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PMC:3589482 / 18126-18620 JSONTXT

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bionlp-st-ge-2016-spacy-parsed

Id Subject Object Predicate Lexical cue
T22652 493-494 . denotes .
T22651 486-493 NN denotes control
T22650 478-485 VBG denotes loading
T22649 476-477 DT denotes a
T22648 473-475 IN denotes as
T22647 467-472 NNP denotes GAPDH
T22646 463-466 IN denotes for
T22645 454-462 VBN denotes reprobed
T22644 450-453 VBD denotes was
T22643 445-449 NNP denotes Blot
T22642 443-444 . denotes .
T22641 436-443 VBZ denotes lysates
T22640 431-435 NN denotes cell
T22639 425-430 JJ denotes whole
T22638 422-424 IN denotes in
T22637 411-421 NN denotes expression
T22636 403-410 NN denotes protein
T22635 394-402 CD denotes SerpinB2
T22634 391-393 IN denotes of
T22633 382-390 NN denotes analysis
T22632 371-381 NNP denotes Immunoblot
T22631 369-370 -RRB- denotes )
T22630 368-369 NNP denotes B
T22629 367-368 -LRB- denotes (
T22628 365-366 . denotes .
T22627 355-365 NN denotes triplicate
T22626 352-354 IN denotes in
T22625 342-351 VBN denotes performed
T22624 330-341 NNS denotes experiments
T22623 318-329 JJ denotes independent
T22622 314-317 CD denotes two
T22621 308-313 JJS denotes least
T22596 189-192 CD denotes 100
T22595 184-188 IN denotes with
T22594 178-183 NNS denotes times
T22593 168-177 JJ denotes indicated
T22592 164-167 DT denotes the
T22591 160-163 IN denotes for
T22590 152-159 VBN denotes treated
T22589 147-151 VBD denotes were
T22588 135-146 NNS denotes macrophages
T22587 132-134 CD denotes .7
T22586 126-132 CD denotes RAW264
T22585 124-125 . denotes .
T22584 119-124 NNS denotes cells
T22583 108-118 NN denotes macrophage
T22582 101-107 JJ denotes murine
T22581 98-100 IN denotes in
T22580 87-97 NN denotes expression
T22579 79-86 NN denotes protein
T22578 75-78 CC denotes and
T22577 70-74 NNP denotes mRNA
T22576 61-69 NNP denotes SerpinB2
T22575 58-60 IN denotes of
T22574 48-57 NN denotes induction
T22573 44-47 NNP denotes LPS
T22620 305-307 IN denotes at
T22619 302-304 IN denotes of
T22618 287-301 NN denotes representative
T22617 284-286 VBZ denotes is
T22616 279-283 NN denotes plot
T22615 275-278 DT denotes The
T22614 273-274 . denotes .
T22613 266-273 VB denotes β-actin
T22612 263-265 TO denotes to
T22611 254-262 JJ denotes relative
T22610 252-253 , denotes ,
T22609 246-252 NNS denotes levels
T22608 241-245 NNP denotes mRNA
T22607 232-240 NNP denotes SerpinB2
T22606 225-231 JJ denotes murine
T22605 222-224 IN denotes of
T22604 213-221 NN denotes analysis
T22603 208-212 NNP denotes qPCR
T22602 206-207 -RRB- denotes )
T22601 205-206 NNP denotes A
T22600 204-205 -LRB- denotes (
T22599 202-203 . denotes .
T22598 199-202 NNP denotes LPS
T22597 193-198 JJ denotes ng/ml
R16266 T22573 T22574 compound LPS,induction
R16267 T22574 T22580 nmod induction,expression
R16268 T22575 T22574 prep of,induction
R16269 T22576 T22577 compound SerpinB2,mRNA
R16270 T22577 T22575 pobj mRNA,of
R16271 T22578 T22577 cc and,mRNA
R16272 T22579 T22580 compound protein,expression
R16273 T22580 T22580 ROOT expression,expression
R16274 T22581 T22580 prep in,expression
R16275 T22582 T22584 amod murine,cells
R16276 T22583 T22584 compound macrophage,cells
R16277 T22584 T22581 pobj cells,in
R16278 T22585 T22580 punct .,expression
R16279 T22586 T22588 nummod RAW264,macrophages
R16280 T22587 T22588 nummod .7,macrophages
R16281 T22588 T22590 nsubjpass macrophages,treated
R16282 T22589 T22590 auxpass were,treated
R16283 T22590 T22590 ROOT treated,treated
R16284 T22591 T22590 prep for,treated
R16285 T22592 T22594 det the,times
R16286 T22593 T22594 amod indicated,times
R16287 T22594 T22591 pobj times,for
R16288 T22595 T22590 prep with,treated
R16289 T22596 T22598 nummod 100,LPS
R16290 T22597 T22598 amod ng/ml,LPS
R16291 T22598 T22595 pobj LPS,with
R16292 T22599 T22590 punct .,treated
R16293 T22600 T22604 punct (,analysis
R16294 T22601 T22604 det A,analysis
R16295 T22602 T22603 punct ),qPCR
R16296 T22603 T22604 compound qPCR,analysis
R16297 T22604 T22604 ROOT analysis,analysis
R16298 T22605 T22604 prep of,analysis
R16299 T22606 T22609 amod murine,levels
R16300 T22607 T22608 compound SerpinB2,mRNA
R16301 T22608 T22609 compound mRNA,levels
R16302 T22609 T22605 pobj levels,of
R16303 T22610 T22604 punct ",",analysis
R16304 T22611 T22604 amod relative,analysis
R16305 T22612 T22611 prep to,relative
R16306 T22613 T22612 pobj β-actin,to
R16307 T22614 T22604 punct .,analysis
R16308 T22615 T22616 det The,plot
R16309 T22616 T22617 nsubj plot,is
R16310 T22617 T22617 ROOT is,is
R16311 T22618 T22617 attr representative,is
R16312 T22619 T22618 prep of,representative
R16313 T22620 T22621 advmod at,least
R16314 T22621 T22622 advmod least,two
R16315 T22622 T22624 nummod two,experiments
R16316 T22623 T22624 amod independent,experiments
R16317 T22624 T22619 pobj experiments,of
R16318 T22625 T22624 acl performed,experiments
R16319 T22626 T22625 prep in,performed
R16320 T22627 T22626 pobj triplicate,in
R16321 T22628 T22617 punct .,is
R16322 T22629 T22633 punct (,analysis
R16323 T22630 T22633 nmod B,analysis
R16324 T22631 T22630 punct ),B
R16325 T22632 T22633 compound Immunoblot,analysis
R16326 T22633 T22641 nsubj analysis,lysates
R16327 T22634 T22633 prep of,analysis
R16328 T22635 T22637 nummod SerpinB2,expression
R16329 T22636 T22637 compound protein,expression
R16330 T22637 T22634 pobj expression,of
R16331 T22638 T22637 prep in,expression
R16332 T22639 T22640 amod whole,cell
R16333 T22640 T22641 compound cell,lysates
R16334 T22641 T22641 ROOT lysates,lysates
R16335 T22642 T22641 punct .,lysates
R16336 T22643 T22645 nsubjpass Blot,reprobed
R16337 T22644 T22645 auxpass was,reprobed
R16338 T22645 T22645 ROOT reprobed,reprobed
R16339 T22646 T22645 prep for,reprobed
R16340 T22647 T22646 pobj GAPDH,for
R16341 T22648 T22645 prep as,reprobed
R16342 T22649 T22651 det a,control
R16343 T22650 T22651 compound loading,control
R16344 T22651 T22648 pobj control,as
R16345 T22652 T22645 punct .,reprobed

pmc-enju-pas

Id Subject Object Predicate Lexical cue
T22492 486-493 NN denotes control
T22491 478-485 NN denotes loading
T22490 476-477 DT denotes a
T22489 473-475 IN denotes as
T22488 467-472 NN denotes GAPDH
T22487 463-466 IN denotes for
T22486 454-462 VB denotes reprobed
T22485 450-453 VB denotes was
T22484 445-449 NN denotes Blot
T22483 436-443 NN denotes lysates
T22482 431-435 NN denotes cell
T22481 425-430 JJ denotes whole
T22480 422-424 IN denotes in
T22479 411-421 NN denotes expression
T22478 403-410 NN denotes protein
T22477 394-402 NN denotes SerpinB2
T22476 391-393 IN denotes of
T22475 382-390 NN denotes analysis
T22474 371-381 NN denotes Immunoblot
T22473 369-370 -RRB- denotes )
T22472 368-369 NN denotes B
T22471 367-368 -LRB- denotes (
T22470 355-366 FW denotes triplicate.
T22469 352-354 IN denotes in
T22468 342-351 VB denotes performed
T22467 330-341 NN denotes experiments
T22466 318-329 JJ denotes independent
T22465 314-317 CD denotes two
T22464 308-313 JJ denotes least
T22463 305-307 IN denotes at
T22462 302-304 IN denotes of
T22461 287-301 JJ denotes representative
T22460 284-286 VB denotes is
T22459 279-283 NN denotes plot
T22458 275-278 DT denotes The
T22457 266-273 NN denotes β-actin
T22456 263-265 TO denotes to
T22455 254-262 JJ denotes relative
T22454 252-253 -COMMA- denotes ,
T22453 246-252 NN denotes levels
T22452 241-245 NN denotes mRNA
T22451 232-240 NN denotes SerpinB2
T22450 225-231 JJ denotes murine
T22449 222-224 IN denotes of
T22448 213-221 NN denotes analysis
T22447 208-212 NN denotes qPCR
T22446 206-207 -RRB- denotes )
T22445 205-206 NN denotes A
T22444 204-205 -LRB- denotes (
T22443 199-203 NN denotes LPS.
T22442 193-198 NN denotes ng/ml
T22441 189-192 CD denotes 100
T22440 184-188 IN denotes with
T22439 178-183 NN denotes times
T22438 168-177 VB denotes indicated
T22437 164-167 DT denotes the
T22436 160-163 IN denotes for
T22435 152-159 VB denotes treated
T22434 147-151 VB denotes were
T22433 135-146 NN denotes macrophages
T22432 126-134 NN denotes RAW264.7
T22431 119-124 NN denotes cells
T22430 108-118 NN denotes macrophage
T22429 101-107 JJ denotes murine
T22428 98-100 IN denotes in
T22427 87-97 NN denotes expression
T22426 79-86 NN denotes protein
T22425 75-78 CC denotes and
T22424 70-74 NN denotes mRNA
T22423 61-69 NN denotes SerpinB2
T22422 58-60 IN denotes of
T22421 48-57 NN denotes induction
T22420 44-47 NN denotes LPS
R16169 T22421 T22420 arg1Of induction,LPS
R16170 T22421 T22422 arg1Of induction,of
R16171 T22421 T22428 arg1Of induction,in
R16172 T22424 T22423 arg1Of mRNA,SerpinB2
R16173 T22424 T22425 arg1Of mRNA,and
R16174 T22425 T22422 arg2Of and,of
R16175 T22427 T22425 arg2Of expression,and
R16176 T22427 T22426 arg1Of expression,protein
R16177 T22431 T22428 arg2Of cells,in
R16178 T22431 T22429 arg1Of cells,murine
R16179 T22431 T22430 arg1Of cells,macrophage
R16180 T22433 T22432 arg1Of macrophages,RAW264.7
R16181 T22433 T22434 arg1Of macrophages,were
R16182 T22433 T22435 arg2Of macrophages,treated
R16183 T22435 T22434 arg2Of treated,were
R16184 T22435 T22436 arg1Of treated,for
R16185 T22438 T22439 arg1Of indicated,times
R16186 T22439 T22440 arg1Of times,with
R16187 T22441 T22442 arg1Of 100,ng/ml
R16188 T22443 T22440 arg2Of LPS.,with
R16189 T22443 T22441 arg1Of LPS.,100
R16190 T22443 T22444 arg1Of LPS.,(
R16191 T22445 T22444 arg2Of A,(
R16192 T22446 T22444 arg3Of ),(
R16193 T22448 T22436 arg2Of analysis,for
R16194 T22448 T22437 arg1Of analysis,the
R16195 T22448 T22438 arg2Of analysis,indicated
R16196 T22448 T22447 arg1Of analysis,qPCR
R16197 T22448 T22449 arg1Of analysis,of
R16198 T22453 T22449 arg2Of levels,of
R16199 T22453 T22450 arg1Of levels,murine
R16200 T22453 T22451 arg1Of levels,SerpinB2
R16201 T22453 T22452 arg1Of levels,mRNA
R16202 T22453 T22454 arg1Of levels,","
R16203 T22453 T22455 arg1Of levels,relative
R16204 T22455 T22456 arg1Of relative,to
R16205 T22457 T22456 arg2Of β-actin,to
R16206 T22459 T22458 arg1Of plot,The
R16207 T22459 T22460 arg1Of plot,is
R16208 T22459 T22461 arg1Of plot,representative
R16209 T22461 T22460 arg2Of representative,is
R16210 T22461 T22462 arg1Of representative,of
R16211 T22465 T22463 arg1Of two,at
R16212 T22465 T22464 arg1Of two,least
R16213 T22467 T22462 arg2Of experiments,of
R16214 T22467 T22465 arg1Of experiments,two
R16215 T22467 T22466 arg1Of experiments,independent
R16216 T22467 T22468 arg2Of experiments,performed
R16217 T22468 T22469 arg1Of performed,in
R16218 T22472 T22471 arg2Of B,(
R16219 T22473 T22471 arg3Of ),(
R16220 T22475 T22469 arg2Of analysis,in
R16221 T22475 T22470 arg1Of analysis,triplicate.
R16222 T22475 T22471 arg1Of analysis,(
R16223 T22475 T22474 arg1Of analysis,Immunoblot
R16224 T22475 T22476 arg1Of analysis,of
R16225 T22479 T22476 arg2Of expression,of
R16226 T22479 T22477 arg1Of expression,SerpinB2
R16227 T22479 T22478 arg1Of expression,protein
R16228 T22479 T22480 arg1Of expression,in
R16229 T22483 T22480 arg2Of lysates,in
R16230 T22483 T22481 arg1Of lysates,whole
R16231 T22483 T22482 arg1Of lysates,cell
R16232 T22484 T22485 arg1Of Blot,was
R16233 T22484 T22486 arg2Of Blot,reprobed
R16234 T22486 T22485 arg2Of reprobed,was
R16235 T22486 T22487 arg1Of reprobed,for
R16236 T22486 T22489 arg1Of reprobed,as
R16237 T22488 T22487 arg2Of GAPDH,for
R16238 T22492 T22489 arg2Of control,as
R16239 T22492 T22490 arg1Of control,a
R16240 T22492 T22491 arg1Of control,loading

bionlp-st-ge-2016-test-proteins

Id Subject Object Predicate Lexical cue
T22412 467-472 Protein denotes GAPDH
T22411 394-402 Protein denotes SerpinB2
T22410 266-273 Protein denotes β-actin
T22409 232-240 Protein denotes SerpinB2
T22408 61-69 Protein denotes SerpinB2

bionlp-st-ge-2016-uniprot

Id Subject Object Predicate Lexical cue
T22511 467-472 http://www.uniprot.org/uniprot/P04406 denotes GAPDH
T22510 266-273 http://www.uniprot.org/uniprot/P60709 denotes β-actin
T22509 394-402 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2
T22508 232-240 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2
T22507 61-69 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2

GO-CC

Id Subject Object Predicate Lexical cue
T22414 431-435 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T22413 119-124 http://purl.obolibrary.org/obo/GO_0005623 denotes cells

sentences

Id Subject Object Predicate Lexical cue
T22399 445-494 Sentence denotes Blot was reprobed for GAPDH as a loading control.
T22398 275-444 Sentence denotes The plot is representative of at least two independent experiments performed in triplicate. (B) Immunoblot analysis of SerpinB2 protein expression in whole cell lysates.
T22397 126-274 Sentence denotes RAW264.7 macrophages were treated for the indicated times with 100 ng/ml LPS. (A) qPCR analysis of murine SerpinB2 mRNA levels, relative to β-actin.
T22396 44-125 Sentence denotes LPS induction of SerpinB2 mRNA and protein expression in murine macrophage cells.
T118 0-125 Sentence denotes 10.1371/journal.pone.0057855.g001 Figure 1 LPS induction of SerpinB2 mRNA and protein expression in murine macrophage cells.
T119 126-274 Sentence denotes RAW264.7 macrophages were treated for the indicated times with 100 ng/ml LPS. (A) qPCR analysis of murine SerpinB2 mRNA levels, relative to β-actin.
T120 275-444 Sentence denotes The plot is representative of at least two independent experiments performed in triplicate. (B) Immunoblot analysis of SerpinB2 protein expression in whole cell lysates.
T121 445-494 Sentence denotes Blot was reprobed for GAPDH as a loading control.

simple1

Id Subject Object Predicate Lexical cue
T22419 467-472 Protein denotes GAPDH
T22418 394-402 Protein denotes SerpinB2
T22417 266-273 Protein denotes β-actin
T22416 232-240 Protein denotes SerpinB2
T22415 61-69 Protein denotes SerpinB2

BioNLP16_DUT

Id Subject Object Predicate Lexical cue
T22506 411-421 Gene_expression denotes expression
T22505 246-252 Transcription denotes levels
T22504 87-97 Gene_expression denotes expression
T22503 48-57 Positive_regulation denotes induction
T22502 467-472 Protein denotes GAPDH
T22501 394-402 Protein denotes SerpinB2
T22500 266-273 Protein denotes β-actin
T22499 232-240 Protein denotes SerpinB2
T22498 61-69 Protein denotes SerpinB2
R16241 T22498 T22503 themeOf SerpinB2,induction
R16242 T22498 T22504 themeOf SerpinB2,expression
R16243 T22499 T22505 themeOf SerpinB2,levels
R16244 T22501 T22506 themeOf SerpinB2,expression
R16245 T22504 T22503 themeOf expression,induction

BioNLP16_Messiy

Id Subject Object Predicate Lexical cue
T22534 411-421 Gene_expression denotes expression
T22533 48-57 Positive_regulation denotes induction
T22532 87-97 Gene_expression denotes expression
T22531 467-472 Protein denotes GAPDH
T22530 394-402 Protein denotes SerpinB2
T22529 266-273 Protein denotes β-actin
T22528 232-240 Protein denotes SerpinB2
T22527 61-69 Protein denotes SerpinB2
R16252 T22527 T22533 themeOf SerpinB2,induction
R16253 T22527 T22532 themeOf SerpinB2,expression
R16254 T22530 T22534 themeOf SerpinB2,expression
R16255 T22532 T22533 themeOf expression,induction

DLUT931

Id Subject Object Predicate Lexical cue
T22519 411-421 Gene_expression denotes expression
T22518 87-97 Gene_expression denotes expression
T22517 48-57 Positive_regulation denotes induction
T22516 467-472 Protein denotes GAPDH
T22515 394-402 Protein denotes SerpinB2
T22514 266-273 Protein denotes β-actin
T22513 232-240 Protein denotes SerpinB2
T22512 61-69 Protein denotes SerpinB2
R16246 T22512 T22517 themeOf SerpinB2,induction
R16247 T22512 T22518 themeOf SerpinB2,expression
R16248 T22515 T22519 themeOf SerpinB2,expression
R16249 T22518 T22517 themeOf expression,induction

bionlp-st-ge-2016-test-ihmc

Id Subject Object Predicate Lexical cue
T22572 79-97 Gene_expression denotes protein expression
T22571 382-443 Gene_expression denotes analysis of SerpinB2 protein expression in whole cell lysates
T22570 476-493 Regulation denotes a loading control
T22569 61-74 Protein denotes SerpinB2 mRNA
T22568 108-118 Entity denotes macrophage
T22567 126-146 Entity denotes RAW264.7 macrophages
T22566 208-212 Protein denotes qPCR
T22565 193-202 Entity denotes ng/ml LPS
T22564 101-124 Entity denotes murine macrophage cells
T22563 467-472 Protein denotes GAPDH
T22562 241-245 Protein denotes mRNA
T22561 222-253 Protein denotes of murine SerpinB2 mRNA levels,
T22560 394-402 Protein denotes SerpinB2
T22559 44-47 Entity denotes LPS
T22558 79-86 Protein denotes protein
T22557 266-273 Protein denotes β-actin
T22556 61-69 Protein denotes SerpinB2
T22555 394-410 Protein denotes SerpinB2 protein
R16264 T22555 T22571 themeOf SerpinB2 protein,analysis of SerpinB2 protein expression in whole cell lysates
R16265 T22558 T22572 themeOf protein,protein expression

bionlp-st-ge-2016-test-tees

Id Subject Object Predicate Lexical cue
T22544 467-472 Protein denotes GAPDH
T22543 445-449 Protein denotes Blot
T22542 411-421 Gene_expression denotes expression
T22541 394-410 Protein denotes SerpinB2 protein
T22540 266-273 Protein denotes β-actin
T22539 232-245 Protein denotes SerpinB2 mRNA
T22538 48-57 Positive_regulation denotes induction
T22537 87-97 Gene_expression denotes expression
T22536 48-57 Positive_regulation denotes induction
T22535 61-74 Protein denotes SerpinB2 mRNA
R16256 T22535 T22536 themeOf SerpinB2 mRNA,induction
R16257 T22535 T22537 themeOf SerpinB2 mRNA,expression
R16258 T22537 T22538 themeOf expression,induction
R16259 T22541 T22542 themeOf SerpinB2 protein,expression

testone

Id Subject Object Predicate Lexical cue
T22382 411-421 Gene_expression denotes expression
T22381 87-97 Gene_expression denotes expression
T22380 48-57 Positive_regulation denotes induction
T22379 467-472 Protein denotes GAPDH
T22378 394-402 Protein denotes SerpinB2
T22377 266-273 Protein denotes β-actin
T22376 232-240 Protein denotes SerpinB2
T22375 61-69 Protein denotes SerpinB2
R16160 T22375 T22380 themeOf SerpinB2,induction
R16161 T22378 T22382 themeOf SerpinB2,expression
R16162 T22381 T22380 themeOf expression,induction

test3

Id Subject Object Predicate Lexical cue
T22395 467-472 Protein denotes GAPDH
T22394 411-421 Gene_expression denotes expression
T22393 394-402 Protein denotes SerpinB2
T22392 266-273 Protein denotes β-actin
T22391 232-240 Protein denotes SerpinB2
T22390 87-97 Gene_expression denotes expression
T22389 61-69 Protein denotes SerpinB2
T22388 48-57 Positive_regulation denotes induction
T22387 467-472 Protein denotes GAPDH
T22386 394-402 Protein denotes SerpinB2
T22385 266-273 Protein denotes β-actin
T22384 232-240 Protein denotes SerpinB2
T22383 61-69 Protein denotes SerpinB2
R16163 T22389 T22390 themeOf SerpinB2,expression
R16164 T22390 T22388 themeOf expression,induction
R16165 T22393 T22394 themeOf SerpinB2,expression