{"action":"created","issue":{"url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/45","labels_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/45/labels{/name}","comments_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/45/comments","events_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/45/events","html_url":"https://github.com/BgeeDB/expression-annotations/issues/45","id":106752052,"number":45,"title":"GTEx normality check in phs000424.v5.pht002742.v5.p1.c1.GTEx_Subject_Phenotypes.GRU.txt","user":{"login":"ANiknejad","id":2682520,"avatar_url":"https://avatars.githubusercontent.com/u/2682520?v=3","gravatar_id":"","url":"https://api.github.com/users/ANiknejad","html_url":"https://github.com/ANiknejad","followers_url":"https://api.github.com/users/ANiknejad/followers","following_url":"https://api.github.com/users/ANiknejad/following{/other_user}","gists_url":"https://api.github.com/users/ANiknejad/gists{/gist_id}","starred_url":"https://api.github.com/users/ANiknejad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ANiknejad/subscriptions","organizations_url":"https://api.github.com/users/ANiknejad/orgs","repos_url":"https://api.github.com/users/ANiknejad/repos","events_url":"https://api.github.com/users/ANiknejad/events{/privacy}","received_events_url":"https://api.github.com/users/ANiknejad/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":13,"created_at":"2015-09-16T11:15:35Z","updated_at":"2015-09-30T11:36:30Z","closed_at":null,"body":"For cause of death: cf column DTHFUCOD First Underlying Cause Of Death\r\nirst underlying Cause of Death A disease or injury, leading to the cause of death listed in immediate_cause_of_death.\r\n\r\nThe inconsistency in reporting information (ex:'probable MI' and 'probable myocardial infarction' and 'possible myocardial infarction') generates more than 200 death reasons...\r\nSome of them are easy to remove regarding 'normality' (ex: all 'toxic' one) but others are less clear,\r\nso help welcome.\r\nI propose to select at least 'trauma', 'suicide by hanging', 'GSW' (gun shot wound) as fine for normal conditions. \r\n\r\naaa\r\nabdominal aortic aneurysm secondary to arterial thrombosis left lower extremity\r\naccident unspecified\r\nAcute Cerebellar infarct with obstructive hydrocephalus\r\nacute cocaine intoxication\r\nacute mi\r\nAcute myocardial infarction\r\nacute renal failure\r\nacute renal failure secondary to polycystic kidney disease\r\nAcute Respiratory Distress Syndrome\r\nalcohol abuse\r\nalcoholic cirrhosis of liver\r\nallergic reaction\r\nals\r\nanoxia\r\nanoxia secondary to hanging\r\nanoxic brain injury\r\nanoxic brain injury secondary to cardiac arrest\r\nAnoxic encephalopathy\r\narrest [as an cardiac arrest]\r\narrest; cardiac\r\nasphyxia secondary to hanging\r\nAsphyxiation\r\naspiration\r\naspiration pneumonia due to regurgitated food\r\nassault by other and unspecified firearm and gun discharge\r\nAsyphyxiation\r\nasystole\r\natherosclerotic cardiovascular disease\r\nAtrial fibrillation\r\nBlunt force trauma\r\nblunt force trauma to head\r\nBlunt Injury\r\nbowel obstruction\r\nbreathing arrested\r\nbreathing difficult\r\ncad\r\nCardiac arrest\r\ncardiac arrest, unspecified\r\ncardiac asystole\r\nCardio-Pulmonary Arrest\r\nCardiovascular\r\ncardiovascular collapse\r\ncardiovascular disease other\r\ncardiovascular; collapse\r\nCardivascular\r\ncause unknown; death\r\nCerebral Vascular Accident\r\nCerebral Vascular Accident (Intracranial hemorrhage)\r\nCerebral vascular accident secondary to anti-coagulation\r\ncerebrovascular dis\r\ncerebrovascular disease\r\nchange in mental status\r\nchest pain\r\nCHF\r\nCHF exacerbation\r\ncomplications from ALS\r\ncontact with blunt object, undetermined intent, sequela\r\nCOPD\r\nCOPD/pulmonary edema\r\nCPA\r\nCVA\r\ncva - cerebrovascular accident\r\nCVA traumatic brain injury\r\ndehydration\r\nDiabetic Emergency\r\ndissection aortic\r\nDrug Intoxication\r\nDTHFUCOD\r\nDysphagia with recurrent aspiration\r\nelectrolyte imbalance\r\nembolism pulm\r\nempyema, lung\r\nend stage COPD\r\nend stage liver disease\r\nend-stage renal disease\r\nend-stage renal failure\r\nepilepsy\r\nESLD\r\nESRD\r\nEtOH abuse\r\ngi - gastrointestinal bleed\r\ngi bleed\r\nGSW\r\nGSW to back\r\ngun shot wound\r\ngunshot wound\r\nGunshot Wound to Head\r\nHanging\r\nhead injury\r\nHead trauma secondary to MVA\r\nHeart Attack/Stroke\r\nHeart disease\r\nheart disease (MI)\r\nHeart failure\r\nhepatic encephalopathy\r\nhepatitis acute\r\nHepatorenal Syndrome\r\nhypertension\r\nhypoxemia\r\nICH\r\ninfarcted bowel secondary to AAA repair\r\ninjury\r\ninjury from an external force\r\ninjury of head\r\nintent self harm by hanging strangulation / suffocation\r\nIntercranial Hemmorage\r\nIntracranial hemmorhage\r\nIntracranial hemmorhage secondary to Arteriovenous malformation\r\nIntracranial Hemorrhage\r\nintracranial hemorrhages\r\nintracranial; hemorrhage\r\nintraperitoneal bleed\r\nischemic cardiomyopathy\r\nKidney diseases\r\nkidney failure\r\nlactic acidosis\r\nLiver disease, alcoholic\r\nliver failure\r\nLiver Transplant\r\nlung cancer\r\nMetabolic acidosis related to diabetic ketoacidosis\r\nMI\r\nmi - myocardial infarction\r\nmi, myocardial infarction\r\nmotor vehicle accident\r\nMotor vehicle accident trauma\r\nmotorcycle accident\r\nmotor-vehicle accident [mva] nos\r\nMSOF secondary to NSTEMI\r\nmultiple blunt force trauma\r\nmultiple blunt force trauma secondary to motor vehicle accident\r\nmultiple blunt force trauma secondary to MVA\r\nmva - motor vehicle accident\r\nMVA Trauma\r\nmyocardial infarction\r\nN/A\r\nNA\r\nnatural causes\r\nNONE\r\nnon-ischemic cardiomyopathy\r\nnon-ST elevation myocardial infarction\r\nNSTEMI\r\nNSTEMI with anoxic brain injury due to prolonged CPA\r\npe\r\npe - pulmonary embolism\r\nphv00169091.v5.p1.c1\r\nPneumonia\r\npneumothorax\r\nPontine Bleed\r\npossible myocardial infarction\r\nposterior wall myocardial infarction\r\nprescription drug overdose\r\nprobable  myocardial infarction\r\nprobable drug overdose\r\nprobable MI\r\nprobable myocardial infarction\r\nprobable overdose\r\npulmonary arrest\r\npulmonary disease\r\npulmonary embolism\r\nRenal failure\r\nResp-Asphyxiation\r\nrespiration; arrest\r\nrespiratory arrest\r\nrespiratory difficulty\r\nRespiratory disease\r\ns/p Hanging\r\nsah\r\nSAH and intraventricular hemorrhage secondary to head injury\r\nSeizure\r\nseizure disorder\r\nseizures\r\nSelf Inflicted GSW to head\r\nsepsis\r\nShock secondary to burns\r\nshortness of breath (sob)\r\nSIGSW\r\nsinus [sinusal] tachycardia nos\r\nsmoke asphyxiation\r\nsmoke inhalation-respiratory disease\r\nStroke\r\nSubarachnoid hemorrhage\r\nsubdural hematoma secondary to fall\r\nsubdural hemorrhage following injury\r\nsuicide by hanging\r\nsuicide-hanging\r\nsuspected overdose\r\nthrombocytopenia\r\ntia\r\ntoxic effect of unspecified substance\r\ntrauma\r\ntrauma due to fall\r\ntrauma SAH/SDH\r\ntrauma, head\r\ntrauma;multiple\r\nTrauma-blunt force trauma secondary to MVA\r\ntrauma-head bleed result of a fall\r\ntraumatic brain injury\r\nunknown\r\nunknown cause of death\r\nvascular cerebral accident\r\n"},"comment":{"url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/comments/144369637","html_url":"https://github.com/BgeeDB/expression-annotations/issues/45#issuecomment-144369637","issue_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/45","id":144369637,"user":{"login":"aechchiki","id":13200013,"avatar_url":"https://avatars.githubusercontent.com/u/13200013?v=3","gravatar_id":"","url":"https://api.github.com/users/aechchiki","html_url":"https://github.com/aechchiki","followers_url":"https://api.github.com/users/aechchiki/followers","following_url":"https://api.github.com/users/aechchiki/following{/other_user}","gists_url":"https://api.github.com/users/aechchiki/gists{/gist_id}","starred_url":"https://api.github.com/users/aechchiki/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aechchiki/subscriptions","organizations_url":"https://api.github.com/users/aechchiki/orgs","repos_url":"https://api.github.com/users/aechchiki/repos","events_url":"https://api.github.com/users/aechchiki/events{/privacy}","received_events_url":"https://api.github.com/users/aechchiki/received_events","type":"User","site_admin":false},"created_at":"2015-09-30T11:36:30Z","updated_at":"2015-09-30T11:36:30Z","body":"@mimiblis , I also discarded ~70 individuals according to BMI out of range...  btw, I guess that being overweight is not a criterion to be excluded from organ donation, in fact \"There is no binding donor weight limit, but a little more than half of transplant centers cap donor body mass index at 35\" (Source: http://well.blogs.nytimes.com/2012/08/06/transplant-centers-struggle-with-donors-obesity/?_r=0 ). \r\nIn our dataset, I also observed that individuals who died because of drug intoxication could donate his organs, so.... lol :P "}}