PubMed:32586363
Annnotations
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 |