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PMC:3589482 / 20015-20359 JSONTXT

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bionlp-st-ge-2016-spacy-parsed

Id Subject Object Predicate Lexical cue
T10330 343-344 . denotes .
T10329 341-343 CD denotes 87
T10328 340-341 NN denotes −
T10327 329-339 NN denotes nucleotide
T10326 326-328 IN denotes of
T10325 315-325 JJ denotes downstream
T10324 311-314 VBP denotes lie
T10323 306-310 RB denotes also
T10322 302-305 NNP denotes PMA
T10321 299-301 TO denotes to
T10320 290-298 NN denotes promoter
T10319 281-289 NNP denotes SerpinB2
T10318 274-280 NN denotes murine
T10317 270-273 DT denotes the
T10316 267-269 IN denotes of
T10315 258-266 NN denotes response
T10314 254-257 DT denotes the
T10313 244-253 VBG denotes mediating
T10312 235-243 NNS denotes elements
T10311 224-234 JJ denotes cis-acting
T10310 219-223 IN denotes that
T10309 208-218 VBG denotes indicating
T10308 206-207 , denotes ,
T10307 203-206 NNP denotes PMA
T10306 200-202 TO denotes to
T10305 189-199 JJ denotes responsive
T10304 179-188 RB denotes partially
T10303 173-178 RB denotes still
T10302 169-172 VBD denotes was
T10301 159-168 VBP denotes construct
T10300 150-158 NN denotes promoter
T10299 141-149 NNP denotes SerpinB2
T10298 134-140 NN denotes murine
T10297 131-133 CD denotes 87
T10296 130-131 NN denotes −
T10295 126-129 DT denotes the
T10294 124-125 , denotes ,
T10293 116-124 NN denotes response
T10292 112-115 NNP denotes PMA
T10291 108-111 DT denotes the
T10290 100-107 VBD denotes reduced
T10289 89-99 RB denotes marginally
T10288 85-88 CC denotes and
T10287 76-84 NN denotes response
T10286 72-75 NNP denotes LPS
T10285 68-71 DT denotes the
T10284 57-67 VBD denotes eliminated
T10283 54-56 CD denotes 87
T10282 53-54 CD denotes −
T10281 50-52 TO denotes to
T10280 46-49 CD denotes 189
T10279 45-46 CD denotes −
T10278 40-44 IN denotes from
T10277 31-39 NN denotes promoter
T10276 22-30 NNP denotes SerpinB2
T10275 18-21 DT denotes the
T10274 15-17 IN denotes of
T10273 6-14 NN denotes deletion
T10272 0-5 IN denotes While
R7559 T10272 T10284 mark While,eliminated
R7560 T10273 T10284 nsubj deletion,eliminated
R7561 T10274 T10273 prep of,deletion
R7562 T10275 T10277 det the,promoter
R7563 T10276 T10277 compound SerpinB2,promoter
R7564 T10277 T10274 pobj promoter,of
R7565 T10278 T10273 prep from,deletion
R7566 T10279 T10284 dep −,eliminated
R7567 T10280 T10284 dep 189,eliminated
R7568 T10281 T10284 prep to,eliminated
R7569 T10282 T10281 pobj −,to
R7570 T10283 T10284 nsubj 87,eliminated
R7571 T10284 T10302 advcl eliminated,was
R7572 T10285 T10287 det the,response
R7573 T10286 T10287 compound LPS,response
R7574 T10287 T10284 dobj response,eliminated
R7575 T10288 T10287 cc and,response
R7576 T10289 T10290 advmod marginally,reduced
R7577 T10290 T10284 conj reduced,eliminated
R7578 T10291 T10293 det the,response
R7579 T10292 T10293 compound PMA,response
R7580 T10293 T10290 dobj response,reduced
R7581 T10294 T10301 punct ",",construct
R7582 T10295 T10300 det the,promoter
R7583 T10296 T10300 nmod −,promoter
R7584 T10297 T10298 nummod 87,murine
R7585 T10298 T10300 compound murine,promoter
R7586 T10299 T10300 compound SerpinB2,promoter
R7587 T10300 T10301 compound promoter,construct
R7588 T10301 T10302 nsubj construct,was
R7589 T10302 T10302 ROOT was,was
R7590 T10303 T10302 advmod still,was
R7591 T10304 T10305 advmod partially,responsive
R7592 T10305 T10302 acomp responsive,was
R7593 T10306 T10305 prep to,responsive
R7594 T10307 T10306 pobj PMA,to
R7595 T10308 T10302 punct ",",was
R7596 T10309 T10302 advcl indicating,was
R7597 T10310 T10324 mark that,lie
R7598 T10311 T10312 amod cis-acting,elements
R7599 T10312 T10324 nsubj elements,lie
R7600 T10313 T10312 acl mediating,elements
R7601 T10314 T10315 det the,response
R7602 T10315 T10313 dobj response,mediating
R7603 T10316 T10315 prep of,response
R7604 T10317 T10320 det the,promoter
R7605 T10318 T10320 amod murine,promoter
R7606 T10319 T10320 compound SerpinB2,promoter
R7607 T10320 T10316 pobj promoter,of
R7608 T10321 T10324 aux to,lie
R7609 T10322 T10321 pobj PMA,to
R7610 T10323 T10324 advmod also,lie
R7611 T10324 T10309 ccomp lie,indicating
R7612 T10325 T10324 dobj downstream,lie
R7613 T10326 T10325 prep of,downstream
R7614 T10327 T10328 compound nucleotide,−
R7615 T10328 T10326 pobj −,of
R7616 T10329 T10328 nummod 87,−
R7617 T10330 T10302 punct .,was

pmc-enju-pas

Id Subject Object Predicate Lexical cue
T9855 340-343 CD denotes −87
T9854 329-339 NN denotes nucleotide
T9853 326-328 IN denotes of
T9852 315-325 JJ denotes downstream
T9851 311-314 VB denotes lie
T9850 306-310 RB denotes also
T9849 302-305 NN denotes PMA
T9848 299-301 TO denotes to
T9847 290-298 NN denotes promoter
T9846 281-289 NN denotes SerpinB2
T9845 274-280 JJ denotes murine
T9844 270-273 DT denotes the
T9843 267-269 IN denotes of
T9842 258-266 NN denotes response
T9841 254-257 DT denotes the
T9840 244-253 VB denotes mediating
T9839 235-243 NN denotes elements
T9838 224-234 JJ denotes cis-acting
T9837 219-223 IN denotes that
T9836 208-218 VB denotes indicating
T9835 206-207 -COMMA- denotes ,
T9834 203-206 NN denotes PMA
T9833 200-202 TO denotes to
T9832 189-199 JJ denotes responsive
T9831 179-188 RB denotes partially
T9830 173-178 RB denotes still
T9829 169-172 VB denotes was
T9828 159-168 NN denotes construct
T9827 150-158 NN denotes promoter
T9826 141-149 NN denotes SerpinB2
T9825 134-140 JJ denotes murine
T9824 130-133 CD denotes −87
T9823 126-129 DT denotes the
T9822 124-125 -COMMA- denotes ,
T9821 116-124 NN denotes response
T9820 112-115 NN denotes PMA
T9819 108-111 DT denotes the
T9818 100-107 VB denotes reduced
T9817 89-99 RB denotes marginally
T9816 85-88 CC denotes and
T9815 76-84 NN denotes response
T9814 72-75 NN denotes LPS
T9813 68-71 DT denotes the
T9812 57-67 VB denotes eliminated
T9811 53-56 CD denotes −87
T9810 50-52 TO denotes to
T9809 45-49 CD denotes −189
T9808 40-44 IN denotes from
T9807 31-39 NN denotes promoter
T9806 22-30 NN denotes SerpinB2
T9805 18-21 DT denotes the
T9804 15-17 IN denotes of
T9803 6-14 NN denotes deletion
T9802 0-5 IN denotes While
R7206 T9803 T9804 arg1Of deletion,of
R7207 T9803 T9810 arg1Of deletion,to
R7208 T9803 T9812 arg1Of deletion,eliminated
R7209 T9803 T9818 arg1Of deletion,reduced
R7210 T9807 T9804 arg2Of promoter,of
R7211 T9807 T9805 arg1Of promoter,the
R7212 T9807 T9806 arg1Of promoter,SerpinB2
R7213 T9807 T9808 arg1Of promoter,from
R7214 T9809 T9808 arg2Of −189,from
R7215 T9811 T9810 arg2Of −87,to
R7216 T9812 T9816 arg1Of eliminated,and
R7217 T9815 T9812 arg2Of response,eliminated
R7218 T9815 T9813 arg1Of response,the
R7219 T9815 T9814 arg1Of response,LPS
R7220 T9816 T9802 arg2Of and,While
R7221 T9818 T9816 arg2Of reduced,and
R7222 T9818 T9817 arg1Of reduced,marginally
R7223 T9821 T9818 arg2Of response,reduced
R7224 T9821 T9819 arg1Of response,the
R7225 T9821 T9820 arg1Of response,PMA
R7226 T9828 T9823 arg1Of construct,the
R7227 T9828 T9824 arg1Of construct,−87
R7228 T9828 T9825 arg1Of construct,murine
R7229 T9828 T9826 arg1Of construct,SerpinB2
R7230 T9828 T9827 arg1Of construct,promoter
R7231 T9828 T9829 arg1Of construct,was
R7232 T9828 T9832 arg1Of construct,responsive
R7233 T9829 T9802 arg1Of was,While
R7234 T9829 T9822 arg1Of was,","
R7235 T9829 T9830 arg1Of was,still
R7236 T9829 T9835 arg1Of was,","
R7237 T9829 T9836 modOf was,indicating
R7238 T9832 T9829 arg2Of responsive,was
R7239 T9832 T9831 arg1Of responsive,partially
R7240 T9832 T9833 arg1Of responsive,to
R7241 T9834 T9833 arg2Of PMA,to
R7242 T9839 T9838 arg1Of elements,cis-acting
R7243 T9839 T9840 arg1Of elements,mediating
R7244 T9839 T9851 arg1Of elements,lie
R7245 T9842 T9840 arg2Of response,mediating
R7246 T9842 T9841 arg1Of response,the
R7247 T9842 T9843 arg1Of response,of
R7248 T9842 T9848 arg1Of response,to
R7249 T9847 T9843 arg2Of promoter,of
R7250 T9847 T9844 arg1Of promoter,the
R7251 T9847 T9845 arg1Of promoter,murine
R7252 T9847 T9846 arg1Of promoter,SerpinB2
R7253 T9849 T9848 arg2Of PMA,to
R7254 T9851 T9836 arg2Of lie,indicating
R7255 T9851 T9837 arg1Of lie,that
R7256 T9851 T9850 arg1Of lie,also
R7257 T9851 T9852 arg1Of lie,downstream
R7258 T9852 T9853 arg1Of downstream,of
R7259 T9854 T9853 arg2Of nucleotide,of
R7260 T9854 T9855 arg1Of nucleotide,−87

bionlp-st-ge-2016-test-proteins

Id Subject Object Predicate Lexical cue
T9536 281-289 Protein denotes SerpinB2
T9535 141-149 Protein denotes SerpinB2
T9534 22-30 Protein denotes SerpinB2

bionlp-st-ge-2016-uniprot

Id Subject Object Predicate Lexical cue
T9896 281-289 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2
T9895 141-149 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2
T9894 22-30 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2

GO-BP

Id Subject Object Predicate Lexical cue
T9547 112-124 http://purl.obolibrary.org/obo/GO_1904627 denotes PMA response
T9546 72-84 http://purl.obolibrary.org/obo/GO_0032496 denotes LPS response

sentences

Id Subject Object Predicate Lexical cue
T9476 0-344 Sentence denotes While deletion of the SerpinB2 promoter from −189 to −87 eliminated the LPS response and marginally reduced the PMA response, the −87 murine SerpinB2 promoter construct was still partially responsive to PMA, indicating that cis-acting elements mediating the response of the murine SerpinB2 promoter to PMA also lie downstream of nucleotide −87.
T129 0-344 Sentence denotes While deletion of the SerpinB2 promoter from −189 to −87 eliminated the LPS response and marginally reduced the PMA response, the −87 murine SerpinB2 promoter construct was still partially responsive to PMA, indicating that cis-acting elements mediating the response of the murine SerpinB2 promoter to PMA also lie downstream of nucleotide −87.

simple1

Id Subject Object Predicate Lexical cue
T9564 281-289 Protein denotes SerpinB2
T9563 141-149 Protein denotes SerpinB2
T9562 22-30 Protein denotes SerpinB2

BioNLP16_DUT

Id Subject Object Predicate Lexical cue
T9887 244-253 Positive_regulation denotes mediating
T9886 258-266 Positive_regulation denotes response
T9885 6-14 Negative_regulation denotes deletion
T9884 100-107 Negative_regulation denotes reduced
T9877 22-30 Protein denotes SerpinB2
T9876 281-289 Protein denotes SerpinB2
T9875 141-149 Protein denotes SerpinB2
R7270 T9876 T9886 themeOf SerpinB2,response
R7271 T9877 T9884 themeOf SerpinB2,reduced
R7272 T9877 T9885 themeOf SerpinB2,deletion
R7275 T9886 T9887 themeOf response,mediating

BioNLP16_Messiy

Id Subject Object Predicate Lexical cue
T9940 6-14 Negative_regulation denotes deletion
T9936 22-30 Protein denotes SerpinB2
T9935 281-289 Protein denotes SerpinB2
T9934 141-149 Protein denotes SerpinB2
R7282 T9936 T9940 themeOf SerpinB2,deletion

DLUT931

Id Subject Object Predicate Lexical cue
T9910 22-30 Protein denotes SerpinB2
T9909 281-289 Protein denotes SerpinB2
T9908 141-149 Protein denotes SerpinB2
T9914 6-14 Negative_regulation denotes deletion
R7278 T9910 T9914 themeOf SerpinB2,deletion

bionlp-st-ge-2016-test-ihmc

Id Subject Object Predicate Lexical cue
T10017 302-305 Entity denotes PMA
T10015 329-339 Entity denotes nucleotide
T10014 22-30 Protein denotes SerpinB2
T10012 126-149 Protein denotes the −87 murine SerpinB2
T10004 203-207 Entity denotes PMA,
T10001 281-289 Protein denotes SerpinB2
T9994 72-75 Entity denotes LPS
T9993 112-115 Entity denotes PMA
T9989 15-39 Entity denotes of the SerpinB2 promoter
T9984 150-168 Entity denotes promoter construct
T9976 270-298 Entity denotes the murine SerpinB2 promoter
R7300 T9976 T10001 partOf the murine SerpinB2 promoter,SerpinB2
R7302 T9989 T10014 partOf of the SerpinB2 promoter,SerpinB2

bionlp-st-ge-2016-test-tees

Id Subject Object Predicate Lexical cue
T9957 244-253 Positive_regulation denotes mediating
T9956 258-266 Positive_regulation denotes response
T9955 100-107 Negative_regulation denotes reduced
T9954 6-14 Negative_regulation denotes deletion
T9953 274-298 Protein denotes murine SerpinB2 promoter
T9952 22-39 Protein denotes SerpinB2 promoter
R7288 T9952 T9954 themeOf SerpinB2 promoter,deletion
R7289 T9953 T9956 themeOf murine SerpinB2 promoter,response
R7290 T9954 T9955 themeOf deletion,reduced
R7291 T9956 T9957 themeOf response,mediating

testone

Id Subject Object Predicate Lexical cue
T9442 281-289 Protein denotes SerpinB2
T9441 141-149 Protein denotes SerpinB2
T9440 22-30 Protein denotes SerpinB2

test3

Id Subject Object Predicate Lexical cue
T9455 281-289 Protein denotes SerpinB2
T9454 141-149 Protein denotes SerpinB2
T9453 22-30 Protein denotes SerpinB2
T9467 281-289 Protein denotes SerpinB2
T9466 141-149 Protein denotes SerpinB2
T9465 22-30 Protein denotes SerpinB2
T9464 6-14 Negative_regulation denotes deletion