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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 378-381 Body_part denotes arm http://purl.org/sig/ont/fma/fma24890
T2 760-766 Body_part denotes breast http://purl.org/sig/ont/fma/fma9601
T3 771-776 Body_part denotes colon http://purl.org/sig/ont/fma/fma14543
T4 1003-1020 Body_part denotes respiratory tract http://purl.org/sig/ont/fma/fma265130
T5 2056-2061 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T6 2081-2084 Body_part denotes IgM http://purl.org/sig/ont/fma/fma62873
T7 2086-2089 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T8 2090-2098 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 378-381 Body_part denotes arm http://purl.obolibrary.org/obo/UBERON_0001460
T2 760-766 Body_part denotes breast http://purl.obolibrary.org/obo/UBERON_0000310
T3 771-776 Body_part denotes colon http://purl.obolibrary.org/obo/UBERON_0001155
T4 1003-1020 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 32-40 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 55-61 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T3 292-300 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 305-311 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T5 514-520 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T6 581-598 Disease denotes myeloid leukemias http://purl.obolibrary.org/obo/MONDO_0004643
T7 589-598 Disease denotes leukemias http://purl.obolibrary.org/obo/MONDO_0005059
T8 672-694 Disease denotes non-Hodgkin's lymphoma http://purl.obolibrary.org/obo/MONDO_0018908
T9 676-694 Disease denotes Hodgkin's lymphoma http://purl.obolibrary.org/obo/MONDO_0004952
T10 686-694 Disease denotes lymphoma http://purl.obolibrary.org/obo/MONDO_0005062
T11 708-716 Disease denotes leukemia http://purl.obolibrary.org/obo/MONDO_0005059
T12 771-783 Disease denotes colon cancer http://purl.obolibrary.org/obo/MONDO_0021063
T13 777-783 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T14 952-963 Disease denotes retinopathy http://purl.obolibrary.org/obo/MONDO_0005283
T15 980-995 Disease denotes cardiac disease http://purl.obolibrary.org/obo/MONDO_0005267
T16 1003-1030 Disease denotes respiratory tract infection http://purl.obolibrary.org/obo/MONDO_0024355
T17 1021-1030 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T18 1060-1068 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 1122-1139 Disease denotes Diabetes Mellitus http://purl.obolibrary.org/obo/MONDO_0005015
T20 1189-1195 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T21 1212-1229 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275
T22 1312-1318 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T23 1846-1854 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 2063-2071 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 2157-2165 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 2261-2269 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T27 2306-2312 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T28 3291-3299 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T29 3315-3321 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 93-94 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 117-118 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 138-139 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 169-179 http://purl.obolibrary.org/obo/BFO_0000030 denotes OBJECTIVES
T5 358-359 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 378-381 http://www.ebi.ac.uk/efo/EFO_0001410 denotes arm
T7 760-766 http://purl.obolibrary.org/obo/UBERON_0000310 denotes breast
T8 771-776 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colon
T9 927-929 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T10 1775-1776 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 2001-2002 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 2056-2061 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T13 2109-2110 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 2138-2142 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T15 2168-2173 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T16 2318-2321 http://purl.obolibrary.org/obo/CLO_0001562 denotes a 2
T17 2318-2321 http://purl.obolibrary.org/obo/CLO_0001563 denotes a 2
T18 2590-2593 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1:1
T19 3063-3066 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T20 3195-3198 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T21 3708-3711 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T22 3751-3752 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 10-28 Chemical denotes hydroxychloroquine http://purl.obolibrary.org/obo/CHEBI_5801
T2 225-243 Chemical denotes hydroxychloroquine http://purl.obolibrary.org/obo/CHEBI_5801
T3 392-397 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T4 1260-1264 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T5 1529-1547 Chemical denotes hydroxychloroquine http://purl.obolibrary.org/obo/CHEBI_5801
T6 1651-1669 Chemical denotes hydroxychloroquine http://purl.obolibrary.org/obo/CHEBI_5801
T7 1671-1675 Chemical denotes Amin http://purl.obolibrary.org/obo/CHEBI_32952
T8 2111-2123 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T9 2119-2123 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T10 2144-2147 Chemical denotes NAT http://purl.obolibrary.org/obo/CHEBI_82508
T11 2713-2718 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T12 2782-2787 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T13 2914-2919 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T14 3734-3740 Chemical denotes Letter http://purl.obolibrary.org/obo/CHEBI_6446

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-168 Sentence denotes Effect of hydroxychloroquine on COVID-19 prevention in cancer patients undergoing treatment: a structured summary of a study protocol for a randomised controlled trial.
T2 169-180 Sentence denotes OBJECTIVES:
T3 181-335 Sentence denotes In this study, we investigate the effect of hydroxychloroquine on the prevention of Novel Coronavirus Disease (COVID-19) in cancer patients being treated.
T4 336-349 Sentence denotes TRIAL DESIGN:
T5 350-451 Sentence denotes This is a multi-centre, two-arm, parallel-group, triple-blind, phase 2-3 randomised controlled trial.
T6 452-465 Sentence denotes PARTICIPANTS:
T7 466-547 Sentence denotes All patients over the age of 15 from 5 types of cancer are included in the study.
T8 548-836 Sentence denotes Patients with acute lymphoid and myeloid leukemias in the first line treated with curative intent, patients with high-grade non-Hodgkin's lymphoma treated with leukemia protocols and patients with non-metastatic breast and colon cancer in the first line of treatment will enter the study.
T9 837-1319 Sentence denotes The exclusion criteria will include known sensitivity to Hydroxychloroquine, weight below 35 kilograms, history of retinopathy, history of any cardiac disease, acute respiratory tract infection in the last 2 months, having COVID-19 in the first two weeks of entering the trial, having Diabetes Mellitus, having an immuno-suppressive disease other than cancer, having chronic pulmonary disease and taking immuno-suppressant drug other than chemotherapeutic agents for current cancer.
T10 1320-1437 Sentence denotes This study is performed in five academic centres affiliated to Mashhad University of Medical Sciences, Mashhad, Iran.
T11 1438-1466 Sentence denotes INTERVENTION AND COMPARATOR:
T12 1467-1579 Sentence denotes Patients are randomly assigned to two groups; one being given hydroxychloroquine and the other is given placebo.
T13 1580-1814 Sentence denotes During two months of treatment, the two groups are treated with either hydroxychloroquine (Amin® Pharmaceutical Company, Isfahan, Iran) or placebo (identical in terms of shape, colour, smell) as a single 200 mg tablet every other day.
T14 1815-1892 Sentence denotes Patients will be monitored for COVID-19 symptoms during the follow-up period.
T15 1893-2174 Sentence denotes If signs or symptoms occur (fever, cough, shortness of breath), they will be examined and investigated with a high-resolution computed tomography (CT) scan of the lungs, COVID-19 specific IgM, IgG antibody assay and a nucleic acid amplification test (NAT) for the SARS-CoV-2 virus.
T16 2175-2189 Sentence denotes MAIN OUTCOMES:
T17 2190-2335 Sentence denotes The primary end point of this study is to investigate the incidence of COVID-19 in patients being treated for their cancer over a 2-month period.
T18 2336-2350 Sentence denotes RANDOMISATION:
T19 2351-2414 Sentence denotes Randomisation will be performed using randomly permuted blocks.
T20 2415-2530 Sentence denotes By using an online website (www.randomization.com) the randomization sequence will be produced by quadruple blocks.
T21 2531-2594 Sentence denotes The allocation ratio in intervention and control groups is 1:1.
T22 2595-2614 Sentence denotes BLINDING (MASKING):
T23 2615-2719 Sentence denotes Participants and caregivers do not know whether the patient is in the intervention or the control group.
T24 2720-2799 Sentence denotes The outcome assessor and the data analyst are also blinded to group assignment.
T25 2800-2839 Sentence denotes NUMBERS TO BE RANDOMISED (SAMPLE SIZE):
T26 2840-2920 Sentence denotes The calculated total sample size is 60 patients, with 30 patients in each group.
T27 2921-2934 Sentence denotes TRIAL STATUS:
T28 2935-2996 Sentence denotes The trial began on April 14, 2020 and recruitment is ongoing.
T29 2997-3163 Sentence denotes Recruitment is anticipated to be completed by June 14, 2020 There has been no change in study protocol since approval, protocol version 1 was approved April 12, 2020.
T30 3164-3183 Sentence denotes TRIAL REGISTRATION:
T31 3184-3460 Sentence denotes This trial has been registered by the title of "Effect of Hydroxychloroquine on Novel Coronavirus Disease (COVID-19) prevention in cancer patients under treatment" in Iranian Registry of Clinical Trials (IRCT) with code "IRCT20200405046958N1", https://www.irct.ir/trial/46946.
T32 3461-3497 Sentence denotes Registration date is April 14, 2020.
T33 3498-3512 Sentence denotes FULL PROTOCOL:
T34 3513-3621 Sentence denotes The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1).
T35 3622-3802 Sentence denotes In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 55-61 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T2 305-311 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T3 514-520 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T4 581-598 Phenotype denotes myeloid leukemias http://purl.obolibrary.org/obo/HP_0012324
T5 672-694 Phenotype denotes non-Hodgkin's lymphoma http://purl.obolibrary.org/obo/HP_0012539
T6 708-716 Phenotype denotes leukemia http://purl.obolibrary.org/obo/HP_0001909
T7 771-783 Phenotype denotes colon cancer http://purl.obolibrary.org/obo/HP_0003003
T8 952-963 Phenotype denotes retinopathy http://purl.obolibrary.org/obo/HP_0000488
T9 997-1030 Phenotype denotes acute respiratory tract infection http://purl.obolibrary.org/obo/HP_0011948
T10 1122-1139 Phenotype denotes Diabetes Mellitus http://purl.obolibrary.org/obo/HP_0000819
T11 1189-1195 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T12 1312-1318 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T13 1921-1926 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T14 1928-1933 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T15 1935-1954 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T16 2306-2312 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T17 3315-3321 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664

hydroxychloroquine

Id Subject Object Predicate Lexical cue hp_id
T1 55-61 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T2 305-311 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T3 514-520 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T4 581-598 Phenotype denotes myeloid leukemias http://purl.obolibrary.org/obo/HP_0012324
T5 672-694 Phenotype denotes non-Hodgkin's lymphoma http://purl.obolibrary.org/obo/HP_0012539
T6 708-716 Phenotype denotes leukemia http://purl.obolibrary.org/obo/HP_0001909
T7 771-783 Phenotype denotes colon cancer http://purl.obolibrary.org/obo/HP_0003003
T8 952-963 Phenotype denotes retinopathy http://purl.obolibrary.org/obo/HP_0000488
T9 997-1030 Phenotype denotes acute respiratory tract infection http://purl.obolibrary.org/obo/HP_0011948
T10 1122-1139 Phenotype denotes Diabetes Mellitus http://purl.obolibrary.org/obo/HP_0000819
T11 1189-1195 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T12 1312-1318 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T13 1921-1926 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T14 1928-1933 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T15 1935-1954 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T16 2306-2312 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664
T17 3315-3321 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664