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PMC:7340597 / 4089-6528 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T2 783-790 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T3 783-790 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T4 1073-1086 https://glytoucan.org/Structures/Glycans/G93424OB denotes galactomannan
T5 1142-1155 https://glytoucan.org/Structures/Glycans/G93424OB denotes galactomannan
T6 1157-1159 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T7 1511-1513 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T10 304-308 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T11 459-465 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T12 557-572 Body_part denotes digestive tract http://purl.org/sig/ont/fma/fma317863
T13 783-790 Body_part denotes heparin http://purl.org/sig/ont/fma/fma82839
T14 1088-1093 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T15 1098-1104 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T16 1547-1552 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T17 1636-1640 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T18 1741-1746 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T19 1775-1779 Body_part denotes Lung http://purl.org/sig/ont/fma/fma7195
T20 1967-1972 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T7 304-308 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T8 459-465 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T9 557-572 Body_part denotes digestive tract http://purl.obolibrary.org/obo/UBERON_0001555
T10 1088-1093 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T11 1098-1104 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T12 1547-1552 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T13 1636-1640 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T14 1775-1779 Body_part denotes Lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
171 49-57 Species denotes patients Tax:9606
172 84-131 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
173 133-143 Species denotes SARS-COV-2 Tax:2697049
174 358-368 Species denotes SARS-CoV-2 Tax:2697049
175 1412-1420 Species denotes patients Tax:9606
176 1557-1568 Species denotes Aspergillus Tax:746128
177 596-607 Chemical denotes chloroquine MESH:D002738
178 783-790 Chemical denotes heparin MESH:D006493
179 792-796 Chemical denotes LMWH MESH:D006495
180 799-809 Chemical denotes nadroparin MESH:D017762
181 1073-1086 Chemical denotes galactomannan MESH:C012990
182 1142-1155 Chemical denotes galactomannan MESH:C012990
183 1157-1159 Chemical denotes GM MESH:C012990
184 1511-1513 Chemical denotes GM MESH:C012990
185 188-207 Disease denotes respiratory failure MESH:D012131
186 887-910 Disease denotes pulmonary aspergillosis MESH:D055732
187 972-995 Disease denotes Pulmonary aspergillosis MESH:D055732
188 1316-1339 Disease denotes pulmonary aspergillosis MESH:D055732
189 1472-1481 Disease denotes infection MESH:D007239
197 1666-1674 Species denotes patients Tax:9606
198 2005-2013 Chemical denotes formalin MESH:D005557
199 2027-2035 Chemical denotes paraffin MESH:D010232
200 2065-2076 Chemical denotes Hematoxylin MESH:D006416
201 2081-2086 Chemical denotes eosin MESH:D004801
202 2088-2091 Chemical denotes H&E
203 2098-2111 Chemical denotes periodic acid MESH:D010504
205 2266-2273 Species denotes patient Tax:9606

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T60 84-131 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T61 84-117 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T62 133-137 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T63 188-207 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T64 358-366 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 897-910 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T66 982-995 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T67 1295-1304 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T68 1326-1339 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T69 1426-1430 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T70 1472-1481 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T71 2134-2137 Disease denotes PAS http://purl.obolibrary.org/obo/MONDO_0004277

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T23 216-218 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T24 304-308 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T25 304-308 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T26 557-572 http://purl.obolibrary.org/obo/UBERON_0001555 denotes digestive tract
T27 875-882 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T28 1161-1168 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T29 1273-1274 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 1509-1510 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 1636-1640 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T32 1636-1640 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T33 1741-1746 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T34 1775-1779 http://purl.obolibrary.org/obo/UBERON_0002048 denotes Lung
T35 1775-1779 http://www.ebi.ac.uk/efo/EFO_0000934 denotes Lung
T36 1867-1868 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 1880-1881 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T38 1967-1972 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T3 596-607 Chemical denotes chloroquine http://purl.obolibrary.org/obo/CHEBI_3638
T4 783-790 Chemical denotes heparin http://purl.obolibrary.org/obo/CHEBI_28304
T5 813-815 Chemical denotes IE http://purl.obolibrary.org/obo/CHEBI_137259
T6 1073-1086 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T7 1142-1155 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T8 1157-1159 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T10 1198-1201 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T11 1230-1237 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T12 1511-1513 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T14 1529-1532 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T15 1588-1591 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T16 2098-2111 Chemical denotes periodic acid http://purl.obolibrary.org/obo/CHEBI_29149
T17 2107-2111 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T18 2134-2137 Chemical denotes PAS http://purl.obolibrary.org/obo/CHEBI_27565

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T12 188-207 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 399-420 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T2 407-420 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T2 1073-1086 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 1142-1155 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T4 1157-1159 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T5 1511-1513 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T35 0-10 Sentence denotes 2 Methods
T36 12-44 Sentence denotes 2.1 Study population and design
T37 45-357 Sentence denotes All patients with laboratory confirmed severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) admitted to the ICU due to acute hypoxemic respiratory failure between 22 March 2020 and 30 April 2020 and with available postmortem needle core biopsy of the lung were eligible for inclusion in this case series.
T38 358-493 Sentence denotes SARS-CoV-2 was diagnosed using real-time reverse transcription polymerase chain reaction (RT-PCR) on sputum and/or bronchial aspirates.
T39 494-832 Sentence denotes Routine ICU management included, among other things, selective digestive tract decontamination (SDD), chloroquine until the Dutch National Institute for Public Health and Environment advised against its use at the end of March 2020, and high dose anticoagulation with low-molecular-weight heparin (LMWH) (nadroparin 87 IE/kg twice daily).
T40 833-971 Sentence denotes Bronchoscopy, with or without lavage, and testing for pulmonary aspergillosis were performed at the discretion of the attending physician.
T41 972-1137 Sentence denotes Pulmonary aspergillosis was diagnosed using clinical, radiological and mycological data and included galactomannan (serum and sputum), tracheal or bronchial culture.
T42 1138-1262 Sentence denotes For galactomannan (GM) testing from bronchoalveolar lavage (BAL) fluid Platelia Aspergillis antigen ELISA (Biorad) was used.
T43 1263-1436 Sentence denotes Recently, a case definition for influenza associated pulmonary aspergillosis (IAPA) was proposed by an expert panel, which could be used to classify patients with CAPA [14].
T44 1437-1592 Sentence denotes Diagnostic criteria include proven infection with clinical symptoms and a GM index of ≥1 on BAL or of ≥0ꞏ5 on serum; or Aspergillus spp. cultured from BAL.
T45 1594-1640 Sentence denotes 2.2 Postmortem needle core biopsy of the lung
T46 1641-1774 Sentence denotes With permission from the patients' families, postmortem core needle biopsies were performed on both lungs within an hour after death.
T47 1775-1879 Sentence denotes Lung biopsies were ultrasound and CT guided and combined with surface anatomic landmarks as a reference.
T48 1880-1973 Sentence denotes A minimum of three histologic 14 gauge true cut needle biopsies were performed in both lungs.
T49 1974-2064 Sentence denotes Biopsy specimens were fixed in formalin, embedded in paraffin, and cut into 3 μm sections.
T50 2065-2193 Sentence denotes Hematoxylin and eosin (H&E), and periodic acid–Schiff with diastase (PAS-D) stains were applied according to routine procedures.
T51 2195-2220 Sentence denotes 2.3 Statistical analysis
T52 2221-2290 Sentence denotes Descriptive statistics were used to describe patient characteristics.
T53 2291-2347 Sentence denotes For statistical analysis IBM SPSS version 25.0 was used.
T54 2348-2439 Sentence denotes The local Medical Ethics Committee (Medical Research Committees United) approved the study.

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T52 84-96 SP_7 denotes severe acute
T53 97-108 SP_7;UBERON:0001004 denotes respiratory
T54 109-131 SP_7 denotes syndrome coronavirus 2
T55 133-143 SP_7 denotes SARS-COV-2
T56 188-199 UBERON:0001004 denotes respiratory
T57 267-277 GO:0016265 denotes postmortem
T58 304-308 UBERON:0002048 denotes lung
T59 358-368 SP_7 denotes SARS-CoV-2
T60 399-420 GO:0001171 denotes reverse transcription
T61 459-465 UBERON:0007311 denotes sputum
T62 473-482 UBERON:0004242 denotes bronchial
T63 557-566 GO:0007586;UBERON:0001555 denotes digestive
T64 567-572 UBERON:0001555 denotes tract
T65 596-607 CHEBI:3638;DG_10;CHEBI:3638 denotes chloroquine
T66 741-756 GO:0050817 denotes anticoagulation
T67 783-790 CHEBI:24505;CHEBI:24505 denotes heparin
T68 887-896 UBERON:0002048 denotes pulmonary
T69 972-981 UBERON:0002048 denotes Pulmonary
T70 1073-1086 CHEBI:27680;CHEBI:27680 denotes galactomannan
T71 1088-1093 UBERON:0001977 denotes serum
T72 1098-1104 UBERON:0007311 denotes sputum
T73 1107-1115 UBERON:0003126 denotes tracheal
T74 1119-1128 UBERON:0004242 denotes bronchial
T75 1142-1155 CHEBI:27680;CHEBI:27680 denotes galactomannan
T76 1174-1189 UBERON:0002031 denotes bronchoalveolar
T77 1190-1196 UBERON:0004821 denotes lavage
T78 1230-1237 CHEBI:59132;CHEBI:59132 denotes antigen
T79 1316-1325 UBERON:0002048 denotes pulmonary
T80 1547-1552 UBERON:0001977 denotes serum
T81 1557-1568 NCBITaxon:5052 denotes Aspergillus
T82 1599-1609 GO:0016265 denotes Postmortem
T83 1636-1640 UBERON:0002048 denotes lung
T84 1686-1696 GO:0016265 denotes postmortem
T85 1741-1746 UBERON:0000170 denotes lungs
T86 1768-1773 GO:0016265 denotes death
T87 1775-1779 UBERON:0002048 denotes Lung
T88 1845-1853 UBERON:0001062 denotes anatomic
T89 1967-1972 UBERON:0000170 denotes lungs
T90 2005-2013 CHEBI:16842;CHEBI:16842 denotes formalin
T91 2065-2076 CHEBI:51686;CHEBI:51686 denotes Hematoxylin
T92 2088-2089 CHEBI:51686;CHEBI:51686 denotes H
T93 2098-2111 CHEBI:29149;CHEBI:29149 denotes periodic acid
T30595 99-105 UBERON:0000170 denotes spirat
T75123 138-146 CHEBI:16842;CHEBI:16842 denotes COV-2) a
T96536 199-210 CHEBI:51686;CHEBI:51686 denotes failure be
T48493 222-223 CHEBI:51686;CHEBI:51686 denotes c
T9930 232-245 CHEBI:29149;CHEBI:29149 denotes d 30 April 20
T72105 655-665 GO:0016265 denotes ealth and
T2841 692-697 UBERON:0000170 denotes its
T58291 833-842 UBERON:0002048 denotes Bronchosc
T96902 869-885 CHEBI:35705;CHEBI:35705 denotes , and testing fo
T96250 954-966 CHEBI:8378;CHEBI:8378 denotes ending physi
T21854 1079-1084 GO:0016265 denotes omann
T57492 1235-1244 UBERON:0002048 denotes en ELISA
T41634 1478-1490 CHEBI:10023;CHEBI:10023 denotes ion with cli
T55502 1556-1571 CHEBI:50858;CHEBI:50858 denotes Aspergillus sp
T68620 1579-1591 CHEBI:8378;CHEBI:8378 denotes red from BAL
T3137 1635-1649 CHEBI:50858;CHEBI:50858 denotes lung With per
T8024 1691-1698 CHEBI:35341;CHEBI:35341 denotes ortem c
T69823 1774-1779 UBERON:0001443 denotes Lung
T65939 1864-1873 UBERON:0002048 denotes as a refe
T56069 1935-1944 CHEBI:35341;CHEBI:35341 denotes biopsies
T93868 1991-1996 UBERON:0001443 denotes were
T38163 2030-2035 UBERON:0000170 denotes affin
T111 2396-2408 CHEBI:8378;CHEBI:8378 denotes arch Committ