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PMC:3589482 / 445-869 JSONTXT

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bionlp-st-ge-2016-spacy-parsed

Id Subject Object Predicate Lexical cue
T856 172-180 NN denotes promoter
T855 163-171 CD denotes SerpinB2
T854 149-162 JJ denotes LPS-regulated
T853 145-148 DT denotes the
T852 141-144 VB denotes map
T851 138-140 TO denotes To
T850 136-137 . denotes .
T849 125-136 NNS denotes macrophages
T848 118-124 JJ denotes murine
T847 115-117 IN denotes in
T846 111-114 NNS denotes hrs
T845 108-110 CD denotes 24
T844 105-107 IN denotes of
T843 98-104 NN denotes period
T842 96-97 DT denotes a
T841 91-95 IN denotes over
T840 81-90 JJ denotes 1000-fold
T839 80-81 CD denotes ∼
T838 77-79 IN denotes by
T837 75-76 -RRB- denotes )
T836 71-75 CD denotes TLR4
T835 70-71 -LRB- denotes (
T834 68-69 CD denotes 4
T833 59-67 NN denotes receptor
T832 49-58 JJ denotes toll-like
T831 45-48 DT denotes the
T830 41-44 IN denotes via
T829 30-40 NN denotes expression
T828 21-29 NNP denotes SerpinB2
T827 14-20 VB denotes induce
T826 10-13 MD denotes can
T825 8-9 , denotes ,
T901 414-422 NN denotes sequence
T900 405-413 NN denotes flanking
T899 403-404 NN denotes ′
T898 402-403 CD denotes 5
T897 395-401 NN denotes murine
T896 391-394 DT denotes the
T895 388-390 IN denotes of
T894 379-387 NN denotes sequence
T893 375-378 NNP denotes DNA
T892 371-374 DT denotes the
T891 362-370 VBD denotes compared
T890 359-361 PRP denotes we
T889 357-358 , denotes ,
T888 349-357 NN denotes addition
T887 346-348 IN denotes In
T886 344-345 . denotes .
T885 333-344 NNS denotes macrophages
T884 326-332 JJ denotes murine
T883 321-325 IN denotes into
T882 313-320 NNS denotes mutants
T881 304-312 NN denotes deletion
T880 296-303 JJ denotes several
T879 292-295 CC denotes and
T878 287-291 NN denotes gene
T877 278-286 NNP denotes SerpinB2
T876 271-277 NN denotes murine
T875 267-270 DT denotes the
T874 264-266 IN denotes of
T873 257-263 NN denotes region
T872 248-256 VBG denotes flanking
T871 247-248 : denotes -
T870 246-247 '' denotes '
T869 245-246 CD denotes 5
T868 242-244 NN denotes kb
T867 240-241 CD denotes 5
T866 239-240 NN denotes ∼
T865 235-238 DT denotes the
T864 232-234 IN denotes by
T863 225-231 VBN denotes driven
T862 214-224 NNS denotes constructs
T861 205-213 NN denotes reporter
T860 193-204 VBD denotes transfected
T859 190-192 PRP denotes we
T858 188-189 , denotes ,
T857 181-188 NNS denotes regions
R412 T825 T827 punct ",",induce
R413 T826 T827 aux can,induce
R414 T827 T827 ROOT induce,induce
R415 T828 T829 compound SerpinB2,expression
R416 T829 T827 dobj expression,induce
R417 T830 T827 prep via,induce
R418 T831 T833 det the,receptor
R419 T832 T833 amod toll-like,receptor
R420 T833 T830 pobj receptor,via
R421 T834 T833 nummod 4,receptor
R422 T835 T833 punct (,receptor
R423 T836 T833 appos TLR4,receptor
R424 T837 T833 punct ),receptor
R425 T838 T827 prep by,induce
R426 T839 T838 pobj ∼,by
R427 T840 T827 advcl 1000-fold,induce
R428 T841 T840 prep over,1000-fold
R429 T842 T843 det a,period
R430 T843 T841 pobj period,over
R431 T844 T843 prep of,period
R432 T845 T846 nummod 24,hrs
R433 T846 T844 pobj hrs,of
R434 T847 T846 prep in,hrs
R435 T848 T849 amod murine,macrophages
R436 T849 T847 pobj macrophages,in
R437 T850 T827 punct .,induce
R438 T851 T852 aux To,map
R439 T852 T860 advcl map,transfected
R440 T853 T857 det the,regions
R441 T854 T857 amod LPS-regulated,regions
R442 T855 T857 nummod SerpinB2,regions
R443 T856 T857 compound promoter,regions
R444 T857 T852 dobj regions,map
R445 T858 T860 punct ",",transfected
R446 T859 T860 nsubj we,transfected
R447 T860 T860 ROOT transfected,transfected
R448 T861 T862 compound reporter,constructs
R449 T862 T860 dobj constructs,transfected
R450 T863 T862 acl driven,constructs
R451 T864 T863 agent by,driven
R452 T865 T873 det the,region
R453 T866 T868 nmod ∼,kb
R454 T867 T866 nummod 5,∼
R455 T868 T872 meta kb,flanking
R456 T869 T868 nummod 5,kb
R457 T870 T869 punct ',5
R458 T871 T872 punct -,flanking
R459 T872 T873 amod flanking,region
R460 T873 T864 pobj region,by
R461 T874 T873 prep of,region
R462 T875 T878 det the,gene
R463 T876 T878 compound murine,gene
R464 T877 T878 compound SerpinB2,gene
R465 T878 T874 pobj gene,of
R466 T879 T878 cc and,gene
R467 T880 T882 amod several,mutants
R468 T881 T882 compound deletion,mutants
R469 T882 T878 conj mutants,gene
R470 T883 T863 prep into,driven
R471 T884 T885 amod murine,macrophages
R472 T885 T883 pobj macrophages,into
R473 T886 T860 punct .,transfected
R474 T887 T891 prep In,compared
R475 T888 T887 pobj addition,In
R476 T889 T891 punct ",",compared
R477 T890 T891 nsubj we,compared
R478 T891 T891 ROOT compared,compared
R479 T892 T894 det the,sequence
R480 T893 T894 compound DNA,sequence
R481 T894 T891 dobj sequence,compared
R482 T895 T894 prep of,sequence
R483 T896 T901 det the,sequence
R484 T897 T901 nmod murine,sequence
R485 T898 T897 nummod 5,murine
R486 T899 T901 compound ′,sequence
R487 T900 T901 compound flanking,sequence
R488 T901 T895 pobj sequence,of

pmc-enju-pas

Id Subject Object Predicate Lexical cue
T307 108-110 CD denotes 24
T306 105-107 IN denotes of
T305 98-104 NN denotes period
T304 96-97 DT denotes a
T303 91-95 IN denotes over
T302 80-90 RB denotes ∼1000-fold
T301 77-79 IN denotes by
T300 75-76 -RRB- denotes )
T299 71-75 NN denotes TLR4
T298 70-71 -LRB- denotes (
T297 68-69 CD denotes 4
T296 59-67 NN denotes receptor
T295 49-58 JJ denotes toll-like
T294 45-48 DT denotes the
T293 41-44 IN denotes via
T292 30-40 NN denotes expression
T291 21-29 NN denotes SerpinB2
T290 14-20 VB denotes induce
T289 10-13 MD denotes can
T288 8-9 -COMMA- denotes ,
T347 362-370 VB denotes compared
T346 359-361 PRP denotes we
T345 357-358 -COMMA- denotes ,
T344 349-357 NN denotes addition
T343 346-348 IN denotes In
T342 333-344 NN denotes macrophages
T341 326-332 JJ denotes murine
T340 321-325 IN denotes into
T339 313-320 NN denotes mutants
T338 304-312 NN denotes deletion
T337 296-303 JJ denotes several
T336 292-295 CC denotes and
T335 287-291 NN denotes gene
T334 278-286 NN denotes SerpinB2
T333 271-277 JJ denotes murine
T332 267-270 DT denotes the
T331 264-266 IN denotes of
T330 257-263 NN denotes region
T329 245-256 JJ denotes 5'-flanking
T328 242-244 NN denotes kb
T327 239-241 CD denotes ∼5
T326 235-238 DT denotes the
T325 232-234 IN denotes by
T324 225-231 VB denotes driven
T323 214-224 NN denotes constructs
T322 205-213 NN denotes reporter
T321 193-204 VB denotes transfected
T320 190-192 PRP denotes we
T319 188-189 -COMMA- denotes ,
T318 181-188 NN denotes regions
T317 172-180 NN denotes promoter
T316 163-171 NN denotes SerpinB2
T315 149-162 JJ denotes LPS-regulated
T314 145-148 DT denotes the
T313 141-144 VB denotes map
T312 138-140 TO denotes To
T311 125-136 NN denotes macrophages
T310 118-124 JJ denotes murine
T309 115-117 IN denotes in
T308 111-114 NN denotes hrs
T356 414-422 NN denotes sequence
T355 405-413 NN denotes flanking
T354 402-404 NN denotes 5′
T353 395-401 JJ denotes murine
T352 391-394 DT denotes the
T351 388-390 IN denotes of
T350 379-387 NN denotes sequence
T349 375-378 NN denotes DNA
T348 371-374 DT denotes the
R100 T290 T288 arg1Of induce,","
R101 T290 T289 arg2Of induce,can
R102 T290 T293 arg1Of induce,via
R103 T290 T301 arg1Of induce,by
R104 T290 T303 arg1Of induce,over
R105 T292 T290 arg2Of expression,induce
R106 T292 T291 arg1Of expression,SerpinB2
R107 T296 T293 arg2Of receptor,via
R108 T296 T294 arg1Of receptor,the
R109 T296 T295 arg1Of receptor,toll-like
R110 T296 T297 arg1Of receptor,4
R111 T296 T298 arg1Of receptor,(
R112 T299 T298 arg2Of TLR4,(
R113 T300 T298 arg3Of ),(
R114 T302 T301 arg2Of ∼1000-fold,by
R115 T305 T303 arg2Of period,over
R116 T305 T304 arg1Of period,a
R117 T305 T306 arg1Of period,of
R118 T305 T309 arg1Of period,in
R119 T308 T306 arg2Of hrs,of
R120 T308 T307 arg1Of hrs,24
R121 T311 T309 arg2Of macrophages,in
R122 T311 T310 arg1Of macrophages,murine
R123 T313 T312 arg1Of map,To
R124 T318 T313 arg2Of regions,map
R125 T318 T314 arg1Of regions,the
R126 T318 T315 arg1Of regions,LPS-regulated
R127 T318 T316 arg1Of regions,SerpinB2
R128 T318 T317 arg1Of regions,promoter
R129 T320 T313 arg1Of we,map
R130 T320 T321 arg1Of we,transfected
R131 T321 T312 modOf transfected,To
R132 T321 T319 arg1Of transfected,","
R133 T323 T321 arg2Of constructs,transfected
R134 T323 T322 arg1Of constructs,reporter
R135 T323 T324 arg2Of constructs,driven
R136 T330 T324 arg1Of region,driven
R137 T330 T325 arg2Of region,by
R138 T330 T326 arg1Of region,the
R139 T330 T327 arg1Of region,∼5
R140 T330 T328 arg1Of region,kb
R141 T330 T329 arg1Of region,5'-flanking
R142 T330 T331 arg1Of region,of
R143 T330 T340 arg1Of region,into
R144 T335 T332 arg1Of gene,the
R145 T335 T333 arg1Of gene,murine
R146 T335 T334 arg1Of gene,SerpinB2
R147 T335 T336 arg1Of gene,and
R148 T336 T331 arg2Of and,of
R149 T339 T336 arg2Of mutants,and
R150 T339 T337 arg1Of mutants,several
R151 T339 T338 arg1Of mutants,deletion
R152 T342 T340 arg2Of macrophages,into
R153 T342 T341 arg1Of macrophages,murine
R154 T344 T343 arg2Of addition,In
R155 T346 T347 arg1Of we,compared
R158 T350 T347 arg2Of sequence,compared
R159 T350 T348 arg1Of sequence,the
R160 T350 T349 arg1Of sequence,DNA
R161 T350 T351 arg1Of sequence,of
R163 T356 T351 arg2Of sequence,of
R164 T356 T352 arg1Of sequence,the
R165 T356 T353 arg1Of sequence,murine
R166 T356 T354 arg1Of sequence,5′
R167 T356 T355 arg1Of sequence,flanking

bionlp-st-ge-2016-test-proteins

Id Subject Object Predicate Lexical cue
T162 21-29 Protein denotes SerpinB2
T163 49-69 Protein denotes toll-like receptor 4
T164 71-75 Protein denotes TLR4
T165 163-171 Protein denotes SerpinB2
T166 278-286 Protein denotes SerpinB2

bionlp-st-ge-2016-uniprot

Id Subject Object Predicate Lexical cue
T539 71-75 http://www.uniprot.org/uniprot/O00206 denotes TLR4
T531 21-29 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2
T532 163-171 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2
T533 278-286 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2

sentences

Id Subject Object Predicate Lexical cue
T102 138-345 Sentence denotes To map the LPS-regulated SerpinB2 promoter regions, we transfected reporter constructs driven by the ∼5 kb 5'-flanking region of the murine SerpinB2 gene and several deletion mutants into murine macrophages.
T6 138-345 Sentence denotes To map the LPS-regulated SerpinB2 promoter regions, we transfected reporter constructs driven by the ∼5 kb 5'-flanking region of the murine SerpinB2 gene and several deletion mutants into murine macrophages.

simple1

Id Subject Object Predicate Lexical cue
T215 21-29 Protein denotes SerpinB2
T216 49-69 Protein denotes toll-like receptor 4
T217 71-75 Protein denotes TLR4
T218 163-171 Protein denotes SerpinB2
T219 278-286 Protein denotes SerpinB2

BioNLP16_DUT

Id Subject Object Predicate Lexical cue
T514 14-20 Positive_regulation denotes induce
T513 30-40 Gene_expression denotes expression
T500 163-171 Protein denotes SerpinB2
T499 278-286 Protein denotes SerpinB2
T498 71-75 Protein denotes TLR4
T496 21-29 Protein denotes SerpinB2
T497 49-69 Protein denotes toll-like receptor 4
R308 T513 T514 themeOf expression,induce
R680 T496 T513 themeOf SerpinB2,expression

BioNLP16_Messiy

Id Subject Object Predicate Lexical cue
T606 21-29 Protein denotes SerpinB2
T607 49-69 Protein denotes toll-like receptor 4
T608 71-75 Protein denotes TLR4
T609 278-286 Protein denotes SerpinB2
T610 163-171 Protein denotes SerpinB2
T623 30-40 Gene_expression denotes expression
T624 14-20 Positive_regulation denotes induce
R718 T606 T623 themeOf SerpinB2,expression
R720 T607 T624 causeOf toll-like receptor 4,induce
R733 T623 T624 themeOf expression,induce

DLUT931

Id Subject Object Predicate Lexical cue
T572 21-29 Protein denotes SerpinB2
T573 49-69 Protein denotes toll-like receptor 4
T574 71-75 Protein denotes TLR4
T575 278-286 Protein denotes SerpinB2
T576 163-171 Protein denotes SerpinB2
T590 30-40 Gene_expression denotes expression
T591 14-20 Positive_regulation denotes induce
R685 T572 T590 themeOf SerpinB2,expression
R686 T573 T591 causeOf toll-like receptor 4,induce
R693 T590 T591 themeOf expression,induce

bionlp-st-ge-2016-test-ihmc

Id Subject Object Predicate Lexical cue
T760 108-136 Localization denotes 24 hrs in murine macrophages
T759 21-40 Gene_expression denotes SerpinB2 expression
T753 278-286 Protein denotes SerpinB2
T748 21-29 Protein denotes SerpinB2
T714 45-76 Protein denotes the toll-like receptor 4 (TLR4)
T715 71-75 Protein denotes TLR4
T719 108-136 Protein denotes 24 hrs in murine macrophages
T720 163-171 Protein denotes SerpinB2
T722 375-378 Entity denotes DNA
T724 118-136 Entity denotes murine macrophages
T726 326-344 Entity denotes murine macrophages
T729 145-189 Entity denotes the LPS-regulated SerpinB2 promoter regions,
T741 149-162 Entity denotes LPS-regulated
T743 264-291 Protein denotes of the murine SerpinB2 gene
R348 T748 T759 themeOf SerpinB2,SerpinB2 expression
R721 T719 T760 themeOf 24 hrs in murine macrophages,24 hrs in murine macrophages
R723 T724 T760 locationOf murine macrophages,24 hrs in murine macrophages

bionlp-st-ge-2016-test-tees

Id Subject Object Predicate Lexical cue
T649 271-291 Protein denotes murine SerpinB2 gene
T648 163-180 Protein denotes SerpinB2 promoter
T647 14-20 Positive_regulation denotes induce
T646 30-40 Gene_expression denotes expression
T645 21-29 Protein denotes SerpinB2
R324 T645 T646 themeOf SerpinB2,expression
R325 T646 T647 themeOf expression,induce

testone

Id Subject Object Predicate Lexical cue
T40 30-40 Gene_expression denotes expression
T39 14-20 Positive_regulation denotes induce
T29 278-286 Protein denotes SerpinB2
T28 163-171 Protein denotes SerpinB2
T27 71-75 Protein denotes TLR4
T26 49-69 Protein denotes toll-like receptor 4
T25 21-29 Protein denotes SerpinB2
R3 T27 T26 equivalentTo TLR4,toll-like receptor 4
R8 T40 T39 themeOf expression,induce
R2 T25 T40 themeOf SerpinB2,expression

test3

Id Subject Object Predicate Lexical cue
T80 278-286 Protein denotes SerpinB2
T79 163-171 Protein denotes SerpinB2
T78 71-75 Protein denotes TLR4
T77 49-69 Protein denotes toll-like receptor 4
T76 30-40 Gene_expression denotes expression
T75 21-29 Protein denotes SerpinB2
T74 14-20 Positive_regulation denotes induce
T58 278-286 Protein denotes SerpinB2
T57 163-171 Protein denotes SerpinB2
T56 71-75 Protein denotes TLR4
T55 49-69 Protein denotes toll-like receptor 4
T54 21-29 Protein denotes SerpinB2
R17 T75 T76 themeOf SerpinB2,expression
R18 T76 T74 themeOf expression,induce
R19 T78 T77 equivalentTo TLR4,toll-like receptor 4