PMC:7152911 / 115793-121124 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1823 34-43 Disease denotes infection MESH:D007239
1834 542-547 Species denotes human Tax:9606
1835 578-584 Species denotes humans Tax:9606
1836 1530-1551 Species denotes Plasmodium falciparum Tax:5833
1837 1818-1823 Species denotes human Tax:9606
1838 1081-1086 Chemical denotes water MESH:D014867
1839 1202-1207 Chemical denotes water MESH:D014867
1840 295-300 Disease denotes death MESH:D003643
1841 352-359 Disease denotes malaria MESH:D008288
1842 403-409 Disease denotes deaths MESH:D003643
1843 1590-1597 Disease denotes malaria MESH:D008288
1859 2203-2229 Species denotes Mycobacterium tuberculosis Tax:1773
1860 2262-2279 Species denotes Naegleria fowleri Tax:5763
1861 2588-2609 Species denotes Clostridium difficile Tax:1496
1862 2737-2746 Species denotes S. aureus Tax:1280
1863 2158-2168 Species denotes Legionella Tax:446
1864 2611-2613 Species denotes CD Tax:1496
1865 2656-2658 Species denotes CD Tax:1496
1866 2715-2726 Chemical denotes methicillin MESH:D008712
1867 2187-2201 Disease denotes Legionnellosis
1868 2244-2256 Disease denotes tuberculosis MESH:D014376
1869 2294-2312 Disease denotes amoebic meningitis MESH:D004404
1870 2504-2514 Disease denotes infections MESH:D007239
1871 2670-2678 Disease denotes diarrhea MESH:D003967
1872 2702-2709 Disease denotes colitis MESH:D003092
1873 2775-2785 Disease denotes infections MESH:D007239
1875 3058-3060 Species denotes CD Tax:1496
1889 4792-4800 Species denotes patients Tax:9606
1890 4961-4970 Species denotes S. aureus Tax:1280
1891 4976-4990 Species denotes S. dysenteriae Tax:622
1892 5157-5162 Species denotes algae Tax:569578
1893 4920-4933 Species denotes Campylobacter Tax:197
1894 4935-4947 Species denotes Enterococcus Tax:1351
1895 4949-4959 Species denotes Salmonella Tax:90371
1896 3509-3514 Chemical denotes water MESH:D014867
1897 5310-5315 Chemical denotes water MESH:D014867
1898 4014-4024 Disease denotes infections MESH:D007239
1899 4225-4234 Disease denotes infection MESH:D007239
1900 4619-4629 Disease denotes infections MESH:D007239
1901 4744-4754 Disease denotes infections MESH:D007239

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T14 969-980 Body_part denotes body fluids http://purl.org/sig/ont/fma/fma280556
T15 969-973 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T16 1335-1339 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T17 2810-2814 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T18 2830-2843 Body_part denotes urinary tract http://purl.org/sig/ont/fma/fma0326482

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T85 34-43 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T86 352-359 Disease denotes malaria http://purl.obolibrary.org/obo/MONDO_0005136
T87 1479-1489 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T88 1557-1567 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T89 1590-1597 Disease denotes malaria http://purl.obolibrary.org/obo/MONDO_0005136
T90 2158-2168 Disease denotes Legionella http://purl.obolibrary.org/obo/MONDO_0005824
T91 2217-2229 Disease denotes tuberculosis http://purl.obolibrary.org/obo/MONDO_0018076
T92 2244-2256 Disease denotes tuberculosis http://purl.obolibrary.org/obo/MONDO_0018076
T93 2302-2312 Disease denotes meningitis http://purl.obolibrary.org/obo/MONDO_0004796|http://purl.obolibrary.org/obo/MONDO_0021108
T95 2504-2514 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T96 2670-2678 Disease denotes diarrhea http://purl.obolibrary.org/obo/MONDO_0001673
T97 2702-2709 Disease denotes colitis http://purl.obolibrary.org/obo/MONDO_0005292
T98 2748-2752 Disease denotes MRSA http://purl.obolibrary.org/obo/MONDO_0100073
T99 2775-2788 Disease denotes infections in http://purl.obolibrary.org/obo/MONDO_0005550
T100 2873-2883 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T101 3039-3049 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T102 3099-3103 Disease denotes MRSA http://purl.obolibrary.org/obo/MONDO_0100073
T103 4014-4024 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T104 4225-4234 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T105 4619-4629 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T106 4726-4754 Disease denotes Hospital-acquired infections http://purl.obolibrary.org/obo/MONDO_0043544

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T102 496-497 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 542-547 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T104 578-584 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T105 969-980 http://purl.obolibrary.org/obo/UBERON_0006314 denotes body fluids
T106 1200-1201 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 1439-1448 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T108 1439-1448 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T109 1505-1514 http://purl.obolibrary.org/obo/NCBITaxon_7157 denotes mosquitos
T110 1701-1708 http://purl.obolibrary.org/obo/BFO_0000030 denotes objects
T111 1745-1752 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T112 1756-1763 http://purl.obolibrary.org/obo/BFO_0000030 denotes objects
T113 1818-1823 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T114 2127-2128 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T115 2329-2337 http://purl.obolibrary.org/obo/NCBITaxon_2 denotes bacteria
T116 2830-2843 http://purl.obolibrary.org/obo/UBERON_0001008 denotes urinary tract
T117 3128-3137 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T118 3128-3137 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T119 3926-3927 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T120 4360-4367 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T121 4372-4379 http://purl.obolibrary.org/obo/BFO_0000030 denotes objects
T122 4557-4560 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T123 4578-4579 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T124 4631-4632 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T125 4834-4837 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T126 5208-5216 http://purl.obolibrary.org/obo/NCBITaxon_2 denotes bacteria

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T33481 1081-1086 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T62506 1202-1207 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T37111 2523-2527 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T33883 2548-2552 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T9618 2564-2567 Chemical denotes MDR http://purl.obolibrary.org/obo/CHEBI_53218
T89888 2611-2613 Chemical denotes CD http://purl.obolibrary.org/obo/CHEBI_8673
T97800 2656-2658 Chemical denotes CD http://purl.obolibrary.org/obo/CHEBI_8673
T69352 2683-2693 Chemical denotes antibiotic http://purl.obolibrary.org/obo/CHEBI_33281
T94262 2715-2726 Chemical denotes methicillin http://purl.obolibrary.org/obo/CHEBI_6827
T56532 3058-3060 Chemical denotes CD http://purl.obolibrary.org/obo/CHEBI_8673
T32162 3509-3514 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T55132 4688-4691 Chemical denotes MDR http://purl.obolibrary.org/obo/CHEBI_53218
T57539 4875-4878 Chemical denotes MDR http://purl.obolibrary.org/obo/CHEBI_53218
T79399 4879-4881 Chemical denotes CD http://purl.obolibrary.org/obo/CHEBI_8673
T26656 4894-4898 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T24591 5190-5198 Chemical denotes sulphate http://purl.obolibrary.org/obo/CHEBI_16189
T38968 5310-5315 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T5 2548-2562 http://purl.obolibrary.org/obo/GO_0042493 denotes drug resistant

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T11 2302-2312 Phenotype denotes meningitis http://purl.obolibrary.org/obo/HP_0001287
T12 2548-2562 Phenotype denotes drug resistant http://purl.obolibrary.org/obo/HP_0020174
T13 2670-2678 Phenotype denotes diarrhea http://purl.obolibrary.org/obo/HP_0002014
T14 2702-2709 Phenotype denotes colitis http://purl.obolibrary.org/obo/HP_0002583
T15 2768-2785 Phenotype denotes severe infections http://purl.obolibrary.org/obo/HP_0032169

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T942 0-64 Sentence denotes 4.2 Environmental monitoring and infection control applications
T943 65-199 Sentence denotes In addition to foodborne and waterborne pathogens, the detection of environmental pathogens is also an important aspect of healthcare.
T944 200-338 Sentence denotes For example, diseases associated with environmental pathogens are one of the leading causes of death in low-income economies (WHO, 2018a).
T945 339-431 Sentence denotes For example, malaria was reported to cause an estimated 435,000 deaths in 2017 (WHO, 2018b).
T946 432-655 Sentence denotes Environmental pathogens are microorganisms that typically spend a substantial part of their lifecycle outside human hosts, but when introduced to humans through contact or inhalation cause disease with measurable frequency.
T947 656-740 Sentence denotes Thus, environmental pathogens are often targets in medical diagnostics applications.
T948 741-981 Sentence denotes However, here, we choose to distinguish environmental monitoring applications, which require pathogen detection in the environment (e.g., in air or on surfaces), from medical diagnostics applications, which require detection in body fluids.
T949 982-1060 Sentence denotes Thus, the distinction is based on the matrix in which the pathogen is present.
T950 1061-1290 Sentence denotes Similar to food and water safety applications, which require biosensors capable of analyzing pathogen-containing complex matrices, such as a water or food matrix, environmental pathogens are present in multiple types of matrices.
T951 1291-1599 Sentence denotes While environmental pathogens can enter the body through direct physical contact, they can also be transmitted through aerosols or interaction with organisms that serve as vectors for the infectious agent, such as mosquitos in the case of Plasmodium falciparum (the infectious agent associated with malaria).
T952 1600-1847 Sentence denotes Thus, the detection of environmental pathogens often requires analysis of matrices, such as air, and objects, such as the surfaces of biomedical devices or objects within healthcare facilities, that are present in the human environment (Lai et al.
T953 1848-1854 Sentence denotes 2009).
T954 1855-1979 Sentence denotes Several comprehensive reviews have been provided on the detection of environmental pathogens (Baeumner, 2003; Justino et al.
T955 1980-1986 Sentence denotes 2017).
T956 1987-2092 Sentence denotes Here, we describe the most common environmental pathogens found both in and outside of clinical settings.
T957 2093-2313 Sentence denotes Common environmental pathogens in a non-clinical setting include Legionella spp., which cause Legionnellosis, Mycobacterium tuberculosis, which causes tuberculosis, and Naegleria fowleri, which causes amoebic meningitis.
T958 2314-2415 Sentence denotes In addition to bacteria and protozoa, fungi, nematodes, and insects are also environmental pathogens.
T959 2416-2868 Sentence denotes Common environmental pathogens in clinical settings associated with healthcare-acquired infections include drug-resistant and multi-drug resistant (MDR) pathogens, such as Clostridium difficile (CD) (Hookman and Barkin, 2009), which causes CD-associated diarrhea and antibiotic-induced colitis, and methicillin-resistant S. aureus (MRSA), which causes severe infections in various parts of the body, including the urinary tract (Gordon and Lowy, 2008).
T960 2869-3021 Sentence denotes The infectious dose of environmental pathogens also varies by orders of magnitude depending on the pathogen as well as age and health of the individual.
T961 3022-3170 Sentence denotes For example, the infectious dose of CD is less than 10 spores, while that of MRSA is greater than 100,000 organisms (Schmid-Hempel and Frank, 2007).
T962 3171-3366 Sentence denotes While it is possible to obtain antibodies for foodborne and waterborne pathogens, it can be challenging to obtain antibodies for various environmental pathogens, including protozoa and nematodes.
T963 3367-3488 Sentence denotes Thus, traditional bioanalytical techniques, such as PCR, are often utilized for the detection of environmental pathogens.
T964 3489-3682 Sentence denotes Similar to food and water safety applications, biosensor-based assays for environmental pathogen detection applications also utilize measurement formats that facilitate the analysis of liquids.
T965 3683-3773 Sentence denotes However, they also require measurement formats for the detection of aerosolized pathogens.
T966 3774-4026 Sentence denotes In addition to airborne transmission, environmental pathogens are transmitted by direct surface contact (similar to many foodborne pathogens), which is a significant mode of transmission in healthcare settings (e.g., of healthcare-acquired infections).
T967 4027-4289 Sentence denotes Standardized guidelines for disinfecting and sterilizing the surfaces of medical equipment, assistive technologies, counters, and doors, among other surfaces, have emerged as an important aspect of infection control in modern healthcare facilities (Fraise et al.
T968 4290-4296 Sentence denotes 2008).
T969 4297-4457 Sentence denotes Thus, the detection of pathogens on the surfaces of biomedical devices and objects present in healthcare facilities is an important research area (Kramer et al.
T970 4458-4476 Sentence denotes 2006; Weber et al.
T971 4477-4483 Sentence denotes 2010).
T972 4484-4718 Sentence denotes For example, bacterial contamination of inanimate surfaces and equipment has been examined as a source of intensive care unit-acquired infections, a global healthcare challenge, especially when caused by MDR pathogens (Russotto et al.
T973 4719-4725 Sentence denotes 2015).
T974 4726-4813 Sentence denotes Hospital-acquired infections are prevalent causes of morbidity in patients (Orsi et al.
T975 4814-4820 Sentence denotes 2002).
T976 4821-5007 Sentence denotes This problem has only been exasperated by the rise of MDR CD, as well as drug-resistant strains of Campylobacter, Enterococcus, Salmonella, S. aureus, and S. dysenteriae (Ventola, 2015).
T977 5008-5140 Sentence denotes In addition to clinical pathogens, it is also of interest to detect pathogens in non-clinical settings (Faucher and Charette, 2015).
T978 5141-5331 Sentence denotes Toxin-producing algae, such as cyanobacteria and sulphate-reducing bacteria, are also important targets for electrochemical biosensors associated with the prevention of water-based diseases.

2_test

Id Subject Object Predicate Lexical cue
32364936-20102582-7713159 1848-1852 20102582 denotes 2009
32364936-12920503-7713160 1959-1963 12920503 denotes 2003
32364936-19340897-7713161 2636-2640 19340897 denotes 2009
32364936-18462090-7713162 2862-2866 18462090 denotes 2008
32364936-17967057-7713163 3164-3168 17967057 denotes 2007
32364936-16914034-7713164 4458-4462 16914034 denotes 2006
32364936-26693023-7713165 4719-4723 26693023 denotes 2015
32364936-12002233-7713166 4814-4818 12002233 denotes 2002
32364936-25859123-7713167 5001-5005 25859123 denotes 2015
32364936-25954260-7713168 5134-5138 25954260 denotes 2015