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PMC:7239617 / 2403-5116 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
63 1705-1718 Chemical denotes galactomannan MESH:C012990
122 1198-1201 Gene denotes AZI Gene:51582
123 1211-1214 Gene denotes AZI Gene:51582
124 1180-1183 Gene denotes AZI Gene:51582
125 1162-1165 Gene denotes AZI Gene:51582
126 1142-1145 Gene denotes AZI Gene:51582
127 186-194 Species denotes patients Tax:9606
128 219-226 Species denotes patient Tax:9606
129 238-245 Species denotes Patient Tax:9606
130 265-272 Species denotes Patient Tax:9606
131 322-329 Species denotes Patient Tax:9606
132 351-358 Species denotes Patient Tax:9606
133 378-385 Species denotes Patient Tax:9606
134 405-412 Species denotes Patient Tax:9606
135 432-439 Species denotes Patient Tax:9606
136 461-468 Species denotes Patient Tax:9606
137 294-301 Species denotes Patient Tax:9606
138 1125-1132 Chemical denotes LPV–RTV
139 1133-1140 Chemical denotes LPV–RTV
140 1146-1153 Chemical denotes LPV–RTV
141 1154-1161 Chemical denotes LPV–RTV
142 1166-1173 Chemical denotes LPV–RTV
143 1184-1191 Chemical denotes LPV–RTV
144 1202-1209 Chemical denotes LPV–RTV
145 153-185 Disease denotes invasive pulmonary aspergillosis MESH:D055744
146 511-519 Disease denotes COVID-19 MESH:C000657245
147 520-532 Disease denotes Hypertension MESH:D006973
148 534-541 Disease denotes obesity MESH:D009765
149 543-566 Disease denotes ischaemic heart disease MESH:D003324
150 567-579 Disease denotes Hypertension MESH:D006973
151 581-589 Disease denotes diabetes MESH:D003920
152 591-611 Disease denotes obesity Hypertension MESH:D006973
153 613-633 Disease denotes obesity Hypertension MESH:D006973
154 635-643 Disease denotes diabetes MESH:D003920
155 645-701 Disease denotes ischaemic heart disease Asthma Hypertension Hypertension MESH:D006973
156 703-722 Disease denotes asthma Hypertension MESH:D006973
157 724-732 Disease denotes diabetes MESH:D003920
158 801-808 Disease denotes Myeloma MESH:D009101
159 893-901 Disease denotes COVID-19 MESH:C000657245
160 910-918 Disease denotes COVID-19 MESH:C000657245
161 927-935 Disease denotes COVID-19 MESH:C000657245
162 944-952 Disease denotes COVID-19 MESH:C000657245
163 961-969 Disease denotes COVID-19 MESH:C000657245
164 978-986 Disease denotes COVID-19 MESH:C000657245
165 1023-1031 Disease denotes COVID-19 MESH:C000657245
166 1033-1042 Disease denotes emphysema MESH:D004646
167 1051-1059 Disease denotes COVID-19 MESH:C000657245
168 1068-1076 Disease denotes COVID-19 MESH:C000657245
169 1106-1114 Disease denotes COVID-19 MESH:C000657245
170 1236-1245 Disease denotes pneumonia MESH:D011014
171 1437-1469 Disease denotes Invasive pulmonary aspergillosis MESH:D055744
180 54-62 Species denotes patients Tax:9606
181 39-53 Disease denotes critically ill MESH:D016638
182 68-76 Disease denotes COVID-19 MESH:C000657245
183 105-137 Disease denotes invasive pulmonary aspergillosis MESH:D055744
193 2135-2138 Gene denotes AZI Gene:51582
194 2095-2102 Chemical denotes LPV–RTV
195 2103-2121 Chemical denotes lopnavir–ritonavir
196 2139-2151 Chemical denotes azithromycin MESH:D017963
197 2153-2156 Chemical denotes HCQ MESH:D006886
198 2157-2175 Chemical denotes hydroxychloroquine MESH:D006886
199 2247-2259 Chemical denotes voriconazole MESH:D065819
200 2265-2276 Chemical denotes caspofungin MESH:D000077336
201 2034-2040 Disease denotes Cancer MESH:D009369
203 2309-2312 Gene denotes Pt3 Gene:7694
205 2372-2385 Chemical denotes Dexamethasone MESH:D003907
207 2581-2602 Species denotes Aspergillus fumigatus Tax:746128

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T7 553-558 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088
T8 655-660 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088
T9 998-1002 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T10 1619-1624 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T11 1699-1704 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T7 553-558 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948
T8 655-660 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948
T9 998-1002 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T10 1619-1624 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T11 1699-1704 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T12 105-137 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T13 153-185 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T14 215-218 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T15 520-532 Phenotype denotes Hypertension http://purl.obolibrary.org/obo/HP_0000822
T16 534-541 Phenotype denotes obesity http://purl.obolibrary.org/obo/HP_0001513
T17 567-579 Phenotype denotes Hypertension http://purl.obolibrary.org/obo/HP_0000822
T18 591-598 Phenotype denotes obesity http://purl.obolibrary.org/obo/HP_0001513
T19 599-611 Phenotype denotes Hypertension http://purl.obolibrary.org/obo/HP_0000822
T20 613-620 Phenotype denotes obesity http://purl.obolibrary.org/obo/HP_0001513
T21 621-633 Phenotype denotes Hypertension http://purl.obolibrary.org/obo/HP_0000822
T22 669-675 Phenotype denotes Asthma http://purl.obolibrary.org/obo/HP_0002099
T23 676-688 Phenotype denotes Hypertension http://purl.obolibrary.org/obo/HP_0000822
T24 689-701 Phenotype denotes Hypertension http://purl.obolibrary.org/obo/HP_0000822
T25 703-709 Phenotype denotes asthma http://purl.obolibrary.org/obo/HP_0002099
T26 710-722 Phenotype denotes Hypertension http://purl.obolibrary.org/obo/HP_0000822
T27 1003-1014 Phenotype denotes atelectasis http://purl.obolibrary.org/obo/HP_0100750
T28 1033-1042 Phenotype denotes emphysema http://purl.obolibrary.org/obo/HP_0002097
T29 1236-1245 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T30 1437-1469 Phenotype denotes Invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T31 2034-2040 Phenotype denotes Cancer http://purl.obolibrary.org/obo/HP_0002664
T32 2218-2228 Phenotype denotes aspiration http://purl.obolibrary.org/obo/HP_0002835

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T17 68-76 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T18 124-137 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T19 172-185 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T20 511-519 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 520-532 Disease denotes Hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T22 534-541 Disease denotes obesity http://purl.obolibrary.org/obo/MONDO_0011122
T23 553-566 Disease denotes heart disease http://purl.obolibrary.org/obo/MONDO_0005267
T24 567-579 Disease denotes Hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T25 581-589 Disease denotes diabetes http://purl.obolibrary.org/obo/MONDO_0005015
T26 591-598 Disease denotes obesity http://purl.obolibrary.org/obo/MONDO_0011122
T27 599-611 Disease denotes Hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T28 613-620 Disease denotes obesity http://purl.obolibrary.org/obo/MONDO_0011122
T29 621-633 Disease denotes Hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T30 635-643 Disease denotes diabetes http://purl.obolibrary.org/obo/MONDO_0005015
T31 655-668 Disease denotes heart disease http://purl.obolibrary.org/obo/MONDO_0005267
T32 669-675 Disease denotes Asthma http://purl.obolibrary.org/obo/MONDO_0004979
T33 676-688 Disease denotes Hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T34 689-701 Disease denotes Hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T35 703-709 Disease denotes asthma http://purl.obolibrary.org/obo/MONDO_0004979
T36 710-722 Disease denotes Hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T37 724-732 Disease denotes diabetes http://purl.obolibrary.org/obo/MONDO_0005015
T38 801-808 Disease denotes Myeloma http://purl.obolibrary.org/obo/MONDO_0005170|http://purl.obolibrary.org/obo/MONDO_0009693
T40 893-901 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T41 910-918 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T42 927-935 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T43 944-952 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T44 961-969 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T45 978-986 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T46 1023-1031 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 1033-1042 Disease denotes emphysema http://purl.obolibrary.org/obo/MONDO_0004849
T48 1051-1059 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T49 1068-1076 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T50 1106-1114 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T51 1236-1245 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T52 1456-1469 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T53 1872-1875 Disease denotes CSP http://purl.obolibrary.org/obo/MONDO_0005078
T54 2034-2040 Disease denotes Cancer http://purl.obolibrary.org/obo/MONDO_0004992
T55 2261-2264 Disease denotes CSP http://purl.obolibrary.org/obo/MONDO_0005078

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T12 249-253 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T13 249-253 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T14 276-282 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T15 304-310 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T16 333-339 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T17 362-366 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T18 362-366 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T19 389-393 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T20 389-393 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T21 416-420 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T22 416-420 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T23 443-449 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T24 472-476 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T25 472-476 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T26 553-558 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T27 553-558 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T28 553-558 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T29 553-558 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T30 655-660 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T31 655-660 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T32 655-660 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T33 655-660 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T34 841-843 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T35 998-1002 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T36 998-1002 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T37 1537-1539 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T38 1613-1615 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T39 1662-1664 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T40 1805-1808 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 2
T41 1944-1946 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T42 1959-1961 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T43 1991-2003 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T30 215-218 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T32 249-253 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T33 362-366 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T34 389-393 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T35 416-420 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T36 472-476 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T37 810-818 Chemical denotes steroids http://purl.obolibrary.org/obo/CHEBI_35341
T38 826-828 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T39 1403-1406 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T40 1407-1410 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T41 1414-1417 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T42 1418-1421 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T43 1422-1425 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T44 1426-1429 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T45 1430-1433 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T46 1480-1483 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T47 1511-1514 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T48 1554-1557 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T49 1558-1571 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T50 1588-1590 Chemical denotes ND http://purl.obolibrary.org/obo/CHEBI_73419
T51 1616-1618 Chemical denotes ND http://purl.obolibrary.org/obo/CHEBI_73419
T52 1637-1639 Chemical denotes ND http://purl.obolibrary.org/obo/CHEBI_73419
T53 1654-1660 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T54 1672-1674 Chemical denotes ND http://purl.obolibrary.org/obo/CHEBI_73419
T55 1705-1718 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T56 2112-2121 Chemical denotes ritonavir http://purl.obolibrary.org/obo/CHEBI_45409
T57 2139-2151 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T58 2157-2175 Chemical denotes hydroxychloroquine http://purl.obolibrary.org/obo/CHEBI_5801
T59 2177-2180 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T60 2230-2232 Chemical denotes ND http://purl.obolibrary.org/obo/CHEBI_73419
T61 2247-2259 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T62 2265-2276 Chemical denotes caspofungin http://purl.obolibrary.org/obo/CHEBI_474180
T63 2372-2385 Chemical denotes Dexamethasone http://purl.obolibrary.org/obo/CHEBI_41879

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T4 1558-1571 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T5 1705-1718 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T10 0-143 Sentence denotes Table Clinical characteristics of nine critically ill patients with COVID-19 probable (n=1) and putative invasive pulmonary aspergillosis (n=8)
T11 144-237 Sentence denotes Putative invasive pulmonary aspergillosis patients (sex, age) Probable IPA patient (sex, age)
T12 238-487 Sentence denotes Patient 1 (male, 53 years) Patient 2 (female, 59 years) Patient3 (female, 69 years) Patient 4 (female, 63 years) Patient 5 (male, 43 years) Patient 6 (male, 79 years) Patient 7 (male, 77 years) Patient 8 (female, 75 years) Patient 9 (male, 47 years)
T13 488-737 Sentence denotes Risk factors of severe COVID-19 Hypertension, obesity, ischaemic heart disease Hypertension, diabetes, obesity Hypertension, obesity Hypertension, diabetes, ischaemic heart disease Asthma Hypertension Hypertension, asthma Hypertension, diabetes None
T14 738-818 Sentence denotes EORTC risk factors None None None None Steroids None None None Myeloma, steroids
T15 819-860 Sentence denotes APACHE II score 26 16 11 20 8 16 25 21 10
T16 861-1100 Sentence denotes Thoracic CT-scan/x-ray* Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19, segmental lung atelectasis Typical COVID-19, emphysema Typical COVID-19 Typical COVID-19 + one peripheral nodule
T17 1101-1217 Sentence denotes Anti-COVID-19 therapies LPV–RTV LPV–RTV, AZI LPV–RTV LPV–RTV AZI LPV–RTV, HCQ, AZI LPV–RTV, HCQ, AZI LPV–RTV, AZI No
T18 1218-1279 Sentence denotes Steroids to treat pneumonia† Yes No Yes Yes No Yes Yes Yes No
T19 1280-1335 Sentence denotes Renal replacement therapy Yes No No Yes No No Yes No No
T20 1336-1382 Sentence denotes Vasopressor Yes Yes Yes Yes No Yes Yes Yes Yes
T21 1383-1436 Sentence denotes Pulmonary specimen‡ BAL BAL BA BAL BAL BAL BAL BAL BA
T22 1437-1479 Sentence denotes Invasive pulmonary aspergillosis diagnosis
T23 1480-1510 Sentence denotes BAL culture§ − + + − + + + + +
T24 1511-1553 Sentence denotes BAL/BA qPCR¶ − − 23·9 − − 34·5 29·0 31·7 −
T25 1554-1618 Sentence denotes BAL galactomannan index 0·89 0·03 ND 0·15 0·12 0·05 3·91 0·36 ND
T26 1619-1649 Sentence denotes Serum qPCR¶ − − − ND − − − − −
T27 1650-1698 Sentence denotes β-D-glucan, pg/mL 523 ND 7·8 105 7 23 135 450 14
T28 1699-1769 Sentence denotes Serum galactomannan index 0·13 0·04 0·03 0·51 0·04 0·02 0·37 0·37 0·09
T29 1770-1818 Sentence denotes Number of mycological criteria 2 1 2 2 1 2 3 3 1
T30 1819-1880 Sentence denotes Antifungal therapy None None None None None None VRC CSP None
T31 1881-1975 Sentence denotes Outcome Alive Alive Alive Death (day 0) Alive Alive Death (day 18) Death (day 11) Death day 3)
T32 1976-2041 Sentence denotes EORTC=European Organization for Research and Treatment of Cancer.
T33 2042-2094 Sentence denotes APACHE= Acute Physiology and Chronic Health Enquiry.
T34 2095-2134 Sentence denotes LPV–RTV=lopnavir–ritonavir combination.
T35 2135-2152 Sentence denotes AZI=azithromycin.
T36 2153-2176 Sentence denotes HCQ=hydroxychloroquine.
T37 2177-2204 Sentence denotes BAL=Bronchoalveolar lavage.
T38 2205-2229 Sentence denotes BA=bronchial aspiration.
T39 2230-2242 Sentence denotes ND=not done.
T40 2243-2260 Sentence denotes VRC=voriconazole.
T41 2261-2277 Sentence denotes CSP=caspofungin.
T42 2278-2369 Sentence denotes * Thoracic CT scan was done in Pt3, Pt4, Pt5, 5 days (median) before respiratory specimens.
T43 2370-2494 Sentence denotes † Dexamethasone intravenous dose of 20 mg once daily from day 1 to day 5, followed by 10 mg once daily from day 6 to day 10;
T44 2495-2550 Sentence denotes ‡ No endotracheal or endobronchial lesion was observed.
T45 2551-2618 Sentence denotes § −=negative; +=positive with Aspergillus fumigatus identification.
T46 2619-2713 Sentence denotes ¶ qPCR=quantitative real-time PCR (−, negative; if positive, number of quantification cycles).