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tner
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bc5cdr

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Token Classification
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named-entity-recognition
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tokens
sequence
tags
sequence
[ "Naloxone", "reverses", "the", "antihypertensive", "effect", "of", "clonidine", "." ]
[ 1, 0, 0, 0, 0, 0, 1, 0 ]
[ "In", "unanesthetized", ",", "spontaneously", "hypertensive", "rats", "the", "decrease", "in", "blood", "pressure", "and", "heart", "rate", "produced", "by", "intravenous", "clonidine", ",", "5", "to", "20", "micrograms", "/", "kg", ",", "was", "inhibited", "or", "reversed", "by", "nalozone", ",", "0", "." ]
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[ "2", "to", "2", "mg", "/", "kg", "." ]
[ 0, 0, 0, 0, 0, 0, 0 ]
[ "The", "hypotensive", "effect", "of", "100", "mg", "/", "kg", "alpha-methyldopa", "was", "also", "partially", "reversed", "by", "naloxone", "." ]
[ 0, 2, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0 ]
[ "Naloxone", "alone", "did", "not", "affect", "either", "blood", "pressure", "or", "heart", "rate", "." ]
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[ "In", "brain", "membranes", "from", "spontaneously", "hypertensive", "rats", "clonidine", ",", "10", "(-", "8", ")", "to", "10", "(-", "5", ")", "M", ",", "did", "not", "influence", "stereoselective", "binding", "of", "[3H]-naloxone", "(", "8", "nM", "),", "and", "naloxone", ",", "10", "(-", "8", ")", "to", "10", "(-", "4", ")", "M", ",", "did", "not", "influence", "clonidine", "-", "suppressible", "binding", "of", "[3H]-dihydroergocryptine", "(", "1", "nM", ").", "These", "findings", "indicate", "that", "in", "spontaneously", "hypertensive", "rats", "the", "effects", "of", "central", "alpha", "-", "adrenoceptor", "stimulation", "involve", "activation", "of", "opiate", "receptors", "." ]
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[ "As", "naloxone", "and", "clonidine", "do", "not", "appear", "to", "interact", "with", "the", "same", "receptor", "site", ",", "the", "observed", "functional", "antagonism", "suggests", "the", "release", "of", "an", "endogenous", "opiate", "by", "clonidine", "or", "alpha-methyldopa" ]
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[ "Lidocaine", "-", "induced", "cardiac", "asystole", "." ]
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[ "Intravenous", "administration", "of", "a", "single", "50", "-", "mg", "bolus", "of", "lidocaine", "in", "a", "67", "-", "year", "-", "old", "man", "resulted", "in", "profound", "depression", "of", "the", "activity", "of", "the", "sinoatrial", "and", "atrioventricular", "nodal", "pacemakers", "." ]
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[ "The", "patient", "had", "no", "apparent", "associated", "conditions", "which", "might", "have", "predisposed", "him", "to", "the", "development", "of", "bradyarrhythmias", ";", "and", ",", "thus", ",", "this", "probably", "represented", "a", "true", "idiosyncrasy", "to", "lidocaine" ]
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[ "Suxamethonium", "infusion", "rate", "and", "observed", "fasciculations", "." ]
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[ "A", "dose", "-", "response", "study", "." ]
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[ "Suxamethonium", "chloride", "(", "Sch", ")", "was", "administered", "i", "." ]
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[ "v", "." ]
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[ "to", "36", "adult", "males", "at", "six", "rates", ":", "0", "." ]
[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
[ "25", "mg", "s", "-", "1", "to", "20", "mg", "s", "-", "1", "." ]
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[ "The", "infusion", "was", "discontinued", "either", "when", "there", "was", "no", "muscular", "response", "to", "tetanic", "stimulation", "of", "the", "ulnar", "nerve", "or", "when", "Sch", "120", "mg", "was", "exceeded", "." ]
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[ "Six", "additional", "patients", "received", "a", "30", "-", "mg", "i", "." ]
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[ "v", "." ]
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[ "bolus", "dose", "." ]
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[ "Fasciculations", "in", "six", "areas", "of", "the", "body", "were", "scored", "from", "0", "to", "3", "and", "summated", "as", "a", "total", "fasciculation", "score", "." ]
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[ "The", "times", "to", "first", "fasciculation", ",", "twitch", "suppression", "and", "tetanus", "suppression", "were", "inversely", "related", "to", "the", "infusion", "rates", "." ]
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[ "Fasciculations", "in", "the", "six", "areas", "and", "the", "total", "fasciculation", "score", "were", "related", "directly", "to", "the", "rate", "of", "infusion", "." ]
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[ "Total", "fasciculation" ]
[ 0, 2 ]
[ "Galanthamine", "hydrobromide", ",", "a", "longer", "acting", "anticholinesterase", "drug", ",", "in", "the", "treatment", "of", "the", "central", "effects", "of", "scopolamine", "(", "Hyoscine", ").", "Galanthamine", "hydrobromide", ",", "an", "anticholinesterase", "drug", "capable", "of", "penetrating", "the", "blood", "-", "brain", "barrier", ",", "was", "used", "in", "a", "patient", "demonstrating", "central", "effects", "of", "scopolamine", "(", "hyoscine", ")", "overdosage", "." ]
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[ "It", "is", "longer", "acting", "than", "physostigmine", "and", "is", "used", "in", "anaesthesia", "to", "reverse", "the", "non", "-", "depolarizing", "neuromuscular", "block", "." ]
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[ "However", ",", "studies", "into", "the", "dose", "necessary", "to", "combating", "scopolamine" ]
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[ "Effects", "of", "uninephrectomy", "and", "high", "protein", "feeding", "on", "lithium", "-", "induced", "chronic", "renal", "failure", "in", "rats", "." ]
[ 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 2, 3, 3, 0, 0, 0 ]
[ "Rats", "with", "lithium", "-", "induced", "nephropathy", "were", "subjected", "to", "high", "protein", "(", "HP", ")", "feeding", ",", "uninephrectomy", "(", "NX", ")", "or", "a", "combination", "of", "these", ",", "in", "an", "attempt", "to", "induce", "glomerular", "hyperfiltration", "and", "further", "progression", "of", "renal", "failure", "." ]
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[ "Newborn", "female", "Wistar", "rats", "were", "fed", "a", "lithium", "-", "containing", "diet", "(", "50", "mmol", "/", "kg", ")", "for", "8", "weeks", "and", "then", "randomized", "to", "normal", "diet", ",", "HP", "diet", "(", "40", "vs", "." ]
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[ "19", "%),", "NX", "or", "HP", "+", "NX", "for", "another", "8", "weeks", "." ]
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[ "Corresponding", "non", "-", "lithium", "pretreated", "groups", "were", "generated", "." ]
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[ "When", "comparing", "all", "lithium", "treated", "versus", "non", "-", "lithium", "-", "treated", "groups", ",", "lithium", "caused", "a", "reduction", "in", "glomerular", "filtration", "rate", "(", "GFR", ")", "without", "significant", "changes", "in", "effective", "renal", "plasma", "flow", "(", "as", "determined", "by", "a", "marker", "secreted", "into", "the", "proximal", "tubules", ")", "or", "lithium", "clearance", "." ]
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[ "Consequently", ",", "lithium", "pretreatment", "caused", "a", "fall", "in", "filtration", "fraction", "and", "an", "increase", "in", "fractional", "Li", "excretion", "." ]
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[ "Lithium", "also", "caused", "proteinuria", "and", "systolic", "hypertension", "in", "absence", "of", "glomerulosclerosis", "." ]
[ 1, 0, 0, 2, 0, 0, 2, 0, 0, 0, 2, 0 ]
[ "HP", "failed", "to", "accentuante", "progression", "of", "renal", "failure", "and", "in", "fact", "tended", "to", "increase", "GFR", "and", "decrease", "plasma", "creatinine", "levels", "in", "lithium", "pretreated", "rats", "." ]
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[ "NX", "caused", "an", "additive", "deterioration", "in", "GFR", "which", ",", "however", ",", "was", "ameliorated", "by", "HP", "." ]
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[ "NX", "+", "HP", "caused", "a", "further", "rise", "in", "blood", "pressure", "in", "Li", "-", "pretreated", "rats", "." ]
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[ "The", "results", "indicate", "that", "Li", "-", "induced", "nephropathy", ",", "even", "when", "the", "GFR", "is", "only", "modestly", "reduced", ",", "is", "associated", "with", "proteinuria", "and", "arterial", "systolic", "hypertension", "." ]
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[ "In", "this", "model", "of", "chronic", "renal", "failure" ]
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[ "Treatment", "of", "Crohn's", "disease", "with", "fusidic", "acid", ":", "an", "antibiotic", "with", "immunosuppressive", "properties", "similar", "to", "cyclosporin", "." ]
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[ "Fusidic", "acid", "is", "an", "antibiotic", "with", "T", "-", "cell", "specific", "immunosuppressive", "effects", "similar", "to", "those", "of", "cyclosporin", "." ]
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[ "Because", "of", "the", "need", "for", "the", "development", "of", "new", "treatments", "for", "Crohn's", "disease", ",", "a", "pilot", "study", "was", "undertaken", "to", "estimate", "the", "pharmacodynamics", "and", "tolerability", "of", "fusidic", "acid", "treatment", "in", "chronic", "active", ",", "therapy", "-", "resistant", "patients", "." ]
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[ "Eight", "Crohn's", "disease", "patients", "were", "included", "." ]
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[ "and", "the", "treatment", "was", "planned", "to", "last", "8", "weeks", "." ]
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[ "There", "were", "no", "serious", "clinical", "side", "effects", ",", "but", "dose", "reduction", "was", "required", "in", "two", "patients", "because", "of", "nausea", "." ]
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[ "Biochemically", ",", "an", "increase", "in", "alkaline", "phosphatases", "was", "noted", "in", "5", "of", "8", "cases", "(", "63", "%),", "and", "the", "greatest", "increases", "were", "seen", "in", "those", "who", "had", "elevated", "levels", "prior", "to", "treatment", "." ]
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[ "All", "reversed", "to", "pre", "-", "treatment", "levels", "after", "cessation", "of", "treatment", "." ]
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[ "Electrocardiographic", "evidence", "of", "myocardial", "injury", "in", "psychiatrically", "hospitalized", "cocaine", "abusers", "." ]
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[ "Sulpiride", "-", "induced", "tardive", "dystonia", "." ]
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[ "Sulpiride", "is", "a", "selective", "D2", "-", "receptor", "antagonist", "with", "antipsychotic", "and", "antidepressant", "properties", "." ]
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[ "Ocular", "and", "auditory", "toxicity", "in", "hemodialyzed", "patients", "receiving", "desferrioxamine", "." ]
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[ "6", "patients", "presented", "clinical", "symptoms", "of", "visual", "or", "auditory", "toxicity", "." ]
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[ "Moreover", ",", "detailed", "ophthalmologic", "and", "audiologic", "studies", "disclosed", "abnormalities", "in", "7", "more", "asymptomatic", "patients", "." ]
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[ "Visual", "toxicity", "was", "of", "retinal", "origin", "and", "was", "characterized", "by", "a", "tritan", "-", "type", "dyschromatopsy", ",", "sometimes", "associated", "with", "a", "loss", "of", "visual", "acuity", "and", "pigmentary", "retinal", "deposits", "." ]
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[ "Myasthenia", "gravis", "presenting", "as", "weakness", "after", "magnesium", "administration", "." ]
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[ "The", "serum", "magnesium", "concentration", "was", "3", "." ]
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[ "0", "mEq", "/", "L", ",", "which", "is", "usually", "well", "tolerated", "." ]
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[ "The", "magnesium", "was", "stopped", "and", "she", "recovered", "over", "a", "few", "days", "." ]
[ 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
[ "While", "she", "was", "weak", ",", "2", "-", "Hz", "repetitive", "stimulation", "revealed", "a", "decrement", "without", "significant", "facilitation", "at", "rapid", "rates", "or", "after", "exercise", ",", "suggesting", "postsynaptic", "neuromuscular", "blockade", "." ]
[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 3, 3, 0 ]
[ "After", "her", "strength", "returned", ",", "repetitive", "stimulation", "was", "normal", ",", "but", "single", "fiber", "EMG", "revealed", "increased", "jitter", "and", "blocking", "." ]
[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
[ "Her", "acetylcholine", "receptor", "antibody", "level", "was", "markedly", "elevated", "." ]
[ 0, 1, 0, 0, 0, 0, 0, 0, 0 ]
[ "Although", "paralysis", "after", "magnesium", "administration", "has", "been", "described", "in", "patients", "with", "known", "myasthenia", "gravis", ",", "it", "has", "not", "previously", "been", "reported", "to", "be", "the", "initial", "or", "only", "manifestation", "of", "the", "disease", "." ]
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[ "Patients", "who", "are", "unusually", "sensitive", "to", "the", "neuromuscular", "effects", "of", "magnesium", "should", "be", "suspected", "of", "having", "an", "underlying", "disorder", "of", "neuromuscular", "transmission" ]
[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 2, 3, 3, 3 ]
[ "Chloroacetaldehyde", "and", "its", "contribution", "to", "urotoxicity", "during", "treatment", "with", "cyclophosphamide", "or", "ifosfamide", "." ]
[ 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0 ]
[ "An", "experimental", "study", "/", "short", "communication", "." ]
[ 0, 0, 0, 0, 0, 0, 0 ]
[ "Based", "on", "clinical", "data", ",", "indicating", "that", "chloroacetaldehyde", "(", "CAA", ")", "is", "an", "important", "metabolite", "of", "oxazaphosphorine", "cytostatics", ",", "an", "experimental", "study", "was", "carried", "out", "in", "order", "to", "elucidate", "the", "role", "of", "CAA", "in", "the", "development", "of", "hemorrhagic", "cystitis", "." ]
[ 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 2, 3, 0 ]
[ "The", "data", "demonstrate", "that", "CAA", "after", "i", "." ]
[ 0, 0, 0, 0, 1, 0, 0, 0 ]
[ "v", "." ]
[ 0, 0 ]
[ "administration", "does", "not", "contribute", "to", "bladder", "damage", "." ]
[ 0, 0, 0, 0, 0, 2, 3, 0 ]
[ "When", "instilled", "directly", "into", "the", "bladder", ",", "CAA", "exerts", "urotoxic", "effects", ",", "it", "is", ",", "however", ",", "susceptible", "to", "detoxification", "with", "mesna" ]
[ 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1 ]
[ "Source", "of", "pain", "and", "primitive", "dysfunction", "in", "migraine", ":", "an", "identical", "site", "?", "Twenty", "common", "migraine", "patients", "received", "a", "one", "sided", "frontotemporal", "application", "of", "nitroglycerin", "(", "10", "patients", ")", "or", "placebo", "ointment", "(", "10", "patients", ")", "in", "a", "double", "blind", "study", "." ]
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[ "Early", "onset", "migraine", "attacks", "were", "induced", "by", "nitroglycerin", "in", "seven", "out", "of", "10", "patients", "versus", "no", "patient", "in", "the", "placebo", "group", "." ]
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[ "Subsequently", "20", "migraine", "patients", ",", "who", "developed", "an", "early", "onset", "attack", "with", "frontotemporal", "nitroglycerin", ",", "received", "the", "drug", "in", "a", "second", "induction", "test", "at", "other", "body", "areas", "." ]
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[ "No", "early", "onset", "migraine", "was", "observed", "." ]
[ 0, 0, 0, 2, 0, 0, 0 ]
[ "Thus", "the", "migraine", "-", "inducing", "effect", "of", "nitroglycerin", "seems", "to", "depend", "on", "direct", "stimulation", "of", "the", "habitual", "site", "of", "pain", ",", "suggesting", "that", "the", "frontotemporal", "region", "is", "of", "crucial", "importance", "in", "the", "development", "of", "a", "migraine", "crisis", "." ]
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[ "This", "is", "not", "consistent", "with", "a", "CNS", "origin", "of", "migraine" ]
[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 2 ]
[ "Clotiazepam", "-", "induced", "acute", "hepatitis", "." ]
[ 1, 0, 0, 0, 2, 0 ]
[ "We", "report", "the", "case", "of", "a", "patient", "who", "developed", "acute", "hepatitis", "with", "extensive", "hepatocellular", "necrosis", ",", "7", "months", "after", "the", "onset", "of", "administration", "of", "clotiazepam", ",", "a", "thienodiazepine", "derivative", "." ]
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[ "Clotiazepam", "withdrawal", "was", "followed", "by", "prompt", "recovery", "." ]
[ 1, 0, 0, 0, 0, 0, 0, 0 ]
[ "The", "administration", "of", "several", "benzodiazepines", ",", "chemically", "related", "to", "clotiazepam", ",", "did", "not", "interfere", "with", "recovery", "and", "did", "not", "induce", "any", "relapse", "of", "hepatitis", "." ]
[ 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0 ]
[ "This", "observation", "shows", "that", "clotiazepam", "can", "induce", "acute", "hepatitis", "and", "suggests", "that", "there", "is", "no", "cross", "hepatotoxicity", "between", "clotiazepam", "and", "several", "benzodiazepines" ]
[ 0, 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 2, 0, 1, 0, 0, 1 ]
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Dataset Card for "tner/bc5cdr"

Dataset Summary

BioCreative V CDR NER dataset formatted in a part of TNER project. The original dataset consists of long documents which cannot be fed on LM because of the length, so we split them into sentences to reduce their size.

  • Entity Types: Chemical, Disease

Dataset Structure

Data Instances

An example of train looks as follows.

{
    'tags': [2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0],
    'tokens': ['Fasciculations', 'in', 'six', 'areas', 'of', 'the', 'body', 'were', 'scored', 'from', '0', 'to', '3', 'and', 'summated', 'as', 'a', 'total', 'fasciculation', 'score', '.']
}

Label ID

The label2id dictionary can be found at here.

{
    "O": 0,
    "B-Chemical": 1,
    "B-Disease": 2,
    "I-Disease": 3,
    "I-Chemical": 4
}

Data Splits

name train validation test
bc5cdr 5228 5330 5865

Citation Information 

@article{wei2016assessing,
  title={Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task},
  author={Wei, Chih-Hsuan and Peng, Yifan and Leaman, Robert and Davis, Allan Peter and Mattingly, Carolyn J and Li, Jiao and Wiegers, Thomas C and Lu, Zhiyong},
  journal={Database},
  volume={2016},
  year={2016},
  publisher={Oxford Academic}
}
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Edit dataset card
Repository:
T-NER
Paper:
academic.oup.com
Dataset:
BioCreative V CDR
Domain:
Biomedical
Number of Entity:
2
Size of downloaded dataset files:
4.34 MB
Size of the auto-converted Parquet files:
1.12 MB
Number of rows:
16,423

Models trained or fine-tuned on tner/bc5cdr

Browse 15 models trained on this dataset