BB-norm+ner@ldeleger:BB-norm+ner-24678646 JSONTXT

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bionlp-ost-19-BB-norm-ner-train

Below, discontinuous spans are shown in the chain model. You can change it to the bag model.

Id Subject Object Predicate Lexical cue NCBI_Taxonomy OntoBiotope
T1 0-153 Title denotes Natural history of colonization with methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE): a systematic review.
T2 154-443 Paragraph denotes No published systematic reviews have assessed the natural history of colonization with methicillin-resistant Staphylococcus aureus (MRSA) or vancomycin-resistant Enterococcus (VRE). Time to clearance of colonization has important implications for patient care and infection control policy.
T3 444-653 Paragraph denotes We performed parallel searches in OVID Medline for studies that reported the time to documented clearance of MRSA and VRE colonization in the absence of treatment, published between January 1990 and July 2012.
T4 654-1897 Paragraph denotes For MRSA, we screened 982 articles, identified 16 eligible studies (13 observational studies and 3 randomized controlled trials), for a total of 1,804 non-duplicated subjects. For VRE, we screened 284 articles, identified 13 eligible studies (12 observational studies and 1 randomized controlled trial), for a total of 1,936 non-duplicated subjects. Studies reported varying definitions of clearance of colonization; no study reported time of initial colonization. Studies varied in the frequency of sampling, assays used for sampling, and follow-up period. The median duration of total follow-up was 38 weeks for MRSA and 25 weeks for VRE. Based on pooled analyses, the model-estimated median time to clearance was 88 weeks after documented colonization for MRSA-colonized patients and 26 weeks for VRE-colonized patients. In a secondary analysis, clearance rates for MRSA and VRE were compared by restricting the duration of follow-up for the MRSA studies to the maximum observed time point for VRE studies (43 weeks). With this restriction, the model-fitted median time to documented clearance for MRSA would occur at 41 weeks after documented colonization, demonstrating the sensitivity of the pooled estimate to length of study follow-up.
T5 1898-2508 Paragraph denotes Few available studies report the natural history of MRSA and VRE colonization. Lack of a consistent definition of clearance, uncertainty regarding the time of initial colonization, variation in frequency of sampling for persistent colonization, assays employed and variation in duration of follow-up are limitations of the existing published literature. The heterogeneity of study characteristics limits interpretation of pooled estimates of time to clearance, however, studies included in this review suggest an increase in documented clearance over time, a result which is sensitive to duration of follow-up.
T6 37-58 Phenotype denotes methicillin-resistant OBT:002817
T7 59-80 Microorganism denotes Staphylococcus aureus 1280
T8 82-86 Phenotype denotes MRSA OBT:002817
T9 82-86 Microorganism denotes MRSA 1280
T10 92-112 Phenotype denotes vancomycin-resistant OBT:002874
T11 113-125 Microorganism denotes Enterococcus 1350
T12 127-130 Phenotype denotes VRE OBT:002874
T13 127-130 Microorganism denotes VRE 1350
T14 241-262 Phenotype denotes methicillin-resistant OBT:002817
T15 263-284 Microorganism denotes Staphylococcus aureus 1280
T16 286-290 Phenotype denotes MRSA OBT:002817
T17 286-290 Microorganism denotes MRSA 1280
T18 295-315 Phenotype denotes vancomycin-resistant OBT:002874
T19 316-328 Microorganism denotes Enterococcus 1350
T20 330-333 Phenotype denotes VRE OBT:002874
T21 330-333 Microorganism denotes VRE 1350
T22 401-408 Habitat denotes patient OBT:003269
T23 553-557 Phenotype denotes MRSA OBT:002817
T24 553-557 Microorganism denotes MRSA 1280
T25 562-565 Phenotype denotes VRE OBT:002874
T26 562-565 Microorganism denotes VRE 1350
T27 658-662 Phenotype denotes MRSA OBT:002817
T28 658-662 Microorganism denotes MRSA 1280
T29 834-837 Phenotype denotes VRE OBT:002874
T30 834-837 Microorganism denotes VRE 1350
T31 1268-1272 Phenotype denotes MRSA OBT:002817
T32 1268-1272 Microorganism denotes MRSA 1280
T33 1290-1293 Phenotype denotes VRE OBT:002874
T34 1290-1293 Microorganism denotes VRE 1350
T37 1413-1436 Habitat denotes MRSA-colonized patients OBT:003269
T35 1413-1417 Phenotype denotes MRSA OBT:002817
T36 1413-1417 Microorganism denotes MRSA 1280
T40 1454-1476 Habitat denotes VRE-colonized patients OBT:003269
T38 1454-1457 Phenotype denotes VRE OBT:002874
T39 1454-1457 Microorganism denotes VRE 1350
T41 1523-1527 Phenotype denotes MRSA OBT:002817
T42 1523-1527 Microorganism denotes MRSA 1280
T43 1532-1535 Phenotype denotes VRE OBT:002874
T44 1532-1535 Microorganism denotes VRE 1350
T45 1599-1603 Phenotype denotes MRSA OBT:002817
T46 1599-1603 Microorganism denotes MRSA 1280
T47 1651-1654 Phenotype denotes VRE OBT:002874
T48 1651-1654 Microorganism denotes VRE 1350
T49 1755-1759 Phenotype denotes MRSA OBT:002817
T50 1755-1759 Microorganism denotes MRSA 1280
T51 1950-1954 Phenotype denotes MRSA OBT:002817
T52 1950-1954 Microorganism denotes MRSA 1280
T53 1959-1962 Phenotype denotes VRE OBT:002874
T54 1959-1962 Microorganism denotes VRE 1350