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PMC:3589482 / 6738-7109 JSONTXT

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bionlp-st-ge-2016-spacy-parsed

Id Subject Object Predicate Lexical cue
T3794 370-371 . denotes .
T3793 369-370 -RRB- denotes )
T3792 359-369 NNPS denotes Biosystems
T3791 351-358 NNP denotes Applied
T3790 350-351 -LRB- denotes (
T3789 348-349 -RRB- denotes )
T3788 335-348 NNP denotes Mm00607939_s1
T3787 334-335 -LRB- denotes (
T3786 326-333 JJ denotes β-actin
T3785 322-325 CC denotes and
T3784 320-321 -RRB- denotes )
T3783 307-320 NNP denotes Mm00843434_s1
T3782 306-307 -LRB- denotes (
T3781 300-305 NNP denotes Cebpb
T3780 298-299 , denotes ,
T3779 297-298 -RRB- denotes )
T3778 284-297 NNP denotes Mm00440905_m1
T3777 283-284 -LRB- denotes (
T3776 265-282 NNP denotes Serpinb2/SerpinB2
T3775 261-264 IN denotes for
T3774 253-260 NNS denotes primers
T3773 249-252 NNP denotes 20X
T3772 238-248 NNP denotes Expression
T3771 233-237 NNP denotes Gene
T3770 231-232 NNP denotes ®
T3769 225-231 NNP denotes TaqMan
T3768 219-224 VBG denotes using
T3767 209-218 VBN denotes performed
T3766 205-208 VBD denotes was
T3765 200-204 NNP denotes qPCR
T3764 198-199 . denotes .
T3763 197-198 -RRB- denotes )
T3762 187-197 NNPS denotes Biosystems
T3761 179-186 NNP denotes Applied
T3760 178-179 -LRB- denotes (
T3759 169-177 NNP denotes Reagents
T3758 155-168 NNP denotes Transcription
T3757 147-154 VB denotes Reverse
T3756 145-146 NNP denotes ®
T3755 139-145 NNP denotes TaqMan
T3754 133-138 VBG denotes using
T3753 121-132 VBN denotes transcribed
T3752 113-120 JJ denotes reverse
T3751 109-112 VBD denotes was
T3750 105-108 NNP denotes RNA
T3749 99-104 JJ denotes total
T3748 96-98 IN denotes of
T3747 93-95 NN denotes µg
T3746 91-92 CD denotes 1
T3745 89-90 , denotes ,
T3744 80-89 NN denotes synthesis
T3743 75-79 NNP denotes cDNA
T3742 71-74 IN denotes For
T3741 69-70 . denotes .
T3740 64-69 NNS denotes cells
T3739 59-63 IN denotes from
T3738 55-58 NNP denotes RNA
T3737 49-54 JJ denotes total
T3736 41-48 VB denotes isolate
T3735 38-40 TO denotes to
T3734 33-37 VBN denotes used
T3733 29-32 VBD denotes was
T3732 27-28 -RRB- denotes )
T3731 21-27 NNP denotes Qiagen
T3730 20-21 -LRB- denotes (
T3729 16-19 NNP denotes Kit
T3728 11-15 NNP denotes Mini
T3727 4-10 NNP denotes RNeasy
T3726 0-3 DT denotes The
R2705 T3726 T3729 det The,Kit
R2706 T3727 T3729 compound RNeasy,Kit
R2707 T3728 T3729 compound Mini,Kit
R2708 T3729 T3734 nsubjpass Kit,used
R2709 T3730 T3729 punct (,Kit
R2710 T3731 T3729 appos Qiagen,Kit
R2711 T3732 T3729 punct ),Kit
R2712 T3733 T3734 auxpass was,used
R2713 T3734 T3734 ROOT used,used
R2714 T3735 T3736 aux to,isolate
R2715 T3736 T3734 xcomp isolate,used
R2716 T3737 T3738 amod total,RNA
R2717 T3738 T3736 dobj RNA,isolate
R2718 T3739 T3736 prep from,isolate
R2719 T3740 T3739 pobj cells,from
R2720 T3741 T3734 punct .,used
R2721 T3742 T3751 prep For,was
R2722 T3743 T3744 compound cDNA,synthesis
R2723 T3744 T3742 pobj synthesis,For
R2724 T3745 T3751 punct ",",was
R2725 T3746 T3747 nummod 1,µg
R2726 T3747 T3751 nsubj µg,was
R2727 T3748 T3747 prep of,µg
R2728 T3749 T3750 amod total,RNA
R2729 T3750 T3748 pobj RNA,of
R2730 T3751 T3751 ROOT was,was
R2731 T3752 T3753 advmod reverse,transcribed
R2732 T3753 T3751 conj transcribed,was
R2733 T3754 T3753 advcl using,transcribed
R2734 T3755 T3756 compound TaqMan,®
R2735 T3756 T3757 nsubj ®,Reverse
R2736 T3757 T3754 xcomp Reverse,using
R2737 T3758 T3759 compound Transcription,Reagents
R2738 T3759 T3757 dobj Reagents,Reverse
R2739 T3760 T3762 punct (,Biosystems
R2740 T3761 T3762 compound Applied,Biosystems
R2741 T3762 T3759 appos Biosystems,Reagents
R2742 T3763 T3762 punct ),Biosystems
R2743 T3764 T3757 punct .,Reverse
R2744 T3765 T3767 nsubjpass qPCR,performed
R2745 T3766 T3767 auxpass was,performed
R2746 T3767 T3767 ROOT performed,performed
R2747 T3768 T3767 advcl using,performed
R2748 T3769 T3773 compound TaqMan,20X
R2749 T3770 T3773 compound ®,20X
R2750 T3771 T3773 compound Gene,20X
R2751 T3772 T3773 compound Expression,20X
R2752 T3773 T3774 compound 20X,primers
R2753 T3774 T3768 dobj primers,using
R2754 T3775 T3768 prep for,using
R2755 T3776 T3775 pobj Serpinb2/SerpinB2,for
R2756 T3777 T3778 punct (,Mm00440905_m1
R2757 T3778 T3776 appos Mm00440905_m1,Serpinb2/SerpinB2
R2758 T3779 T3776 punct ),Serpinb2/SerpinB2
R2759 T3780 T3776 punct ",",Serpinb2/SerpinB2
R2760 T3781 T3776 conj Cebpb,Serpinb2/SerpinB2
R2761 T3782 T3783 punct (,Mm00843434_s1
R2762 T3783 T3781 appos Mm00843434_s1,Cebpb
R2763 T3784 T3783 punct ),Mm00843434_s1
R2764 T3785 T3781 cc and,Cebpb
R2765 T3786 T3781 conj β-actin,Cebpb
R2766 T3787 T3786 punct (,β-actin
R2767 T3788 T3786 appos Mm00607939_s1,β-actin
R2768 T3789 T3786 punct ),β-actin
R2769 T3790 T3792 punct (,Biosystems
R2770 T3791 T3792 compound Applied,Biosystems
R2771 T3792 T3786 appos Biosystems,β-actin
R2772 T3793 T3767 punct ),performed
R2773 T3794 T3767 punct .,performed

pmc-enju-pas

Id Subject Object Predicate Lexical cue
T3673 351-352 -RRB- denotes A
T3672 341-351 NNP denotes 7939_s1) (
T3671 334-341 NNP denotes (Mm0060
T3670 332-333 -LRB- denotes n
T3669 331-332 -RRB- denotes i
T3668 318-331 NN denotes s1) and β-act
T3667 317-318 -LRB- denotes _
T3666 310-317 NN denotes 0843434
T3665 307-310 CC denotes Mm0
T3664 306-307 -RRB- denotes (
T3663 292-305 NN denotes 05_m1), Cebpb
T3662 291-292 -LRB- denotes 9
T3661 286-291 NN denotes 00440
T3660 285-286 -COMMA- denotes m
T3659 284-285 -RRB- denotes M
T3658 271-284 NN denotes b2/SerpinB2 (
T3657 270-271 -LRB- denotes n
T3656 253-270 NN denotes primers for Serpi
T3655 250-253 IN denotes 0X
T3654 243-250 NN denotes ssion 2
T3653 240-243 NN denotes pre
T3652 230-240 NN denotes n® Gene Ex
T3651 226-230 NNP denotes aqMa
T3650 219-226 NNP denotes using T
T3649 214-219 VB denotes rmed
T3648 205-214 VB denotes was perfo
T3647 202-205 VB denotes CR
T3646 198-202 NN denotes . qP
T3645 197-198 -RRB- denotes )
T3644 187-197 NNP denotes Biosystems
T3643 179-186 NNP denotes Applied
T3642 178-179 -LRB- denotes (
T3641 169-177 NN denotes Reagents
T3640 155-168 NN denotes Transcription
T3639 147-154 NNP denotes Reverse
T3638 139-146 NNP denotes TaqMan®
T3637 133-138 VB denotes using
T3636 121-132 VB denotes transcribed
T3635 113-120 RB denotes reverse
T3634 109-112 VB denotes was
T3633 105-108 NN denotes RNA
T3632 99-104 JJ denotes total
T3631 96-98 IN denotes of
T3630 93-95 NN denotes µg
T3629 91-92 CD denotes 1
T3628 89-90 -COMMA- denotes ,
T3627 80-89 NN denotes synthesis
T3626 75-79 NN denotes cDNA
T3625 71-74 IN denotes For
T3624 64-69 NN denotes cells
T3623 59-63 IN denotes from
T3622 55-58 NN denotes RNA
T3621 49-54 JJ denotes total
T3620 41-48 VB denotes isolate
T3619 38-40 TO denotes to
T3618 33-37 VB denotes used
T3617 29-32 VB denotes was
T3616 27-28 -RRB- denotes )
T3615 21-27 NN denotes Qiagen
T3614 20-21 -LRB- denotes (
T3613 16-19 NNP denotes Kit
T3612 11-15 NNP denotes Mini
T3611 4-10 NNP denotes RNeasy
T3610 0-3 DT denotes The
R2630 T3613 T3614 arg1Of Kit,(
R2632 T3613 T3618 arg2Of Kit,used
R2633 T3613 T3620 arg1Of Kit,isolate
R2634 T3615 T3614 arg2Of Qiagen,(
R2637 T3620 T3618 arg3Of isolate,used
R2638 T3620 T3619 arg1Of isolate,to
R2639 T3620 T3623 arg1Of isolate,from
R2640 T3622 T3620 arg2Of RNA,isolate
R2641 T3622 T3621 arg1Of RNA,total
R2642 T3624 T3623 arg2Of cells,from
R2643 T3627 T3625 arg2Of synthesis,For
R2644 T3627 T3626 arg1Of synthesis,cDNA
R2645 T3630 T3629 arg1Of µg,1
R2646 T3630 T3631 arg1Of µg,of
R2647 T3630 T3634 arg1Of µg,was
R2648 T3630 T3636 arg2Of µg,transcribed
R2649 T3630 T3637 arg1Of µg,using
R2650 T3633 T3631 arg2Of RNA,of
R2651 T3633 T3632 arg1Of RNA,total
R2652 T3636 T3625 arg1Of transcribed,For
R2653 T3636 T3628 arg1Of transcribed,","
R2654 T3636 T3634 arg2Of transcribed,was
R2655 T3636 T3635 arg1Of transcribed,reverse
R2656 T3636 T3637 modOf transcribed,using
R2657 T3639 T3638 arg1Of Reverse,TaqMan®
R2658 T3641 T3637 arg2Of Reagents,using
R2659 T3641 T3639 arg1Of Reagents,Reverse
R2660 T3641 T3640 arg1Of Reagents,Transcription
R2661 T3641 T3642 arg1Of Reagents,(
R2662 T3641 T3647 modOf Reagents,CR
R2663 T3644 T3642 arg2Of Biosystems,(
R2664 T3644 T3643 arg1Of Biosystems,Applied
R2665 T3645 T3642 arg3Of ),(
R2666 T3646 T3647 arg1Of . qP,CR
R2667 T3646 T3648 arg2Of . qP,was perfo
R2668 T3648 T3647 arg2Of was perfo,CR
R2669 T3649 T3648 arg3Of rmed ,was perfo
R2670 T3651 T3650 arg1Of aqMa,using T
R2671 T3654 T3649 arg2Of ssion 2,rmed
R2672 T3654 T3651 arg1Of ssion 2,aqMa
R2673 T3654 T3652 arg1Of ssion 2,n® Gene Ex
R2674 T3654 T3653 arg1Of ssion 2,pre
R2675 T3654 T3655 arg1Of ssion 2,0X
R2676 T3654 T3670 arg1Of ssion 2,n
R2677 T3656 T3657 arg1Of primers for Serpi,n
R2678 T3656 T3660 arg1Of primers for Serpi,m
R2679 T3658 T3657 arg2Of b2/SerpinB2 (,n
R2680 T3659 T3657 arg3Of M,n
R2681 T3660 T3665 arg1Of m,Mm0
R2682 T3661 T3660 arg2Of 00440,m
R2683 T3661 T3662 arg1Of 00440,9
R2684 T3663 T3662 arg2Of "05_m1), Cebpb",9
R2685 T3664 T3662 arg3Of (,9
R2686 T3665 T3655 arg2Of Mm0,0X
R2687 T3666 T3665 arg2Of 0843434,Mm0
R2688 T3666 T3667 arg1Of 0843434,_
R2689 T3668 T3667 arg2Of s1) and β-act,_
R2690 T3669 T3667 arg3Of i,_
R2691 T3672 T3670 arg2Of 7939_s1) (,n
R2692 T3672 T3671 arg1Of 7939_s1) (,(Mm0060
R2693 T3673 T3670 arg3Of A,n
R2627 T3613 T3610 arg1Of Kit,The
R2628 T3613 T3611 arg1Of Kit,RNeasy
R2629 T3613 T3612 arg1Of Kit,Mini
R2631 T3613 T3617 arg1Of Kit,was
R2635 T3616 T3614 arg3Of ),(
R2636 T3618 T3617 arg2Of used,was

bionlp-st-ge-2016-test-proteins

Id Subject Object Predicate Lexical cue
T3590 326-333 Protein denotes β-actin
T3589 300-305 Protein denotes Cebpb
T3588 274-282 Protein denotes SerpinB2
T3587 265-273 Protein denotes Serpinb2

bionlp-st-ge-2016-uniprot

Id Subject Object Predicate Lexical cue
T3680 326-333 http://www.uniprot.org/uniprot/P60709 denotes β-actin
T3679 300-305 http://www.uniprot.org/uniprot/P28033 denotes Cebpb

GO-BP

Id Subject Object Predicate Lexical cue
T3594 233-248 http://purl.obolibrary.org/obo/GO_0010467 denotes Gene Expression
T3593 155-168 http://purl.obolibrary.org/obo/GO_0006351 denotes Transcription
T3592 147-168 http://purl.obolibrary.org/obo/GO_0001171 denotes Reverse Transcription
T3591 80-89 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis

GO-CC

Id Subject Object Predicate Lexical cue
T3595 64-69 http://purl.obolibrary.org/obo/GO_0005623 denotes cells

sentences

Id Subject Object Predicate Lexical cue
T3582 71-371 Sentence denotes For cDNA synthesis, 1 µg of total RNA was reverse transcribed using TaqMan® Reverse Transcription Reagents (Applied Biosystems). qPCR was performed using TaqMan® Gene Expression 20X primers for Serpinb2/SerpinB2 (Mm00440905_m1), Cebpb (Mm00843434_s1) and β-actin (Mm00607939_s1) (Applied Biosystems).
T3581 0-70 Sentence denotes The RNeasy Mini Kit (Qiagen) was used to isolate total RNA from cells.
T43 0-70 Sentence denotes The RNeasy Mini Kit (Qiagen) was used to isolate total RNA from cells.
T44 71-371 Sentence denotes For cDNA synthesis, 1 µg of total RNA was reverse transcribed using TaqMan® Reverse Transcription Reagents (Applied Biosystems). qPCR was performed using TaqMan® Gene Expression 20X primers for Serpinb2/SerpinB2 (Mm00440905_m1), Cebpb (Mm00843434_s1) and β-actin (Mm00607939_s1) (Applied Biosystems).

simple1

Id Subject Object Predicate Lexical cue
T3603 326-333 Protein denotes β-actin
T3602 300-305 Protein denotes Cebpb
T3601 274-282 Protein denotes SerpinB2
T3600 265-273 Protein denotes Serpinb2

BioNLP16_DUT

Id Subject Object Predicate Lexical cue
T3678 238-248 Gene_expression denotes Expression
T3677 326-333 Protein denotes β-actin
T3676 300-305 Protein denotes Cebpb
T3675 274-282 Protein denotes SerpinB2
T3674 265-273 Protein denotes Serpinb2
R2694 T3674 T3678 themeOf Serpinb2,Expression
R2695 T3675 T3678 themeOf SerpinB2,Expression
R2696 T3676 T3678 themeOf Cebpb,Expression
R2697 T3677 T3678 themeOf β-actin,Expression

BioNLP16_Messiy

Id Subject Object Predicate Lexical cue
T3692 326-333 Protein denotes β-actin
T3691 300-305 Protein denotes Cebpb
T3690 274-282 Protein denotes SerpinB2
T3689 265-273 Protein denotes Serpinb2

DLUT931

Id Subject Object Predicate Lexical cue
T3684 326-333 Protein denotes β-actin
T3683 300-305 Protein denotes Cebpb
T3682 274-282 Protein denotes SerpinB2
T3681 265-273 Protein denotes Serpinb2

bionlp-st-ge-2016-test-ihmc

Id Subject Object Predicate Lexical cue
T3719 225-260 Gene_expression denotes TaqMan® Gene Expression 20X primers
T3718 59-69 Entity denotes from cells
T3717 99-108 Protein denotes total RNA
T3716 49-58 Protein denotes total RNA
T3713 300-321 Protein denotes Cebpb (Mm00843434_s1)
T3712 11-28 Protein denotes Mini Kit (Qiagen)
T3711 326-349 Protein denotes β-actin (Mm00607939_s1)
T3710 225-237 Protein denotes TaqMan® Gene
T3709 139-198 Entity denotes TaqMan® Reverse Transcription Reagents (Applied Biosystems)
T3708 75-89 Entity denotes cDNA synthesis
T3707 265-299 Protein denotes Serpinb2/SerpinB2 (Mm00440905_m1),
R2698 T3710 T3719 themeOf TaqMan® Gene,TaqMan® Gene Expression 20X primers

bionlp-st-ge-2016-test-tees

Id Subject Object Predicate Lexical cue
T3699 335-348 Protein denotes Mm00607939_s1
T3698 326-333 Protein denotes β-actin
T3697 307-320 Protein denotes Mm00843434_s1
T3696 300-305 Protein denotes Cebpb
T3695 284-297 Protein denotes Mm00440905_m1
T3694 274-282 Protein denotes SerpinB2
T3693 265-273 Protein denotes Serpinb2

testone

Id Subject Object Predicate Lexical cue
T3571 326-333 Protein denotes β-actin
T3570 300-305 Protein denotes Cebpb
T3569 274-282 Protein denotes SerpinB2
T3568 265-273 Protein denotes Serpinb2

test3

Id Subject Object Predicate Lexical cue
T3579 326-333 Protein denotes β-actin
T3578 300-305 Protein denotes Cebpb
T3577 274-282 Protein denotes SerpinB2
T3576 265-273 Protein denotes Serpinb2
T3575 326-333 Protein denotes β-actin
T3574 300-305 Protein denotes Cebpb
T3573 274-282 Protein denotes SerpinB2
T3572 265-273 Protein denotes Serpinb2