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PMC:7214328 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 2599-2604 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 2599-2604 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 496-501 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T2 517-522 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T3 693-698 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T4 1543-1552 Phenotype denotes dry cough http://purl.obolibrary.org/obo/HP_0031246
T5 1554-1559 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T6 1561-1568 Phenotype denotes anosmia http://purl.obolibrary.org/obo/HP_0000458
T7 1570-1577 Phenotype denotes ageusia http://purl.obolibrary.org/obo/HP_0041051
T8 1582-1590 Phenotype denotes diarrhea http://purl.obolibrary.org/obo/HP_0002014
T9 1758-1763 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T10 1799-1804 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T11 1915-1920 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T12 2374-2379 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 0-8 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 85-88 Disease denotes PCP http://purl.obolibrary.org/obo/MONDO_0019121
T3 143-151 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 815-823 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 1373-1381 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 1532-1535 Disease denotes PCP http://purl.obolibrary.org/obo/MONDO_0019121
T7 1561-1568 Disease denotes anosmia http://purl.obolibrary.org/obo/MONDO_0010528
T8 1582-1590 Disease denotes diarrhea http://purl.obolibrary.org/obo/MONDO_0001673
T9 1653-1661 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T10 1849-1851 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T11 1949-1957 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T12 2066-2069 Disease denotes PCP http://purl.obolibrary.org/obo/MONDO_0019121
T13 2092-2100 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T14 2414-2423 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 339-343 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T2 644-648 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T3 1020-1021 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 1058-1059 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 1109-1116 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T6 1186-1187 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 1363-1364 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1440-1442 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T9 1541-1542 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 1614-1620 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T11 2081-2082 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 2101-2105 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T13 2205-2209 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T14 2232-2233 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 2253-2257 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T16 2395-2400 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T17 2457-2464 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airways
T18 2591-2597 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airway
T19 2831-2836 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T20 3188-3195 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T21 3205-3208 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T22 3309-3313 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T23 3422-3429 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T24 3455-3456 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 3522-3523 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T26 3973-3980 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T27 4025-4026 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 85-88 Chemical denotes PCP http://purl.obolibrary.org/obo/CHEBI_17642|http://purl.obolibrary.org/obo/CHEBI_8058
T3 1532-1535 Chemical denotes PCP http://purl.obolibrary.org/obo/CHEBI_17642|http://purl.obolibrary.org/obo/CHEBI_8058
T5 2066-2069 Chemical denotes PCP http://purl.obolibrary.org/obo/CHEBI_17642|http://purl.obolibrary.org/obo/CHEBI_8058

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 1394-1408 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding
T2 2771-2785 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding
T3 3163-3177 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding
T4 3502-3516 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding
T5 3580-3594 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-46 Sentence denotes COVID-19 Retesting in the Primary Care Setting
T2 48-60 Sentence denotes Dear Editor:
T3 61-234 Sentence denotes Primary care providers (PCP) play an essential role in preventing transmission of COVID-19 by determining when patients should discontinue home isolation and return to work.
T4 235-1101 Sentence denotes Current Centers for Disease Control and Prevention guidelines addressing such decisions include (1) non-test-based strategy, which advises that patients may discontinue home isolation after at least 72 hours have passed since recovery (defined as resolution of fever without use of fever-reducing medications) and improvement in respiratory symptoms and at least 7 days have passed since symptom onset or (2) test-based strategy, which advises resolution of fever and improvement in respiratory symptoms and negative results of an FDA Emergency Use Authorized molecular assay for COVID-19 from at least 2 consecutive nasopharyngeal swab specimens collected ≥24 hours apart.1 In some instances, more stringent criteria are warranted to reduce the risk of transmission in settings where a patient may be returning to work at a transportation hub or healthcare setting.
T5 1102-1230 Sentence denotes Repeat testing in the convalescent period is typically advised in patients entering a congregate setting after hospitalization.2
T6 1231-1325 Sentence denotes PCPs often encounter scenarios where these recommendations do not provide sufficient guidance.
T7 1326-1434 Sentence denotes For example, we recently encountered a case of SARS-CoV-2 prolonged viral shedding in an ambulatory patient.
T8 1435-1687 Sentence denotes This 34-year-old man without chronic medical problems or prescribed medications presented to his PCP with a dry cough, fever, anosmia, ageusia and diarrhea of 4 days duration and tested positive by molecular assay for COVID-19 from nasopharyngeal swab.
T9 1688-1805 Sentence denotes After 3 weeks, the patient reported resolution of all symptoms except cough, which was diagnosed as post-viral cough.
T10 1806-1899 Sentence denotes Because the patient worked at the airport, he sought medical advice before returning to work.
T11 1900-2026 Sentence denotes Due to ongoing cough, repeat molecular assay for COVID-19 from nasopharyngeal swab was performed and was found to be positive.
T12 2027-2070 Sentence denotes This case poses many challenges to the PCP.
T13 2071-2128 Sentence denotes What does a positive COVID-19 test tell us at this stage?
T14 2129-2188 Sentence denotes Can the patient return to work or remain on home isolation?
T15 2189-2222 Sentence denotes When should the test be repeated?
T16 2223-2473 Sentence denotes Although a positive molecular test result may not correlate with viral load or infectivity, it seems reasonable to assume that patients with prolonged cough may aerosolize virus and transmit infection even if viral loads in the upper airways are low.
T17 2474-2863 Sentence denotes This is supported by emerging data demonstrating that viral clearance can be delayed in samples collected from lower airway, stool and nasopharyngeal swabs.3 Indeed, certain populations, such as those immunocompromised, pregnant and advanced age individuals, are known to be at risk for prolonged viral shedding.4 Reports have shown that some patients shed virus for weeks or even months.5
T18 2864-3037 Sentence denotes Further, PCPs must evaluate the risk of transmission when considering retesting in patients with ongoing symptoms since current guidelines do not indicate this is necessary.
T19 3038-3178 Sentence denotes And, guidance will be needed on whether retesting should be performed in asymptomatic individuals at high risk for prolonged viral shedding.
T20 3179-3353 Sentence denotes To date, testing guidance has prioritized hospitalized patients and health care workers in order to allocate and conserve limited test kits and personal protective equipment.
T21 3354-3595 Sentence denotes As more resources become available, we anticipate liberalization of testing to include retesting in (a) those with symptoms suggestive of prolonged viral shedding and (b) those asymptomatic yet at increased risk for prolonged viral shedding.
T22 3596-3724 Sentence denotes We note that there are individual differences in rate of recovery, viral clearance, as well as the risk of forward transmission.
T23 3725-3819 Sentence denotes PCPs are strategically poised to consider all factors and determine the best course of action.
T24 3820-4042 Sentence denotes Given the absence of guidelines, for our patient who worked in the public transit industry, we recommended continued home isolation and repeat molecular testing in 1 week, with negative results permitting a return to work.
T25 4044-4098 Sentence denotes The authors have no conflicts of interest to disclose.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 0-8 Disease denotes COVID-19 MESH:C000657245
13 172-180 Species denotes patients Tax:9606
14 379-387 Species denotes patients Tax:9606
15 1022-1029 Species denotes patient Tax:9606
16 1168-1176 Species denotes patients Tax:9606
17 143-151 Disease denotes COVID-19 MESH:C000657245
18 496-501 Disease denotes fever MESH:D005334
19 517-522 Disease denotes fever MESH:D005334
20 564-584 Disease denotes respiratory symptoms MESH:D012818
21 693-698 Disease denotes fever MESH:D005334
22 718-738 Disease denotes respiratory symptoms MESH:D012818
23 815-823 Disease denotes COVID-19 MESH:C000657245
38 1373-1383 Species denotes SARS-CoV-2 Tax:2697049
39 1426-1433 Species denotes patient Tax:9606
40 1707-1714 Species denotes patient Tax:9606
41 1818-1825 Species denotes patient Tax:9606
42 1543-1552 Disease denotes dry cough MESH:D003371
43 1554-1559 Disease denotes fever MESH:D005334
44 1561-1568 Disease denotes anosmia MESH:D000857
45 1570-1577 Disease denotes ageusia MESH:D000370
46 1582-1590 Disease denotes diarrhea MESH:D003967
47 1653-1661 Disease denotes COVID-19 MESH:C000657245
48 1758-1763 Disease denotes cough MESH:D003371
49 1799-1804 Disease denotes cough MESH:D003371
50 1915-1920 Disease denotes cough MESH:D003371
51 1949-1957 Disease denotes COVID-19 MESH:C000657245
58 2137-2144 Species denotes patient Tax:9606
59 2350-2358 Species denotes patients Tax:9606
60 2817-2825 Species denotes patients Tax:9606
61 2092-2100 Disease denotes COVID-19 MESH:C000657245
62 2374-2379 Disease denotes cough MESH:D003371
63 2414-2423 Disease denotes infection MESH:D007239
67 2947-2955 Species denotes patients Tax:9606
68 3234-3242 Species denotes patients Tax:9606
69 3861-3868 Species denotes patient Tax:9606