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PMC:7264932 / 1064-2573 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
50 1052-1055 Gene denotes CRP Gene:1401
51 1072-1076 Gene denotes IL-6 Gene:3569
52 687-694 Species denotes Patient Tax:9606
53 743-750 Species denotes Patient Tax:9606
54 918-939 Species denotes Aspergillus fumigatus Tax:746128
55 940-961 Species denotes Aspergillus fumigatus Tax:746128
56 962-972 Species denotes SARS-CoV-2 Tax:2697049
57 723-741 Disease denotes pulmonary fibrosis MESH:D011658
58 1217-1230 Disease denotes Renal failure MESH:D051437
59 1266-1298 Disease denotes invasive pulmonary aspergillosis MESH:D055744
61 617-630 Chemical denotes galactomannan MESH:C012990
66 1349-1352 Gene denotes CRP Gene:1401
67 1354-1372 Gene denotes C-reactive protein Gene:1401
68 1374-1378 Gene denotes IL-6 Gene:3569
69 1400-1432 Disease denotes invasive pulmonary aspergillosis MESH:D055744
79 46-54 Species denotes patients Tax:9606
80 97-112 Species denotes influenza virus Tax:11309
81 117-148 Species denotes respiratory syncytial virus); a Tax:1439707
82 303-324 Species denotes Aspergillus fumigatus Tax:746128
83 377-385 Species denotes patients Tax:9606
84 275-288 Chemical denotes galactomannan MESH:C012990
85 60-68 Disease denotes COVID-19 MESH:C000657245
86 201-206 Disease denotes fever MESH:D005334
87 473-491 Disease denotes COVID-19 pneumonia MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T4 397-402 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T5 659-664 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T6 861-866 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T7 1161-1170 Body_part denotes Leucocyte http://purl.org/sig/ont/fma/fma62852
T8 1196-1207 Body_part denotes Lymphocytes http://purl.org/sig/ont/fma/fma62863
T9 1365-1372 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T10 1380-1393 Body_part denotes interleukin 6 http://purl.org/sig/ont/fma/fma264829
T11 1380-1391 Body_part denotes interleukin http://purl.org/sig/ont/fma/fma86578

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 397-402 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T2 659-664 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T3 861-866 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T14 201-206 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T15 357-360 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T16 482-491 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T17 518-521 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T18 723-741 Phenotype denotes pulmonary fibrosis http://purl.obolibrary.org/obo/HP_0002206
T19 1037-1040 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T20 1217-1230 Phenotype denotes Renal failure http://purl.obolibrary.org/obo/HP_0000083
T21 1266-1298 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T22 1395-1398 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T23 1400-1432 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T20 60-68 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 97-106 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T22 473-481 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 482-491 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T24 723-741 Disease denotes pulmonary fibrosis http://purl.obolibrary.org/obo/MONDO_0002771
T25 962-970 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 1093-1096 Disease denotes PCT http://purl.obolibrary.org/obo/MONDO_0008296|http://purl.obolibrary.org/obo/MONDO_0015104
T28 1217-1230 Disease denotes Renal failure http://purl.obolibrary.org/obo/MONDO_0001106
T29 1285-1298 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T30 1419-1432 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T31 1490-1493 Disease denotes PCT http://purl.obolibrary.org/obo/MONDO_0008296|http://purl.obolibrary.org/obo/MONDO_0015104

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T4 107-112 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T5 139-144 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T6 147-148 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 207-208 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 395-396 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 397-402 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T10 707-711 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T11 707-711 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T12 763-767 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T13 763-767 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T14 1078-1080 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T15 1161-1170 http://purl.obolibrary.org/obo/CL_0000738 denotes Leucocyte
T16 1380-1393 http://purl.obolibrary.org/obo/PR_000001393 denotes interleukin 6

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T8 275-288 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T9 357-360 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T11 518-521 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T13 617-630 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T14 707-711 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T15 763-767 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T16 805-808 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T17 1037-1040 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T19 1072-1074 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T21 1320-1323 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T22 1365-1372 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T23 1374-1376 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T25 1395-1398 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T27 1439-1446 Chemical denotes lactate http://purl.obolibrary.org/obo/CHEBI_24996

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 293-299 http://purl.obolibrary.org/obo/GO_0040007 denotes growth

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 275-288 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T2 617-630 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 786-799 GlycoEpitope denotes Galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T4 842-855 GlycoEpitope denotes Galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T7 0-372 Sentence denotes In the initial bronchoalveolar lavage of both patients only COVID-19 was found (PCR negative for influenza virus and respiratory syncytial virus); a follow-up bronchoalveolar lavage because of ongoing fever a few days later (days 5 and 6 after ICU admission) showed elevated galactomannan and growth of Aspergillus fumigatus in standard culture, suggesting IPA (Table 1 ).
T8 373-522 Sentence denotes All patients received a chest computed tomography scan before ICU admittance with typical signs for COVID-19 pneumonia but no specific signs for IPA.
T9 523-597 Sentence denotes Follow-up computed tomography scans were not performed for safety reasons.
T10 598-686 Sentence denotes Table 1 Results of galactomannan (bronchoalveolar lavage and serum) and standard culture
T11 687-785 Sentence denotes Patient 1(80 years, male, suspected pulmonary fibrosis) Patient 2(70 years, male, no risk factors)
T12 786-841 Sentence denotes Galactomannan from BAL (ODI; normal range <1.0) 6.3 6.1
T13 842-900 Sentence denotes Galactomannan from serum (ODI; normal range <0.5) 1.5 <0.5
T14 901-961 Sentence denotes Standard culture Aspergillus fumigatus Aspergillus fumigatus
T15 962-1005 Sentence denotes SARS-CoV-2 (at follow up) positive positive
T16 1006-1050 Sentence denotes Laboratory parameters, mean at IPA diagnosis
T17 1051-1070 Sentence denotes  CRP (mg/dL) 26 5.1
T18 1071-1091 Sentence denotes  IL-6 (pg/mL) 460 82
T19 1092-1112 Sentence denotes  PCT (ng/mL) 3.7 0.4
T20 1113-1140 Sentence denotes  D-Dimer (μg/L) 4820 14 151
T21 1141-1159 Sentence denotes  LDH (U/L) 481 530
T22 1160-1194 Sentence denotes  Leucocyte count (G/L) 10.38 14.55
T23 1195-1216 Sentence denotes  Lymphocytes (%) 15 7
T24 1217-1238 Sentence denotes Renal failure Yes Yes
T25 1239-1304 Sentence denotes Classical risk factors for invasive pulmonary aspergillosis No No
T26 1305-1509 Sentence denotes Abbreviations: BAL, bronchoalveolar lavage; CRP, C-reactive protein; IL-6, interleukin 6; IPA, invasive pulmonary aspergillosis; LDH, lactate dehydrogenase; ODI, optical density index; PCT, procalcitonin.