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jnlpba-st-training

Id Subject Object Predicate Lexical cue
T1 13-41 protein denotes tumour necrosis factor alpha
T2 71-105 cell_type denotes peripheral blood mononuclear cells
T3 454-471 cell_type denotes mononuclear cells
T4 512-540 protein denotes tumour necrosis factor alpha
T5 542-551 protein denotes TNF-alpha
T6 632-641 protein denotes TNF-alpha
T7 663-680 cell_type denotes mononuclear cells
T8 872-881 protein denotes TNF-alpha
T9 1008-1017 protein denotes TNF-alpha
T10 1110-1119 protein denotes NF-kappaB
T11 1123-1143 protein denotes transcription factor
T12 1161-1170 protein denotes TNF-alpha
T13 1194-1203 protein denotes TNF-alpha
T14 1243-1252 protein denotes TNF-alpha

genia-medco-coref

Id Subject Object Predicate Lexical cue
C1 125-160 NP denotes thalassaemia or sickle cell anaemia
C2 181-196 NP denotes desferrioxamine
C3 364-385 NP denotes desferrioxamine (DFX)
C4 475-478 NP denotes DFX
C6 512-552 NP denotes tumour necrosis factor alpha (TNF-alpha)
C5 489-552 NP denotes the bioavailability of tumour necrosis factor alpha (TNF-alpha)
C7 553-558 NP denotes which
C8 712-747 NP denotes thalassaemia or sickle cell anaemia
C9 754-757 NP denotes DFX
C10 850-863 NP denotes DFX treatment
C11 921-924 NP denotes its
C12 964-967 NP denotes its
C13 1063-1076 NP denotes DFX treatment
C14 1110-1119 NP denotes NF-kappaB
C15 1121-1224 NP denotes a transcription factor involved in both TNF-alpha gene transcription and TNF-alpha signalling (P<0.005)
C16 1314-1327 NP denotes DFX treatment
R1 C3 C2 coref-ident desferrioxamine (DFX),desferrioxamine
R2 C4 C3 coref-ident DFX,desferrioxamine (DFX)
R3 C7 C5 coref-relat which,the bioavailability of tumour necrosis factor alpha (TNF-alpha)
R4 C8 C1 coref-ident thalassaemia or sickle cell anaemia,thalassaemia or sickle cell anaemia
R5 C9 C4 coref-ident DFX,DFX
R6 C11 C6 coref-pron its,tumour necrosis factor alpha (TNF-alpha)
R7 C12 C6 coref-pron its,tumour necrosis factor alpha (TNF-alpha)
R8 C13 C10 coref-ident DFX treatment,DFX treatment
R9 C15 C14 coref-appos a transcription factor involved in both TNF-alpha gene transcription and TNF-alpha signalling (P<0.005),NF-kappaB
R10 C16 C13 coref-ident DFX treatment,DFX treatment

semrep-sample

Id Subject Object Predicate Lexical cue
E1-ti-1 13-41 cui:C1456820 denotes tumour necrosis factor alpha
E2-ti-1 42-52 cui:C0185117 denotes expression
E3-ti-1 57-67 cui:C0037083 denotes signalling
E4-ti-1 71-105 cui:C1321301 denotes peripheral blood mononuclear cells
E5-ti-1 111-119 cui:C0030705 denotes patients
E6-ti-1 125-137 cui:C0039730 denotes thalassaemia
E7-ti-1 141-160 cui:C0002895 denotes sickle cell anaemia
E8-ti-1 166-175 cui:C0087111 denotes treatment
E9-ti-1 181-196 cui:C0011145 denotes desferrioxamine
T1 68-70 LOCATION_OF denotes in
T2 120-124 PROCESS_OF denotes with
T3 120-124 PROCESS_OF denotes with
T4 176-180 PART_OF denotes with
T5 120-124 ASSOCIATED_WITH denotes with
T6 120-124 ASSOCIATED_WITH denotes with
E1-ab-1 198-204 cui:C0332185 denotes Recent
E2-ab-1 233-237 cui:C1521828 denotes rate
E3-ab-1 241-252 cui:C0449258 denotes progression
E4-ab-1 260-273 cui:C0019693 denotes HIV-1 disease
E5-ab-1 302-320 cui:C0002875 denotes thalassaemia major
E6-ab-1 321-329 cui:C0030705 denotes patients
E7-ab-1 335-344 cui:C0087111 denotes treatment
E8-ab-1 350-360 cui:C0444956 denotes high doses
E9-ab-1 364-379 cui:C0011145 denotes desferrioxamine
T7 302-329 PROCESS_OF denotes thalassaemia major patients
T8 299-301 PROCESS_OF denotes in
E1-ab-2 391-398 cui:C0221192 denotes authors
E2-ab-2 454-471 cui:C0806987 denotes mononuclear cells
E3-ab-2 475-478 cui:C0011145 denotes DFX
E4-ab-2 493-508 cui:C0005508 denotes bioavailability
E5-ab-2 512-540 cui:C1456820 denotes tumour necrosis factor alpha
E6-ab-2 565-576 cui:C0175727 denotes stimulatory
E7-ab-2 577-583 cui:C1280500 denotes effect
E8-ab-2 587-592 cui:C0019704 denotes HIV-1
T9 479-488 INHIBITS denotes decreases
E1-ab-3 614-619 cui:C0008972 denotes study
E2-ab-3 632-641 cui:C1456820 denotes TNF-alpha
E3-ab-3 642-657 cui:C0005508 denotes bioavailability
E4-ab-3 663-680 cui:C0806987 denotes mononuclear cells
E5-ab-3 698-706 cui:C0030705 denotes patients
E6-ab-3 712-724 cui:C0039730 denotes thalassaemia
E7-ab-3 728-747 cui:C0002895 denotes sickle cell anaemia
E8-ab-3 754-757 cui:C0011145 denotes DFX
E9-ab-3 786-794 cui:C1550501 denotes subjects
T10 658-662 LOCATION_OF denotes from
T11 690-694 LOCATION_OF denotes from
T12 707-711 PROCESS_OF denotes with
E1-ab-4 850-853 cui:C0011145 denotes DFX
E2-ab-4 872-881 cui:C1456820 denotes TNF-alpha
E3-ab-4 882-897 cui:C0005508 denotes bioavailability
E4-ab-4 910-920 cui:C0311403 denotes inhibiting
E5-ab-4 925-937 cui:C0678587 denotes steady state
E6-ab-4 968-980 cui:C0544461 denotes inactivation
E7-ab-4 1008-1017 cui:C0439095 denotes TNF-alpha
E8-ab-4 1008-1034 cui:C0255813 denotes TNF-alpha receptor type II
T13 989-996 INTERACTS_WITH denotes binding
E1-ab-5 1063-1066 cui:C0011145 denotes DFX
E2-ab-5 1110-1119 cui:C0079904 denotes NF-kappaB
E3-ab-5 1123-1143 cui:C0040648 denotes transcription factor
E4-ab-5 1161-1170 cui:C1448177 denotes TNF-alpha
E5-ab-5 1171-1189 cui:C0040649 denotes gene transcription
E6-ab-5 1194-1203 cui:C1448177 denotes TNF-alpha
E7-ab-5 1204-1214 cui:C0037083 denotes signalling
T14 1144-1152 AFFECTS denotes involved
T15 1144-1152 AFFECTS denotes involved
E1-ab-6 1243-1252 cui:C1456820 denotes TNF-alpha
E2-ab-6 1253-1268 cui:C0005508 denotes bioavailability
E3-ab-6 1273-1283 cui:C0037083 denotes signalling
E4-ab-6 1300-1308 cui:C0030705 denotes patients
E5-ab-6 1314-1317 cui:C0011145 denotes DFX
T16 1297-1299 PROCESS_OF denotes in
E1-ab-7 1334-1343 cui:C0441712 denotes mechanism
E2-ab-7 1362-1369 cui:C0205421 denotes delayed
E3-ab-7 1370-1381 cui:C0449258 denotes progression
E4-ab-7 1389-1404 cui:C0019693 denotes HIV-1 infection
R1 E4-ti-1 T1 subjectOf peripheral blood mononuclear cells,in
R2 E1-ti-1 T1 objectOf tumour necrosis factor alpha,in
R3 E6-ti-1 T2 subjectOf thalassaemia,with
R4 E5-ti-1 T2 objectOf patients,with
R5 E7-ti-1 T3 subjectOf sickle cell anaemia,with
R6 E5-ti-1 T3 objectOf patients,with
R7 E9-ti-1 T4 subjectOf desferrioxamine,with
R8 E5-ti-1 T4 objectOf patients,with
R9 E9-ti-1 T5 subjectOf desferrioxamine,with
R10 E6-ti-1 T5 objectOf thalassaemia,with
R11 E9-ti-1 T6 subjectOf desferrioxamine,with
R12 E7-ti-1 T6 objectOf sickle cell anaemia,with
R13 E5-ab-1 T7 subjectOf thalassaemia major,thalassaemia major patients
R14 E6-ab-1 T7 objectOf patients,thalassaemia major patients
R15 E4-ab-1 T8 subjectOf HIV-1 disease,in
R16 E6-ab-1 T8 objectOf patients,in
R17 E3-ab-2 T9 subjectOf DFX,decreases
R18 E5-ab-2 T9 objectOf tumour necrosis factor alpha,decreases
R19 E4-ab-3 T10 subjectOf mononuclear cells,from
R20 E2-ab-3 T10 objectOf TNF-alpha,from
R21 E5-ab-3 T11 subjectOf patients,from
R22 E2-ab-3 T11 objectOf TNF-alpha,from
R23 E6-ab-3 T12 subjectOf thalassaemia,with
R24 E5-ab-3 T12 objectOf patients,with
R25 E2-ab-4 T13 subjectOf TNF-alpha,binding
R26 E8-ab-4 T13 objectOf TNF-alpha receptor type II,binding
R27 E3-ab-5 T14 subjectOf transcription factor,involved
R28 E5-ab-5 T14 objectOf gene transcription,involved
R29 E3-ab-5 T15 subjectOf transcription factor,involved
R30 E7-ab-5 T15 objectOf signalling,involved
R31 E3-ab-6 T16 subjectOf signalling,in
R32 E4-ab-6 T16 objectOf patients,in

pubmed-sentences-benchmark

Id Subject Object Predicate Lexical cue
S1 0-197 Sentence denotes Reduction of tumour necrosis factor alpha expression and signalling in peripheral blood mononuclear cells from patients with thalassaemia or sickle cell anaemia upon treatment with desferrioxamine.
S2 198-386 Sentence denotes Recent evidence indicates that the rate of progression of the HIV-1 disease is significantly reduced in thalassaemia major patients upon treatment with high doses of desferrioxamine (DFX).
S3 387-605 Sentence denotes The authors have previously demonstrated that in vitro exposure of mononuclear cells to DFX decreases the bioavailability of tumour necrosis factor alpha (TNF-alpha) which has a stimulatory effect on HIV-1 replication.
S4 606-814 Sentence denotes In this study, therefore, TNF-alpha bioavailability from mononuclear cells isolated from 10 patients with thalassaemia or sickle cell anaemia given DFX as compared to 10 untreated subjects has been evaluated.
S5 815-1044 Sentence denotes Evidence is presented showing that DFX treatment reduces TNF-alpha bioavailability (P<0.05) by inhibiting its steady state (P<0.05) and by enhancing its inactivation through binding to soluble TNF-alpha receptor type II (P<0.05).
S6 1045-1225 Sentence denotes We also show that DFX treatment limits the in vivo activation of NF-kappaB, a transcription factor involved in both TNF-alpha gene transcription and TNF-alpha signalling (P<0.005).
S7 1226-1328 Sentence denotes We conclude that TNF-alpha bioavailability and signalling are impaired in patients upon DFX treatment.
S8 1329-1413 Sentence denotes This mechanism may contribute to delayed progression of the HIV-1 infection in vivo.

GENIAcorpus

Id Subject Object Predicate Lexical cue
T1 13-41 protein_molecule denotes tumour necrosis factor alpha
T2 71-105 cell_type denotes peripheral blood mononuclear cells
T3 111-119 multi_cell denotes patients
T4 125-137 other_name denotes thalassaemia
T5 141-160 other_name denotes sickle cell anaemia
T6 181-196 other_organic_compound denotes desferrioxamine
T7 260-265 virus denotes HIV-1
T8 302-314 other_name denotes thalassaemia
T9 321-329 multi_cell denotes patients
T10 364-379 other_organic_compound denotes desferrioxamine
T11 454-471 cell_type denotes mononuclear cells
T12 475-478 other_organic_compound denotes DFX
T13 512-540 protein_molecule denotes tumour necrosis factor alpha
T14 542-551 protein_molecule denotes TNF-alpha
T15 587-592 virus denotes HIV-1
T16 632-641 protein_molecule denotes TNF-alpha
T17 663-680 cell_type denotes mononuclear cells
T18 698-706 multi_cell denotes patients
T19 712-724 other_name denotes thalassaemia
T20 728-747 other_name denotes sickle cell anaemia
T21 754-757 other_organic_compound denotes DFX
T22 776-794 multi_cell denotes untreated subjects
T23 850-853 other_organic_compound denotes DFX
T24 872-881 protein_molecule denotes TNF-alpha
T25 1008-1017 protein_molecule denotes TNF-alpha
T26 1063-1066 other_organic_compound denotes DFX
T27 1088-1106 other_name denotes in vivo activation
T28 1110-1119 protein_complex denotes NF-kappaB
T29 1123-1143 protein_family_or_group denotes transcription factor
T30 1161-1170 protein_molecule denotes TNF-alpha
T31 1194-1203 protein_molecule denotes TNF-alpha
T32 1243-1252 protein_molecule denotes TNF-alpha
T33 1300-1308 multi_cell denotes patients
T34 1314-1317 other_organic_compound denotes DFX
T35 1389-1394 virus denotes HIV-1

metamap-sample

Id Subject Object Predicate Lexical cue
T1 713-725 C0039730 denotes halassaemia
T2 126-138 C0039730 denotes halassaemia
T3 729-748 C0002895 denotes ickle cell anaemia
T4 142-160 C0002895 denotes ickle cell anaemia
T5 1244-1253 C1456820 denotes NF-alpha
T6 873-882 C1456820 denotes NF-alpha
T7 633-642 C1456820 denotes NF-alpha
T8 513-541 C1456820 denotes umour necrosis factor alpha
T9 14-42 C1456820 denotes umour necrosis factor alpha
T10 1315-1318 C0011145 denotes FX
T11 1064-1066 C0011145 denotes FX
T12 851-854 C0011145 denotes FX
T13 755-758 C0011145 denotes FX
T14 476-479 C0011145 denotes FX
T15 365-380 C0011145 denotes esferrioxamine
T16 182-197 C0011145 denotes esferrioxamine.
T17 1301-1309 C0030705 denotes atients
T18 699-707 C0030705 denotes atients
T19 322-330 C0030705 denotes atients
T20 112-120 C0030705 denotes atients
T21 1274-1284 C3537152 denotes ignalling
T22 1205-1215 C3537152 denotes ignalling
T23 58-68 C3537152 denotes ignalling
T24 480-489 C0392756 denotes ecreases
T25 292-299 C0392756 denotes educed
T26 1-10 C0392756 denotes eduction
T27 1319-1328 C0087111 denotes reatment.
T28 1068-1077 C0087111 denotes reatment
T29 855-864 C0087111 denotes reatment
T30 336-345 C0087111 denotes reatment
T31 167-176 C0087111 denotes reatment
T32 43-53 C0185117 denotes xpression
T33 1390-1395 C0019704 denotes IV-1
T34 588-593 C0019704 denotes IV-1
T35 261-266 C0019704 denotes IV-1
T36 1254-1269 C0005508 denotes ioavailability
T37 883-898 C0005508 denotes ioavailability
T38 643-658 C0005508 denotes ioavailability
T39 494-509 C0005508 denotes ioavailability
T40 1230-1238 C0917903 denotes onclude
T41 1371-1381 C0242656 denotes rogression
T42 242-253 C0242656 denotes rogression
T43 1009-1035 C0255813 denotes NF-alpha receptor type II
T44 1217-1218 C2603361 denotes <
T45 1254-1269 C1706947 denotes ioavailability
T46 883-898 C1706947 denotes ioavailability
T47 643-658 C1706947 denotes ioavailability
T48 494-509 C1706947 denotes ioavailability
T49 805-814 C0220825 denotes valuated.
T50 911-921 C3463820 denotes nhibiting
T51 1172-1190 C0040649 denotes ene transcription
T52 594-605 C0598312 denotes eplication.
T53 1124-1143 C0040648 denotes ranscription factor
T54 1396-1405 C0009450 denotes nfection
T55 1054-1058 C1547282 denotes how
T56 838-845 C1547282 denotes howing
T57 816-824 C0332120 denotes vidence
T58 206-214 C0332120 denotes vidence
T59 1406-1413 C1515655 denotes n vivo.
T60 1089-1096 C1515655 denotes n vivo
T61 455-472 C0806987 denotes ononuclear cells
T62 392-399 C0221193 denotes uthors
T63 1078-1084 C0439801 denotes imits
T64 1335-1344 C0441712 denotes echanism
T65 828-837 C0449450 denotes resented
T66 615-620 C2603343 denotes tudy,
T67 926-938 C0678587 denotes teady state
T68 1097-1120 C1523116 denotes ctivation of NF-kappaB,
T69 303-321 C0002875 denotes halassaemia major
T70 948-951 C1515981 denotes nd
T71 1289-1297 C0221099 denotes mpaired
T72 969-981 C0544461 denotes nactivation
T73 682-690 C0205409 denotes solated
T74 762-770 C1707455 denotes ompared
T75 777-786 C0332155 denotes ntreated
T76 955-964 C2349975 denotes nhancing
T77 578-584 C1280500 denotes ffect
T78 443-451 C0332157 denotes xposure
T79 1349-1359 C1880177 denotes ontribute
T80 1363-1370 C0205421 denotes elayed
T81 1145-1153 C1314939 denotes nvolved
T82 234-238 C0871208 denotes ate
T83 787-795 C1706203 denotes ubjects
T84 199-205 C0332185 denotes ecent
T85 1009-1018 C2003941 denotes NF-alpha
T86 1001-1008 C1749467 denotes oluble
T87 990-997 C1167622 denotes inding

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 512-518 HP_0002664 denotes tumour
T2 740-747 HP_0001903 denotes anaemia