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PMC:7650537 / 6141-9621 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T1 1836-1843 https://glytoucan.org/Structures/Glycans/G15021LG denotes glucose

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T45 95-100 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T46 194-199 Body_part denotes Blood http://purl.org/sig/ont/fma/fma9670
T47 423-428 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T48 451-456 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T49 536-539 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T50 984-989 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T51 1013-1017 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T52 1424-1429 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T53 1538-1543 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T54 1685-1689 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T55 1836-1843 Body_part denotes glucose http://purl.org/sig/ont/fma/fma82743
T56 1852-1861 Body_part denotes glutamine http://purl.org/sig/ont/fma/fma82752
T57 1924-1929 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T58 2106-2111 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T59 2205-2210 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T60 2310-2314 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T61 2364-2368 Body_part denotes calf http://purl.org/sig/ont/fma/fma24984
T62 2369-2374 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T63 2474-2479 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T64 2783-2787 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T65 2819-2824 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 95-100 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T2 194-199 Body_part denotes Blood http://purl.obolibrary.org/obo/UBERON_0000178
T3 423-428 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T4 451-456 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T5 1924-1929 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T6 2205-2210 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T7 2369-2374 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T8 2819-2824 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T34 172-180 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 183-192 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T36 315-323 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 525-533 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 750-758 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 925-933 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 1009-1012 Disease denotes CLS http://purl.obolibrary.org/obo/MONDO_0001956|http://purl.obolibrary.org/obo/MONDO_0010561
T42 1403-1412 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T43 3350-3358 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T39 27-32 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T40 156-157 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 194-199 http://purl.obolibrary.org/obo/UBERON_0000178 denotes Blood
T42 194-199 http://www.ebi.ac.uk/efo/EFO_0000296 denotes Blood
T43 258-259 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 333-338 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T45 340-342 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T46 386-387 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 405-407 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T48 451-456 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T49 451-456 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T50 484-490 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T51 748-749 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 870-871 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T53 923-924 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 979-983 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T55 979-983 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T56 984-989 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T57 1013-1023 http://purl.obolibrary.org/obo/CLO_0000031 denotes Cell Lines
T58 1074-1075 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 1252-1263 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing was
T60 1424-1429 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T61 1460-1462 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T62 1538-1543 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T63 1685-1689 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T64 1766-1770 http://purl.obolibrary.org/obo/PR_000001318 denotes SELL
T65 1915-1919 http://purl.obolibrary.org/obo/PR_000001318 denotes SELL
T66 1922-1923 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T67 2004-2009 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T68 2106-2111 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T69 2160-2164 http://purl.obolibrary.org/obo/PR_000001318 denotes SELL
T70 2199-2204 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T71 2272-2273 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 2310-2314 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T73 2364-2368 http://www.ebi.ac.uk/efo/EFO_0003051 denotes calf
T74 2415-2416 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75 2474-2479 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T76 2500-2503 http://purl.obolibrary.org/obo/CLO_0050644 denotes w/v
T77 2597-2600 http://purl.obolibrary.org/obo/CLO_0050644 denotes w/v
T78 2707-2713 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T79 2783-2787 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T80 2800-2801 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 2802-2807 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T82 2817-2818 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T83 2919-2924 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T84 3086-3087 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T85 3244-3248 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T86 3276-3280 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T25 1820-1826 Chemical denotes NaHCO3 http://purl.obolibrary.org/obo/CHEBI_32139
T26 1836-1843 Chemical denotes glucose http://purl.obolibrary.org/obo/CHEBI_17234|http://purl.obolibrary.org/obo/CHEBI_4167
T28 1850-1861 Chemical denotes L-glutamine http://purl.obolibrary.org/obo/CHEBI_18050|http://purl.obolibrary.org/obo/CHEBI_30011|http://purl.obolibrary.org/obo/CHEBI_58359
T31 1852-1861 Chemical denotes glutamine http://purl.obolibrary.org/obo/CHEBI_28300
T32 1876-1886 Chemical denotes Penicillin http://purl.obolibrary.org/obo/CHEBI_17334
T33 2129-2138 Chemical denotes phosphate http://purl.obolibrary.org/obo/CHEBI_18367|http://purl.obolibrary.org/obo/CHEBI_26020|http://purl.obolibrary.org/obo/CHEBI_35780|http://purl.obolibrary.org/obo/CHEBI_43474
T37 2525-2534 Chemical denotes phosphate http://purl.obolibrary.org/obo/CHEBI_18367|http://purl.obolibrary.org/obo/CHEBI_26020|http://purl.obolibrary.org/obo/CHEBI_35780|http://purl.obolibrary.org/obo/CHEBI_43474
T41 2579-2587 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T42 2602-2616 Chemical denotes crystal violet http://purl.obolibrary.org/obo/CHEBI_41688
T43 2631-2639 Chemical denotes methanol http://purl.obolibrary.org/obo/CHEBI_17790

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T11 2744-2753 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T12 2864-2873 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T47 0-4 Sentence denotes 2.1.
T48 5-81 Sentence denotes Reference Samples and Tests Chosen for Evaluation of Immunoassay Performance
T49 82-193 Sentence denotes Thirty-seven serum samples were obtained from 26 outpatient patients with a PCR-confirmed SARS-CoV-2 infection.
T50 194-422 Sentence denotes Blood was drawn between four and 60 days (median 19 days) after a positive real-time RT-PCR result in which parts of the SARS-CoV-2 E or N genes [18] were detected in oropharyngeal swabs with a cycle threshold ≤35 (median 26.8).
T51 423-491 Sentence denotes Serum was obtained from the blood and stored at −20 °C until tested.
T52 492-672 Sentence denotes These sera are likely to contain SARS-CoV-2 IgG/total antibodies and, therefore, were considered to determine the serological assay sensitivities (as previously suggested by [19]).
T53 673-869 Sentence denotes This variant of the sensitivity calculation only took into account whether a SARS-CoV-2-infected patient was reactive at all, regardless of when this reactivity was developed (reference method 1).
T54 870-1000 Sentence denotes A plaque reduction neutralization assay (PRNT) using a SARS-CoV-2 isolate designated as Kiel M16502/2020 and Vero cells (order no.
T55 1001-1135 Sentence denotes 605372, CLS Cell Lines Service GmbH, Eppelheim, Germany) was included as a further reference for the calculation of the sensitivities.
T56 1136-1196 Sentence denotes All sera classified as reactive in the PRNT were considered.
T57 1197-1251 Sentence denotes This also covered follow-up sera (reference method 2).
T58 1252-1379 Sentence denotes Testing was done under biosafety level 3 conditions and was in accordance to previous reports [20,21] with minor modifications.
T59 1380-1475 Sentence denotes One to two days before infection, 1.0 × 105 cells were seeded into each well of 48-well plates.
T60 1476-1561 Sentence denotes These were then incubated under standard conditions until the cells became confluent.
T61 1562-1921 Sentence denotes Directly prior to the PRNT, patient sera were heat-inactivated at 56 °C for 30 min and then diluted from 1:10 to 1:1280 in cell culture medium consisting of Dulbecco’s modified Eagle’s medium (DMEM) (Bio&SELL GmbH, Feucht, Germany) supplemented with 3.7 g/L NaHCO3, 4.5 g/L glucose, 2 mM L-glutamine, and 1% (v/v) Penicillin/Streptomycin/Fungi-Mix (Bio&SELL).
T62 1922-2101 Sentence denotes A serum dilution series was made by mixing 50 µL of each dilution step with 50 µL virus suspension containing 100 plaque-forming units, followed by an incubation for 1 h at 37 °C.
T63 2102-2289 Sentence denotes The cells were washed with phosphate-buffered saline (Bio&SELL), inoculated with 100 μL of these virus serum dilutions, and incubated for one hour at room temperature on a rocking shaker.
T64 2290-2448 Sentence denotes Then, 100 µL of the cell culture medium supplemented with 20% (v/v) fetal calf serum (FCS) was added to each well to achieve a FCS concentration of 10% (v/v).
T65 2449-2640 Sentence denotes After four to five days, cells were fixed with 4% (w/v) paraformaldehyde in phosphate-buffered saline and stained with an aqueous solution of 0.1% (w/v) crystal violet and 20% (v/v) methanol.
T66 2641-2682 Sentence denotes The stained plates were photo-documented.
T67 2683-2816 Sentence denotes All dilution steps were tested in quadruplicates, and plaque formation was compared to an untreated cell control and a virus control.
T68 2817-2988 Sentence denotes A serum dilution >1:10, which prevented plaque formation in at least 50% of the wells compared to the virus control, was classified as reactive and probably as protective.
T69 2989-3047 Sentence denotes The reciprocal titers were used to visualize the kinetics.
T70 3048-3153 Sentence denotes If an exact titer could not be given, a geometric mean value was calculated from the two adjacent titers.
T71 3154-3305 Sentence denotes For the calculation of assay specificities, 100 archived sera collected during the summer 2018 (N = 50) and during winter 2018/2019 (N = 50) were used.
T72 3306-3372 Sentence denotes None of these sera were expected to contain SARS-CoV-2 antibodies.
T73 3373-3480 Sentence denotes The inclusion of such pre-pandemic sera for the demonstration of specificity was previously suggested [19].

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
119 0-3 Gene denotes 2.1 Gene:6700
129 326-327 Gene denotes E Gene:43740570
130 331-332 Gene denotes N Gene:43740575
131 131-141 Species denotes outpatient Tax:9606
132 142-150 Species denotes patients Tax:9606
133 315-325 Species denotes SARS-CoV-2 Tax:2697049
134 770-777 Species denotes patient Tax:9606
135 525-535 Species denotes SARS-CoV-2 Tax:2697049
136 172-192 Disease denotes SARS-CoV-2 infection MESH:C000657245
137 750-769 Disease denotes SARS-CoV-2-infected MESH:C000657245
153 925-935 Species denotes SARS-CoV-2 Tax:2697049
154 1590-1597 Species denotes patient Tax:9606
155 1719-1753 Chemical denotes Dulbecco’s modified Eagle’s medium
156 1755-1759 Chemical denotes DMEM
157 1820-1826 Chemical denotes NaHCO3 MESH:D017693
158 1836-1843 Chemical denotes glucose MESH:D005947
159 1850-1861 Chemical denotes L-glutamine MESH:D005973
160 1876-1886 Chemical denotes Penicillin MESH:D010406
161 1887-1899 Chemical denotes Streptomycin MESH:D013307
162 2129-2154 Chemical denotes phosphate-buffered saline
163 2505-2521 Chemical denotes paraformaldehyde MESH:C003043
164 2525-2550 Chemical denotes phosphate-buffered saline
165 2602-2616 Chemical denotes crystal violet MESH:D005840
166 2631-2639 Chemical denotes methanol MESH:D000432
167 1403-1412 Disease denotes infection MESH:D007239
171 3287-3288 Gene denotes N Gene:43740575
172 3250-3251 Gene denotes N Gene:43740575
173 3350-3360 Species denotes SARS-CoV-2 Tax:2697049