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jnlpba-st-training

Id Subject Object Predicate Lexical cue
T1 0-34 cell_type denotes Peripheral blood mononuclear cells
T2 117-164 protein denotes oxidative-stress sensitive transcription factor
T3 165-174 protein denotes NF-kappaB
T4 257-266 protein denotes NF-kappaB
T5 382-391 protein denotes NF-kappaB
T6 570-579 protein denotes NF-kappaB
T7 602-645 cell_type denotes isolated peripheral blood mononuclear cells
T8 765-774 protein denotes NF-kappaB
T9 888-900 protein denotes NF-kappaBp65
T10 944-953 protein denotes NF-kappaB
T11 1034-1048 protein denotes thrombomodulin
T12 1367-1376 protein denotes NF-kappaB
T13 1405-1448 cell_type denotes isolated peripheral blood mononuclear cells
T14 1490-1510 protein denotes transcription factor
T15 1511-1520 protein denotes NF-kappaB
T16 1532-1575 cell_type denotes isolated peripheral blood mononuclear cells
T17 1663-1672 protein denotes NF-kappaB
T18 1782-1791 protein denotes NF-kappaB

genia-medco-coref

Id Subject Object Predicate Lexical cue
C2 63-83 NP denotes diabetic nephropathy
C1 49-83 NP denotes patients with diabetic nephropathy
C3 113-174 NP denotes the oxidative-stress sensitive transcription factor NF-kappaB
C4 232-266 NP denotes the transcription factor NF-kappaB
C6 431-451 NP denotes diabetic nephropathy
C5 417-451 NP denotes patients with diabetic nephropathy
C7 460-539 NP denotes an Electrophoretic Mobility Shift Assay based semiquantitative detection system
C8 540-545 NP denotes which
C9 594-645 NP denotes ex vivo isolated peripheral blood mononuclear cells
C10 676-714 NP denotes diabetes mellitus (Type I and Type II)
C12 730-750 NP denotes diabetic nephropathy
C11 716-750 NP denotes Patients with diabetic nephropathy
C13 944-970 NP denotes NF-kappaB binding activity
C14 1149-1175 NP denotes a 3 day intervention study
C15 1179-1184 NP denotes which
C16 1286-1306 NP denotes diabetic nephropathy
C17 1397-1448 NP denotes ex vivo isolated peripheral blood mononuclear cells
C18 1486-1520 NP denotes the transcription factor NF-kappaB
C19 1593-1610 NP denotes diabetes mellitus
C20 1641-1661 NP denotes diabetic nephropathy
C21 1782-1808 NP denotes NF-kappaB binding activity
R1 C4 C3 coref-ident the transcription factor NF-kappaB,the oxidative-stress sensitive transcription factor NF-kappaB
R2 C6 C2 coref-ident diabetic nephropathy,diabetic nephropathy
R3 C5 C1 coref-ident patients with diabetic nephropathy,patients with diabetic nephropathy
R4 C8 C7 coref-relat which,an Electrophoretic Mobility Shift Assay based semiquantitative detection system
R5 C12 C6 coref-ident diabetic nephropathy,diabetic nephropathy
R6 C11 C5 coref-ident Patients with diabetic nephropathy,patients with diabetic nephropathy
R7 C15 C14 coref-relat which,a 3 day intervention study
R8 C16 C12 coref-ident diabetic nephropathy,diabetic nephropathy
R9 C17 C9 coref-ident ex vivo isolated peripheral blood mononuclear cells,ex vivo isolated peripheral blood mononuclear cells
R10 C18 C4 coref-ident the transcription factor NF-kappaB,the transcription factor NF-kappaB
R11 C19 C10 coref-ident diabetes mellitus,diabetes mellitus (Type I and Type II)
R12 C20 C16 coref-ident diabetic nephropathy,diabetic nephropathy
R13 C21 C13 coref-ident NF-kappaB binding activity,NF-kappaB binding activity

semrep-sample

Id Subject Object Predicate Lexical cue
E1-ti-1 0-34 cui:C1321301 denotes Peripheral blood mononuclear cells
E2-ti-1 49-57 cui:C0030705 denotes patients
E3-ti-1 63-83 cui:C0011881 denotes diabetic nephropathy
E4-ti-1 89-98 cui:C0205217 denotes increased
E5-ti-1 117-133 cui:C0242606 denotes oxidative-stress
E6-ti-1 134-143 cui:C0332324 denotes sensitive
E7-ti-1 144-164 cui:C0040648 denotes transcription factor
E8-ti-1 165-174 cui:C0079904 denotes NF-kappaB
T1 58-62 PROCESS_OF denotes with
E1-ab-1 176-185 cui:C0205217 denotes Increased
E2-ab-1 186-202 cui:C0242606 denotes oxidative stress
E3-ab-1 207-217 cui:C0750530 denotes subsequent
E4-ab-1 236-256 cui:C0040648 denotes transcription factor
E5-ab-1 257-266 cui:C0079904 denotes NF-kappaB
E6-ab-1 290-301 cui:C1527148 denotes development
E7-ab-1 305-309 cui:C0205087 denotes late
E8-ab-1 310-332 cui:C0271672 denotes diabetic complications
E1-ab-2 355-371 cui:C0242606 denotes oxidative stress
E2-ab-2 382-391 cui:C0079904 denotes NF-kappaB
E3-ab-2 417-425 cui:C0030705 denotes patients
E4-ab-2 431-451 cui:C0011881 denotes diabetic nephropathy
E5-ab-2 463-499 cui:C0949632 denotes Electrophoretic Mobility Shift Assay
E6-ab-2 506-522 cui:C0522525 denotes semiquantitative
E7-ab-2 523-532 cui:C1511790 denotes detection
E8-ab-2 533-539 cui:C0449913 denotes system
E9-ab-2 570-579 cui:C0079904 denotes NF-kappaB
E10-ab-2 611-645 cui:C1321301 denotes peripheral blood mononuclear cells
T2 426-430 PROCESS_OF denotes with
E1-ab-3 662-670 cui:C0030705 denotes patients
E2-ab-3 676-693 cui:C0011849 denotes diabetes mellitus
E3-ab-3 695-699 cui:C1547052 denotes Type
E4-ab-3 706-713 cui:C0441730 denotes Type II
T3 671-675 PROCESS_OF denotes with
E1-ab-4 716-724 cui:C0030705 denotes Patients
E2-ab-4 730-750 cui:C0011881 denotes diabetic nephropathy
E3-ab-4 758-764 cui:C0205250 denotes higher
E4-ab-4 765-774 cui:C0079904 denotes NF-kappaB
E5-ab-4 783-791 cui:C0439167 denotes activity
E6-ab-4 795-832 cui:C0949632 denotes Electrophoretic Mobility Shift Assays
E7-ab-4 837-845 cui:C0442821 denotes stronger
E8-ab-4 878-887 cui:C1515877 denotes activated
E9-ab-4 906-914 cui:C0030705 denotes patients
E10-ab-4 923-928 cui:C0022646 denotes renal
E11-ab-4 929-942 cui:C0009566 denotes complications
T4 725-729 PROCESS_OF denotes with
T5 923-942 LOCATION_OF denotes renal complications
E1-ab-5 944-953 cui:C0079904 denotes NF-kappaB
E2-ab-5 962-970 cui:C0439167 denotes activity
E3-ab-5 1001-1012 cui:C0001925 denotes albuminuria
E4-ab-5 1034-1048 cui:C0145779 denotes thrombomodulin
E5-ab-5 1049-1070 cui:C0683150 denotes plasma concentrations
E6-ab-5 1098-1109 cui:C0001925 denotes albuminuria
E7-ab-5 1121-1144 cui:C0856169 denotes endothelial dysfunction
T6 1110-1120 ASSOCIATED_WITH denotes associated
E1-ab-6 1151-1156 cui:C1442459 denotes 3 day
E2-ab-6 1157-1175 cui:C0021810 denotes intervention study
E3-ab-6 1199-1210 cui:C0003402 denotes antioxidant
E4-ab-6 1211-1224 cui:C0023791 denotes thioctic acid
E5-ab-6 1226-1243 cui:C0023791 denotes alpha-lipoic acid
E6-ab-6 1249-1252 cui:C0439228 denotes day
E7-ab-6 1267-1271 cui:C0205455 denotes nine
E8-ab-6 1272-1280 cui:C0030705 denotes patients
E9-ab-6 1286-1306 cui:C0011881 denotes diabetic nephropathy
E10-ab-6 1307-1323 cui:C0242606 denotes oxidative stress
E11-ab-6 1327-1341 cui:C0444263 denotes plasma samples
E12-ab-6 1367-1376 cui:C0214222 denotes NF-kappaB
E13-ab-6 1385-1393 cui:C0439167 denotes activity
E14-ab-6 1414-1448 cui:C1321301 denotes peripheral blood mononuclear cells
T7 1199-1224 ISA denotes antioxidant thioctic acid
T8 1281-1285 PROCESS_OF denotes with
E1-ab-7 1490-1510 cui:C0040648 denotes transcription factor
E2-ab-7 1511-1520 cui:C0079904 denotes NF-kappaB
E3-ab-7 1541-1575 cui:C1321301 denotes peripheral blood mononuclear cells
E4-ab-7 1579-1587 cui:C0030705 denotes patients
E5-ab-7 1593-1610 cui:C0011849 denotes diabetes mellitus
E6-ab-7 1641-1661 cui:C0011881 denotes diabetic nephropathy
T9 1576-1578 PART_OF denotes of
T10 1588-1592 PROCESS_OF denotes with
E1-ab-8 1663-1672 cui:C0214222 denotes NF-kappaB
E2-ab-8 1699-1703 cui:C0449719 denotes part
E3-ab-8 1717-1733 cui:C0242606 denotes oxidative stress
E4-ab-8 1740-1753 cui:C0023791 denotes thioctic acid
E5-ab-8 1755-1772 cui:C0023791 denotes alpha-lipoic acid
E6-ab-8 1774-1781 cui:C0392756 denotes reduced
E7-ab-8 1782-1791 cui:C0214222 denotes NF-kappaB
E8-ab-8 1800-1808 cui:C0439167 denotes activity
T11 1673-1683 STIMULATES denotes activation
R1 E3-ti-1 T1 subjectOf diabetic nephropathy,with
R2 E2-ti-1 T1 objectOf patients,with
R3 E4-ab-2 T2 subjectOf diabetic nephropathy,with
R4 E3-ab-2 T2 objectOf patients,with
R5 E2-ab-3 T3 subjectOf diabetes mellitus,with
R6 E1-ab-3 T3 objectOf patients,with
R7 E2-ab-4 T4 subjectOf diabetic nephropathy,with
R8 E1-ab-4 T4 objectOf Patients,with
R9 E10-ab-4 T5 subjectOf renal,renal complications
R10 E11-ab-4 T5 objectOf complications,renal complications
R11 E4-ab-5 T6 subjectOf thrombomodulin,associated
R12 E7-ab-5 T6 objectOf endothelial dysfunction,associated
R13 E4-ab-6 T7 subjectOf thioctic acid,antioxidant thioctic acid
R14 E3-ab-6 T7 objectOf antioxidant,antioxidant thioctic acid
R15 E10-ab-6 T8 subjectOf oxidative stress,with
R16 E8-ab-6 T8 objectOf patients,with
R17 E3-ab-7 T9 subjectOf peripheral blood mononuclear cells,of
R18 E4-ab-7 T9 objectOf patients,of
R19 E5-ab-7 T10 subjectOf diabetes mellitus,with
R20 E4-ab-7 T10 objectOf patients,with
R21 E4-ab-8 T11 subjectOf thioctic acid,activation
R22 E1-ab-8 T11 objectOf NF-kappaB,activation

pubmed-sentences-benchmark

Id Subject Object Predicate Lexical cue
S1 0-175 Sentence denotes Peripheral blood mononuclear cells isolated from patients with diabetic nephropathy show increased activation of the oxidative-stress sensitive transcription factor NF-kappaB.
S2 176-333 Sentence denotes Increased oxidative stress and subsequent activation of the transcription factor NF-kappaB has been linked to the development of late diabetic complications.
S3 334-646 Sentence denotes To determine whether oxidative stress dependent NF-kappaB activation is evident in patients with diabetic nephropathy we used an Electrophoretic Mobility Shift Assay based semiquantitative detection system which enabled us to determine NF-kappaB activation in ex vivo isolated peripheral blood mononuclear cells.
S4 647-715 Sentence denotes We examined 33 patients with diabetes mellitus (Type I and Type II).
S5 716-943 Sentence denotes Patients with diabetic nephropathy showed higher NF-kappaB binding activity in Electrophoretic Mobility Shift Assays and stronger immunohistological staining for activated NF-kappaBp65 than patients without renal complications.
S6 944-1145 Sentence denotes NF-kappaB binding activity correlated with the degree of albuminuria (r = 0.316) and with thrombomodulin plasma concentrations (r = 0.33), indicative for albuminuria associated endothelial dysfunction.
S7 1146-1456 Sentence denotes In a 3 day intervention study in which 600 mg of the antioxidant thioctic acid (alpha-lipoic acid) per day were given to nine patients with diabetic nephropathy oxidative stress in plasma samples was decreased by 48% and NF-kappaB binding activity in ex vivo isolated peripheral blood mononuclear cells by 38%.
S8 1457-1662 Sentence denotes In conclusion, activation of the transcription factor NF-kappaB in ex vivo isolated peripheral blood mononuclear cells of patients with diabetes mellitus correlates with the degree of diabetic nephropathy.
S9 1663-1809 Sentence denotes NF-kappaB activation is at least in part dependent on oxidative stress since thioctic acid (alpha-lipoic acid) reduced NF-kappaB binding activity.

GENIAcorpus

Id Subject Object Predicate Lexical cue
T1 0-34 cell_type denotes Peripheral blood mononuclear cells
T2 49-57 multi_cell denotes patients
T3 63-83 other_name denotes diabetic nephropathy
T4 117-164 protein_family_or_group denotes oxidative-stress sensitive transcription factor
T5 165-174 protein_complex denotes NF-kappaB
T6 186-202 other_name denotes oxidative stress
T7 257-266 protein_complex denotes NF-kappaB
T8 310-332 other_name denotes diabetic complications
T9 355-371 other_name denotes oxidative stress
T10 382-391 protein_complex denotes NF-kappaB
T11 417-425 multi_cell denotes patients
T12 431-451 other_name denotes diabetic nephropathy
T13 463-499 other_name denotes Electrophoretic Mobility Shift Assay
T14 570-579 protein_complex denotes NF-kappaB
T15 602-645 cell_type denotes isolated peripheral blood mononuclear cells
T16 662-670 multi_cell denotes patients
T17 676-693 other_name denotes diabetes mellitus
T18 730-750 other_name denotes diabetic nephropathy
T19 765-774 protein_complex denotes NF-kappaB
T20 795-832 other_name denotes Electrophoretic Mobility Shift Assays
T21 888-900 protein_subunit denotes NF-kappaBp65
T22 906-914 multi_cell denotes patients
T23 923-942 other_name denotes renal complications
T24 944-953 protein_complex denotes NF-kappaB
T25 1001-1012 other_name denotes albuminuria
T26 1034-1048 protein_molecule denotes thrombomodulin
T27 1098-1109 other_name denotes albuminuria
T28 1211-1224 other_organic_compound denotes thioctic acid
T29 1226-1243 other_organic_compound denotes alpha-lipoic acid
T30 1272-1280 multi_cell denotes patients
T31 1286-1306 other_name denotes diabetic nephropathy
T32 1307-1323 other_name denotes oxidative stress
T33 1367-1376 protein_complex denotes NF-kappaB
T34 1405-1448 cell_type denotes isolated peripheral blood mononuclear cells
T35 1490-1510 protein_family_or_group denotes transcription factor
T36 1511-1520 protein_complex denotes NF-kappaB
T37 1532-1575 cell_type denotes isolated peripheral blood mononuclear cells
T38 1579-1587 multi_cell denotes patients
T39 1593-1610 other_name denotes diabetes mellitus
T40 1641-1661 other_name denotes diabetic nephropathy
T41 1663-1672 protein_complex denotes NF-kappaB
T42 1717-1733 other_name denotes oxidative stress
T43 1740-1753 other_organic_compound denotes thioctic acid
T44 1755-1772 other_organic_compound denotes alpha-lipoic acid
T45 1782-1791 protein_complex denotes NF-kappaB

metamap-sample

Id Subject Object Predicate Lexical cue
T1 1308-1324 C0242606 denotes xidative stress
T2 356-372 C0242606 denotes xidative stress
T3 187-203 C0242606 denotes xidative stress
T4 118-134 C0242606 denotes xidative-stress
T5 1580-1588 C0030705 denotes atients
T6 1273-1281 C0030705 denotes atients
T7 717-725 C0030705 denotes atients
T8 907-915 C0030705 denotes atients
T9 663-671 C0030705 denotes atients
T10 418-426 C0030705 denotes atients
T11 50-58 C0030705 denotes atients
T12 752-758 C1547282 denotes howed
T13 85-89 C1547282 denotes how
T14 1533-1541 C0205409 denotes solated
T15 1406-1414 C0205409 denotes solated
T16 603-611 C0205409 denotes solated
T17 36-44 C0205409 denotes solated
T18 1542-1576 C1321301 denotes eripheral blood mononuclear cells
T19 612-646 C1321301 denotes eripheral blood mononuclear cells.
T20 1-35 C1321301 denotes eripheral blood mononuclear cells
T21 1664-1684 C1523116 denotes F-kappaB activation
T22 1287-1307 C1442864 denotes iabetic nephropathy
T23 731-751 C1442864 denotes iabetic nephropathy
T24 432-452 C1442864 denotes iabetic nephropathy
T25 177-186 C0205217 denotes ncreased
T26 90-99 C0205217 denotes ncreased
T27 135-143 C1550474 denotes ensitive
T28 1756-1773 C0023791 denotes lpha-lipoic acid)
T29 1741-1754 C0023791 denotes hioctic acid
T30 1227-1244 C0023791 denotes lpha-lipoic acid)
T31 1212-1225 C0023791 denotes hioctic acid
T32 1158-1176 C0021810 denotes ntervention study
T33 1200-1211 C0003402 denotes ntioxidant
T34 1594-1611 C0011849 denotes iabetes mellitus
T35 766-775 C0079904 denotes F-kappaB
T36 1783-1799 C1523084 denotes F-kappaB binding
T37 1368-1385 C1523084 denotes F-kappaB binding
T38 945-961 C1523084 denotes F-kappaB binding
T39 1265-1267 C1883351 denotes o
T40 335-336 C1883351 denotes o
T41 558-560 C1883351 denotes o
T42 1525-1532 C2348480 denotes x vivo
T43 1398-1405 C2348480 denotes x vivo
T44 595-602 C2348480 denotes x vivo
T45 311-333 C0342257 denotes iabetic complications.
T46 924-929 C0022646 denotes enal
T47 1386-1394 C1561536 denotes ctivity
T48 963-971 C1561536 denotes ctivity
T49 1632-1638 C0449286 denotes egree
T50 992-998 C0449286 denotes egree
T51 1705-1714 C0851827 denotes ependent
T52 373-382 C0851827 denotes ependent
T53 1111-1121 C0332281 denotes ssociated
T54 501-506 C1705938 denotes ased
T55 1461-1471 C1707478 denotes onclusion,
T56 547-554 C0562342 denotes nabled
T57 651-659 C0332128 denotes xamined
T58 1259-1264 C1442162 denotes iven
T59 1700-1704 C0449719 denotes art
T60 707-714 C0441730 denotes ype II)
T61 456-460 C1273517 denotes sed
T62 1122-1145 C0856169 denotes ndothelial dysfunction.
T63 1328-1342 C0444263 denotes lasma samples
T64 930-943 C0009566 denotes omplications.
T65 1190-1191 C2346927 denotes g
T66 187-196 C0311404 denotes xidative
T67 534-540 C0449913 denotes ystem
T68 1050-1071 C0683150 denotes lasma concentrations
T69 1347-1356 C0205216 denotes ecreased
T70 1026-1029 C1515981 denotes nd
T71 776-792 C2266866 denotes inding activity
T72 1035-1049 C1420720 denotes hrombomodulin
T73 972-982 C1707520 denotes orrelated
T74 866-874 C0487602 denotes taining
T75 291-302 C0678723 denotes evelopment
T76 306-310 C0205087 denotes ate
T77 407-414 C0332120 denotes vident
T78 277-283 C1517892 denotes inked
T79 524-533 C1511790 denotes etection
T80 1152-1153 C0439086 denotes
T81 879-887 C1879547 denotes ctivated
T82 208-218 C0332282 denotes ubsequent
T83 1268-1271 C0205455 denotes ine
T84 838-846 C0442821 denotes tronger
T85 759-765 C0205250 denotes igher

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 440-451 HP_0000112 denotes nephropathy
T2 676-693 HP_0000819 denotes diabetes mellitus
T3 739-750 HP_0000112 denotes nephropathy
T4 1001-1012 HP_0012592 denotes albuminuria
T5 1098-1109 HP_0012592 denotes albuminuria
T6 1295-1306 HP_0000112 denotes nephropathy
T7 1593-1610 HP_0000819 denotes diabetes mellitus
T8 1650-1661 HP_0000112 denotes nephropathy