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PMC:7234792 / 3798-5532 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
86 154-161 Species denotes patient Tax:9606
87 326-333 Species denotes patient Tax:9606
88 902-912 Species denotes SARS-CoV-2 Tax:2697049
89 246-258 Chemical denotes azithromycin MESH:D017963
90 384-396 Chemical denotes azithromycin MESH:D017963
91 440-451 Chemical denotes clindamycin MESH:D002981
92 992-998 Chemical denotes oxygen MESH:D010100
93 1076-1086 Chemical denotes prednisone MESH:D011241
94 1426-1439 Chemical denotes galactomannan MESH:C012990
95 201-206 Disease denotes cough MESH:D003371
96 211-219 Disease denotes dyspnoea MESH:D004417
97 282-287 Disease denotes fever MESH:D005334
98 362-370 Disease denotes coughing MESH:D003371
99 831-840 Disease denotes pneumonia MESH:D011014
100 943-948 Disease denotes cough MESH:D003371
101 971-976 Disease denotes fever MESH:D005334
102 1181-1190 Disease denotes pneumonia MESH:D011014
103 1306-1331 Disease denotes invasive fungal infection MESH:D000072742
104 1394-1402 Disease denotes COVID-19 MESH:C000657245
105 1608-1616 Disease denotes COVID-19 MESH:C000657245
106 1683-1691 Disease denotes COVID-19 MESH:C000657245
107 1716-1733 Disease denotes pulmonary disease MESH:D008171

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T28 29-34 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T29 66-82 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T30 117-122 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T31 533-538 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T32 577-593 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T33 709-724 Body_part denotes left lower lobe http://purl.org/sig/ont/fma/fma7371
T34 766-782 Body_part denotes right upper lobe http://purl.org/sig/ont/fma/fma7333
T35 1420-1425 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T21 29-34 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T22 78-82 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T23 533-538 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T24 589-593 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T25 720-724 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T26 778-782 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T27 1420-1425 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T17 831-840 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T18 902-910 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 1181-1190 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T20 1315-1331 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T21 1322-1331 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T22 1608-1616 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 1683-1691 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 1716-1733 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T61 29-34 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T62 41-42 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 117-122 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T64 291-292 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 410-411 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 524-525 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T67 533-538 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T68 634-635 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 668-669 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T70 730-731 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 868-869 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T72 890-892 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T73 1017-1019 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T74 1170-1180 http://purl.obolibrary.org/obo/OBI_0000245 denotes organising
T75 1237-1238 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76 1418-1419 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 1692-1693 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T43 246-258 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T44 384-396 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T45 440-451 Chemical denotes clindamycin http://purl.obolibrary.org/obo/CHEBI_3745
T46 890-892 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T49 992-998 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T50 1076-1086 Chemical denotes prednisone http://purl.obolibrary.org/obo/CHEBI_8382
T51 1426-1439 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T52 1581-1584 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 1426-1439 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T10 201-206 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T11 211-219 Phenotype denotes dyspnoea http://purl.obolibrary.org/obo/HP_0002094
T12 282-287 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T13 344-350 Phenotype denotes rigors http://purl.obolibrary.org/obo/HP_0025145
T14 362-370 Phenotype denotes coughing http://purl.obolibrary.org/obo/HP_0012735
T15 831-840 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T16 943-948 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T17 950-957 Phenotype denotes malaise http://purl.obolibrary.org/obo/HP_0012378
T18 959-965 Phenotype denotes rigors http://purl.obolibrary.org/obo/HP_0025145
T19 971-976 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T20 1181-1190 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T21 1253-1270 Phenotype denotes reverse halo sign http://purl.obolibrary.org/obo/HP_0032983
T22 1306-1331 Phenotype denotes invasive fungal infection http://purl.obolibrary.org/obo/HP_0020101

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T25 0-139 Sentence denotes On hospital day 2, CT of the chest found a rounded opacity in the right lower lobe (figure 1B); the remainder of the lungs appeared normal.
T26 140-271 Sentence denotes On day 4, the patient's peak temperature was 37·8°C, and his cough and dyspnoea had improved; intravenous azithromycin was stopped.
T27 272-371 Sentence denotes On day 5, fever to a peak of 38·9°C occurred, and the patient developed rigors and severe coughing.
T28 372-523 Sentence denotes Intravenous azithromycin (500 mg once a day) was restarted and oral clindamycin (300 mg once every 6 h) was administered, without clinical improvement.
T29 524-667 Sentence denotes A repeat chest CT on day 6 showed enlargement of the right lower lobe opacity, which had become surrounded by a large new ground glass opacity.
T30 668-797 Sentence denotes A new rounded opacity was present in the left lower lobe, and a new multilobulated opacity in the right upper lobe (figure 1C–E).
T31 798-867 Sentence denotes The CT report suggested atypical pneumonia of fungal or viral origin.
T32 868-935 Sentence denotes A repeat RT-PCR of an NP swab for SARS-CoV-2 was negative on day 7.
T33 936-1036 Sentence denotes Severe cough, malaise, rigors, and fever continued, and oxygen saturation was 92–94% at ambient air.
T34 1037-1191 Sentence denotes Antibiotics were stopped on day 8, and prednisone 40 mg was given orally on the mornings of day 8 and day 9 for presumed cryptogenic organising pneumonia.
T35 1192-1499 Sentence denotes Consulting radiologists noted CT evidence of a halo sign and reverse halo sign (figure 1B and 1E),7 suggestive of invasive fungal infection and not characteristic of previously reported CT findings for COVID-19.1, 8 On day 8, a serum galactomannan assay was ordered and pulmonary consultation was requested.
T36 1500-1585 Sentence denotes The pulmonary consultant recommended bronchoscopy with transbronchial biopsy and BAL.
T37 1586-1734 Sentence denotes Given the epidemic of COVID-19 in New York City at the time, the pulmonary team still considered COVID-19 a possible cause of the pulmonary disease.