "label" : "Diarrhea" @@ -1082,7 +1082,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0002094", "label" : "Dyspnea" @@ -1095,7 +1095,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0033677", "label" : "Acute respiratory distress syndrome" @@ -1346,7 +1346,7 @@ "karyotypicSex" : "UNKNOWN_KARYOTYPE", "phenotypicFeatures" : [ { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0031936", "label" : "Delayed ability to walk" @@ -1358,7 +1358,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0003707", "label" : "Calf muscle pseudohypertrophy" @@ -1371,7 +1371,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0009046", "label" : "Difficulty running" @@ -1384,7 +1384,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0003458", "label" : "EMG: myopathic abnormalities" @@ -1396,7 +1396,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0003236", "label" : "Elevated circulating creatine kinase concentration" @@ -1526,7 +1526,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000238", "label" : "Hydrocephalus" @@ -1550,7 +1550,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0002507", "label" : "Semilobar holoprosencephaly" @@ -1575,7 +1575,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001750", "label" : "Single ventricle" @@ -1599,7 +1599,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001272", "label" : "Cerebellar atrophy" @@ -1623,7 +1623,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0100702", "label" : "Arachnoid cyst" @@ -1647,7 +1647,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001272", "label" : "Cerebellar atrophy" @@ -1671,7 +1671,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001263", "label" : "Global developmental delay" @@ -1696,7 +1696,7 @@ } } ], - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001347", "label" : "Hyperreflexia" @@ -1720,7 +1720,7 @@ "id" : "OMIM:154700", "label" : "Marfan syndrome" }, - "excluded" : true + "excluded" : false } ], "id" : "proband C", @@ -1778,7 +1778,7 @@ "karyotypicSex" : "UNKNOWN_KARYOTYPE", "phenotypicFeatures" : [ { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0002616", "label" : "Aortic root aneurysm" @@ -2023,7 +2023,7 @@ "karyotypicSex" : "UNKNOWN_KARYOTYPE", "phenotypicFeatures" : [ { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001558", "label" : "Decreased fetal movement" @@ -2035,7 +2035,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0025672", "label" : "Fetal skin edema" @@ -2048,7 +2048,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0010557", "label" : "Overlapping fingers" @@ -2061,7 +2061,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001561", "label" : "Polyhydramnios" @@ -2080,7 +2080,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0030931", "label" : "1-minute APGAR score of 4" @@ -2093,7 +2093,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0030922", "label" : "5-minute APGAR score of 2" @@ -2106,7 +2106,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0033469", "label" : "10-minute APGAR score of 1" @@ -2119,7 +2119,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0012027", "label" : "Laryngeal edema" @@ -2132,7 +2132,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0001290", "label" : "Generalized hypotonia" @@ -2163,7 +2163,7 @@ "id" : "MONDO:0008327", "label" : "exfoliation syndrome" }, - "excluded" : true, + "excluded" : false, "primarySite" : { "id" : "UBERON:0004549", "label" : "right eye" @@ -2632,7 +2632,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000545", "label" : "Myopia" @@ -2650,7 +2650,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "NCIT:C50618", "label" : "Intraocular Pressure Increased" @@ -2750,7 +2750,7 @@ "label" : "Group E" } ], - "excluded" : true, + "excluded" : false, "primarySite" : { "id" : "UBERON:0004548", "label" : "left eye" @@ -3144,7 +3144,7 @@ ], "phenotypicFeatures" : [ { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0030084", "label" : "Clinodactyly" @@ -3162,7 +3162,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000555", "label" : "Leukocoria" @@ -3180,7 +3180,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000486", "label" : "Strabismus" @@ -3198,7 +3198,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000541", "label" : "Retinal detachment" @@ -3274,7 +3274,7 @@ "id" : "NCIT:C4024", "label" : "Esophageal Squamous Cell Carcinoma" }, - "excluded" : true + "excluded" : false } ], "id" : "proband A", @@ -3420,7 +3420,7 @@ "id" : "MONDO:0005148", "label" : "type 2 diabetes mellitus" }, - "excluded" : true + "excluded" : false }, { "ageOfOnset" : { @@ -3432,7 +3432,7 @@ "id" : "MONDO:0001134", "label" : "essential hypertension" }, - "excluded" : true + "excluded" : false } ], "id" : "65-year-old man", @@ -3552,7 +3552,7 @@ ], "phenotypicFeatures" : [ { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0008994", "label" : "Proximal muscle weakness in lower limbs" @@ -3564,7 +3564,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0007289", "label" : "Limb fasciculations" @@ -3576,7 +3576,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0008956", "label" : "Proximal lower limb amyotrophy" @@ -3600,7 +3600,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0003391", "label" : "Gowers sign" @@ -3612,7 +3612,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0003551", "label" : "Difficulty climbing stairs" @@ -3624,7 +3624,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0006886", "label" : "Impaired distal vibration sensation" @@ -3820,7 +3820,7 @@ "label" : "Stage IV" } ], - "excluded" : true + "excluded" : false } ], "id" : "patient1", @@ -4046,7 +4046,7 @@ "karyotypicSex" : "UNKNOWN_KARYOTYPE", "phenotypicFeatures" : [ { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0100518", "label" : "Dysuria" @@ -4057,7 +4057,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000790", "label" : "Hematuria" @@ -4081,7 +4081,7 @@ "id" : "MONDO:0016649", "label" : "Warburg micro syndrome" }, - "excluded" : true + "excluded" : false } ], "id" : "case1", @@ -4115,7 +4115,7 @@ "karyotypicSex" : "UNKNOWN_KARYOTYPE", "phenotypicFeatures" : [ { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0034248", "label" : "Increased fetal lens echogenicity" @@ -4141,7 +4141,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000369", "label" : "Low-set ears" @@ -4153,7 +4153,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0008936", "label" : "Axial hypotonia" @@ -4165,7 +4165,7 @@ } }, { - "excluded" : true, + "excluded" : false, "featureType" : { "id" : "HP:0000568", "label" : "Microphthalmia" diff --git a/t/pxf2bff/out/individuals.yaml b/t/pxf2bff/out/individuals.yaml index cd915a3c..f07f2a6a 100644 --- a/t/pxf2bff/out/individuals.yaml +++ b/t/pxf2bff/out/individuals.yaml @@ -7,7 +7,7 @@ diseaseCode: id: MONDO:0100308 label: atactic disorder - excluded: true + excluded: 0 id: 16-year-old boy info: phenopacket: @@ -205,14 +205,14 @@ iso8601duration: P16Y6M timeObserved: *4 phenotypicFeatures: - - excluded: true + - excluded: 0 featureType: id: HP:0001288 label: Gait disturbance onset: age: iso8601duration: P10Y - - excluded: true + - excluded: 0 featureType: id: HP:0001324 label: Muscle weakness @@ -222,77 +222,77 @@ onset: age: iso8601duration: P10Y - - excluded: true + - excluded: 0 featureType: id: HP:0002066 label: Gait ataxia onset: age: iso8601duration: P16Y - - excluded: true + - excluded: 0 featureType: id: HP:0001308 label: Tongue fasciculations onset: age: iso8601duration: P16Y - - excluded: true + - excluded: 0 featureType: id: HP:0002080 label: Intention tremor onset: age: iso8601duration: P16Y - - excluded: true + - excluded: 0 featureType: id: HP:0002075 label: Dysdiadochokinesis onset: age: iso8601duration: P16Y - - excluded: true + - excluded: 0 featureType: id: HP:0001251 label: Ataxia onset: age: iso8601duration: P16Y - - excluded: true + - excluded: 0 featureType: id: HP:0001284 label: Areflexia onset: age: iso8601duration: P16Y - - excluded: true + - excluded: 0 featureType: id: HP:0011448 label: Ankle clonus onset: age: iso8601duration: P16Y - - excluded: true + - excluded: 0 featureType: id: HP:0003690 label: Limb muscle weakness onset: age: iso8601duration: P16Y - - excluded: true + - excluded: 1 featureType: id: HP:0003474 label: Somatic sensory dysfunction onset: age: iso8601duration: P16Y - - excluded: true + - excluded: 1 featureType: id: HP:0002599 label: Head titubation onset: age: iso8601duration: P16Y - - excluded: true + - excluded: 1 featureType: id: HP:0031910 label: Abnormal cranial nerve physiology @@ -387,7 +387,7 @@ description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report' id: PMID:30808312 - excluded: true + excluded: 0 featureType: id: HP:0001629 label: Ventricular septal defect @@ -403,7 +403,7 @@ description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report' id: PMID:30808312 - excluded: true + excluded: 0 featureType: id: HP:0000280 label: Coarse facial features @@ -415,7 +415,7 @@ description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report' id: PMID:30808312 - excluded: true + excluded: 0 featureType: id: HP:0008689 label: Bilateral cryptorchidism @@ -431,7 +431,7 @@ description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report' id: PMID:30808312 - excluded: true + excluded: 0 featureType: id: HP:0001561 label: Polyhydramnios @@ -447,7 +447,7 @@ description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report' id: PMID:30808312 - excluded: true + excluded: 0 featureType: id: HP:0000054 label: Micropenis @@ -463,7 +463,7 @@ description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report' id: PMID:30808312 - excluded: true + excluded: 0 featureType: id: HP:0001798 label: Anonychia @@ -479,7 +479,7 @@ description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report' id: PMID:30808312 - excluded: true + excluded: 0 featureType: id: HP:0001320 label: Cerebellar vermis hypoplasia @@ -491,7 +491,7 @@ description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report' id: PMID:30808312 - excluded: true + excluded: 0 featureType: id: HP:0000518 label: Cataract @@ -507,7 +507,7 @@ description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report' id: PMID:30808312 - excluded: true + excluded: 0 featureType: id: HP:0002198 label: Dilated fourth ventricle @@ -519,7 +519,7 @@ description: 'COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report' id: PMID:30808312 - excluded: true + excluded: 0 featureType: id: HP:0100333 label: Unilateral cleft lip @@ -534,17 +534,17 @@ - diseaseCode: id: MONDO:0005015 label: diabetes mellitus - excluded: true + excluded: 1 - diseaseCode: id: MONDO:0004994 label: cardiomyopathy - excluded: true + excluded: 0 - ageOfOnset: timestamp: 2020-03-17T00:00:00Z diseaseCode: id: MONDO:0100096 label: COVID-19 - excluded: true + excluded: 0 id: P123542 info: phenopacket: @@ -640,31 +640,31 @@ timestamp: 2020-03-20T00:00:00Z timeObserved: *6 phenotypicFeatures: - - excluded: true + - excluded: 0 featureType: id: HP:0001945 label: 'Fever ' onset: timestamp: 2021-02-01T05:00:00Z - - excluded: true + - excluded: 0 featureType: id: HP:0030157 label: Flank pain onset: timestamp: 2021-02-01T05:00:00Z - - excluded: true + - excluded: 0 featureType: id: HP:0000790 label: Hematuria onset: timestamp: 2021-02-01T05:00:00Z - - excluded: true + - excluded: 0 featureType: id: HP:0012625 label: Stage 3 chronic kidney disease onset: timestamp: 2021-02-01T05:00:00Z - - excluded: true + - excluded: 0 featureType: id: HP:0003326 label: Myalgia @@ -672,7 +672,7 @@ interval: end: 2020-03-20T00:00:00Z start: 2020-03-18T00:00:00Z - - excluded: true + - excluded: 0 featureType: id: HP:0002014 label: Diarrhea @@ -680,7 +680,7 @@ interval: end: 2020-03-20T00:00:00Z start: 2020-03-18T00:00:00Z - - excluded: true + - excluded: 0 featureType: id: HP:0002094 label: Dyspnea @@ -688,7 +688,7 @@ interval: end: 2020-03-20T00:00:00Z start: 2020-03-18T00:00:00Z - - excluded: true + - excluded: 0 featureType: id: HP:0033677 label: Acute respiratory distress syndrome @@ -847,14 +847,14 @@ version: 2022-03-05 karyotypicSex: UNKNOWN_KARYOTYPE phenotypicFeatures: - - excluded: true + - excluded: 0 featureType: id: HP:0031936 label: Delayed ability to walk onset: age: iso8601duration: P1Y6M - - excluded: true + - excluded: 0 featureType: id: HP:0003707 label: Calf muscle pseudohypertrophy @@ -862,7 +862,7 @@ ontologyClass: id: HP:0011463 label: Childhood onset - - excluded: true + - excluded: 0 featureType: id: HP:0009046 label: Difficulty running @@ -870,14 +870,14 @@ ontologyClass: id: HP:0011463 label: Childhood onset - - excluded: true + - excluded: 0 featureType: id: HP:0003458 label: 'EMG: myopathic abnormalities' onset: age: iso8601duration: P10Y - - excluded: true + - excluded: 0 featureType: id: HP:0003236 label: Elevated circulating creatine kinase concentration @@ -960,7 +960,7 @@ reference: description: Xiong J, et al., 2019 id: PMID:30855487 - excluded: true + excluded: 0 featureType: id: HP:0000238 label: Hydrocephalus @@ -974,7 +974,7 @@ reference: description: Xiong J, et al., 2019 id: PMID:30855487 - excluded: true + excluded: 0 featureType: id: HP:0002507 label: Semilobar holoprosencephaly @@ -989,7 +989,7 @@ reference: description: Xiong J, et al., 2019 id: PMID:30855487 - excluded: true + excluded: 0 featureType: id: HP:0001750 label: Single ventricle @@ -1003,7 +1003,7 @@ reference: description: Xiong J, et al., 2019 id: PMID:30855487 - excluded: true + excluded: 0 featureType: id: HP:0001272 label: Cerebellar atrophy @@ -1017,7 +1017,7 @@ reference: description: Xiong J, et al., 2019 id: PMID:30855487 - excluded: true + excluded: 0 featureType: id: HP:0100702 label: Arachnoid cyst @@ -1031,7 +1031,7 @@ reference: description: Xiong J, et al., 2019 id: PMID:30855487 - excluded: true + excluded: 0 featureType: id: HP:0001272 label: Cerebellar atrophy @@ -1045,7 +1045,7 @@ reference: description: Xiong J, et al., 2019 id: PMID:30855487 - excluded: true + excluded: 0 featureType: id: HP:0001263 label: Global developmental delay @@ -1060,7 +1060,7 @@ reference: description: Xiong J, et al., 2019 id: PMID:30855487 - excluded: true + excluded: 0 featureType: id: HP:0001347 label: Hyperreflexia @@ -1074,7 +1074,7 @@ - diseaseCode: id: OMIM:154700 label: Marfan syndrome - excluded: true + excluded: 0 id: proband C info: phenopacket: @@ -1115,7 +1115,7 @@ version: 2.1 karyotypicSex: UNKNOWN_KARYOTYPE phenotypicFeatures: - - excluded: true + - excluded: 0 featureType: id: HP:0002616 label: Aortic root aneurysm @@ -1270,14 +1270,14 @@ version: 2022-03-05 karyotypicSex: UNKNOWN_KARYOTYPE phenotypicFeatures: - - excluded: true + - excluded: 0 featureType: id: HP:0001558 label: Decreased fetal movement onset: gestationalAge: weeks: 23 - - excluded: true + - excluded: 0 featureType: id: HP:0025672 label: Fetal skin edema @@ -1285,7 +1285,7 @@ gestationalAge: days: 4 weeks: 32 - - excluded: true + - excluded: 0 featureType: id: HP:0010557 label: Overlapping fingers @@ -1293,7 +1293,7 @@ gestationalAge: days: 4 weeks: 32 - - excluded: true + - excluded: 0 featureType: id: HP:0001561 label: Polyhydramnios @@ -1304,7 +1304,7 @@ gestationalAge: days: 4 weeks: 32 - - excluded: true + - excluded: 0 featureType: id: HP:0030931 label: 1-minute APGAR score of 4 @@ -1312,7 +1312,7 @@ ontologyClass: id: HP:0003577 label: Congenital onset - - excluded: true + - excluded: 0 featureType: id: HP:0030922 label: 5-minute APGAR score of 2 @@ -1320,7 +1320,7 @@ ontologyClass: id: HP:0003577 label: Congenital onset - - excluded: true + - excluded: 0 featureType: id: HP:0033469 label: 10-minute APGAR score of 1 @@ -1328,7 +1328,7 @@ ontologyClass: id: HP:0003577 label: Congenital onset - - excluded: true + - excluded: 0 featureType: id: HP:0012027 label: Laryngeal edema @@ -1336,7 +1336,7 @@ ontologyClass: id: HP:0003577 label: Congenital onset - - excluded: true + - excluded: 0 featureType: id: HP:0001290 label: Generalized hypotonia @@ -1353,7 +1353,7 @@ diseaseCode: id: MONDO:0008327 label: exfoliation syndrome - excluded: true + excluded: 0 primarySite: id: UBERON:0004549 label: right eye @@ -1625,7 +1625,7 @@ iso8601duration: P71Y1M timeObserved: *16 phenotypicFeatures: - - excluded: true + - excluded: 1 featureType: id: HP:0000539 label: Abnormality of refraction @@ -1635,7 +1635,7 @@ onset: age: iso8601duration: P70Y - - excluded: true + - excluded: 0 featureType: id: HP:0000545 label: Myopia @@ -1645,7 +1645,7 @@ onset: age: iso8601duration: P71Y1M - - excluded: true + - excluded: 0 featureType: id: NCIT:C50618 label: Intraocular Pressure Increased @@ -1655,15 +1655,15 @@ onset: age: iso8601duration: P71Y1M - - excluded: true + - excluded: 1 featureType: id: HP:0007686 label: Abnormal pupillary function - - excluded: true + - excluded: 1 featureType: id: HP:0012629 label: Phakodonesis - - excluded: true + - excluded: 1 featureType: id: SNOMEDCT:414775001 label: monovision @@ -1701,7 +1701,7 @@ diseaseStage: - id: LOINC:LA24739-7 label: Group E - excluded: true + excluded: 0 primarySite: id: UBERON:0004548 label: left eye @@ -1949,7 +1949,7 @@ iso8601duration: P6M timeObserved: *18 phenotypicFeatures: - - excluded: true + - excluded: 0 featureType: id: HP:0030084 label: Clinodactyly @@ -1959,7 +1959,7 @@ onset: age: iso8601duration: P3M - - excluded: true + - excluded: 0 featureType: id: HP:0000555 label: Leukocoria @@ -1969,7 +1969,7 @@ onset: age: iso8601duration: P4M - - excluded: true + - excluded: 0 featureType: id: HP:0000486 label: Strabismus @@ -1979,7 +1979,7 @@ onset: age: iso8601duration: P5M15D - - excluded: true + - excluded: 0 featureType: id: HP:0000541 label: Retinal detachment @@ -2021,7 +2021,7 @@ diseaseCode: id: NCIT:C4024 label: Esophageal Squamous Cell Carcinoma - excluded: true + excluded: 0 id: proband A info: phenopacket: @@ -2115,14 +2115,14 @@ diseaseCode: id: MONDO:0005148 label: type 2 diabetes mellitus - excluded: true + excluded: 0 - ageOfOnset: age: iso8601duration: P55Y diseaseCode: id: MONDO:0001134 label: essential hypertension - excluded: true + excluded: 0 id: 65-year-old man info: phenopacket: @@ -2204,49 +2204,49 @@ label: enzyme unit per liter value: 234 phenotypicFeatures: - - excluded: true + - excluded: 0 featureType: id: HP:0008994 label: Proximal muscle weakness in lower limbs onset: age: iso8601duration: P65Y - - excluded: true + - excluded: 0 featureType: id: HP:0007289 label: Limb fasciculations onset: age: iso8601duration: P65Y - - excluded: true + - excluded: 0 featureType: id: HP:0008956 label: Proximal lower limb amyotrophy onset: age: iso8601duration: P65Y - - excluded: true + - excluded: 1 featureType: id: HP:0003808 label: Abnormal muscle tone onset: age: iso8601duration: P65Y - - excluded: true + - excluded: 0 featureType: id: HP:0003391 label: Gowers sign onset: age: iso8601duration: P65Y - - excluded: true + - excluded: 0 featureType: id: HP:0003551 label: Difficulty climbing stairs onset: age: iso8601duration: P65Y - - excluded: true + - excluded: 0 featureType: id: HP:0006886 label: Impaired distal vibration sensation @@ -2364,7 +2364,7 @@ diseaseStage: - id: NCIT:C27971 label: Stage IV - excluded: true + excluded: 0 id: patient1 info: phenopacket: @@ -2514,14 +2514,14 @@ version: 2022-06-11 karyotypicSex: UNKNOWN_KARYOTYPE phenotypicFeatures: - - excluded: true + - excluded: 0 featureType: id: HP:0100518 label: Dysuria severity: id: HP:0012828 label: Severe - - excluded: true + - excluded: 0 featureType: id: HP:0000790 label: Hematuria @@ -2533,7 +2533,7 @@ diseaseCode: id: MONDO:0016649 label: Warburg micro syndrome - excluded: true + excluded: 0 id: case1 info: phenopacket: @@ -2556,7 +2556,7 @@ version: v2022-04-04 karyotypicSex: UNKNOWN_KARYOTYPE phenotypicFeatures: - - excluded: true + - excluded: 0 featureType: id: HP:0034248 label: Increased fetal lens echogenicity @@ -2564,7 +2564,7 @@ gestationalAge: days: 2 weeks: 27 - - excluded: true + - excluded: 1 featureType: id: HP:0000568 label: Microphthalmia @@ -2572,21 +2572,21 @@ gestationalAge: days: 2 weeks: 27 - - excluded: true + - excluded: 0 featureType: id: HP:0000369 label: Low-set ears onset: age: iso8601duration: P4D - - excluded: true + - excluded: 0 featureType: id: HP:0008936 label: Axial hypotonia onset: age: iso8601duration: P4D - - excluded: true + - excluded: 0 featureType: id: HP:0000568 label: Microphthalmia