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PMC:3589482 / 28792-29545 JSONTXT

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bionlp-st-ge-2016-spacy-parsed

Id Subject Object Predicate Lexical cue
T24494 751-752 . denotes .
T24493 742-751 NN denotes arrowhead
T24492 739-741 DT denotes an
T24491 734-738 IN denotes with
T24490 724-733 VBN denotes indicated
T24489 721-723 VBZ denotes is
T24488 713-720 NN denotes complex
T24487 699-712 JJ denotes LPS-inducible
T24486 695-698 DT denotes The
T24485 693-694 . denotes .
T24484 685-693 NN denotes antibody
T24483 679-684 NNP denotes C/EBP
T24482 670-678 JJ denotes specific
T24481 660-669 VBN denotes indicated
T24480 656-659 DT denotes the
T24479 651-655 IN denotes with
T24478 637-650 NN denotes preincubation
T24477 631-636 IN denotes after
T24476 628-630 IN denotes by
T24475 622-627 NN denotes probe
T24474 618-621 CD denotes 185
T24473 617-618 NN denotes −
T24472 616-617 CD denotes /
T24471 613-616 CD denotes 212
T24470 612-613 NN denotes −
T24469 608-611 DT denotes the
T24468 603-607 IN denotes with
T24467 593-602 VBN denotes performed
T24466 588-592 VBD denotes were
T24465 581-587 NNS denotes assays
T24464 570-580 NNP denotes Supershift
T24463 568-569 -RRB- denotes )
T24462 567-568 NNP denotes C
T24461 566-567 -LRB- denotes (
T24460 564-565 . denotes .
T24459 555-564 NNS denotes complexes
T24458 543-554 JJ denotes DNA-protein
T24452 506-507 -RRB- denotes )
T24451 505-506 NNP denotes A
T24450 504-505 -LRB- denotes (
T24449 501-503 IN denotes in
T24448 491-500 VBN denotes described
T24447 474-490 NNS denotes oligonucleotides
T24446 465-473 VBD denotes stranded
T24445 458-464 JJ denotes double
T24444 454-457 DT denotes the
T24443 451-453 IN denotes of
T24442 446-450 DT denotes each
T24441 443-445 IN denotes of
T24440 436-442 NN denotes excess
T24439 430-435 NN denotes molar
T24438 421-429 JJ denotes 100-fold
T24437 419-420 DT denotes a
T24436 415-418 CC denotes and
T24435 409-414 NN denotes probe
T24434 405-408 CD denotes 185
T24433 404-405 NN denotes −
T24432 403-404 CD denotes /
T24431 400-403 CD denotes 212
T24430 399-400 NN denotes −
T24429 390-398 NN denotes promoter
T24428 381-389 NNP denotes SerpinB2
T24427 374-380 NN denotes murine
T24426 360-373 VBN denotes radiolabelled
T24425 356-359 DT denotes the
T24424 351-355 IN denotes with
T24423 341-350 VBN denotes performed
T24422 335-340 NNS denotes EMSAs
T24421 323-334 NN denotes competition
T24420 318-322 NNP denotes Cold
T24419 316-317 -RRB- denotes )
T24418 315-316 NNP denotes B
T24417 314-315 -LRB- denotes (
T24416 312-313 . denotes .
T24415 307-312 NN denotes probe
T24414 305-306 -RRB- denotes )
T24413 300-305 NNP denotes C/EBP
T24412 292-299 NN denotes albumin
T24411 288-291 NN denotes rat
T24410 287-288 -LRB- denotes (
T24409 281-286 NNP denotes C/EBP
T24408 274-280 NN denotes region
T24407 270-273 NNP denotes DEI
T24406 261-269 NN denotes promoter
T24405 253-260 NN denotes albumin
T24404 249-252 NN denotes rat
T24403 245-248 DT denotes the
T24402 240-244 IN denotes with
T24401 237-239 CC denotes or
T24400 232-236 NN denotes site
T24399 226-231 NNP denotes C/EBP
T24398 224-225 -RRB- denotes )
T24397 219-224 NNP denotes C/EBP
T24396 212-218 JJ denotes mutant
T24395 211-212 -LRB- denotes (
T24394 203-210 VBN denotes mutated
T24393 200-202 CC denotes or
T24392 198-199 -RRB- denotes )
T24391 193-198 NNP denotes C/EBP
T24390 184-192 CD denotes SerpinB2
T24389 183-184 -LRB- denotes (
T24388 176-182 JJ denotes intact
T24387 173-175 DT denotes an
T24386 162-172 VBG denotes containing
T24385 156-161 NN denotes probe
T24384 152-155 CD denotes 185
T24383 151-152 NN denotes −
T24382 150-151 CD denotes /
T24381 147-150 CD denotes 212
T24380 146-147 NN denotes −
T24379 137-145 NN denotes promoter
T24378 128-136 NNP denotes SerpinB2
T24377 121-127 NN denotes murine
T24376 117-120 DT denotes the
T24375 110-116 CC denotes either
T24374 105-109 IN denotes with
T24373 95-104 VBN denotes incubated
T24372 89-94 NNS denotes cells
T24371 83-88 CD denotes 264.7
T24370 79-82 NNP denotes RAW
T24369 77-78 -RRB- denotes )
T24368 74-77 NNP denotes LPS
T24367 73-74 -LRB- denotes (
T24366 65-72 VBD denotes treated
T24365 61-64 NNP denotes LPS
T24364 58-60 NN denotes hr
T24363 55-57 CD denotes 10
T24362 51-54 CC denotes and
T24361 49-50 -RRB- denotes )
T24360 47-49 NNP denotes UN
T24359 46-47 -LRB- denotes (
T24358 36-45 JJ denotes untreated
T24357 31-35 IN denotes from
T24356 22-30 NNS denotes extracts
T24355 14-21 JJ denotes nuclear
T24354 9-13 IN denotes with
T24353 4-8 NNP denotes EMSA
T24352 2-3 -RRB- denotes )
T24351 1-2 NNP denotes A
T24350 0-1 -LRB- denotes (
T24457 539-542 DT denotes the
T24456 536-538 IN denotes of
T24455 524-535 NN denotes specificity
T24454 520-523 DT denotes the
T24453 508-519 VBP denotes demonstrate
R17446 T24350 T24353 punct (,EMSA
R17447 T24351 T24353 nmod A,EMSA
R17448 T24352 T24353 punct ),EMSA
R17449 T24353 T24366 nsubj EMSA,treated
R17450 T24354 T24353 prep with,EMSA
R17451 T24355 T24356 amod nuclear,extracts
R17452 T24356 T24354 pobj extracts,with
R17453 T24357 T24356 prep from,extracts
R17454 T24358 T24360 amod untreated,UN
R17455 T24359 T24360 punct (,UN
R17456 T24360 T24357 pobj UN,from
R17457 T24361 T24360 punct ),UN
R17458 T24362 T24360 cc and,UN
R17459 T24363 T24365 nummod 10,LPS
R17460 T24364 T24365 compound hr,LPS
R17461 T24365 T24360 conj LPS,UN
R17462 T24366 T24366 ROOT treated,treated
R17463 T24367 T24370 punct (,RAW
R17464 T24368 T24370 nmod LPS,RAW
R17465 T24369 T24370 punct ),RAW
R17466 T24370 T24372 nmod RAW,cells
R17467 T24371 T24370 nummod 264.7,RAW
R17468 T24372 T24366 dobj cells,treated
R17469 T24373 T24372 acl incubated,cells
R17470 T24374 T24373 prep with,incubated
R17471 T24375 T24385 preconj either,probe
R17472 T24376 T24385 det the,probe
R17473 T24377 T24385 nmod murine,probe
R17474 T24378 T24379 compound SerpinB2,promoter
R17475 T24379 T24385 nmod promoter,probe
R17476 T24380 T24385 nmod −,probe
R17477 T24381 T24385 nummod 212,probe
R17478 T24382 T24385 nummod /,probe
R17479 T24383 T24385 nmod −,probe
R17480 T24384 T24385 nummod 185,probe
R17481 T24385 T24374 pobj probe,with
R17482 T24386 T24385 acl containing,probe
R17483 T24387 T24400 det an,site
R17484 T24388 T24400 amod intact,site
R17485 T24389 T24391 punct (,C/EBP
R17486 T24390 T24391 nummod SerpinB2,C/EBP
R17487 T24391 T24388 appos C/EBP,intact
R17488 T24392 T24391 punct ),C/EBP
R17489 T24393 T24388 cc or,intact
R17490 T24394 T24388 conj mutated,intact
R17491 T24395 T24397 punct (,C/EBP
R17492 T24396 T24397 amod mutant,C/EBP
R17493 T24397 T24400 meta C/EBP,site
R17494 T24398 T24397 punct ),C/EBP
R17495 T24399 T24400 compound C/EBP,site
R17496 T24400 T24386 dobj site,containing
R17497 T24401 T24374 cc or,with
R17498 T24402 T24374 conj with,with
R17499 T24403 T24404 det the,rat
R17500 T24404 T24415 nsubj rat,probe
R17501 T24405 T24409 compound albumin,C/EBP
R17502 T24406 T24409 compound promoter,C/EBP
R17503 T24407 T24408 compound DEI,region
R17504 T24408 T24409 compound region,C/EBP
R17505 T24409 T24415 punct C/EBP,probe
R17506 T24410 T24412 punct (,albumin
R17507 T24411 T24412 compound rat,albumin
R17508 T24412 T24409 parataxis albumin,C/EBP
R17509 T24413 T24415 compound C/EBP,probe
R17510 T24414 T24415 punct ),probe
R17511 T24415 T24402 pobj probe,with
R17512 T24416 T24366 punct .,treated
R17513 T24417 T24417 ROOT (,(
R17514 T24418 T24417 dep B,(
R17515 T24419 T24418 punct ),B
R17516 T24420 T24422 compound Cold,EMSAs
R17517 T24421 T24422 compound competition,EMSAs
R17518 T24422 T24448 nsubj EMSAs,described
R17519 T24423 T24422 acl performed,EMSAs
R17520 T24424 T24423 prep with,performed
R17521 T24425 T24447 det the,oligonucleotides
R17522 T24426 T24427 amod radiolabelled,murine
R17523 T24427 T24447 nmod murine,oligonucleotides
R17524 T24428 T24429 compound SerpinB2,promoter
R17525 T24429 T24447 nmod promoter,oligonucleotides
R17526 T24430 T24447 nmod −,oligonucleotides
R17527 T24431 T24447 nummod 212,oligonucleotides
R17528 T24432 T24447 nummod /,oligonucleotides
R17529 T24433 T24446 npadvmod −,stranded
R17530 T24434 T24435 nummod 185,probe
R17531 T24435 T24433 appos probe,−
R17532 T24436 T24435 cc and,probe
R17533 T24437 T24440 det a,excess
R17534 T24438 T24440 amod 100-fold,excess
R17535 T24439 T24440 compound molar,excess
R17536 T24440 T24435 conj excess,probe
R17537 T24441 T24440 prep of,excess
R17538 T24442 T24441 pobj each,of
R17539 T24443 T24442 prep of,each
R17540 T24444 T24445 det the,double
R17541 T24445 T24443 pobj double,of
R17542 T24446 T24447 amod stranded,oligonucleotides
R17543 T24447 T24448 nsubj oligonucleotides,described
R17544 T24448 T24448 ROOT described,described
R17545 T24449 T24448 prep in,described
R17546 T24450 T24451 punct (,A
R17547 T24451 T24449 pobj A,in
R17548 T24452 T24448 punct ),described
R17549 T24453 T24453 ROOT demonstrate,demonstrate
R17550 T24454 T24455 det the,specificity
R17551 T24455 T24453 dobj specificity,demonstrate
R17552 T24456 T24455 prep of,specificity
R17553 T24457 T24459 det the,complexes
R17554 T24458 T24459 amod DNA-protein,complexes
R17555 T24459 T24456 pobj complexes,of
R17556 T24460 T24453 punct .,demonstrate
R17557 T24461 T24467 punct (,performed
R17558 T24462 T24465 nmod C,assays
R17559 T24463 T24462 punct ),C
R17560 T24464 T24465 compound Supershift,assays
R17561 T24465 T24467 nsubjpass assays,performed
R17562 T24466 T24467 auxpass were,performed
R17563 T24467 T24467 ROOT performed,performed
R17564 T24468 T24467 prep with,performed
R17565 T24469 T24470 det the,−
R17566 T24470 T24468 pobj −,with
R17567 T24471 T24473 nummod 212,−
R17568 T24472 T24473 nummod /,−
R17569 T24473 T24470 appos −,−
R17570 T24474 T24475 nummod 185,probe
R17571 T24475 T24473 appos probe,−
R17572 T24476 T24475 prep by,probe
R17573 T24477 T24475 prep after,probe
R17574 T24478 T24477 pobj preincubation,after
R17575 T24479 T24478 prep with,preincubation
R17576 T24480 T24484 det the,antibody
R17577 T24481 T24484 amod indicated,antibody
R17578 T24482 T24484 amod specific,antibody
R17579 T24483 T24484 compound C/EBP,antibody
R17580 T24484 T24479 pobj antibody,with
R17581 T24485 T24473 punct .,−
R17582 T24486 T24488 det The,complex
R17583 T24487 T24488 amod LPS-inducible,complex
R17584 T24488 T24490 nsubjpass complex,indicated
R17585 T24489 T24490 auxpass is,indicated
R17586 T24490 T24490 ROOT indicated,indicated
R17587 T24491 T24490 prep with,indicated
R17588 T24492 T24493 det an,arrowhead
R17589 T24493 T24491 pobj arrowhead,with
R17590 T24494 T24490 punct .,indicated

pmc-enju-pas

Id Subject Object Predicate Lexical cue
T24233 742-751 NN denotes arrowhead
T24232 739-741 DT denotes an
T24231 734-738 IN denotes with
T24230 724-733 VB denotes indicated
T24229 721-723 VB denotes is
T24228 713-720 NN denotes complex
T24227 699-712 JJ denotes LPS-inducible
T24226 695-698 DT denotes The
R17402 T24228 T24226 arg1Of complex,The
R17403 T24228 T24227 arg1Of complex,LPS-inducible
R17404 T24228 T24229 arg1Of complex,is
R17405 T24228 T24230 arg2Of complex,indicated
R17406 T24230 T24229 arg2Of indicated,is
R17407 T24230 T24231 arg1Of indicated,with
R17408 T24233 T24231 arg2Of arrowhead,with
R17409 T24233 T24232 arg1Of arrowhead,an

bionlp-st-ge-2016-test-proteins

Id Subject Object Predicate Lexical cue
T24195 381-389 Protein denotes SerpinB2
T24194 292-299 Protein denotes albumin
T24193 253-260 Protein denotes albumin
T24192 184-192 Protein denotes SerpinB2
T24191 128-136 Protein denotes SerpinB2

bionlp-st-ge-2016-uniprot

Id Subject Object Predicate Lexical cue
T24252 381-389 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2
T24251 184-192 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2
T24250 128-136 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2

GO-MF

Id Subject Object Predicate Lexical cue
T24197 685-693 http://purl.obolibrary.org/obo/GO_0003823 denotes antibody

GO-CC

Id Subject Object Predicate Lexical cue
T24204 685-693 http://purl.obolibrary.org/obo/GO_0042571 denotes antibody
T24203 685-693 http://purl.obolibrary.org/obo/GO_0019815 denotes antibody
T24202 547-564 http://purl.obolibrary.org/obo/GO_0043234 denotes protein complexes
T24201 543-564 http://purl.obolibrary.org/obo/GO_0097522 denotes DNA-protein complexes
T24200 543-564 http://purl.obolibrary.org/obo/GO_0032993 denotes DNA-protein complexes
T24199 543-564 http://purl.obolibrary.org/obo/GO_0001114 denotes DNA-protein complexes
T24198 89-94 http://purl.obolibrary.org/obo/GO_0005623 denotes cells

sentences

Id Subject Object Predicate Lexical cue
T24178 695-752 Sentence denotes The LPS-inducible complex is indicated with an arrowhead.
T24177 0-694 Sentence denotes (A) EMSA with nuclear extracts from untreated (UN) and 10 hr LPS treated (LPS) RAW 264.7 cells incubated with either the murine SerpinB2 promoter −212/−185 probe containing an intact (SerpinB2 C/EBP) or mutated (mutant C/EBP) C/EBP site or with the rat albumin promoter DEI region C/EBP (rat albumin C/EBP) probe. (B) Cold competition EMSAs performed with the radiolabelled murine SerpinB2 promoter −212/−185 probe and a 100-fold molar excess of each of the double stranded oligonucleotides described in (A) demonstrate the specificity of the DNA-protein complexes. (C) Supershift assays were performed with the −212/−185 probe by after preincubation with the indicated specific C/EBP antibody.
T179 0-694 Sentence denotes (A) EMSA with nuclear extracts from untreated (UN) and 10 hr LPS treated (LPS) RAW 264.7 cells incubated with either the murine SerpinB2 promoter −212/−185 probe containing an intact (SerpinB2 C/EBP) or mutated (mutant C/EBP) C/EBP site or with the rat albumin promoter DEI region C/EBP (rat albumin C/EBP) probe. (B) Cold competition EMSAs performed with the radiolabelled murine SerpinB2 promoter −212/−185 probe and a 100-fold molar excess of each of the double stranded oligonucleotides described in (A) demonstrate the specificity of the DNA-protein complexes. (C) Supershift assays were performed with the −212/−185 probe by after preincubation with the indicated specific C/EBP antibody.
T180 695-752 Sentence denotes The LPS-inducible complex is indicated with an arrowhead.

simple1

Id Subject Object Predicate Lexical cue
T24211 381-389 Protein denotes SerpinB2
T24210 292-299 Protein denotes albumin
T24209 253-260 Protein denotes albumin
T24208 184-192 Protein denotes SerpinB2
T24207 128-136 Protein denotes SerpinB2

BioNLP16_DUT

Id Subject Object Predicate Lexical cue
T24247 381-389 Protein denotes SerpinB2
T24246 292-299 Protein denotes albumin
T24245 253-260 Protein denotes albumin
T24244 184-192 Protein denotes SerpinB2
T24243 128-136 Protein denotes SerpinB2

BioNLP16_Messiy

Id Subject Object Predicate Lexical cue
T24275 381-389 Protein denotes SerpinB2
T24274 292-299 Protein denotes albumin
T24273 253-260 Protein denotes albumin
T24272 184-192 Protein denotes SerpinB2
T24271 128-136 Protein denotes SerpinB2

DLUT931

Id Subject Object Predicate Lexical cue
T24260 381-389 Protein denotes SerpinB2
T24259 292-299 Protein denotes albumin
T24258 253-260 Protein denotes albumin
T24257 184-192 Protein denotes SerpinB2
T24256 128-136 Protein denotes SerpinB2

bionlp-st-ge-2016-test-ihmc

Id Subject Object Predicate Lexical cue
T24332 184-192 Protein denotes SerpinB2
T24330 536-564 Entity denotes of the DNA-protein complexes
T24329 695-720 Entity denotes The LPS-inducible complex
T24328 226-236 Entity denotes C/EBP site
T24327 253-260 Protein denotes albumin
T24326 381-389 Protein denotes SerpinB2
T24325 55-72 Entity denotes 10 hr LPS treated
T24324 465-500 Entity denotes stranded oligonucleotides described
T24323 184-198 Protein denotes SerpinB2 C/EBP
T24321 679-684 Protein denotes C/EBP
T24320 292-299 Protein denotes albumin
T24319 288-305 Protein denotes rat albumin C/EBP
T24318 226-231 Protein denotes C/EBP
T24317 670-693 Protein denotes specific C/EBP antibody
T24315 245-306 Entity denotes the rat albumin promoter DEI region C/EBP (rat albumin C/EBP)
T24314 356-414 Entity denotes the radiolabelled murine SerpinB2 promoter −212/−185 probe
T24312 245-306 Protein denotes the rat albumin promoter DEI region C/EBP (rat albumin C/EBP)
T24311 212-224 Protein denotes mutant C/EBP
T24310 74-77 Entity denotes LPS
T24309 14-30 Entity denotes nuclear extracts
T24307 270-273 Protein denotes DEI

bionlp-st-ge-2016-test-tees

Id Subject Object Predicate Lexical cue
T24291 679-693 Protein denotes C/EBP antibody
T24290 95-104 Positive_regulation denotes incubated
T24289 162-172 Positive_regulation denotes containing
T24288 176-182 Positive_regulation denotes intact
T24287 95-104 Positive_regulation denotes incubated
T24286 95-104 Positive_regulation denotes incubated
T24285 95-104 Positive_regulation denotes incubated
T24284 288-305 Protein denotes rat albumin C/EBP
T24283 274-286 Protein denotes region C/EBP
T24282 249-269 Protein denotes rat albumin promoter
T24281 226-236 Protein denotes C/EBP site
T24280 184-198 Protein denotes SerpinB2 C/EBP
R17415 T24280 T24288 themeOf SerpinB2 C/EBP,intact
R17416 T24282 T24285 themeOf rat albumin promoter,incubated
R17417 T24283 T24286 themeOf region C/EBP,incubated
R17418 T24284 T24287 themeOf rat albumin C/EBP,incubated
R17419 T24288 T24289 themeOf intact,containing
R17420 T24289 T24290 themeOf containing,incubated

testone

Id Subject Object Predicate Lexical cue
T24158 381-389 Protein denotes SerpinB2
T24157 292-299 Protein denotes albumin
T24156 253-260 Protein denotes albumin
T24155 184-192 Protein denotes SerpinB2
T24154 128-136 Protein denotes SerpinB2

test3

Id Subject Object Predicate Lexical cue
T24175 381-389 Protein denotes SerpinB2
T24174 292-299 Protein denotes albumin
T24173 253-260 Protein denotes albumin
T24172 184-192 Protein denotes SerpinB2
T24171 128-136 Protein denotes SerpinB2
T24167 381-389 Protein denotes SerpinB2
T24166 292-299 Protein denotes albumin
T24165 253-260 Protein denotes albumin
T24164 184-192 Protein denotes SerpinB2
T24163 128-136 Protein denotes SerpinB2