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PMC:3589482 / 4117-4342 JSONTXT

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bionlp-st-ge-2016-spacy-parsed

Id Subject Object Predicate Lexical cue
T2957 224-225 . denotes .
T2956 223-224 NNP denotes ]
T2955 221-223 CD denotes 16
T2954 220-221 NNP denotes [
T2953 211-219 NNS denotes pathways
T2952 201-210 NNP denotes MAPK/CREB
T2951 197-200 CD denotes p38
T2950 193-196 CC denotes and
T2949 187-192 NNP denotes NF-κB
T2948 186-187 NNP denotes /
T2947 182-186 NNP denotes IKKβ
T2946 178-181 DT denotes the
T2945 175-177 IN denotes of
T2944 163-174 NN denotes cooperation
T2943 160-162 IN denotes by
T2942 148-159 VBN denotes upregulated
T2941 144-147 VBD denotes was
T2940 133-143 NN denotes expression
T2939 127-132 WP$ denotes whose
T2938 120-126 NN denotes factor
T2937 118-119 DT denotes a
T2936 115-117 IN denotes as
T2935 104-114 VBN denotes identified
T2934 100-103 VBD denotes was
T2933 91-99 NNP denotes SerpinB2
T2932 89-90 , denotes ,
T2931 85-89 NNP denotes MAPK
T2930 81-84 CD denotes p38
T2929 78-80 IN denotes of
T2928 67-77 JJ denotes downstream
T2927 59-66 NNS denotes factors
T2926 46-58 JJ denotes pro-survival
T2925 32-45 JJ denotes LPS-inducible
T2924 20-31 VBG denotes identifying
T2923 17-19 IN denotes at
T2922 11-16 VBN denotes aimed
T2921 3-10 NNS denotes studies
T2920 0-2 IN denotes In
R2042 T2920 T2935 prep In,identified
R2044 T2921 T2920 pobj studies,In
R2045 T2922 T2921 acl aimed,studies
R2046 T2923 T2922 prep at,aimed
R2048 T2924 T2923 pcomp identifying,at
R2049 T2925 T2927 amod LPS-inducible,factors
R2050 T2926 T2927 amod pro-survival,factors
R2054 T2927 T2924 dobj factors,identifying
R2055 T2928 T2927 amod downstream,factors
R2056 T2929 T2928 prep of,downstream
R2058 T2930 T2931 nummod p38,MAPK
R2059 T2931 T2929 pobj MAPK,of
R2060 T2932 T2935 punct ",",identified
R2061 T2933 T2935 nsubjpass SerpinB2,identified
R2062 T2934 T2935 auxpass was,identified
R2064 T2935 T2935 ROOT identified,identified
R2065 T2936 T2935 prep as,identified
R2066 T2937 T2938 det a,factor
R2067 T2938 T2936 pobj factor,as
R2069 T2939 T2940 poss whose,expression
R2070 T2940 T2942 nsubjpass expression,upregulated
R2071 T2941 T2942 auxpass was,upregulated
R2073 T2942 T2935 advcl upregulated,identified
R2074 T2943 T2942 agent by,upregulated
R2075 T2944 T2943 pobj cooperation,by
R2077 T2945 T2944 prep of,cooperation
R2078 T2946 T2949 det the,NF-κB
R2080 T2947 T2949 compound IKKβ,NF-κB
R2081 T2948 T2949 compound /,NF-κB
R2083 T2949 T2945 pobj NF-κB,of
R2084 T2950 T2949 cc and,NF-κB
R2085 T2951 T2953 nummod p38,pathways
R2086 T2952 T2953 compound MAPK/CREB,pathways
R2088 T2953 T2944 conj pathways,cooperation
R2089 T2954 T2956 nmod [,]
R2091 T2955 T2956 nummod 16,]
R2092 T2956 T2953 appos ],pathways
R2093 T2957 T2935 punct .,identified

pmc-enju-pas

Id Subject Object Predicate Lexical cue
T1863 120-126 NN denotes factor
T1879 223-224 -RRB- denotes ]
T1878 221-223 CD denotes 16
T1877 220-221 -LRB- denotes [
T1876 211-219 NN denotes pathways
T1875 201-210 NN denotes MAPK/CREB
T1874 197-200 NN denotes p38
T1873 193-196 CC denotes and
T1872 182-192 NN denotes IKKβ/NF-κB
T1871 178-181 DT denotes the
T1870 175-177 IN denotes of
T1869 163-174 NN denotes cooperation
T1868 160-162 IN denotes by
T1867 148-159 VB denotes upregulated
T1866 144-147 VB denotes was
T1865 133-143 NN denotes expression
T1864 127-132 WP-DOLLAR- denotes whose
T1862 118-119 DT denotes a
T1861 115-117 IN denotes as
T1860 104-114 VB denotes identified
T1859 100-103 VB denotes was
T1858 91-99 NN denotes SerpinB2
T1857 89-90 -COMMA- denotes ,
T1856 85-89 NN denotes MAPK
T1855 81-84 NN denotes p38
T1854 78-80 IN denotes of
T1853 67-77 RB denotes downstream
T1852 59-66 NN denotes factors
T1851 46-58 JJ denotes pro-survival
T1850 32-45 JJ denotes LPS-inducible
T1849 20-31 VB denotes identifying
T1848 17-19 IN denotes at
T1847 11-16 VB denotes aimed
T1846 3-10 NN denotes studies
T1845 0-2 IN denotes In
R1251 T1846 T1845 arg2Of studies,In
R1252 T1846 T1847 arg2Of studies,aimed
R1253 T1847 T1848 arg1Of aimed,at
R1254 T1849 T1848 arg2Of identifying,at
R1255 T1852 T1849 arg2Of factors,identifying
R1256 T1852 T1850 arg1Of factors,LPS-inducible
R1257 T1852 T1851 arg1Of factors,pro-survival
R1258 T1852 T1853 arg1Of factors,downstream
R1259 T1853 T1854 arg1Of downstream,of
R1260 T1856 T1854 arg2Of MAPK,of
R1261 T1856 T1855 arg1Of MAPK,p38
R1262 T1858 T1859 arg1Of SerpinB2,was
R1263 T1858 T1860 arg2Of SerpinB2,identified
R1264 T1860 T1845 arg1Of identified,In
R1265 T1860 T1857 arg1Of identified,","
R1266 T1860 T1859 arg2Of identified,was
R1267 T1860 T1861 arg1Of identified,as
R1268 T1863 T1861 arg2Of factor,as
R1269 T1863 T1862 arg1Of factor,a
R1270 T1863 T1864 arg2Of factor,whose
R1271 T1865 T1864 arg1Of expression,whose
R1272 T1865 T1866 arg1Of expression,was
R1273 T1865 T1867 arg2Of expression,upregulated
R1274 T1867 T1866 arg2Of upregulated,was
R1275 T1869 T1867 arg1Of cooperation,upregulated
R1276 T1869 T1868 arg2Of cooperation,by
R1277 T1869 T1870 arg1Of cooperation,of
R1278 T1872 T1873 arg1Of IKKβ/NF-κB,and
R1279 T1874 T1873 arg2Of p38,and
R1280 T1876 T1870 arg2Of pathways,of
R1281 T1876 T1871 arg1Of pathways,the
R1282 T1876 T1872 arg1Of pathways,IKKβ/NF-κB
R1283 T1876 T1874 arg1Of pathways,p38
R1284 T1876 T1875 arg1Of pathways,MAPK/CREB
R1285 T1876 T1877 arg1Of pathways,[
R1286 T1878 T1877 arg2Of 16,[
R1287 T1879 T1877 arg3Of ],[

bionlp-st-ge-2016-coref

Id Subject Object Predicate Lexical cue
T1294 118-126 Antecedent denotes a factor
T1293 127-132 Anaphor denotes whose
T1292 91-99 Antecedent denotes SerpinB2
T1291 118-126 Anaphor denotes a factor
R821 T1291 T1292 boundBy a factor,SerpinB2
R822 T1293 T1291 boundBy whose,a factor

bionlp-st-ge-2016-test-proteins

Id Subject Object Predicate Lexical cue
T1312 182-186 Protein denotes IKKβ
T1311 91-99 Protein denotes SerpinB2

bionlp-st-ge-2016-uniprot

Id Subject Object Predicate Lexical cue
T2111 91-99 http://www.uniprot.org/uniprot/P05120 denotes SerpinB2
T2127 206-210 http://www.uniprot.org/uniprot/O43889 denotes CREB
T2126 206-210 http://www.uniprot.org/uniprot/P16220 denotes CREB
T2125 206-210 http://www.uniprot.org/uniprot/Q8TEY5 denotes CREB
T2124 206-210 http://www.uniprot.org/uniprot/P18848 denotes CREB
T2123 182-186 http://www.uniprot.org/uniprot/O14920 denotes IKKβ
T2129 206-210 http://www.uniprot.org/uniprot/Q02930 denotes CREB
T2128 206-210 http://www.uniprot.org/uniprot/P15336 denotes CREB

GO-BP

Id Subject Object Predicate Lexical cue
T1373 46-58 http://purl.obolibrary.org/obo/GO_0043066 denotes pro-survival
T1372 197-200 http://purl.obolibrary.org/obo/GO_0004707 denotes p38
T1371 81-84 http://purl.obolibrary.org/obo/GO_0004707 denotes p38
T1370 85-89 http://purl.obolibrary.org/obo/GO_0004707 denotes MAPK

GO-MF

Id Subject Object Predicate Lexical cue
T1387 197-200 http://purl.obolibrary.org/obo/GO_0004707 denotes p38
T1386 81-84 http://purl.obolibrary.org/obo/GO_0004707 denotes p38
T1385 85-89 http://purl.obolibrary.org/obo/GO_0004707 denotes MAPK

sentences

Id Subject Object Predicate Lexical cue
T1217 0-225 Sentence denotes In studies aimed at identifying LPS-inducible pro-survival factors downstream of p38 MAPK, SerpinB2 was identified as a factor whose expression was upregulated by cooperation of the IKKβ/NF-κB and p38 MAPK/CREB pathways [16].
T27 0-225 Sentence denotes In studies aimed at identifying LPS-inducible pro-survival factors downstream of p38 MAPK, SerpinB2 was identified as a factor whose expression was upregulated by cooperation of the IKKβ/NF-κB and p38 MAPK/CREB pathways [16].

simple1

Id Subject Object Predicate Lexical cue
T1410 182-186 Protein denotes IKKβ
T1409 91-99 Protein denotes SerpinB2

BioNLP16_DUT

Id Subject Object Predicate Lexical cue
T2068 182-186 Protein denotes IKKβ
T2067 91-99 Protein denotes SerpinB2
T2089 133-143 Gene_expression denotes expression
T2088 148-159 Positive_regulation denotes upregulated
R1455 T2067 T2089 themeOf SerpinB2,expression
R1456 T2067 T2088 themeOf SerpinB2,upregulated
R1469 T2089 T2088 themeOf expression,upregulated

BioNLP16_Messiy

Id Subject Object Predicate Lexical cue
T2227 182-186 Protein denotes IKKβ
T2226 91-99 Protein denotes SerpinB2
T2248 148-159 Positive_regulation denotes upregulated
T2247 133-143 Gene_expression denotes expression
R1516 T2226 T2247 themeOf SerpinB2,expression
R1517 T2226 T2248 causeOf SerpinB2,upregulated
R1521 T2247 T2248 themeOf expression,upregulated

DLUT931

Id Subject Object Predicate Lexical cue
T2168 148-159 Positive_regulation denotes upregulated
T2167 133-143 Gene_expression denotes expression
T2146 182-186 Protein denotes IKKβ
T2145 91-99 Protein denotes SerpinB2
R1483 T2145 T2167 themeOf SerpinB2,expression
R1495 T2167 T2168 themeOf expression,upregulated

bionlp-st-ge-2016-test-ihmc

Id Subject Object Predicate Lexical cue
T2478 127-159 Positive_regulation denotes whose expression was upregulated
T2455 201-210 Protein denotes MAPK/CREB
T2454 182-192 Protein denotes IKKβ/NF-κB
T2450 91-99 Protein denotes SerpinB2
T2447 81-89 Protein denotes p38 MAPK
T2445 81-84 Protein denotes p38
T2441 182-192 Protein denotes IKKβ/NF-κB
T2419 187-192 Protein denotes NF-κB
T2412 206-210 Protein denotes CREB
T2377 201-210 Protein denotes MAPK/CREB

bionlp-st-ge-2016-test-tees

Id Subject Object Predicate Lexical cue
T2296 148-159 Positive_regulation denotes upregulated
T2295 148-159 Positive_regulation denotes upregulated
T2294 148-159 Positive_regulation denotes upregulated
T2293 163-174 Gene_expression denotes cooperation
T2292 163-174 Gene_expression denotes cooperation
T2291 163-174 Gene_expression denotes cooperation
T2290 133-143 Gene_expression denotes expression
T2289 206-210 Protein denotes CREB
T2288 197-205 Protein denotes p38 MAPK
T2287 182-192 Protein denotes IKKβ/NF-κB
T2286 91-99 Protein denotes SerpinB2
T2285 81-89 Protein denotes p38 MAPK
R1547 T2286 T2290 themeOf SerpinB2,expression
R1553 T2287 T2291 themeOf IKKβ/NF-κB,cooperation
R1554 T2288 T2292 themeOf p38 MAPK,cooperation
R1555 T2289 T2293 themeOf CREB,cooperation
R1556 T2290 T2294 themeOf expression,upregulated
R1557 T2290 T2295 themeOf expression,upregulated
R1559 T2290 T2296 themeOf expression,upregulated
R1560 T2291 T2294 causeOf cooperation,upregulated
R1561 T2292 T2295 causeOf cooperation,upregulated
R1562 T2293 T2296 causeOf cooperation,upregulated

testone

Id Subject Object Predicate Lexical cue
T1125 148-159 Positive_regulation denotes upregulated
T1107 182-186 Protein denotes IKKβ
T1106 91-99 Protein denotes SerpinB2

test3

Id Subject Object Predicate Lexical cue
T1176 182-186 Protein denotes IKKβ
T1175 91-99 Protein denotes SerpinB2
T1148 182-186 Protein denotes IKKβ
T1147 91-99 Protein denotes SerpinB2