BB-kb+ner@ldeleger:BB-kb+ner-19396518 JSONTXT

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bionlp-ost-19-BB-kb-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 0-104 Title denotes Rapid detection of eight causative pathogens for the diagnosis of bacterial meningitis by real-time PCR.
T2 105-1735 Paragraph denotes We aimed to detect causative pathogens in cerebrospinal fluid (CSF) collected from patients diagnosed with bacterial meningitis by real-time polymerase chain reaction (PCR). In addition to Streptococcus pneumoniae, Haemophilus influenzae, and Mycoplasma pneumoniae described previously, five other pathogens, Neisseria meningitidis, Escherichia coli, Streptococcus agalactiae, Staphylococcus aureus, and Listeria monocytogenes, were targeted, based on a large-scale surveillance in Japan. Results in CSF from neonates and children (n=150), and from adults (n=18) analyzed by real-time PCR with molecular beacon probes were compared with those of conventional culturing. The total time from DNA extraction from CSF to PCR analysis was 1.5 h. The limit of detection for these pathogens ranged from 5 copies to 28 copies per tube. Nonspecific positive reactions were not recognized for 37 microorganisms in clinical isolates as a negative control. The pathogens were detected in 72.0% of the samples by real-time PCR, but in only 48.2% by culture, although the microorganisms were completely concordant. With the real-time PCR, the detection rate of H. influenzae from CSF was high, at 45.2%, followed by S. pneumoniae (21.4%), S. agalactiae (2.4%), E. coli (1.8%), L. monocytogenes (0.6%), and M. pneumoniae (0.6%). The detection rate with PCR was significantly better than that with cultures in patients with antibiotic administration (chi2=18.3182; P=0.0000). In conclusion, detection with real-time PCR is useful for rapidly identifying the causative pathogens of meningitis and for examining the clinical course of chemotherapy.
T3 35-44 Phenotype denotes pathogens OBT:000375
T4 134-143 Phenotype denotes pathogens OBT:002806
T5 147-166 Habitat denotes cerebrospinal fluid OBT:000550
T6 168-171 Habitat denotes CSF OBT:000550
T7 188-232 Habitat denotes patients diagnosed with bacterial meningitis OBT:003269
T8 294-318 Microorganism denotes Streptococcus pneumoniae 1313
T9 320-342 Microorganism denotes Haemophilus influenzae 727
T10 348-369 Microorganism denotes Mycoplasma pneumoniae 2104
T11 403-412 Phenotype denotes pathogens OBT:002806
T12 414-436 Microorganism denotes Neisseria meningitidis 487
T13 438-454 Microorganism denotes Escherichia coli 562
T14 456-480 Microorganism denotes Streptococcus agalactiae 1311
T15 482-503 Microorganism denotes Staphylococcus aureus 1280
T16 509-531 Microorganism denotes Listeria monocytogenes 1639
T17 605-635 Habitat denotes CSF from neonates and children OBT:000550
T18-0 605-608 _FRAGMENT denotes CSF OBT:000550
T18-1 649-660 Habitat denotes from adults
T19 614-622 Habitat denotes neonates OBT:003453|OBT:003269
T20 627-635 Habitat denotes children OBT:003188|OBT:003269
T21 654-660 Habitat denotes adults OBT:003245|OBT:003269
T22 815-818 Habitat denotes CSF OBT:000550
T23 879-888 Phenotype denotes pathogens OBT:002806
T24 1009-1017 Habitat denotes clinical OBT:003220
T25 1054-1063 Phenotype denotes pathogens OBT:002806
T26 1252-1265 Microorganism denotes H. influenzae 727
T27 1271-1274 Habitat denotes CSF OBT:000550
T28 1307-1320 Microorganism denotes S. pneumoniae 1313
T29 1330-1343 Microorganism denotes S. agalactiae 1311
T30 1352-1359 Microorganism denotes E. coli 562
T31 1368-1384 Microorganism denotes L. monocytogenes 1639
T32 1397-1410 Microorganism denotes M. pneumoniae 1313
T33 1499-1538 Habitat denotes patients with antibiotic administration OBT:003269
T34 1657-1666 Phenotype denotes pathogens OBT:002806
E2 294-318 Exhibits denotes Streptococcus pneumoniae
E4 320-342 Exhibits denotes Haemophilus influenzae
E6 348-369 Exhibits denotes Mycoplasma pneumoniae
E8 414-436 Exhibits denotes Neisseria meningitidis
E10 438-454 Exhibits denotes Escherichia coli
E12 456-480 Exhibits denotes Streptococcus agalactiae
E14 482-503 Exhibits denotes Staphylococcus aureus
E16 509-531 Exhibits denotes Listeria monocytogenes
E17 1252-1265 Lives_In denotes H. influenzae
E18 1252-1265 Lives_In denotes H. influenzae
E19 1307-1320 Lives_In denotes S. pneumoniae
E20 1307-1320 Lives_In denotes S. pneumoniae
E21 1330-1343 Lives_In denotes S. agalactiae
E22 1330-1343 Lives_In denotes S. agalactiae
E23 1352-1359 Lives_In denotes E. coli
E24 1352-1359 Lives_In denotes E. coli
E25 1368-1384 Lives_In denotes L. monocytogenes
E26 1368-1384 Lives_In denotes L. monocytogenes
E27 1397-1410 Lives_In denotes M. pneumoniae
E28 1397-1410 Lives_In denotes M. pneumoniae
R1 E2 T8 Microorganism Streptococcus pneumoniae,Streptococcus pneumoniae
R2 E2 T11 Property Streptococcus pneumoniae,pathogens
R3 E4 T9 Microorganism Haemophilus influenzae,Haemophilus influenzae
R4 E4 T11 Property Haemophilus influenzae,pathogens
R5 E6 T10 Microorganism Mycoplasma pneumoniae,Mycoplasma pneumoniae
R6 E6 T11 Property Mycoplasma pneumoniae,pathogens
R7 E8 T12 Microorganism Neisseria meningitidis,Neisseria meningitidis
R8 E8 T11 Property Neisseria meningitidis,pathogens
R9 E10 T13 Microorganism Escherichia coli,Escherichia coli
R10 E10 T11 Property Escherichia coli,pathogens
R11 E12 T14 Microorganism Streptococcus agalactiae,Streptococcus agalactiae
R12 E12 T11 Property Streptococcus agalactiae,pathogens
R13 E14 T15 Microorganism Staphylococcus aureus,Staphylococcus aureus
R14 E14 T11 Property Staphylococcus aureus,pathogens
R15 E16 T16 Microorganism Listeria monocytogenes,Listeria monocytogenes
R16 E16 T11 Property Listeria monocytogenes,pathogens
R17 E17 T26 Microorganism H. influenzae,H. influenzae
R18 E17 T27 Location H. influenzae,CSF
R19 E18 T26 Microorganism H. influenzae,H. influenzae
R20 E18 T33 Location H. influenzae,patients with antibiotic administration
R21 E19 T28 Microorganism S. pneumoniae,S. pneumoniae
R22 E19 T27 Location S. pneumoniae,CSF
R23 E20 T28 Microorganism S. pneumoniae,S. pneumoniae
R24 E20 T33 Location S. pneumoniae,patients with antibiotic administration
R25 E21 T29 Microorganism S. agalactiae,S. agalactiae
R26 E21 T33 Location S. agalactiae,patients with antibiotic administration
R27 E22 T29 Microorganism S. agalactiae,S. agalactiae
R28 E22 T27 Location S. agalactiae,CSF
R29 E23 T30 Microorganism E. coli,E. coli
R30 E23 T27 Location E. coli,CSF
R31 E24 T30 Microorganism E. coli,E. coli
R32 E24 T33 Location E. coli,patients with antibiotic administration
R33 E25 T31 Microorganism L. monocytogenes,L. monocytogenes
R34 E25 T27 Location L. monocytogenes,CSF
R35 E26 T31 Microorganism L. monocytogenes,L. monocytogenes
R36 E26 T33 Location L. monocytogenes,patients with antibiotic administration
R37 E27 T32 Microorganism M. pneumoniae,M. pneumoniae
R38 E27 T27 Location M. pneumoniae,CSF
R39 E28 T32 Microorganism M. pneumoniae,M. pneumoniae
R40 E28 T33 Location M. pneumoniae,patients with antibiotic administration
C-T18-0 T18-1 T18-0 _lexicallyChainedTo from adults,CSF