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PMC:3585731 / 36446-36731 JSONTXT

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testone

Id Subject Object Predicate Lexical cue
T16761 224-236 Positive_regulation denotes upregulation
T16760 204-213 Regulation denotes dependent
T16759 133-141 Positive_regulation denotes response
T16758 105-119 Phosphorylation denotes phosphorylated
T16757 65-75 Gene_expression denotes expressing
T16756 32-41 Negative_regulation denotes knockdown
T16736 214-218 Protein denotes TNFα
T16735 199-203 Protein denotes RIP1
T16734 145-149 Protein denotes TNFα
T16733 95-99 Protein denotes Akt2
T16732 87-91 Protein denotes Akt1
R11139 T16732 T16757 themeOf Akt1,expressing
R11140 T16733 T16758 themeOf Akt2,phosphorylated
R11141 T16735 T16760 causeOf RIP1,dependent
R11142 T16736 T16761 themeOf TNFα,upregulation
R11148 T16761 T16760 themeOf upregulation,dependent

pmc-enju-pas

Id Subject Object Predicate Lexical cue
T17247 92-94 CC denotes or
T17279 283-284 -RRB- denotes )
T17278 281-283 NN denotes 8H
T17277 276-280 NNP denotes Fig.
T17276 275-276 -LRB- denotes (
T17275 264-274 NN denotes conditions
T17274 252-263 JJ denotes necroptotic
T17273 246-251 IN denotes under
T17272 237-245 VB denotes occurred
T17271 224-236 NN denotes upregulation
T17270 219-223 NN denotes mRNA
T17269 214-218 NN denotes TNFα
T17268 199-213 JJ denotes RIP1-dependent
T17267 192-198 JJ denotes robust
T17266 186-191 NN denotes cases
T17265 181-185 DT denotes both
T17264 178-180 IN denotes in
T17263 174-177 CC denotes and
T17262 172-173 -RRB- denotes )
T17261 169-172 NN denotes S9E
T17260 164-168 NN denotes Fig.
T17259 163-164 -LRB- denotes (
T17258 154-162 NN denotes zVAD.fmk
T17257 150-153 CC denotes and
T17256 145-149 NN denotes TNFα
T17255 142-144 TO denotes to
T17254 133-141 NN denotes response
T17253 130-132 IN denotes in
T17252 123-129 NN denotes Thr308
T17251 120-122 IN denotes on
T17250 105-119 VB denotes phosphorylated
T17249 100-104 VB denotes were
T17248 95-99 NN denotes Akt2
T17246 87-91 NN denotes Akt1
T17245 76-86 JJ denotes endogenous
T17244 65-75 VB denotes expressing
T17243 53-64 NN denotes fibroblasts
T17242 48-52 NN denotes lung
T17241 46-47 -COMMA- denotes ,
T17240 42-46 NN denotes data
T17239 32-41 JJ denotes knockdown
T17238 28-31 NN denotes Akt
T17237 20-27 JJ denotes earlier
T17236 16-19 PRP-DOLLAR- denotes our
T17235 11-15 IN denotes with
T17234 0-10 JJ denotes Consistent
R11477 T17234 T17235 arg1Of Consistent,with
R11478 T17240 T17235 arg2Of data,with
R11479 T17240 T17236 arg1Of data,our
R11480 T17240 T17237 arg1Of data,earlier
R11481 T17240 T17238 arg1Of data,Akt
R11482 T17240 T17239 arg1Of data,knockdown
R11483 T17243 T17234 arg1Of fibroblasts,Consistent
R11484 T17243 T17242 arg1Of fibroblasts,lung
R11485 T17243 T17244 arg1Of fibroblasts,expressing
R11486 T17243 T17249 arg1Of fibroblasts,were
R11487 T17243 T17250 arg2Of fibroblasts,phosphorylated
R11488 T17246 T17247 arg1Of Akt1,or
R11489 T17247 T17244 arg2Of or,expressing
R11490 T17247 T17245 arg1Of or,endogenous
R11491 T17248 T17247 arg2Of Akt2,or
R11492 T17250 T17234 modOf phosphorylated,Consistent
R11493 T17250 T17241 arg1Of phosphorylated,","
R11494 T17250 T17249 arg2Of phosphorylated,were
R11495 T17250 T17251 arg1Of phosphorylated,on
R11496 T17250 T17253 arg1Of phosphorylated,in
R11497 T17250 T17263 arg1Of phosphorylated,and
R11498 T17252 T17251 arg2Of Thr308,on
R11499 T17254 T17253 arg2Of response,in
R11500 T17254 T17255 arg1Of response,to
R11501 T17256 T17257 arg1Of TNFα,and
R11502 T17257 T17255 arg2Of and,to
R11503 T17257 T17259 arg1Of and,(
R11504 T17258 T17257 arg2Of zVAD.fmk,and
R11505 T17261 T17259 arg2Of S9E,(
R11506 T17261 T17260 arg1Of S9E,Fig.
R11507 T17262 T17259 arg3Of ),(
R11508 T17266 T17264 arg2Of cases,in
R11509 T17266 T17265 arg1Of cases,both
R11510 T17271 T17267 arg1Of upregulation,robust
R11511 T17271 T17268 arg1Of upregulation,RIP1-dependent
R11512 T17271 T17269 arg1Of upregulation,TNFα
R11513 T17271 T17270 arg1Of upregulation,mRNA
R11514 T17271 T17272 arg1Of upregulation,occurred
R11515 T17272 T17263 arg2Of occurred,and
R11516 T17272 T17264 arg1Of occurred,in
R11517 T17272 T17273 arg1Of occurred,under
R11518 T17275 T17273 arg2Of conditions,under
R11519 T17275 T17274 arg1Of conditions,necroptotic
R11520 T17275 T17276 arg1Of conditions,(
R11521 T17278 T17276 arg2Of 8H,(
R11522 T17278 T17277 arg1Of 8H,Fig.
R11523 T17279 T17276 arg3Of ),(

bionlp-st-ge-2016-test-proteins

Id Subject Object Predicate Lexical cue
T16891 214-218 Protein denotes TNFα
T16890 199-203 Protein denotes RIP1
T16889 145-149 Protein denotes TNFα
T16888 95-99 Protein denotes Akt2
T16887 87-91 Protein denotes Akt1

bionlp-st-ge-2016-uniprot

Id Subject Object Predicate Lexical cue
T17426 199-203 http://www.uniprot.org/uniprot/Q13546 denotes RIP1
T17420 214-218 http://www.uniprot.org/uniprot/P01375 denotes TNFα
T17419 145-149 http://www.uniprot.org/uniprot/P01375 denotes TNFα
T17409 28-31 http://www.uniprot.org/uniprot/Q9Y243 denotes Akt
T17396 28-31 http://www.uniprot.org/uniprot/P31751 denotes Akt
T17383 28-31 http://www.uniprot.org/uniprot/P31749 denotes Akt

UBERON-AE

Id Subject Object Predicate Lexical cue
T16825 48-52 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung

sentences

Id Subject Object Predicate Lexical cue
T16836 0-285 Sentence denotes Consistent with our earlier Akt knockdown data, lung fibroblasts expressing endogenous Akt1 or Akt2 were phosphorylated on Thr308 in response to TNFα and zVAD.fmk (Fig. S9E) and in both cases robust RIP1-dependent TNFα mRNA upregulation occurred under necroptotic conditions (Fig. 8H).
T226 0-285 Sentence denotes Consistent with our earlier Akt knockdown data, lung fibroblasts expressing endogenous Akt1 or Akt2 were phosphorylated on Thr308 in response to TNFα and zVAD.fmk (Fig. S9E) and in both cases robust RIP1-dependent TNFα mRNA upregulation occurred under necroptotic conditions (Fig. 8H).

simple1

Id Subject Object Predicate Lexical cue
T16951 214-218 Protein denotes TNFα
T16950 199-203 Protein denotes RIP1
T16949 145-149 Protein denotes TNFα
T16948 95-99 Protein denotes Akt2
T16947 87-91 Protein denotes Akt1

BioNLP16_DUT

Id Subject Object Predicate Lexical cue
T17371 204-213 Positive_regulation denotes dependent
T17370 65-75 Gene_expression denotes expressing
T17369 224-236 Positive_regulation denotes upregulation
T17357 214-218 Protein denotes TNFα
T17356 199-203 Protein denotes RIP1
T17355 145-149 Protein denotes TNFα
T17354 95-99 Protein denotes Akt2
T17353 87-91 Protein denotes Akt1
R11573 T17353 T17370 themeOf Akt1,expressing
R11574 T17354 T17370 themeOf Akt2,expressing
R11575 T17357 T17369 themeOf TNFα,upregulation
R11580 T17369 T17371 themeOf upregulation,dependent

BioNLP16_Messiy

Id Subject Object Predicate Lexical cue
T17904 224-236 Positive_regulation denotes upregulation
T17903 204-213 Positive_regulation denotes dependent
T17902 65-75 Gene_expression denotes expressing
T17890 214-218 Protein denotes TNFα
T17889 199-203 Protein denotes RIP1
T17888 145-149 Protein denotes TNFα
T17887 95-99 Protein denotes Akt2
T17886 87-91 Protein denotes Akt1
R12003 T17886 T17902 themeOf Akt1,expressing
R12004 T17887 T17902 themeOf Akt2,expressing
R12005 T17889 T17903 causeOf RIP1,dependent
R12006 T17890 T17904 themeOf TNFα,upregulation
R12011 T17904 T17903 themeOf upregulation,dependent

DLUT931

Id Subject Object Predicate Lexical cue
T17871 204-213 Positive_regulation denotes dependent
T17870 224-236 Positive_regulation denotes upregulation
T17869 105-119 Phosphorylation denotes phosphorylated
T17868 65-75 Gene_expression denotes expressing
T17855 214-218 Protein denotes TNFα
T17854 199-203 Protein denotes RIP1
T17853 145-149 Protein denotes TNFα
T17852 95-99 Protein denotes Akt2
T17851 87-91 Protein denotes Akt1
R11981 T17851 T17868 themeOf Akt1,expressing
R11982 T17852 T17868 themeOf Akt2,expressing
R11983 T17853 T17869 themeOf TNFα,phosphorylated
R11984 T17854 T17871 causeOf RIP1,dependent
R11985 T17855 T17870 themeOf TNFα,upregulation
R11995 T17870 T17871 themeOf upregulation,dependent

bionlp-st-ge-2016-test-ihmc

Id Subject Object Predicate Lexical cue
T18108 53-99 Gene_expression denotes fibroblasts expressing endogenous Akt1 or Akt2
T18107 53-99 Gene_expression denotes fibroblasts expressing endogenous Akt1 or Akt2
T18102 192-236 Positive_regulation denotes robust RIP1-dependent TNFα mRNA upregulation
T18081 192-223 Protein denotes robust RIP1-dependent TNFα mRNA
T18076 154-162 Entity denotes zVAD.fmk
T18075 53-99 Entity denotes fibroblasts expressing endogenous Akt1 or Akt2
T18072 164-167 Protein denotes Fig
T18060 95-99 Protein denotes Akt2
T18054 123-129 Entity denotes Thr308
T18047 28-31 Protein denotes Akt
T18046 214-218 Protein denotes TNFα
T18043 76-91 Protein denotes endogenous Akt1
T18033 145-149 Protein denotes TNFα
T18031 199-213 Protein denotes RIP1-dependent
R12064 T18043 T18107 themeOf endogenous Akt1,fibroblasts expressing endogenous Akt1 or Akt2
R12070 T18060 T18108 themeOf Akt2,fibroblasts expressing endogenous Akt1 or Akt2
R12075 T18081 T18102 themeOf robust RIP1-dependent TNFα mRNA,robust RIP1-dependent TNFα mRNA upregulation

bionlp-st-ge-2016-spacy-parsed

Id Subject Object Predicate Lexical cue
T17769 284-285 . denotes .
T17768 283-284 -RRB- denotes )
T17767 281-283 NNP denotes 8H
T17766 276-280 NNP denotes Fig.
T17765 275-276 -LRB- denotes (
T17764 264-274 NNS denotes conditions
T17763 252-263 JJ denotes necroptotic
T17762 246-251 IN denotes under
T17761 237-245 VBD denotes occurred
T17760 224-236 NN denotes upregulation
T17759 219-223 NNP denotes mRNA
T17758 214-218 NNP denotes TNFα
T17757 199-213 NN denotes RIP1-dependent
T17756 192-198 JJ denotes robust
T17755 186-191 NNS denotes cases
T17754 181-185 DT denotes both
T17753 178-180 IN denotes in
T17752 174-177 CC denotes and
T17751 172-173 -RRB- denotes )
T17750 169-172 CD denotes S9E
T17749 167-168 . denotes .
T17748 164-167 NNP denotes Fig
T17747 163-164 -LRB- denotes (
T17746 154-162 NNP denotes zVAD.fmk
T17745 150-153 CC denotes and
T17744 145-149 NNP denotes TNFα
T17743 142-144 TO denotes to
T17742 133-141 NN denotes response
T17741 130-132 IN denotes in
T17740 123-129 NNP denotes Thr308
T17739 120-122 IN denotes on
T17738 105-119 VBN denotes phosphorylated
T17737 100-104 VBD denotes were
T17736 95-99 JJ denotes Akt2
T17735 92-94 CC denotes or
T17734 87-91 JJ denotes Akt1
T17733 76-86 JJ denotes endogenous
T17732 65-75 VBG denotes expressing
T17731 53-64 NNS denotes fibroblasts
T17730 48-52 NN denotes lung
T17729 46-47 , denotes ,
T17728 42-46 NNS denotes data
T17727 32-41 JJ denotes knockdown
T17726 28-31 NNP denotes Akt
T17725 20-27 JJR denotes earlier
T17724 16-19 PRP$ denotes our
T17723 11-15 IN denotes with
T17722 0-10 JJ denotes Consistent
R11876 T17722 T17722 ROOT Consistent,Consistent
R11877 T17723 T17722 prep with,Consistent
R11878 T17724 T17728 poss our,data
R11879 T17725 T17728 amod earlier,data
R11880 T17726 T17728 compound Akt,data
R11881 T17727 T17728 compound knockdown,data
R11882 T17728 T17723 pobj data,with
R11883 T17729 T17728 punct ",",data
R11884 T17730 T17731 compound lung,fibroblasts
R11885 T17731 T17728 conj fibroblasts,data
R11886 T17732 T17723 pcomp expressing,with
R11887 T17733 T17734 amod endogenous,Akt1
R11888 T17734 T17738 nsubjpass Akt1,phosphorylated
R11889 T17735 T17734 cc or,Akt1
R11890 T17736 T17734 conj Akt2,Akt1
R11891 T17737 T17738 auxpass were,phosphorylated
R11892 T17738 T17738 ROOT phosphorylated,phosphorylated
R11893 T17739 T17738 prep on,phosphorylated
R11894 T17740 T17739 pobj Thr308,on
R11895 T17741 T17738 prep in,phosphorylated
R11896 T17742 T17741 pobj response,in
R11897 T17743 T17742 prep to,response
R11898 T17744 T17743 pobj TNFα,to
R11899 T17745 T17744 cc and,TNFα
R11900 T17746 T17744 conj zVAD.fmk,TNFα
R11901 T17747 T17748 punct (,Fig
R11902 T17748 T17746 appos Fig,zVAD.fmk
R11903 T17749 T17738 punct .,phosphorylated
R11904 T17750 T17750 ROOT S9E,S9E
R11905 T17751 T17750 punct ),S9E
R11906 T17752 T17750 cc and,S9E
R11907 T17753 T17761 prep in,occurred
R11908 T17754 T17755 det both,cases
R11909 T17755 T17753 pobj cases,in
R11910 T17756 T17757 amod robust,RIP1-dependent
R11911 T17757 T17760 compound RIP1-dependent,upregulation
R11912 T17758 T17760 compound TNFα,upregulation
R11913 T17759 T17760 compound mRNA,upregulation
R11914 T17760 T17761 nsubj upregulation,occurred
R11915 T17761 T17750 conj occurred,S9E
R11916 T17762 T17761 prep under,occurred
R11917 T17763 T17764 amod necroptotic,conditions
R11918 T17764 T17762 pobj conditions,under
R11919 T17765 T17767 punct (,8H
R11920 T17766 T17767 compound Fig.,8H
R11921 T17767 T17761 parataxis 8H,occurred
R11922 T17768 T17767 punct ),8H
R11923 T17769 T17761 punct .,occurred

bionlp-st-ge-2016-test-tees

Id Subject Object Predicate Lexical cue
T17959 65-75 Gene_expression denotes expressing
T17958 65-75 Gene_expression denotes expressing
T17957 214-223 Protein denotes TNFα mRNA
T17956 199-203 Protein denotes RIP1
T17955 169-172 Protein denotes S9E
T17950 95-99 Protein denotes Akt2
T17949 76-91 Protein denotes endogenous Akt1
T17954 164-167 Protein denotes Fig
T17953 154-162 Protein denotes zVAD.fmk
T17952 145-149 Protein denotes TNFα
T17951 123-129 Protein denotes Thr308
T17965 224-236 Positive_regulation denotes upregulation
T17964 105-119 Phosphorylation denotes phosphorylated
T17963 105-119 Phosphorylation denotes phosphorylated
T17962 105-119 Phosphorylation denotes phosphorylated
T17961 105-119 Phosphorylation denotes phosphorylated
T17960 105-119 Phosphorylation denotes phosphorylated
R12028 T17949 T17958 themeOf endogenous Akt1,expressing
R12029 T17950 T17959 themeOf Akt2,expressing
R12030 T17951 T17960 themeOf Thr308,phosphorylated
R12031 T17952 T17961 themeOf TNFα,phosphorylated
R12032 T17953 T17962 themeOf zVAD.fmk,phosphorylated
R12033 T17954 T17963 themeOf Fig,phosphorylated
R12034 T17955 T17964 themeOf S9E,phosphorylated
R12035 T17957 T17965 themeOf TNFα mRNA,upregulation

test3

Id Subject Object Predicate Lexical cue
T16820 224-236 Positive_regulation denotes upregulation
T16819 214-218 Protein denotes TNFα
T16818 204-213 Regulation denotes dependent
T16817 199-203 Protein denotes RIP1
T16816 145-149 Protein denotes TNFα
T16815 105-119 Phosphorylation denotes phosphorylated
T16814 95-99 Protein denotes Akt2
T16813 87-91 Protein denotes Akt1
T16812 65-75 Gene_expression denotes expressing
T16811 32-41 Negative_regulation denotes knockdown
T16780 214-218 Protein denotes TNFα
T16779 199-203 Protein denotes RIP1
T16778 145-149 Protein denotes TNFα
T16777 95-99 Protein denotes Akt2
T16776 87-91 Protein denotes Akt1
R11162 T16813 T16815 themeOf Akt1,phosphorylated
R11163 T16813 T16812 themeOf Akt1,expressing
R11164 T16814 T16815 themeOf Akt2,phosphorylated
R11165 T16814 T16812 themeOf Akt2,expressing
R11166 T16817 T16818 causeOf RIP1,dependent
R11167 T16819 T16820 themeOf TNFα,upregulation
R11168 T16820 T16818 themeOf upregulation,dependent