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PMC:7234792 / 1608-3797 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
35 1752-1790 Disease denotes new right upper lobe nodular opacities MESH:D003318
50 762-764 Gene denotes μL Gene:4591
51 1299-1301 Gene denotes μL Gene:4591
52 52-59 Species denotes patient Tax:9606
53 708-715 Species denotes patient Tax:9606
54 925-932 Species denotes patient Tax:9606
55 1167-1177 Species denotes SARS-CoV-2 Tax:2697049
56 1247-1257 Species denotes SARS-CoV-2 Tax:2697049
57 386-392 Chemical denotes Oxygen MESH:D010100
58 549-559 Chemical denotes vancomycin MESH:D014640
59 587-598 Chemical denotes ceftriaxone MESH:D002443
60 1346-1358 Chemical denotes azithromycin MESH:D017963
61 79-84 Disease denotes fever MESH:D005334
62 102-111 Disease denotes dry cough MESH:D003371
63 117-136 Disease denotes shortness of breath MESH:D004417

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T3 34-38 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T4 287-292 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T5 316-321 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088
T6 685-693 Body_part denotes appendix http://purl.org/sig/ont/fma/fma14542
T7 718-734 Body_part denotes white blood cell http://purl.org/sig/ont/fma/fma62852
T8 730-734 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T9 752-757 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T10 803-813 Body_part denotes lymphocyte http://purl.org/sig/ont/fma/fma62863
T11 837-842 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T12 902-906 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T13 1307-1310 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T14 1452-1460 Body_part denotes appendix http://purl.org/sig/ont/fma/fma14542
T15 1493-1498 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T16 1511-1516 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T17 1551-1556 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T18 1600-1604 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T19 1631-1636 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T20 1653-1669 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T21 1728-1733 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T22 1756-1772 Body_part denotes right upper lobe http://purl.org/sig/ont/fma/fma7333
T23 1844-1860 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T24 1896-1912 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T25 1988-2003 Body_part denotes left lower lobe http://purl.org/sig/ont/fma/fma7371
T26 2062-2078 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T27 2137-2141 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T3 287-292 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T4 316-321 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948
T5 724-729 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T6 837-842 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T7 902-906 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T8 1493-1498 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T9 1511-1516 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T10 1551-1556 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T11 1600-1604 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T12 1631-1636 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T13 1665-1669 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T14 1728-1733 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T15 1768-1772 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T16 1856-1860 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T17 1908-1912 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T18 1999-2003 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T19 2074-2078 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T20 2137-2141 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T13 459-461 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T14 1055-1064 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T15 1167-1175 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 1247-1255 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T20 282-285 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T21 287-292 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T22 287-292 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T23 316-321 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T24 316-321 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T25 316-321 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T26 316-321 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T27 609-610 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 724-729 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T29 730-734 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T30 752-757 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T31 787-789 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T32 801-802 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 837-842 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T34 902-906 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T35 902-906 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T36 982-983 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 1008-1012 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T38 1019-1021 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T39 1142-1144 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T40 1220-1221 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 1263-1266 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T42 1267-1268 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 1300-1303 http://purl.obolibrary.org/obo/CLO_0007203 denotes L.6
T44 1311-1319 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T45 1372-1373 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 1424-1429 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T47 1493-1498 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T48 1511-1516 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T49 1538-1539 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T50 1551-1556 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T51 1600-1604 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T52 1600-1604 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T53 1622-1623 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T54 1631-1636 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T55 1719-1720 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T56 1728-1733 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T57 1804-1805 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 1982-1983 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 2137-2141 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T60 2137-2141 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T30 312-314 Chemical denotes Hg http://purl.obolibrary.org/obo/CHEBI_16170|http://purl.obolibrary.org/obo/CHEBI_25195
T32 386-392 Chemical denotes Oxygen http://purl.obolibrary.org/obo/CHEBI_15379
T33 549-559 Chemical denotes vancomycin http://purl.obolibrary.org/obo/CHEBI_28001|http://purl.obolibrary.org/obo/CHEBI_76842
T35 587-598 Chemical denotes ceftriaxone http://purl.obolibrary.org/obo/CHEBI_29007
T36 1019-1021 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T39 1142-1144 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T42 1346-1358 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T4 79-84 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T5 86-92 Phenotype denotes chills http://purl.obolibrary.org/obo/HP_0025143
T6 94-100 Phenotype denotes rigors http://purl.obolibrary.org/obo/HP_0025145
T7 102-111 Phenotype denotes dry cough http://purl.obolibrary.org/obo/HP_0031246
T8 117-136 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T9 1943-1960 Phenotype denotes reverse halo sign http://purl.obolibrary.org/obo/HP_0032983

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T9 0-137 Sentence denotes On the afternoon of his first day back at work, the patient had rapid onset of fever, chills, rigors, dry cough, and shortness of breath.
T10 138-385 Sentence denotes On arrival at the emergency department of Mount Sinai Hospital, on the same afternoon as symptom onset (hospital day 1), his temperature was 39·4°C, blood pressure 142/80 mm Hg, heart rate 130 beats per min, and respiratory rate20 breaths per min.
T11 386-442 Sentence denotes Oxygen saturation ranged from 89% to 99% at ambient air.
T12 443-530 Sentence denotes On examination, he appeared acutely ill and in mild distress with normal breath sounds.
T13 531-703 Sentence denotes Plasmalyte (2 L), vancomycin (1 g once every 12 h), and ceftriaxone (2 g once a day) were administered intravenously; all medications are detailed in the appendix (pp 1–2).
T14 704-836 Sentence denotes The patient's white blood cell count was 13 900 cells per μL (reference range 4500–11 000), with a lymphocyte count of 9·2% (15–50).
T15 837-920 Sentence denotes Chest radiograph revealed an ill-defined nodule in the right mid-lung (figure 1A ).
T16 921-962 Sentence denotes The patient was admitted to the hospital.
T17 963-1065 Sentence denotes On hospital day 1, a respiratory viral panel test of an NP swab was negative, including for influenza.
T18 1066-1178 Sentence denotes On day 2, RT-PCR (Roche Cobas 6800 System, Roche, Basel, Switzerland) of an NP swab was negative for SARS-CoV-2.
T19 1179-1391 Sentence denotes This assay targets open-reading frame 1, a region that is unique to SARS-CoV-2, and has a sensitivity of 1–5 copies per μL.6 An HIV test was negative, and intravenous azithromycin (500 mg once a day) was started.
T20 1392-1470 Sentence denotes The remainder of the laboratory tests are summarised in the appendix (pp 1–2).
T21 1471-1536 Sentence denotes Figure 1 Imaging with chest radiograph, chest CT, and radial EBUS
T22 1537-1718 Sentence denotes (A) Admission chest radiograph (hospital day 1) with right mid-lung nodule (arrow). (B) First chest CT (day 2) with right lower lobe rounded opacity with possible halo sign (arrow).
T23 1719-2158 Sentence denotes A second chest CT (day 6) showed new right upper lobe nodular opacities (C; arrows), a new large ground glass opacity in the right lower lobe (D; arrow); and enlargement of the right lower lobe rounded opacity with possible reverse halo sign (E; green arrow) and a new left lower lobe rounded opacity (E; blue arrow). (F) Radial EBUS image of right lower lobe rounded opacity (arrow) used to target the transbronchial lung biopsy on day 9.
T24 2159-2189 Sentence denotes EBUS=endobronchial ultrasound.