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prim-sec-outcomes

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id stringlengths 7 12	tokens sequencelengths 2 210	labels sequencelengths 2 210
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19805710_S9	[ "secondary", "outcomes", "were", "changes", "from", "pretreatment", "to", "posttreatment", "in", "percentage", "of", "the", "estimated", "energy", "requirement", "and", "body", "mass", "index", "z", "score", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 4, 4, 4, 4, 4, 0, 3, 4, 4, 4, 4, 0 ]
19805710_S11	[ "results", "after", "treatment", ",", "the", "behavioral", "plus", "nutrition", "education", "intervention", "as", "compared", "with", "the", "nutrition", "education", "intervention", "alone", "had", "a", "statistically", "greater", "average", "increase", "on", "the", "primary", "and", "secondary", "outcomes", "of", "caloric", "intake", "(", "mean", ",", "872", "vs", "489", "cal/d", ",", "respectively", ")", ",", "percentage", "of", "the", "estimated", "energy", "requirement", "(", "mean", ",", "148", "%", "vs", "127", "%", ",", "respectively", ")", ",", "weight", "gain", "(", "mean", ",", "1.47", "vs", "0.92", "kg", ",", "respectively", ")", ",", "and", "body", "mass", "index", "z", "score", "(", "0.38", "vs", "0.18", ",", "respectively", ")", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0 ]
23749007_S8	[ "main", "outcome", "measures", "were", "amount", "of", "drainage", "and", "duration", "of", "drain", "days", "." ]	[ 0, 0, 0, 0, 1, 2, 2, 0, 1, 2, 2, 2, 0 ]
23343686_S6	[ "main", "outcome", "measures", "myocardial", "ischaemia", "as", "assessed", "by", "intracoronary", "(", "i.c", ".", ")" ]	[ 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0 ]
12437457_S12	[ "main", "outcome", "measures", "the", "number", "and", "appearance", "of", "lesions", "were", "evaluated", "before", ",", "during", ",", "and", "after", "treatment", "." ]	[ 0, 0, 0, 0, 1, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
11779598_S7	[ "main", "outcome", "measure", "(", "s", ")", "insulin", ",", "t", ",", "dheas", ",", "fsh", ",", "lh", ",", "body", "mass", "index", "(", "bmi", ")", ",", "waist-to-hip", "ratio", ",", "endometrial", "thickness", ",", "cervical", "score", ",", "ovulation", ",", "and", "pregnancy", "rates", "in", "clomiphene-induced", "cycles", "after", "metformin", "therapy", "." ]	[ 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0 ]
19232615_S7	[ "the", "primary", "outcomes", "is", "the", "mortality", "rate", "at", "6", "months", "follow-up", "." ]	[ 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0 ]
24101715_S4	[ "the", "primary", "blinded", "outcome", "measures", "addressed", "change", "in", "overall", "functioning", "and", "in", "severity", "of", "the", "primary", "anxiety", "diagnosis", "after", "3", "months", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 1, 2, 2, 2, 2, 2, 0, 0, 0, 0 ]
25572620_S4	[ "the", "primary", "outcome", "was", "biochemically-verified", "(", "i.e.", ",", "salivary", "cotinine", ")", "smoking", "cessation", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2 ]
22585469_S8	[ "results", "there", "was", "no", "significant", "difference", "in", "the", "primary", "outcome", "\"", "good", "laryngoscopic", "views", "\"", "(", "cormack-lehane", "grade", "1", "and", "2", ")", "compared", "with", "\"", "poor", "laryngoscopic", "views", "\"", "(", "cormack-lehane", "grade", "3", "and", "4", ")", "between", "the", "lfs", "and", "the", "macintosh", "." ]	[ 0, 0, 1, 2, 2, 2, 0, 0, 1, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
9609624_S5	[ "the", "primary", "efficacy", "parameters", "were", "total", "american", "urological", "association", "(", "aua", ")", "symptom", "score", "and", "maximum", "urinary", "flow", "(", "qmax", ")", "." ]	[ 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 0, 1, 2, 2, 2, 2, 2, 0 ]
12496956_S5	[ "the", "primary", "outcome", "measure", "was", "an", "instrument", "rating", "six", "repetitive", "behaviors", ":", "need", "to", "know", ",", "repeating", ",", "ordering", ",", "need", "to", "tell/ask", ",", "self-injury", ",", "and", "touching", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 ]
12021824_S3	[ "objectives", "the", "primary", "objective", "of", "this", "study", "was", "to", "determine", "whether", "drug", "administration", "instructions", "informing", "subjects", "of", "a", "placebo", "condition", "affect", "the", "drug", "response", "and", "affect", "the", "saliva", "concentration", "of", "the", "stimulant", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0 ]
24352377_S8	[ "main", "outcomes", "and", "measures", "using", "functional", "magnetic", "resonance", "imaging", ",", "we", "examined", "effects", "of", "oxytocin", "on", "behavioral", "neural", "responses", "of", "the", "participants", "to", "a", "social", "psychological", "task", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 0, 1, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
24352377_S10	[ "therefore", ",", "our", "main", "outcomes", "and", "measures", "were", "the", "frequency", "of", "the", "nonverbal", "information-based", "judgments", "(", "nvjs", ")", ",", "the", "response", "time", "for", "nvjs", ",", "and", "brain", "activity", "of", "the", "medial", "prefrontal", "cortex", "during", "nvjs", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 ]
12638099_S7	[ "main", "outcome", "measures", "primary", ":", "day", "1", "mean", "pain", "relief", "(", "0-", "to", "5-point", "verbal", "response", "scale", ")", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 ]
22079469_S4	[ "according", "to", "the", "primary", "endpoint", ",", "systemic", "glucocorticoid", "treatment", "for", "graft-versus-host", "disease", "was", "given", "to", "60", "of", "the", "92", "participants", "(", "65", "%", ")", "in", "the", "bdp", "arm", ",", "versus", "31", "of", "46", "participants", "(", "67", "%", ")", "in", "the", "placebo", "arm", "." ]	[ 0, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
22079469_S5	[ "the", "secondary", "efficacy", "endpoints", "showed", "no", "statistically", "significant", "differences", "between", "the", "two", "arms", "." ]	[ 0, 3, 4, 4, 0, 3, 4, 4, 4, 0, 0, 0, 0, 0 ]
23101741_S2	[ "this", "report", "describes", "a", "secondary", "outcome", "measurement", "from", "this", "trial", ",", "eeg", "activity", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 4, 0 ]
24229362_S5	[ "primary", "endpoints", "are", "the", "level", "of", "educational", "achievement", "one", "year", "after", "the", "cessation", "of", "first-line", "cancer", "therapy", ",", "and", "the", "value", "of", "vo2max", "one", "year", "after", "the", "cessation", "of", "first-line", "cancer", "therapy", "." ]	[ 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 ]
24229362_S6	[ "secondary", "endpoints", "are", "quality", "of", "life", "measured", "by", "validated", "questionnaires", "and", "interviews", ",", "and", "physical", "performance", "." ]	[ 0, 0, 0, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
25087908_S5	[ "primary", "outcomes", "were", "change", "in", "total", "scores", "on", "the", "caregiver-completed", "social", "responsiveness", "scale", "and", "clinician-ratings", "on", "the", "clinical", "global", "impressions-improvement", "scale", "." ]	[ 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 ]
24930383_S6	[ "the", "primary", "endpoint", "of", "this", "study", "was", "the", "imt", "change", "after", "36", "months", "of", "statin", "treatment", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0 ]
18523583_S9	[ "after", "6-months", "of", "exercise", "intervention", ",", "we", "observed", "a", "dose", "dependent", "increase", "in", "all", "parasympathetically", "derived", "time", "and", "frequency", "domain", "measurements", "across", "exercise", "groups", "after", "adjustment", "for", "age", ",", "ethnicity", ",", "antidepressants", ",", "and", "baseline", "rmssd", "(", "all", ",", "p", "<", "0.001", ")", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, 0, 0, 0, 0, 0, 0, 0, 0 ]
15713151_S7	[ "main", "outcome", "measures", "intra-operative", "blood", "loss", ",", "post-operative", "blood", "loss", ",", "blood", "transfusion", "rates", ",", "operative", "morbidity", ",", "uterine", "blood", "flow", "and", "ovarian", "function", "." ]	[ 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 ]
15673801_S4	[ "the", "primary", "outcome", "was", "sustained", "remission", ",", "defined", "as", "a", "birmingham", "vasculitis", "activity", "score", "for", "wegener", "'s", "granulomatosis", "of", "0", "for", "at", "least", "six", "months", "(", "scores", "can", "range", "from", "0", "to", "67", ",", "with", "higher", "scores", "indicating", "more", "active", "disease", ")", "." ]	[ 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
10685722_S4	[ "the", "primary", "outcome", "measures", "were", "the", "changes", "in", "trough", "supine", "systolic", "and", "diastolic", "blood", "pressure", "(", "ssbp", ",", "sdbp", ")", "between", "baseline", "and", "the", "last", "observation", "." ]	[ 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0 ]
21599896_S11	[ "the", "primary", "outcome", "measure", "is", "'patient", "distress", "due", "to", "breathlessness", "'", "measured", "on", "a", "numerical", "rating", "scale", "(", "0-10", ")", "." ]	[ 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0 ]
21892106_S7	[ "primary", "end", "points", "were", "feasibility", ",", "response", "rates", ",", "and", "toxicity", "." ]	[ 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 0 ]
21892106_S8	[ "secondary", "end", "points", "were", "progression-free", "survival", ",", "overall", "survival", ",", "and", "quality", "of", "life", "." ]	[ 0, 0, 0, 0, 3, 4, 4, 4, 4, 0, 0, 3, 4, 4, 0 ]
19433686_S5	[ "results", "at", "3.8", "years", "of", "median", "follow-up", ",", "for", "the", "primary", "end", "point", ",", "recurrence-free", "survival", "(", "rfs", ")", ",", "risk", "was", "reduced", "by", "18", "%", "(", "hazard", "rate", "=", "0.82", ";", "p", "=", ".01", ")", "in", "the", "peg-ifn-alpha-2b", "arm", "compared", "with", "observation", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
24213956_S6	[ "secondary", "outcomes", "included", "kinematic", "parameters", "for", "motor", "control", "and", "the", "motor", "activity", "log", "and", "abilhand", "questionnaire", "for", "daily", "function", "." ]	[ 0, 0, 0, 3, 4, 4, 4, 4, 0, 0, 3, 4, 4, 0, 3, 4, 4, 4, 4, 0 ]
15482502_S10	[ "the", "active", "treatment", "group", "showed", "significant", "improvement", "compared", "with", "controls", "on", "the", "primary", "outcome", "measure", "--", "autism", "diagnostic", "observation", "schedule", "(", "ados", ")", "total", "score", ",", "particularly", "in", "reciprocal", "social", "interaction", "--", "and", "on", "secondary", "measures", "of", "expressive", "language", ",", "communicative", "initiation", "and", "parent-child", "interaction", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2 ]
25022743_S5	[ "primary", "outcome", "was", "total", "sleep", "time", "(", "tst", ")", "recorded", "by", "actigraphy", "over", "each", "2-week", "period", "." ]	[ 0, 0, 0, 1, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0 ]
25022743_S6	[ "secondary", "outcomes", "included", "actigraphically", "recorded", "sleep-onset", "latency", ",", "sleep", "efficiency", ",", "assessments", "of", "child", "behavior", ",", "family", "functioning", ",", "and", "adverse", "events", "." ]	[ 0, 0, 0, 3, 4, 4, 4, 4, 4, 4, 0, 3, 4, 4, 4, 0, 3, 4, 0, 0, 3, 4, 0 ]
26746121_S3	[ "the", "primary", "objective", "was", "to", "evaluate", "the", "effects", "of", "24", "weeks", "of", "buspirone", "on", "the", "autism", "diagnostic", "observation", "schedule", "(", "ados", ")", "composite", "total", "score", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0 ]
26746121_S4	[ "secondary", "objectives", "included", "evaluating", "the", "effects", "of", "buspirone", "on", "social", "competence", ",", "repetitive", "behaviors", ",", "language", ",", "sensory", "dysfunction", ",", "and", "anxiety", "and", "to", "assess", "side", "effects", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 4, 0, 3, 4, 0, 3, 0, 3, 4, 0, 0, 3, 0, 0, 0, 3, 4, 0 ]
19814586_S6	[ "the", "primary", "efficacy", "endpoint", "was", "the", "sum", "of", "pain", "intensity", "difference", "(", "spid", ")", "over", "30", "min", "post-administration", "." ]	[ 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0 ]
19814586_S7	[ "secondary", "efficacy", "endpoints", "included", "pain", "intensity", "difference", "(", "pid", ")", "and", "pain", "relief", "(", "pr", ")", "throughout", "the", "60-min", "post-dose", "assessment", "period", "." ]	[ 0, 0, 0, 0, 3, 4, 4, 4, 4, 4, 0, 3, 4, 4, 4, 4, 0, 0, 0, 0, 0, 0, 0 ]
22151475_S9	[ "the", "primary", "outcome", "will", "be", "measured", "at", "30", "minutes", "after", "treatment", "using", "the", "numerical", "rating", "scale", "(", "nrs", ")", "of", "low", "back", "pain", "while", "the", "patient", "is", "moving", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0 ]
22151475_S10	[ "secondary", "outcomes", "will", "be", "measured", "at", "30", "minutes", "after", "treatment", "using", "the", "nrs", "of", "leg", "pain", ",", "odi", ",", "patient", "global", "impression", "of", "change", ",", "range", "of", "motion", "(", "rom", ")", "of", "the", "lumbar", "spine", ",", "and", "degrees", "of", "straight", "leg", "raising", "(", "slr", ")", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 4, 4, 4, 0, 3, 0, 3, 4, 4, 4, 4, 0, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 0, 3, 4, 4, 4, 4, 4, 4, 4, 0 ]
22151475_S11	[ "post-treatment", "follow-up", "will", "be", "performed", "to", "measure", "primary", "and", "secondary", "outcomes", "with", "the", "exception", "of", "rom", "and", "slr", "at", "2", ",", "4", ",", "and", "24", "weeks", "after", "treatment", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
23578015_S3	[ "primary", "endpoint", "was", "the", "adhd", "rating", "scale", "(", "adhd-rs", ")", "." ]	[ 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 0 ]

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Corpus for token classification of primary and secondary outcomes in scientific articles sentences, in BIO format.

Dataset Details

Dataset Description

Filtered the EBM-NLP corpus Outcomes subset and did the following processing:

split examples into sentences and get the entities for each sentence
verify in each sentences mentions of primary and secondary outcomes using regular expression (with synonyms)
tagged all outcomes according to type when the regex was found in a sentence
removed entity tags for all sentences that were not detected as containing primary or secondary outcome
kept the examples at sentence level
kept original train/test set

Then added data from A. koroleva on primary outcomes (manually annotated corpus). Part of this data is

Then added manually annotated data from a study on primary outcome switching in colorectal cancer articles (this data is only used in test set).

Finally as the filtered EBM-NLP contained a lot of sequences without entities in the end, we sampled from these sequences so that we have an equal number of sequences with and without entities, in train and test set.

Curated by: Mathieu Laï-king
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Language(s) (NLP): English
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From 2 existing corpus one from A. Koroleva and the other is EBM-NLP.

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