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PMC:7170415 / 13840-17305 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
210 102-110 Species denotes patients Tax:9606
211 253-263 Species denotes SARS–CoV-2 Tax:2697049
212 335-345 Species denotes SARS–CoV-2 Tax:2697049
213 159-170 Species denotes respiratory Tax:12814
214 1092-1103 Species denotes respiratory Tax:12814
215 585-593 Chemical denotes aluminum MESH:D000535
216 645-661 Chemical denotes calcium alginate MESH:D000464
217 116-124 Disease denotes COVID-19 MESH:C000657245
225 1690-1694 Gene denotes RdRP Gene:43740578
226 1452-1464 Gene denotes nucleocapsid Gene:43740575
227 1368-1378 Species denotes SARS–CoV-2 Tax:2697049
228 1495-1500 Species denotes human Tax:9606
229 1649-1659 Species denotes SARS–CoV-2 Tax:2697049
230 1788-1798 Species denotes SARS–CoV-2 Tax:2697049
231 1864-1877 Species denotes coronaviruses Tax:11118
239 3237-3244 Species denotes patient Tax:9606
240 3435-3445 Species denotes SARS–CoV-2 Tax:2697049
241 3142-3153 Species denotes respiratory Tax:12814
242 3350-3361 Species denotes respiratory Tax:12814
243 2917-2927 Species denotes SARS–CoV-2 Tax:2697049
244 2824-2833 Disease denotes infection MESH:D007239
245 3111-3119 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T10 159-176 Body_part denotes respiratory tract http://purl.org/sig/ont/fma/fma265130
T11 378-387 Body_part denotes turbinate http://purl.org/sig/ont/fma/fma57456
T12 916-922 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T13 1086-1109 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T14 1235-1238 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 1465-1469 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T16 1509-1513 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T17 1528-1531 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T18 1660-1663 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 1674-1677 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T20 2941-2946 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T21 2951-2956 Body_part denotes urine http://purl.org/sig/ont/fma/fma12274
T22 3136-3159 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T23 3344-3367 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T4 159-176 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T5 916-922 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T6 1086-1109 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T7 1092-1109 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T8 2941-2946 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T9 2951-2956 Body_part denotes urine http://purl.obolibrary.org/obo/UBERON_0001088
T10 3136-3159 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T11 3142-3159 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T12 3344-3367 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T13 3350-3367 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T61 116-124 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T62 253-257 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T63 335-339 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T64 1368-1372 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T65 1649-1653 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T66 1788-1792 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T67 2558-2562 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T68 2824-2833 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T69 2917-2921 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T70 3111-3119 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T71 3435-3439 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T132 27-34 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T133 86-89 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T134 131-135 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T135 262-268 http://purl.obolibrary.org/obo/CLO_0001196 denotes 2 (25)
T136 270-271 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T137 346-353 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T138 481-482 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T139 751-758 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T140 1169-1170 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T141 1186-1190 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T142 1329-1332 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T143 1333-1336 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T144 1465-1469 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T145 1495-1500 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T146 1509-1513 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T147 1600-1612 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T148 1713-1718 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T149 1892-1893 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 1963-1966 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T151 2229-2236 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T152 2238-2240 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T153 2373-2375 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T154 2391-2394 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T155 2441-2443 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T156 2936-2938 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T157 3180-3181 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T158 3235-3236 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T159 3245-3248 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T160 3253-3254 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T161 3264-3268 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T6 220-232 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T7 228-232 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T8 585-593 Chemical denotes aluminum http://purl.obolibrary.org/obo/CHEBI_28984
T9 645-652 Chemical denotes calcium http://purl.obolibrary.org/obo/CHEBI_22984|http://purl.obolibrary.org/obo/CHEBI_29320
T11 653-661 Chemical denotes alginate http://purl.obolibrary.org/obo/CHEBI_58187
T12 883-895 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T13 891-895 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T14 1414-1419 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T15 1478-1480 Chemical denotes N2 http://purl.obolibrary.org/obo/CHEBI_17997
T16 1620-1625 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T17 3004-3016 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T18 3012-3016 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T14 812-821 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T15 1501-1508 http://purl.obolibrary.org/obo/GO_0004526 denotes RNase P
T16 1690-1694 http://purl.obolibrary.org/obo/GO_0003968 denotes RdRP

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T103 0-34 Sentence denotes Laboratory-Based Molecular Testing
T104 35-269 Sentence denotes The current diagnostic strategy recommended by the CDC to identify patients with COVID-19 is to test samples taken from the respiratory tract to assess for the presence of 1 or several nucleic acid targets specific to SARS–CoV-2 (25).
T105 270-444 Sentence denotes A nasopharyngeal specimen is the preferred choice for swab-based SARS–CoV-2 testing, but oropharyngeal, mid-turbinate, or anterior nares samples also are acceptable (31, 32).
T106 445-570 Sentence denotes Samples should be obtained by using a flocked swab, if available, to enhance the collection and release of cellular material.
T107 571-625 Sentence denotes Swabs with an aluminum or plastic shaft are preferred.
T108 626-759 Sentence denotes Swabs that contain calcium alginate, wood, or cotton should be avoided, because they may contain substances that inhibit PCR testing.
T109 760-896 Sentence denotes Ideally, swabs should be transferred into universal transport medium immediately after sample collection to preserve viral nucleic acid.
T110 897-1125 Sentence denotes Samples taken from sputum, endotracheal aspirates, and bronchoalveolar lavage also may be sent directly to the microbiology laboratory for processing, and may have greater sensitivity than upper respiratory tract specimens (33).
T111 1126-1191 Sentence denotes Inadequate sample collection may result in a false-negative test.
T112 1192-1302 Sentence denotes After specimen collection, samples undergo RNA extraction followed by qualitative RT-PCR for target detection.
T113 1303-1385 Sentence denotes In the United States, the CDC has developed the most widely used SARS–CoV-2 assay.
T114 1386-1558 Sentence denotes The kit contains PCR primer–probe sets for 2 regions of the viral nucleocapsid gene (N1 and N2), and for the human RNase P gene to ensure the RNA extraction was successful.
T115 1559-1724 Sentence denotes This assay differs from the World Health Organization primer–probe sets, which target the SARS–CoV-2 RNA-dependent RNA polymerase (RdRP) and envelope (E) genes (25).
T116 1725-1958 Sentence denotes Both assays have high analytic sensitivity and specificity for SARS–CoV-2, with minimal cross-reactivity with other circulating strains of coronaviruses, and both use a cycle threshold of less than 40 as the criterion for positivity.
T117 1959-2242 Sentence denotes The CDC kit may be used by state public health laboratories, other laboratories determined by the state to be qualified, and clinical laboratories that meet the regulatory requirements of the Clinical Laboratories Improvement Amendment (CLIA) to perform high-complexity testing (27).
T118 2243-2377 Sentence denotes Dozens of laboratories have applied for Emergency Use Authorization (EUA) from the FDA for their own laboratory-developed assays (34).
T119 2378-2532 Sentence denotes The FDA also has granted an EUA for several commercial assays (35), further expanding the ability of clinical laboratories to use these platforms (Table).
T120 2533-2539 Sentence denotes Table.
T121 2540-2940 Sentence denotes The 28 Commercial SARS–CoV-2 in Vitro Diagnostic Assays Given an EUA From the FDA as of 4 April 2020 The lack of an established reference standard, use of differing sample collection and preparation methods, and an incomplete understanding of viral dynamics across the time course of infection hamper rigorous assessment of the diagnostic accuracy of the many newly introduced SARS–CoV-2 assays (36).
T122 2941-3054 Sentence denotes Serum and urine are usually negative for the presence of viral nucleic acid, regardless of illness severity (33).
T123 3055-3216 Sentence denotes Of importance, the ability of RT-PCR assays to rule out COVID-19 on the basis of upper respiratory tract samples obtained at a single time point remains unclear.
T124 3217-3465 Sentence denotes Conversely, after a patient has had a positive test result, several authorities have recommended obtaining at least 2 negative upper respiratory tract samples, collected at intervals of 24 hours or longer, to document SARS–CoV-2 clearance (37, 38).