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PMC:7558333 / 5758-7832 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T17 1242-1245 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T18 1572-1577 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T19 1714-1722 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T20 1742-1745 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T21 1853-1858 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T22 2038-2041 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T13 1572-1577 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T14 1853-1858 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T45 1118-1126 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T40 1275-1280 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T41 1297-1298 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 1315-1321 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T43 1355-1356 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T44 1383-1384 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 1548-1553 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T46 1951-1952 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 1967-1973 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T48 2056-2057 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T4 1179-1184 http://purl.obolibrary.org/obo/GO_0019835 denotes Lysis

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T8 238-240 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T9 1598-1600 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T10 1611-1613 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T45 0-4 Sentence denotes 2.2.
T46 5-26 Sentence denotes Aspergillus Detection
T47 27-298 Sentence denotes Respiratory samples, either bronchial or endotracheal aspirates or bronchoalveolar lavages, were systematic twice weekly and Aspergillus detection was performed using culture and real-time quantitative PCR, but GM was not performed to avoid any risk of lab contamination.
T48 299-403 Sentence denotes Briefly, respiratory samples were first digested using v/v digestEUR (Eurobio) for 30 min under shaking.
T49 404-616 Sentence denotes Mycological culture were performed after centrifugation of fluidified samples by inoculation of 100–200 µL of pellet on Sabouraud-Chloramphenicol dextrose Agar plates, and incubated for 7 days at 30 °C and 37 °C.
T50 617-862 Sentence denotes Mold identification at genus or species complex level was performed microscopically, and confirmed at species level using MALDI-ToF mass spectrometry (MALDI Biotyper, Bruker France, Marne-la-Vallée, France), after fungal material extraction [9].
T51 863-1026 Sentence denotes Spectrum profiles were then submitted to the Mass Spectrometry Identification (MSI) online database for definitive identification (https://msi.happy-dev.fr/ [10]).
T52 1027-1331 Sentence denotes For molecular detection, 200 µL of plain fluidified respiratory sample underwent immediate SARS-CoV-2 inactivation by heating at 56 °C overnight in ATL Lysis buffer (Qiagen, Saint-Quentin Fallavier, France), before DNA extraction using the EZ1 DSP virus kit (Qiagen) on a EZ1 Advanced XL device (Qiagen).
T53 1332-1452 Sentence denotes Molecular detection of A. fumigatus was done using a 28S rDNA Aspergillus-targeted PCR, as previously published [11,12].
T54 1453-1802 Sentence denotes In case of Aspergillus positive culture and/or positive PCR in respiratory samples, additional tests were performed on serum, i.e., detection of GM (Platelia GM Aspergillus, Biorad, Marnes-la-Coquette, France), Aspergillus PCR and detection of anti-Aspergillus antibody by ELISA (Platelia IgG Aspergillus, Biorad) and in-house immunoelectrophoresis.
T55 1803-2037 Sentence denotes Briefly, Aspergillus PCR was performed on 1 mL of serum extracted using MagNA Pure 24 Total NA Isolation kit (Roche diagnostics, Meylan, France) on a MagNA Pure 24 device (Roche diagnostics), according to manufacturer recommendations.
T56 2038-2074 Sentence denotes DNA was eluted in a volume of 50 µL.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
143 5-16 Species denotes Aspergillus Tax:746128
146 152-163 Species denotes Aspergillus Tax:746128
147 238-240 Chemical denotes GM MESH:C012990
149 524-563 Chemical denotes Sabouraud-Chloramphenicol dextrose Agar
154 1118-1128 Species denotes SARS-CoV-2 Tax:2697049
155 1355-1367 Species denotes A. fumigatus Tax:746128
156 1394-1405 Species denotes Aspergillus Tax:746128
157 1175-1184 Disease denotes ATL Lysis MESH:D015275
165 1464-1475 Species denotes Aspergillus Tax:746128
166 1664-1675 Species denotes Aspergillus Tax:746128
167 1702-1713 Species denotes Aspergillus Tax:746128
168 1812-1823 Species denotes Aspergillus Tax:746128
169 1598-1600 Chemical denotes GM MESH:C012990
170 1602-1625 Disease denotes Platelia GM Aspergillus MESH:C562602
171 1733-1757 Disease denotes Platelia IgG Aspergillus MESH:D017099

2_test

Id Subject Object Predicate Lexical cue
32664423-28637907-60101697 1021-1023 28637907 denotes 10
32664423-29248586-60101698 1445-1447 29248586 denotes 11
32664423-14766869-60101699 1448-1450 14766869 denotes 12