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jnlpba-st-training

Id Subject Object Predicate Lexical cue
T1 386-402 cell_type denotes monocytoid cells
T2 527-535 protein denotes lysozyme
T3 539-547 protein denotes protease
T4 611-623 cell_line denotes T cell lines
T5 698-716 cell_type denotes HIV-infected cells
T6 731-740 protein denotes NF-kappaB

genia-medco-coref

Id Subject Object Predicate Lexical cue
C1 14-60 NP denotes human immunodeficiency virus type 1 expression
C2 64-85 NP denotes Gardnerella vaginalis
C3 87-111 NP denotes Bacterial vaginosis (BV)
C4 222-243 NP denotes Gardnerella vaginalis
C6 305-307 NP denotes BV
C5 294-307 NP denotes women with BV
C7 309-329 NP denotes G. vaginalis lysates
C8 368-382 NP denotes HIV expression
C9 549-569 NP denotes G. vaginalis lysates
C10 585-599 NP denotes HIV expression
C11 625-645 NP denotes G. vaginalis lysates
C12 783-795 NP denotes G. vaginalis
C13 854-866 NP denotes G. vaginalis
C14 910-922 NP denotes G. vaginalis
C15 945-961 NP denotes HIV transmission
C16 976-990 NP denotes HIV expression
C17 1071-1087 NP denotes HIV transmission
C19 1102-1104 NP denotes BV
C18 1091-1104 NP denotes women with BV
R1 C4 C2 coref-ident Gardnerella vaginalis,Gardnerella vaginalis
R2 C6 C3 coref-ident BV,Bacterial vaginosis (BV)
R3 C8 C1 coref-ident HIV expression,human immunodeficiency virus type 1 expression
R4 C9 C7 coref-ident G. vaginalis lysates,G. vaginalis lysates
R5 C10 C8 coref-ident HIV expression,HIV expression
R6 C11 C9 coref-ident G. vaginalis lysates,G. vaginalis lysates
R7 C12 C4 coref-ident G. vaginalis,Gardnerella vaginalis
R8 C13 C12 coref-ident G. vaginalis,G. vaginalis
R9 C14 C13 coref-ident G. vaginalis,G. vaginalis
R10 C16 C10 coref-ident HIV expression,HIV expression
R11 C17 C15 coref-ident HIV transmission,HIV transmission
R12 C19 C6 coref-ident BV,BV
R13 C18 C5 coref-ident women with BV,women with BV

semrep-sample

Id Subject Object Predicate Lexical cue
E1-ti-1 14-49 cui:C0019704 denotes human immunodeficiency virus type 1
E2-ti-1 50-60 cui:C0185117 denotes expression
E3-ti-1 64-85 cui:C0017098 denotes Gardnerella vaginalis
E1-ab-1 87-106 cui:C0085166 denotes Bacterial vaginosis
E2-ab-1 134-143 cui:C0205217 denotes increased
E3-ab-1 144-148 cui:C1521828 denotes rate
E4-ab-1 152-171 cui:C1519279 denotes sexual transmission
E5-ab-1 175-216 cui:C0019704 denotes human immunodeficiency virus (HIV) type 1
E6-ab-1 222-243 cui:C0017098 denotes Gardnerella vaginalis
E7-ab-1 247-257 cui:C0332183 denotes frequently
E8-ab-1 284-290 cui:C1185740 denotes tracts
E9-ab-1 294-299 cui:C0043210 denotes women
E10-ab-1 305-307 cui:C0085166 denotes BV
T1 267-271 LOCATION_OF denotes from
T2 291-293 PART_OF denotes of
T3 300-304 PROCESS_OF denotes with
E1-ab-2 312-321 cui:C0750103 denotes vaginalis
E2-ab-2 368-371 cui:C0019682 denotes HIV
E3-ab-2 372-382 cui:C0185117 denotes expression
E4-ab-2 386-402 cui:C0333827 denotes monocytoid cells
T4 383-385 LOCATION_OF denotes in
E1-ab-3 404-415 cui:C1292856 denotes Stimulation
E2-ab-3 434-440 cui:C0205250 denotes higher
E3-ab-3 473-482 cui:C0439237 denotes degrees C
E4-ab-3 489-492 cui:C1524031 denotes min
E5-ab-3 512-521 cui:C0087111 denotes treatment
E6-ab-3 527-535 cui:C0026794 denotes lysozyme
E7-ab-3 539-547 cui:C1150095 denotes protease
T5 509-511 METHOD_OF denotes by
T6 522-526 USES denotes with
E1-ab-4 552-561 cui:C0750103 denotes vaginalis
E2-ab-4 575-584 cui:C1515877 denotes activated
E3-ab-4 585-588 cui:C0019682 denotes HIV
E4-ab-4 589-599 cui:C0185117 denotes expression
E5-ab-4 603-610 cui:C0205423 denotes certain
E6-ab-4 613-623 cui:C0007600 denotes cell lines
T7 600-602 LOCATION_OF denotes in
E1-ab-5 628-637 cui:C0750103 denotes vaginalis
E2-ab-5 656-680 cui:C0079517 denotes HIV long-terminal repeat
E3-ab-5 681-694 cui:C0040649 denotes transcription
E4-ab-5 698-701 cui:C0019682 denotes HIV
E5-ab-5 702-710 cui:C0439663 denotes infected
E6-ab-5 711-716 cui:C0007634 denotes cells
E7-ab-5 721-730 cui:C0205217 denotes increased
E8-ab-5 731-740 cui:C0079904 denotes NF-kappaB
E9-ab-5 749-757 cui:C0439167 denotes activity
E10-ab-5 773-779 cui:C1280500 denotes effect
E11-ab-5 786-795 cui:C0750103 denotes vaginalis
E12-ab-5 799-802 cui:C0019682 denotes HIV
E13-ab-5 803-816 cui:C0040649 denotes transcription
T8 773-779 INTERACTS_WITH denotes effect
E1-ab-6 836-839 cui:C0019682 denotes HIV
E2-ab-6 840-850 cui:C0033268 denotes production
E3-ab-6 857-866 cui:C0750103 denotes vaginalis
E4-ab-6 889-894 cui:C1185740 denotes tract
E5-ab-6 881-904 cui:C0729552 denotes genital tract infection
E6-ab-6 913-922 cui:C0750103 denotes vaginalis
E7-ab-6 937-941 cui:C0035647 denotes risk
E8-ab-6 945-961 cui:C1096045 denotes HIV transmission
E9-ab-6 965-975 cui:C0442808 denotes increasing
E10-ab-6 976-979 cui:C0019682 denotes HIV
E11-ab-6 980-990 cui:C0185117 denotes expression
E12-ab-6 1006-1011 cui:C1185740 denotes tract
T9 889-904 LOCATION_OF denotes tract infection
T10 905-909 PROCESS_OF denotes with
T11 991-993 LOCATION_OF denotes in
E1-ab-7 1043-1047 cui:C0449719 denotes part
E2-ab-7 1053-1062 cui:C0205217 denotes increased
E3-ab-7 1063-1067 cui:C1521828 denotes rate
E4-ab-7 1071-1087 cui:C1096045 denotes HIV transmission
E5-ab-7 1091-1096 cui:C0043210 denotes women
E6-ab-7 1102-1104 cui:C0085166 denotes BV
T12 1088-1090 PROCESS_OF denotes in
T13 1097-1101 PROCESS_OF denotes with
R1 E8-ab-1 T1 subjectOf tracts,from
R2 E6-ab-1 T1 objectOf Gardnerella vaginalis,from
R3 E8-ab-1 T2 subjectOf tracts,of
R4 E9-ab-1 T2 objectOf women,of
R5 E10-ab-1 T3 subjectOf BV,with
R6 E9-ab-1 T3 objectOf women,with
R7 E4-ab-2 T4 subjectOf monocytoid cells,in
R8 E2-ab-2 T4 objectOf HIV,in
R9 E5-ab-3 T5 subjectOf treatment,by
R10 E1-ab-3 T5 objectOf Stimulation,by
R11 E5-ab-3 T6 subjectOf treatment,with
R12 E6-ab-3 T6 objectOf lysozyme,with
R13 E6-ab-4 T7 subjectOf cell lines,in
R14 E3-ab-4 T7 objectOf HIV,in
R15 E11-ab-5 T8 subjectOf vaginalis,effect
R16 E12-ab-5 T8 objectOf HIV,effect
R17 E4-ab-6 T9 subjectOf tract,tract infection
R18 E5-ab-6 T9 objectOf genital tract infection,tract infection
R19 E6-ab-6 T10 subjectOf vaginalis,with
R20 E1-ab-6 T10 objectOf HIV,with
R21 E12-ab-6 T11 subjectOf tract,in
R22 E10-ab-6 T11 objectOf HIV,in
R23 E4-ab-7 T12 subjectOf HIV transmission,in
R24 E5-ab-7 T12 objectOf women,in
R25 E6-ab-7 T13 subjectOf BV,with
R26 E5-ab-7 T13 objectOf women,with

pubmed-sentences-benchmark

Id Subject Object Predicate Lexical cue
S1 0-86 Sentence denotes Activation of human immunodeficiency virus type 1 expression by Gardnerella vaginalis.
S2 87-308 Sentence denotes Bacterial vaginosis (BV) is associated with an increased rate of sexual transmission of human immunodeficiency virus (HIV) type 1, and Gardnerella vaginalis is frequently isolated from the genital tracts of women with BV.
S3 309-403 Sentence denotes G. vaginalis lysates were found to significantly stimulate HIV expression in monocytoid cells.
S4 404-548 Sentence denotes Stimulation was significantly higher when lysates were heated at 100 degrees C for 5 min but was reduced by treatment with lysozyme or protease.
S5 549-624 Sentence denotes G. vaginalis lysates also activated HIV expression in certain T cell lines.
S6 625-817 Sentence denotes G. vaginalis lysates activated HIV long-terminal repeat transcription in HIV-infected cells and increased NF-kappaB binding activity, indicating an effect by G. vaginalis on HIV transcription.
S7 818-1012 Sentence denotes The activation of HIV production by G. vaginalis suggests that genital tract infection with G. vaginalis increases the risk of HIV transmission by increasing HIV expression in the genital tract.
S8 1013-1105 Sentence denotes This may explain, at least in part, the increased rate of HIV transmission in women with BV.

GENIAcorpus

Id Subject Object Predicate Lexical cue
T1 14-49 virus denotes human immunodeficiency virus type 1
T2 64-85 mono_cell denotes Gardnerella vaginalis
T3 87-106 other_name denotes Bacterial vaginosis
T4 108-110 other_name denotes BV
T5 175-216 tissue denotes human immunodeficiency virus (HIV) type 1
T6 222-243 mono_cell denotes Gardnerella vaginalis
T7 276-290 body_part denotes genital tracts
T8 294-299 multi_cell denotes women
T9 305-307 other_name denotes BV
T10 309-321 mono_cell denotes G. vaginalis
T11 368-371 virus denotes HIV
T12 386-402 cell_type denotes monocytoid cells
T13 527-535 protein_family_or_group denotes lysozyme
T14 539-547 protein_family_or_group denotes protease
T15 549-561 mono_cell denotes G. vaginalis
T16 585-588 virus denotes HIV
T17 611-623 cell_line denotes T cell lines
T18 625-637 mono_cell denotes G. vaginalis
T19 656-659 virus denotes HIV
T20 698-701 virus denotes HIV
T21 731-740 protein_complex denotes NF-kappaB
T22 783-795 mono_cell denotes G. vaginalis
T23 799-802 virus denotes HIV
T24 836-839 virus denotes HIV
T25 854-866 mono_cell denotes G. vaginalis
T26 881-904 other_name denotes genital tract infection
T27 910-922 mono_cell denotes G. vaginalis
T28 945-948 virus denotes HIV
T29 976-979 virus denotes HIV
T30 998-1011 body_part denotes genital tract
T31 1071-1074 virus denotes HIV
T32 1091-1096 multi_cell denotes women
T33 1102-1104 other_name denotes BV

metamap-sample

Id Subject Object Predicate Lexical cue
T1 15-50 C0019704 denotes uman immunodeficiency virus type 1
T2 586-589 C0019682 denotes IV
T3 369-372 C0019682 denotes IV
T4 823-833 C1879547 denotes ctivation
T5 647-656 C1879547 denotes ctivated
T6 576-585 C1879547 denotes ctivated
T7 1-11 C1879547 denotes ctivation
T8 981-991 C0185117 denotes xpression
T9 590-600 C0185117 denotes xpression
T10 373-383 C0185117 denotes xpression
T11 51-61 C0185117 denotes xpression
T12 1103-1105 C0085166 denotes V.
T13 306-308 C0085166 denotes V.
T14 88-107 C0085166 denotes acterial vaginosis
T15 1072-1075 C0086418 denotes IV
T16 946-949 C0086418 denotes IV
T17 612-617 C0039194 denotes cell
T18 513-522 C0039798 denotes reatment
T19 657-681 C0079517 denotes IV long-terminal repeat
T20 553-562 C0750103 denotes aginalis
T21 313-322 C0750103 denotes aginalis
T22 550-551 C0439267 denotes .
T23 310-311 C0439267 denotes .
T24 938-942 C0035647 denotes isk
T25 540-548 C0030946 denotes rotease.
T26 528-536 C0026794 denotes ysozyme
T27 639-646 C1881488 denotes ysates
T28 563-570 C1881488 denotes ysates
T29 447-454 C1881488 denotes ysates
T30 323-330 C1881488 denotes ysates
T31 1092-1096 C0043210 denotes omen
T32 295-300 C0043210 denotes omen
T33 1072-1075 C0021051 denotes IV
T34 946-949 C0021051 denotes IV
T35 882-905 C2314882 denotes enital tract infection
T36 1007-1012 C1185740 denotes ract.
T37 285-291 C1185740 denotes racts
T38 1064-1068 C0871208 denotes ate
T39 145-149 C0871208 denotes ate
T40 999-1006 C0559522 denotes enital
T41 277-284 C0559522 denotes enital
T42 1054-1063 C0205217 denotes ncreased
T43 135-144 C0205217 denotes ncreased
T44 1069-1088 C1160716 denotes f HIV transmission
T45 943-962 C1160716 denotes f HIV transmission
T46 248-258 C0332183 denotes requently
T47 924-933 C0442805 denotes ncreases
T48 1044-1048 C0449719 denotes art,
T49 336-341 C0150312 denotes ound
T50 405-416 C1948023 denotes timulation
T51 868-876 C1705535 denotes uggests
T52 1035-1040 C0547044 denotes east
T53 732-749 C1523084 denotes F-kappaB binding
T54 490-493 C0702093 denotes in
T55 342-344 C1883351 denotes o
T56 435-441 C0205250 denotes igher
T57 619-624 C0205132 denotes ines.
T58 474-483 C0439237 denotes egrees C
T59 712-717 C0007634 denotes ells
T60 502-509 C0392756 denotes educed
T61 116-131 C0332281 denotes ssociated with
T62 774-779 C1280500 denotes ffect
T63 259-267 C0205409 denotes solated
T64 460-465 C0018837 denotes eated
T65 488-489 C0439084 denotes
T66 604-611 C1704787 denotes ertain
T67 966-976 C0442808 denotes ncreasing
T68 703-711 C0439663 denotes nfected
T69 387-403 C0333827 denotes onocytoid cells.
T70 841-851 C0033268 denotes roduction

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 181-197 HP_0002721 denotes immunodeficiency