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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 101-105 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T2 154-162 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T3 230-234 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T4 235-241 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T5 532-538 Body_part denotes kidney http://purl.org/sig/ont/fma/fma7203
T6 1703-1707 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T7 1814-1825 Body_part denotes thyroiditis http://purl.org/sig/ont/fma/fma9603
T8 1852-1861 Body_part denotes prostatic http://purl.org/sig/ont/fma/fma9600
T9 2458-2461 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T10 3531-3534 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T11 3596-3601 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T12 3714-3719 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T13 4418-4423 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 101-105 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T2 230-234 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T3 235-241 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T4 532-538 Body_part denotes kidney http://purl.obolibrary.org/obo/UBERON_0002113
T5 3596-3601 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T6 3714-3719 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T7 4418-4423 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T12 23-70 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T13 23-56 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T14 72-80 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 264-274 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T16 338-346 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 411-419 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T18 458-495 Disease denotes chronic obstructive pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005002
T19 478-495 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275
T20 497-509 Disease denotes hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T21 511-519 Disease denotes diabetes http://purl.obolibrary.org/obo/MONDO_0005015
T22 524-546 Disease denotes chronic kidney disease http://purl.obolibrary.org/obo/MONDO_0005300
T23 532-546 Disease denotes kidney disease http://purl.obolibrary.org/obo/MONDO_0001343|http://purl.obolibrary.org/obo/MONDO_0005240
T25 654-671 Disease denotes fungal infections http://purl.obolibrary.org/obo/MONDO_0002041
T26 673-695 Disease denotes Invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T27 682-695 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T28 739-748 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T29 749-758 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T30 934-943 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T31 952-977 Disease denotes acute respiratory failure http://purl.obolibrary.org/obo/MONDO_0001208|http://purl.obolibrary.org/obo/MONDO_0021113
T33 1053-1057 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T34 1086-1095 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T35 1110-1123 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T36 1176-1184 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T37 1238-1246 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 1290-1312 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T39 1299-1312 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T40 1394-1402 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T41 1414-1423 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T42 1465-1478 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T43 1539-1556 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275
T44 1620-1644 Disease denotes myelodysplastic syndrome http://purl.obolibrary.org/obo/MONDO_0018881|http://purl.obolibrary.org/obo/MONDO_0044873
T46 1802-1825 Disease denotes Hashimoto’s thyroiditis http://purl.obolibrary.org/obo/MONDO_0007699
T47 1814-1825 Disease denotes thyroiditis http://purl.obolibrary.org/obo/MONDO_0004126
T48 1827-1839 Disease denotes hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T49 1845-1873 Disease denotes benign prostatic hypertrophy http://purl.obolibrary.org/obo/MONDO_0010811
T50 2137-2162 Disease denotes acute respiratory failure http://purl.obolibrary.org/obo/MONDO_0001208|http://purl.obolibrary.org/obo/MONDO_0021113
T52 2280-2282 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T53 2441-2449 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 2580-2590 Disease denotes influenzae http://purl.obolibrary.org/obo/MONDO_0005812
T55 2710-2712 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T56 3014-3021 Disease denotes sterile http://purl.obolibrary.org/obo/MONDO_0005047
T57 3191-3206 Disease denotes silver staining http://purl.obolibrary.org/obo/MONDO_0018952
T58 3397-3416 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T59 3520-3528 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 4041-4063 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T61 4050-4063 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T62 4159-4172 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T63 4399-4412 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T64 4722-4730 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 4733-4742 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T66 4863-4876 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T67 5042-5064 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T68 5051-5064 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T69 5093-5101 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T70 5157-5170 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T71 5215-5223 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T72 5235-5244 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T73 5253-5261 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T74 5404-5412 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T75 5415-5425 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T3 101-105 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T4 101-105 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T5 230-234 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T6 230-234 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T7 282-283 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 532-538 http://purl.obolibrary.org/obo/UBERON_0002113 denotes kidney
T9 532-538 http://www.ebi.ac.uk/efo/EFO_0000927 denotes kidney
T10 532-538 http://www.ebi.ac.uk/efo/EFO_0000929 denotes kidney
T11 699-700 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 830-831 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T13 854-855 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 996-997 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 1348-1349 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 1696-1699 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T17 1701-1707 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T18 1723-1724 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 2025-2026 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 2362-2363 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 2615-2616 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 2717-2718 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 2778-2779 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 3034-3041 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T25 3045-3046 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 3217-3218 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T27 3263-3264 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 3455-3456 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 3476-3477 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T30 3679-3680 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T31 4240-4241 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 4384-4385 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 4418-4423 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T34 4418-4423 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T35 4699-4700 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T36 4714-4715 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 4773-4774 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T38 5128-5129 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 2429-2439 Chemical denotes cefotaxime http://purl.obolibrary.org/obo/CHEBI_204928
T2 2743-2745 Chemical denotes Hg http://purl.obolibrary.org/obo/CHEBI_16170|http://purl.obolibrary.org/obo/CHEBI_25195
T4 2925-2938 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T5 3000-3004 Chemical denotes agar http://purl.obolibrary.org/obo/CHEBI_2509
T6 3191-3197 Chemical denotes silver http://purl.obolibrary.org/obo/CHEBI_30512|http://purl.obolibrary.org/obo/CHEBI_9141
T8 3322-3335 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T9 3439-3443 Chemical denotes agar http://purl.obolibrary.org/obo/CHEBI_2509
T10 3622-3635 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T11 3661-3667 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T12 3787-3793 Chemical denotes silver http://purl.obolibrary.org/obo/CHEBI_30512|http://purl.obolibrary.org/obo/CHEBI_9141
T14 4311-4321 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T15 4520-4533 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T16 4627-4640 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
33 0-8 Species denotes Patients Tax:9606
34 23-70 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
35 72-82 Species denotes SARS-CoV-2 Tax:2697049
36 374-382 Species denotes patients Tax:9606
37 9-17 Disease denotes infected MESH:D007239
38 101-112 Disease denotes lung damage MESH:D008171
39 264-274 Disease denotes infections MESH:D007239
40 317-336 Disease denotes coronavirus disease MESH:D018352
41 338-346 Disease denotes COVID-19 MESH:C000657245
42 411-419 Disease denotes COVID-19 MESH:C000657245
43 458-495 Disease denotes chronic obstructive pulmonary disease MESH:D029424
44 497-509 Disease denotes hypertension MESH:D006973
45 511-519 Disease denotes diabetes MESH:D003920
46 524-546 Disease denotes chronic kidney disease MESH:D051436
47 654-671 Disease denotes fungal infections MESH:D009181
61 880-888 Species denotes patients Tax:9606
62 1022-1030 Species denotes patients Tax:9606
63 1215-1223 Species denotes patients Tax:9606
64 1238-1248 Species denotes SARS-CoV-2 Tax:2697049
65 673-695 Disease denotes Invasive aspergillosis MESH:D055744
66 749-758 Disease denotes pneumonia MESH:D011014
67 958-977 Disease denotes respiratory failure MESH:D012131
68 1035-1039 Disease denotes died MESH:D003643
69 1077-1095 Disease denotes invasive infection MESH:D007239
70 1110-1123 Disease denotes aspergillosis MESH:D001228
71 1176-1184 Disease denotes COVID-19 MESH:C000657245
72 1224-1232 Disease denotes infected MESH:D007239
73 1290-1312 Disease denotes invasive aspergillosis MESH:D055744
86 1696-1699 Gene denotes CD8 Gene:925
87 1484-1491 Species denotes patient Tax:9606
88 1394-1402 Disease denotes COVID-19 MESH:C000657245
89 1414-1423 Disease denotes pneumonia MESH:D011014
90 1446-1478 Disease denotes invasive pulmonary aspergillosis MESH:D055744
91 1539-1556 Disease denotes pulmonary disease MESH:D008171
92 1620-1644 Disease denotes myelodysplastic syndrome MESH:D009190
93 1672-1689 Disease denotes hypereosinophilia MESH:D004802
94 1708-1721 Disease denotes lymphocytosis MESH:D008218
95 1802-1825 Disease denotes Hashimoto’s thyroiditis MESH:D050031
96 1827-1839 Disease denotes hypertension MESH:D006973
97 1845-1873 Disease denotes benign prostatic hypertrophy MESH:D011470
110 1914-1921 Species denotes patient Tax:9606
111 2007-2014 Species denotes patient Tax:9606
112 2194-2201 Species denotes patient Tax:9606
113 2441-2451 Species denotes SARS-CoV-2 Tax:2697049
114 2568-2590 Species denotes Haemophilus influenzae Tax:727
115 2429-2439 Chemical denotes cefotaxime MESH:D002439
116 2045-2050 Disease denotes fever MESH:D005334
117 2055-2060 Disease denotes cough MESH:D003371
118 2082-2089 Disease denotes dyspnea MESH:D004417
119 2143-2162 Disease denotes respiratory failure MESH:D012131
120 2164-2173 Disease denotes tachypnea MESH:D059246
121 2179-2188 Disease denotes hypoxemia MESH:D000860
139 2676-2683 Species denotes patient Tax:9606
140 2860-2881 Species denotes Aspergillus fumigatus Tax:746128
141 3139-3153 Species denotes Aspergillus sp Tax:5065
142 3217-3229 Species denotes A. fumigatus Tax:746128
143 3365-3372 Species denotes patient Tax:9606
144 3476-3488 Species denotes A. fumigatus Tax:746128
145 3520-3530 Species denotes SARS-CoV-2 Tax:2697049
146 3679-3691 Species denotes A. fumigatus Tax:746128
147 2925-2938 Chemical denotes galactomannan MESH:C012990
148 2990-3004 Chemical denotes Sabouraud agar
149 3191-3197 Chemical denotes silver MESH:D012834
150 3322-3335 Chemical denotes galactomannan MESH:C012990
151 3429-3443 Chemical denotes Sabouraud agar
152 3622-3635 Chemical denotes galactomannan MESH:C012990
153 3657-3667 Chemical denotes β-D-glucan
154 3373-3377 Disease denotes died MESH:D003643
155 3397-3416 Disease denotes respiratory failure MESH:D012131
161 3844-3851 Species denotes patient Tax:9606
162 3925-3939 Species denotes Aspergillus sp Tax:5065
163 3787-3793 Chemical denotes silver MESH:D012834
164 3852-3866 Disease denotes critically ill MESH:D016638
165 3872-3891 Disease denotes coronavirus disease MESH:D018352
175 4191-4199 Species denotes patients Tax:9606
176 4217-4224 Species denotes patient Tax:9606
177 4466-4477 Species denotes Aspergillus Tax:746128
178 4520-4533 Chemical denotes galactomannan MESH:C012990
179 4627-4640 Chemical denotes galactomannan MESH:C012990
180 4041-4063 Disease denotes invasive aspergillosis MESH:D055744
181 4140-4172 Disease denotes invasive pulmonary aspergillosis MESH:D055744
182 4176-4190 Disease denotes critically ill MESH:D016638
183 4399-4412 Disease denotes aspergillosis MESH:D001228
191 4701-4708 Species denotes patient Tax:9606
192 4773-4782 Species denotes A. flavus Tax:5059
193 5072-5080 Species denotes patients Tax:9606
194 4722-4742 Disease denotes SARS-CoV-2 infection MESH:C000657245
195 4863-4876 Disease denotes aspergillosis MESH:D001228
196 5042-5064 Disease denotes invasive aspergillosis MESH:D055744
197 5093-5101 Disease denotes COVID-19 MESH:C000657245
204 5193-5200 Species denotes patient Tax:9606
205 5138-5170 Disease denotes invasive pulmonary aspergillosis MESH:D055744
206 5215-5223 Disease denotes COVID-19 MESH:C000657245
207 5235-5244 Disease denotes pneumonia MESH:D011014
208 5253-5261 Disease denotes COVID-19 MESH:C000657245
209 5404-5425 Disease denotes SARS-CoV-2 infections MESH:C000657245

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 120-137 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T2 120-137 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T3 2217-2228 http://purl.obolibrary.org/obo/GO_0006810 denotes transported
T4 2510-2531 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T5 2518-2531 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 2925-2938 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T2 3322-3335 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 3622-3635 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T4 4520-4533 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T5 4627-4640 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T6 154-168 Phenotype denotes cytokine storm http://purl.obolibrary.org/obo/HP_0033041
T7 458-495 Phenotype denotes chronic obstructive pulmonary disease http://purl.obolibrary.org/obo/HP_0006510
T8 497-509 Phenotype denotes hypertension http://purl.obolibrary.org/obo/HP_0000822
T9 524-546 Phenotype denotes chronic kidney disease http://purl.obolibrary.org/obo/HP_0012622
T10 749-758 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T11 958-977 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T12 1414-1423 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T13 1446-1478 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T14 1620-1644 Phenotype denotes myelodysplastic syndrome http://purl.obolibrary.org/obo/HP_0002863
T15 1672-1689 Phenotype denotes hypereosinophilia http://purl.obolibrary.org/obo/HP_0032061
T16 1708-1721 Phenotype denotes lymphocytosis http://purl.obolibrary.org/obo/HP_0100827
T17 1802-1825 Phenotype denotes Hashimoto’s thyroiditis http://purl.obolibrary.org/obo/HP_0000872
T18 1827-1839 Phenotype denotes hypertension http://purl.obolibrary.org/obo/HP_0000822
T19 1845-1873 Phenotype denotes benign prostatic hypertrophy http://purl.obolibrary.org/obo/HP_0008711
T20 2045-2050 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T21 2055-2060 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T22 2082-2089 Phenotype denotes dyspnea http://purl.obolibrary.org/obo/HP_0002094
T23 2143-2162 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T24 2164-2173 Phenotype denotes tachypnea http://purl.obolibrary.org/obo/HP_0002789
T25 2179-2188 Phenotype denotes hypoxemia http://purl.obolibrary.org/obo/HP_0012418
T26 2381-2391 Phenotype denotes aspiration http://purl.obolibrary.org/obo/HP_0002835
T27 2641-2651 Phenotype denotes aspiration http://purl.obolibrary.org/obo/HP_0002835
T28 3063-3073 Phenotype denotes aspiration http://purl.obolibrary.org/obo/HP_0002835
T29 3397-3416 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T30 3572-3583 Phenotype denotes aspirations http://purl.obolibrary.org/obo/HP_0002835
T31 4140-4172 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T32 5138-5170 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T33 5235-5244 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T34 5397-5425 Phenotype denotes severe SARS-CoV-2 infections http://purl.obolibrary.org/obo/HP_0033141

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T6 0-208 Sentence denotes Patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) experience major lung damage due to viral replication and the ensuing cytokine storm and complex inflammatory processes (1).
T7 209-352 Sentence denotes The severe damage to lung tissue can lead to secondary infections within a median of 17 days after onset of coronavirus disease (COVID-19) (2).
T8 353-672 Sentence denotes Most immunocompetent patients who develop severe forms of COVID-19 have >1 underlying condition, such as chronic obstructive pulmonary disease, hypertension, diabetes, or chronic kidney disease (3), but none of these predisposing factors generally are associated with an increased risk for developing fungal infections.
T9 673-829 Sentence denotes Invasive aspergillosis is a well-described complication of severe influenza pneumonia (4,5), but many intensivists seem to overlook this superinfection (6).
T10 830-982 Sentence denotes A recent study reported a 19% incidence among 432 patients admitted to an intensive care unit (ICU) for influenza-related acute respiratory failure (4).
T11 983-1128 Sentence denotes Moreover, in a small autopsy series of patients who died in 2003 from SARS, 10% (2/20) had an invasive infection suggestive of aspergillosis (7).
T12 1129-1325 Sentence denotes As the medical community confronts the ongoing COVID-19 pandemic, determining whether patients infected with SARS-CoV-2 develop fungal complications, especially invasive aspergillosis, is crucial.
T13 1326-1479 Sentence denotes We report the case of a 74-year-old immunocompetent man with severe COVID-19–associated pneumonia who rapidly developed invasive pulmonary aspergillosis.
T14 1480-1557 Sentence denotes The patient had several underlying chronic diseases but no pulmonary disease.
T15 1558-1874 Sentence denotes Among his existing conditions were asymptomatic and untreated myelodysplastic syndrome, diagnosed on the basis of hypereosinophilia, with CD8+ T-cell lymphocytosis, a normal karyotype and low-risk International Prognostic Scoring System score; Hashimoto’s thyroiditis; hypertension; and benign prostatic hypertrophy.
T16 1875-2002 Sentence denotes On the morning of March 23, day 1, the patient fell out of bed, was unable to get up on his own, and called emergency services.
T17 2003-2099 Sentence denotes The patient described a 1-week history of fever and cough followed by onset of dyspnea that day.
T18 2100-2189 Sentence denotes Clinical examination showed signs of acute respiratory failure, tachypnea, and hypoxemia.
T19 2190-2339 Sentence denotes The patient was intubated, transported to the hospital, and transferred to the ICU, where he required mechanical ventilation and vasopressor support.
T20 2340-2440 Sentence denotes The same day, we took a protected distal aspiration before intravenous administration of cefotaxime.
T21 2441-2537 Sentence denotes SARS-CoV-2 viral RNA was detected in this sample by using 2 distinct reverse transcription PCRs.
T22 2538-2671 Sentence denotes The sample revealed 104/mL of Haemophilus influenzae, which was not found in a second protected distal aspiration performed on day 2.
T23 2672-2764 Sentence denotes The patient’s condition worsened, and he had a PaO2/FIO2 ratio <140 mm Hg with FIO2 of 100%.
T24 2765-2851 Sentence denotes We performed a tracheal aspirate on day 4 and sent samples to the mycology laboratory.
T25 2852-3022 Sentence denotes PCR for Aspergillus fumigatus was positive (430 copies/mL; 2.6 log), but galactomannan in the aspirate assay was negative, and culture on Sabouraud agar remained sterile.
T26 3023-3216 Sentence denotes Results of testing of a second tracheal aspiration performed on day 9 yielded branched septate hyphae suggestive of Aspergillus sp. under microscopic examination after silver staining (Figure).
T27 3217-3360 Sentence denotes A. fumigatus PCR was once again positive with a higher number of copies (3,600 copies/mL; 3.55 log); the galactomannan assay was not available.
T28 3361-3417 Sentence denotes The patient died that day of severe respiratory failure.
T29 3418-3510 Sentence denotes Culture on Sabouraud agar later grew a mold identified as A. fumigatus by mass spectrometry.
T30 3511-3584 Sentence denotes Of note, SARS-CoV-2 RNA still was detectable in the tracheal aspirations.
T31 3585-3757 Sentence denotes Results of serum analyses, including galactomannan index determination, β-D-glucan assay, and A. fumigatus PCR, were negative in serum samples collected on day 4 and day 8.
T32 3758-3900 Sentence denotes Figure Microscopic image of silver-stained tracheal aspirate from an immunocompetent patient critically ill with coronavirus disease, France.
T33 3901-3965 Sentence denotes Filaments suggestive of Aspergillus sp. are shown (black arrow).
T34 3966-3996 Sentence denotes Original magnification ×1,000.
T35 3997-4204 Sentence denotes This case fulfills the criteria of putative invasive aspergillosis according to the classification defined by Blot et al. for the diagnosis of invasive pulmonary aspergillosis in critically ill patients (8).
T36 4205-4332 Sentence denotes Because the patient’s illness took a rapid and fatal course, we did not have time to initiate appropriate antifungal treatment.
T37 4333-4455 Sentence denotes As previously reported, respiratory samples led to a diagnosis of aspergillosis, but blood samples lacked sensitivity (4).
T38 4456-4698 Sentence denotes Moreover, Aspergillus PCR contributed to the diagnosis, but the galactomannan was negative, consistent with what we previously reported about the lower sensitivity of the galactomannan compared with PCR and culture in respiratory samples (9).
T39 4699-4904 Sentence denotes A patient with a fatal SARS-CoV-2 infection recently was reported to have A. flavus on tracheal aspirates culture, but other evidence was missing, and diagnosis of aspergillosis was not substantiated (10).
T40 4905-5102 Sentence denotes Additional assessments are urgently needed to thoroughly investigate cases and promptly establish and define the cumulative incidence of invasive aspergillosis in ICU patients with severe COVID-19.
T41 5103-5245 Sentence denotes In conclusion, we report a case of invasive pulmonary aspergillosis in an immunocompetent patient during severe COVID-19–associated pneumonia.
T42 5246-5426 Sentence denotes As the COVID-19 outbreak continues to spread worldwide, other reports are needed to assess the occurrence and frequency of fungal complications during severe SARS-CoV-2 infections.