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PMC:7510993 / 5084-9010 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 227-235 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T2 1257-1262 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T3 3320-3324 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T4 3369-3373 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T43 67-75 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T44 155-163 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T45 271-279 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T46 355-363 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 480-488 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 696-704 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T49 800-808 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T50 1743-1751 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T51 1877-1884 Disease denotes malaria http://purl.obolibrary.org/obo/MONDO_0005136
T52 2185-2193 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T53 2259-2266 Disease denotes malaria http://purl.obolibrary.org/obo/MONDO_0005136
T54 3084-3096 Disease denotes tuberculosis http://purl.obolibrary.org/obo/MONDO_0018076
T55 3125-3127 Disease denotes TB http://purl.obolibrary.org/obo/MONDO_0018076
T56 3292-3294 Disease denotes TB http://purl.obolibrary.org/obo/MONDO_0018076

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T22 224-226 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T23 240-241 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 495-500 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T25 555-567 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T26 608-615 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T27 1220-1221 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 1257-1262 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T29 1278-1279 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 1509-1521 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T31 2272-2274 http://purl.obolibrary.org/obo/CLO_0037161 denotes en
T32 2333-2335 http://purl.obolibrary.org/obo/CLO_0037161 denotes en

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T3 1959-1962 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T4 2052-2055 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T5 2216-2219 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T6 2272-2274 Chemical denotes en http://purl.obolibrary.org/obo/CHEBI_30347
T7 2333-2335 Chemical denotes en http://purl.obolibrary.org/obo/CHEBI_30347
T8 2345-2348 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T9 2450-2453 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T10 2526-2529 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T11 2717-2720 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T12 2800-2803 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T13 2900-2903 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T14 2936-2939 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T15 2982-2985 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T16 3057-3060 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T17 3136-3139 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T18 3332-3335 Chemical denotes PCA http://purl.obolibrary.org/obo/CHEBI_36751|http://purl.obolibrary.org/obo/CHEBI_62248
T20 3363-3366 Chemical denotes PCA http://purl.obolibrary.org/obo/CHEBI_36751|http://purl.obolibrary.org/obo/CHEBI_62248
T22 3432-3435 Chemical denotes PCA http://purl.obolibrary.org/obo/CHEBI_36751|http://purl.obolibrary.org/obo/CHEBI_62248
T24 3480-3483 Chemical denotes BCG http://purl.obolibrary.org/obo/CHEBI_41001
T25 3744-3747 Chemical denotes GDP http://purl.obolibrary.org/obo/CHEBI_17552|http://purl.obolibrary.org/obo/CHEBI_58189
T27 3768-3771 Chemical denotes GDP http://purl.obolibrary.org/obo/CHEBI_17552|http://purl.obolibrary.org/obo/CHEBI_58189

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
108 480-490 Species denotes SARS-CoV-2 Tax:2697049
109 67-75 Disease denotes COVID-19 MESH:C000657245
110 155-163 Disease denotes COVID-19 MESH:C000657245
111 271-279 Disease denotes COVID-19 MESH:C000657245
112 355-363 Disease denotes COVID-19 MESH:C000657245
113 696-704 Disease denotes COVID-19 MESH:C000657245
115 800-808 Disease denotes COVID-19 MESH:C000657245
138 1933-1957 Species denotes bacillus Calmette–Guérin Tax:33892
139 2737-2743 Species denotes people Tax:9606
140 3117-3123 Species denotes people Tax:9606
141 1959-1962 Species denotes BCG Tax:33892
142 2052-2055 Species denotes BCG Tax:33892
143 2216-2219 Species denotes BCG Tax:33892
144 2345-2348 Species denotes BCG Tax:33892
145 2450-2453 Species denotes BCG Tax:33892
146 2526-2529 Species denotes BCG Tax:33892
147 2717-2720 Species denotes BCG Tax:33892
148 2800-2803 Species denotes BCG Tax:33892
149 2900-2903 Species denotes BCG Tax:33892
150 2936-2939 Species denotes BCG Tax:33892
151 2982-2985 Species denotes BCG Tax:33892
152 3057-3060 Species denotes BCG Tax:33892
153 3136-3139 Species denotes BCG Tax:33892
154 3480-3483 Species denotes BCG Tax:33892
155 1743-1751 Disease denotes COVID-19 MESH:C000657245
156 1877-1884 Disease denotes malaria MESH:D008288
157 2185-2193 Disease denotes COVID-19 MESH:C000657245
158 2259-2266 Disease denotes malaria MESH:D008288
159 3084-3096 Disease denotes tuberculosis MESH:D014376

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T27 0-12 Sentence denotes Data sources
T28 13-126 Sentence denotes We compiled geographic data on the number of reported COVID-19 cases per day from December 2019 to June 30, 2020.
T29 127-287 Sentence denotes We collected the numbers of COVID-19 cases for 1,020 countries/regions from various sources (see S1 Appendix for a list of data sources for the COVID-19 cases).
T30 288-448 Sentence denotes We then calculated the length of time (in days) since the onset of COVID-19 spread as defined by the date of the first confirmed case in each country or region.
T31 449-705 Sentence denotes We also examined the number of SARS-CoV-2 PCR tests conducted based on data published by the World Health Organization (WHO) (https://ourworldindata.org/covid-testing) to assess the influence of sampling effort on the number of confirmed cases of COVID-19.
T32 706-778 Sentence denotes For each country or region, we compiled several environmental variables.
T33 779-962 Sentence denotes For mapping cases of COVID-19, the longitude and latitude of the largest city and area for each country or region were extracted from GADM maps and data (https://gadm.org/index.html).
T34 963-1298 Sentence denotes Based on the geocoordinates of the cities, we collected the climatic data of mean precipitation (mm month–1) and temperature (°C) from January to June (WorldClim) using WorldClim version 2.1 climate data (https://www.worldclim.org/data/worldclim21.html) at a resolution of 2.5 arc-minutes grid cells that contained a country or region.
T35 1299-1569 Sentence denotes Regarding international travel linked to the disease transmission, we compiled the average annual number of foreign visitors (per year) for individual countries/regions from data published by the World Tourism Organization (https://www.e-unwto.org/toc/unwtotfb/current).
T36 1570-1693 Sentence denotes We then calculated the relative amount of foreign visitors per population of each country or region to use in the analysis.
T37 1694-1976 Sentence denotes Regarding region-specific host susceptibility to COVID-19, we collected data on the following three epidemiologic properties: the proportion of the population aged over 65 years, the malaria incidence (per year), and information regarding bacillus Calmette–Guérin (BCG) vaccination.
T38 1977-2203 Sentence denotes We included these attributes in our analyses based on the assumptions that BCG vaccination and/or recurrent treatment with anti-malarial medications could be associated with providing some protection against COVID-19 [13, 14].
T39 2204-3129 Sentence denotes We compiled BCG data from the WHO (https://www.who.int/malaria/data/en/) and (https://apps.who.int/gho/data/view.main.80500?lang=en) and the BCG Atlas Team (http://www.bcgatlas.org/) on the following five attributes: i) the number of years since BCG vaccination was started (BCG_year); ii) the present situation regarding BCG vaccination (BCG_type), split into all vaccinated, partly vaccinated, vaccinated once in the past, or never vaccinated; iii) the relative frequency of post-1980 (i.e., the past 40 years) BCG vaccination for people aged less than 1 year old (BCG_rate); iv) the number of BCG vaccinations (MultipleBCG), describing countries as never having vaccinated their citizens with BCG, vaccinated their citizens with BCG only once, vaccinated their citizens with BCG multiple times in the past, or currently vaccinate their citizens with BCG multiple times; and v) tuberculosis cases per 1 million people (TB).
T40 3130-3187 Sentence denotes These BCG-related variables are strongly intercorrelated.
T41 3188-3503 Sentence denotes Therefore, we reduced the dimensions of these variables (BCG_year, BCG_type, BCG_rate, MultipleBCG, and TB) by extracting the first axis of the PCA analysis: the score of the PCA 1 axis was negatively correlated with the five variables, so the PCA 1 score multiplied by –1 was defined as the BCG vaccination effect.
T42 3504-3567 Sentence denotes We also compiled socioeconomic data for each country or region.
T43 3568-3926 Sentence denotes The population size, population density (per km2) (Gridded Population of the World GPW, v4.; https://sedac.ciesin.columbia.edu/data/collection/gpw-v4), gross domestic product (GDP in US dollars), and GDP per person were obtained from national census data (World Development Indicators; https://datacatalog.worldbank.org/dataset/world-development-indicators).