BB-kb+ner@ldeleger:BB-kb+ner-17237163 / 87-1888 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
T2 0-1801 Paragraph denotes Serratia marcescens is an opportunistic pathogen and a major cause of ocular infections. In previous studies of S. marcescens MG1, we showed that biofilm maturation and sloughing were regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). Because of the importance of adhesion in initiating biofilm formation and infection, the primary goal of this study was to determine whether QS is important in adhesion to both abiotic and biotic surfaces, as assessed by determining the degree of attachment to hydrophilic tissue culture plates and human corneal epithelial (HCE) cells. Our results demonstrate that while adhesion to the abiotic surface was AHL regulated, adhesion to the HCE cell biotic surface was not. Type I fimbriae were identified as the critical adhesin for non-QS-mediated attachment to the biotic HCE cell surface but played no role in adhesion to the abiotic surface. While we were not able to identify a single QS-regulated adhesin essential for attachment to the abiotic surface, four AHL-regulated genes involved in adhesion to the abiotic surface were identified. Interestingly, two of these genes, bsmA and bsmB, were also shown to be involved in adhesion to the biotic surface in a non-QS-controlled fashion. Therefore, the expression of these two genes appears to be cocontrolled by regulators other than the QS system for mediation of attachment to HCE cells. We also found that QS in S. marcescens regulates other potential cell surface adhesins, including exopolysaccharide and the outer membrane protein OmpX. We concluded that S. marcescens MG1 utilizes different regulatory systems and adhesins in attachment to biotic and abiotic surfaces and that QS is a main regulatory pathway in adhesion to an abiotic surface but not in adhesion to a biotic surface.
T6 0-19 Microorganism denotes Serratia marcescens 615
T7 26-48 Phenotype denotes opportunistic pathogen OBT:000776
T8 70-76 Habitat denotes ocular OBT:000627
T9 112-129 Microorganism denotes S. marcescens MG1 615
T11 146-164 Phenotype denotes biofilm maturation OBT:001444
T10 146-153 Habitat denotes biofilm OBT:000054
T12 197-249 Phenotype denotes N-acyl homoserine lactone (AHL)-based quorum sensing OBT:000143
T13 251-253 Phenotype denotes QS OBT:000143
T14 285-293 Phenotype denotes adhesion OBT:000029
T16 308-325 Phenotype denotes biofilm formation OBT:001444
T15 308-315 Habitat denotes biofilm OBT:000054
T17 397-399 Phenotype denotes QS OBT:000143
T18 416-424 Phenotype denotes adhesion OBT:000029
T19-0 433-440 _FRAGMENT denotes abiotic OBT:000007
T19-1 452-460 Habitat denotes surfaces
T20 445-460 Habitat denotes biotic surfaces OBT:000007
T21 503-513 Phenotype denotes attachment OBT:000029
T22 517-550 Habitat denotes hydrophilic tissue culture plates OBT:000103
T23 517-543 Habitat denotes hydrophilic tissue culture OBT:000062
T24 555-591 Habitat denotes human corneal epithelial (HCE) cells OBT:000061
T25 555-560 Habitat denotes human OBT:002488
T26 561-568 Habitat denotes corneal OBT:000573
T27 569-579 Habitat denotes epithelial OBT:001091
T28 628-636 Phenotype denotes adhesion OBT:000029
T29 644-659 Habitat denotes abiotic surface OBT:000007
T30 679-687 Phenotype denotes adhesion OBT:000029
T32 695-718 Habitat denotes HCE cell biotic surface OBT:000062
T31 695-703 Habitat denotes HCE cell OBT:000061
T33 792-794 Phenotype denotes QS OBT:000143
T34 804-814 Phenotype denotes attachment OBT:000029
T35 822-845 Habitat denotes biotic HCE cell surface OBT:000062
T36 829-837 Habitat denotes HCE cell OBT:000061
T37 868-876 Phenotype denotes adhesion OBT:000029
T38 884-899 Habitat denotes abiotic surface OBT:000007
T39 945-947 Phenotype denotes QS OBT:000143
T40 980-990 Phenotype denotes attachment OBT:000029
T41 998-1013 Habitat denotes abiotic surface OBT:000007
T42 1052-1060 Phenotype denotes adhesion OBT:000029
T43 1068-1083 Habitat denotes abiotic surface OBT:000007
T44 1185-1193 Phenotype denotes adhesion OBT:000029
T45 1201-1215 Habitat denotes biotic surface OBT:000062
T46 1225-1227 Phenotype denotes QS OBT:000143
T47 1349-1351 Phenotype denotes QS OBT:000143
T48 1376-1386 Phenotype denotes attachment OBT:000029
T49 1390-1399 Habitat denotes HCE cells OBT:000061
T50 1420-1422 Phenotype denotes QS OBT:000143
T51 1426-1439 Microorganism denotes S. marcescens 615
T52 1572-1589 Microorganism denotes S. marcescens MG1 615
T53 1644-1654 Phenotype denotes attachment OBT:000029
T54-0 1658-1664 _FRAGMENT denotes biotic OBT:000062
T54-1 1677-1685 Habitat denotes surfaces
T55 1669-1685 Habitat denotes abiotic surfaces OBT:000007
T56 1695-1697 Phenotype denotes QS OBT:000143
T57 1730-1738 Phenotype denotes adhesion OBT:000029
T58 1745-1760 Habitat denotes abiotic surface OBT:000007
T59 1772-1780 Phenotype denotes adhesion OBT:000029
T60 1786-1800 Habitat denotes biotic surface OBT:000062
E3 0-19 Lives_In denotes Serratia marcescens
E4 0-19 Lives_In denotes Serratia marcescens
E5 0-19 Lives_In denotes Serratia marcescens
E6 0-19 Lives_In denotes Serratia marcescens
E7 0-19 Lives_In denotes Serratia marcescens
E8 0-19 Lives_In denotes Serratia marcescens
E9 0-19 Lives_In denotes Serratia marcescens
E10 0-19 Lives_In denotes Serratia marcescens
E11 0-19 Lives_In denotes Serratia marcescens
E12 0-19 Exhibits denotes Serratia marcescens
E13 0-19 Exhibits denotes Serratia marcescens
E14 0-19 Exhibits denotes Serratia marcescens
E15 0-19 Exhibits denotes Serratia marcescens
E16 0-19 Exhibits denotes Serratia marcescens
E17 0-19 Exhibits denotes Serratia marcescens
E18 0-19 Exhibits denotes Serratia marcescens
E19 0-19 Exhibits denotes Serratia marcescens
E20 0-19 Exhibits denotes Serratia marcescens
E21 112-129 Lives_In denotes S. marcescens MG1
E22 112-129 Exhibits denotes S. marcescens MG1
E23 112-129 Exhibits denotes S. marcescens MG1
E24 1426-1439 Exhibits denotes S. marcescens
E25 1572-1589 Lives_In denotes S. marcescens MG1
E26 1572-1589 Lives_In denotes S. marcescens MG1
E27 1572-1589 Lives_In denotes S. marcescens MG1
E28 1572-1589 Lives_In denotes S. marcescens MG1
E29 1572-1589 Exhibits denotes S. marcescens MG1
E30 1572-1589 Exhibits denotes S. marcescens MG1
E31 1572-1589 Exhibits denotes S. marcescens MG1
E32 1572-1589 Exhibits denotes S. marcescens MG1
R63 E32 T52 Microorganism S. marcescens MG1,S. marcescens MG1
R5 E3 T6 Microorganism Serratia marcescens,Serratia marcescens
R6 E3 T29 Location Serratia marcescens,abiotic surface
R7 E4 T6 Microorganism Serratia marcescens,Serratia marcescens
R8 E4 T49 Location Serratia marcescens,HCE cells
R9 E5 T6 Microorganism Serratia marcescens,Serratia marcescens
R10 E5 T8 Location Serratia marcescens,ocular
R11 E6 T6 Microorganism Serratia marcescens,Serratia marcescens
R12 E6 T32 Location Serratia marcescens,HCE cell biotic surface
R13 E7 T6 Microorganism Serratia marcescens,Serratia marcescens
R14 E7 T45 Location Serratia marcescens,biotic surface
R15 E8 T6 Microorganism Serratia marcescens,Serratia marcescens
R16 E8 T43 Location Serratia marcescens,abiotic surface
R17 E9 T6 Microorganism Serratia marcescens,Serratia marcescens
R18 E9 T38 Location Serratia marcescens,abiotic surface
R19 E10 T6 Microorganism Serratia marcescens,Serratia marcescens
R20 E10 T41 Location Serratia marcescens,abiotic surface
R21 E11 T6 Microorganism Serratia marcescens,Serratia marcescens
R22 E11 T35 Location Serratia marcescens,biotic HCE cell surface
R23 E12 T6 Microorganism Serratia marcescens,Serratia marcescens
R24 E12 T37 Property Serratia marcescens,adhesion
R25 E13 T6 Microorganism Serratia marcescens,Serratia marcescens
R26 E13 T7 Property Serratia marcescens,opportunistic pathogen
R27 E14 T6 Microorganism Serratia marcescens,Serratia marcescens
R28 E14 T48 Property Serratia marcescens,attachment
R29 E15 T6 Microorganism Serratia marcescens,Serratia marcescens
R30 E15 T40 Property Serratia marcescens,attachment
R31 E16 T6 Microorganism Serratia marcescens,Serratia marcescens
R32 E16 T34 Property Serratia marcescens,attachment
R33 E17 T6 Microorganism Serratia marcescens,Serratia marcescens
R34 E17 T30 Property Serratia marcescens,adhesion
R35 E18 T6 Microorganism Serratia marcescens,Serratia marcescens
R36 E18 T44 Property Serratia marcescens,adhesion
R37 E19 T6 Microorganism Serratia marcescens,Serratia marcescens
R38 E19 T28 Property Serratia marcescens,adhesion
R39 E20 T6 Microorganism Serratia marcescens,Serratia marcescens
R40 E20 T42 Property Serratia marcescens,adhesion
R41 E21 T9 Microorganism S. marcescens MG1,S. marcescens MG1
R42 E21 T10 Location S. marcescens MG1,biofilm
R43 E22 T9 Microorganism S. marcescens MG1,S. marcescens MG1
R44 E22 T11 Property S. marcescens MG1,biofilm maturation
R45 E23 T9 Microorganism S. marcescens MG1,S. marcescens MG1
R46 E23 T12 Property S. marcescens MG1,N-acyl homoserine lactone (AHL)-based quorum sensing
R47 E24 T51 Microorganism S. marcescens,S. marcescens
R48 E24 T50 Property S. marcescens,QS
R49 E25 T52 Microorganism S. marcescens MG1,S. marcescens MG1
R50 E25 T58 Location S. marcescens MG1,abiotic surface
R51 E26 T52 Microorganism S. marcescens MG1,S. marcescens MG1
R52 E26 T55 Location S. marcescens MG1,abiotic surfaces
R53 E27 T52 Microorganism S. marcescens MG1,S. marcescens MG1
R54 E27 T60 Location S. marcescens MG1,biotic surface
R55 E28 T52 Microorganism S. marcescens MG1,S. marcescens MG1
R56 E28 T54-0 Location S. marcescens MG1,biotic
R57 E29 T52 Microorganism S. marcescens MG1,S. marcescens MG1
R58 E29 T56 Property S. marcescens MG1,QS
R59 E30 T52 Microorganism S. marcescens MG1,S. marcescens MG1
R60 E30 T53 Property S. marcescens MG1,attachment
R61 E31 T52 Microorganism S. marcescens MG1,S. marcescens MG1
R62 E31 T59 Property S. marcescens MG1,adhesion
R64 E32 T57 Property S. marcescens MG1,adhesion
C-T19-0 T19-1 T19-0 _lexicallyChainedTo surfaces,abiotic
C-T54-0 T54-1 T54-0 _lexicallyChainedTo surfaces,biotic