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PMC:7340597 / 4101-5681 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T2 771-778 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T3 771-778 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T4 1061-1074 https://glytoucan.org/Structures/Glycans/G93424OB denotes galactomannan
T5 1130-1143 https://glytoucan.org/Structures/Glycans/G93424OB denotes galactomannan
T6 1145-1147 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T7 1499-1501 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T10 292-296 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T11 447-453 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T12 545-560 Body_part denotes digestive tract http://purl.org/sig/ont/fma/fma317863
T13 771-778 Body_part denotes heparin http://purl.org/sig/ont/fma/fma82839
T14 1076-1081 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T15 1086-1092 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T16 1535-1540 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T7 292-296 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T8 447-453 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T9 545-560 Body_part denotes digestive tract http://purl.obolibrary.org/obo/UBERON_0001555
T10 1076-1081 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T11 1086-1092 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T12 1535-1540 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
171 37-45 Species denotes patients Tax:9606
172 72-119 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
173 121-131 Species denotes SARS-COV-2 Tax:2697049
174 346-356 Species denotes SARS-CoV-2 Tax:2697049
175 1400-1408 Species denotes patients Tax:9606
176 1545-1556 Species denotes Aspergillus Tax:746128
177 584-595 Chemical denotes chloroquine MESH:D002738
178 771-778 Chemical denotes heparin MESH:D006493
179 780-784 Chemical denotes LMWH MESH:D006495
180 787-797 Chemical denotes nadroparin MESH:D017762
181 1061-1074 Chemical denotes galactomannan MESH:C012990
182 1130-1143 Chemical denotes galactomannan MESH:C012990
183 1145-1147 Chemical denotes GM MESH:C012990
184 1499-1501 Chemical denotes GM MESH:C012990
185 176-195 Disease denotes respiratory failure MESH:D012131
186 875-898 Disease denotes pulmonary aspergillosis MESH:D055732
187 960-983 Disease denotes Pulmonary aspergillosis MESH:D055732
188 1304-1327 Disease denotes pulmonary aspergillosis MESH:D055732
189 1460-1469 Disease denotes infection MESH:D007239

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T60 72-119 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T61 72-105 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T62 121-125 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T63 176-195 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T64 346-354 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 885-898 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T66 970-983 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T67 1283-1292 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T68 1314-1327 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T69 1414-1418 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T70 1460-1469 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T23 204-206 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T24 292-296 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T25 292-296 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T26 545-560 http://purl.obolibrary.org/obo/UBERON_0001555 denotes digestive tract
T27 863-870 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T28 1149-1156 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T29 1261-1262 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 1497-1498 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T3 584-595 Chemical denotes chloroquine http://purl.obolibrary.org/obo/CHEBI_3638
T4 771-778 Chemical denotes heparin http://purl.obolibrary.org/obo/CHEBI_28304
T5 801-803 Chemical denotes IE http://purl.obolibrary.org/obo/CHEBI_137259
T6 1061-1074 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T7 1130-1143 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T8 1145-1147 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T10 1186-1189 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T11 1218-1225 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T12 1499-1501 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T14 1517-1520 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T15 1576-1579 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T12 176-195 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 387-408 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T2 395-408 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T2 1061-1074 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 1130-1143 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T4 1145-1147 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T5 1499-1501 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T36 0-32 Sentence denotes 2.1 Study population and design
T37 33-345 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 346-481 Sentence denotes SARS-CoV-2 was diagnosed using real-time reverse transcription polymerase chain reaction (RT-PCR) on sputum and/or bronchial aspirates.
T39 482-820 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 821-959 Sentence denotes Bronchoscopy, with or without lavage, and testing for pulmonary aspergillosis were performed at the discretion of the attending physician.
T41 960-1125 Sentence denotes Pulmonary aspergillosis was diagnosed using clinical, radiological and mycological data and included galactomannan (serum and sputum), tracheal or bronchial culture.
T42 1126-1250 Sentence denotes For galactomannan (GM) testing from bronchoalveolar lavage (BAL) fluid Platelia Aspergillis antigen ELISA (Biorad) was used.
T43 1251-1424 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 1425-1580 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.

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T52 72-84 SP_7 denotes severe acute
T53 85-96 SP_7;UBERON:0001004 denotes respiratory
T54 97-119 SP_7 denotes syndrome coronavirus 2
T55 121-131 SP_7 denotes SARS-COV-2
T56 176-187 UBERON:0001004 denotes respiratory
T57 255-265 GO:0016265 denotes postmortem
T58 292-296 UBERON:0002048 denotes lung
T59 346-356 SP_7 denotes SARS-CoV-2
T60 387-408 GO:0001171 denotes reverse transcription
T61 447-453 UBERON:0007311 denotes sputum
T62 461-470 UBERON:0004242 denotes bronchial
T63 545-554 GO:0007586;UBERON:0001555 denotes digestive
T64 555-560 UBERON:0001555 denotes tract
T65 584-595 CHEBI:3638;DG_10;CHEBI:3638 denotes chloroquine
T66 729-744 GO:0050817 denotes anticoagulation
T67 771-778 CHEBI:24505;CHEBI:24505 denotes heparin
T68 875-884 UBERON:0002048 denotes pulmonary
T69 960-969 UBERON:0002048 denotes Pulmonary
T70 1061-1074 CHEBI:27680;CHEBI:27680 denotes galactomannan
T71 1076-1081 UBERON:0001977 denotes serum
T72 1086-1092 UBERON:0007311 denotes sputum
T73 1095-1103 UBERON:0003126 denotes tracheal
T74 1107-1116 UBERON:0004242 denotes bronchial
T75 1130-1143 CHEBI:27680;CHEBI:27680 denotes galactomannan
T76 1162-1177 UBERON:0002031 denotes bronchoalveolar
T77 1178-1184 UBERON:0004821 denotes lavage
T78 1218-1225 CHEBI:59132;CHEBI:59132 denotes antigen
T79 1304-1313 UBERON:0002048 denotes pulmonary
T80 1535-1540 UBERON:0001977 denotes serum
T81 1545-1556 NCBITaxon:5052 denotes Aspergillus
T30595 87-93 UBERON:0000170 denotes spirat
T75123 126-134 CHEBI:16842;CHEBI:16842 denotes COV-2) a
T96536 187-198 CHEBI:51686;CHEBI:51686 denotes failure be
T48493 210-211 CHEBI:51686;CHEBI:51686 denotes c
T9930 220-233 CHEBI:29149;CHEBI:29149 denotes d 30 April 20
T72105 643-653 GO:0016265 denotes ealth and
T2841 680-685 UBERON:0000170 denotes its
T58291 821-830 UBERON:0002048 denotes Bronchosc
T96902 857-873 CHEBI:35705;CHEBI:35705 denotes , and testing fo
T96250 942-954 CHEBI:8378;CHEBI:8378 denotes ending physi
T21854 1067-1072 GO:0016265 denotes omann
T57492 1223-1232 UBERON:0002048 denotes en ELISA
T41634 1466-1478 CHEBI:10023;CHEBI:10023 denotes ion with cli
T55502 1544-1559 CHEBI:50858;CHEBI:50858 denotes Aspergillus sp
T68620 1567-1579 CHEBI:8378;CHEBI:8378 denotes red from BAL