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PMC:7306567 / 30317-32058 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T46 252-261 Body_part denotes chemokine http://purl.org/sig/ont/fma/fma241981
T47 272-280 Body_part denotes monocyte http://purl.org/sig/ont/fma/fma62864
T48 296-307 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T49 345-349 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T50 405-409 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T51 440-444 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T52 465-483 Body_part denotes type 2 pneumocytes http://purl.org/sig/ont/fma/fma62501
T53 497-502 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T54 1127-1132 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T55 1158-1163 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T41 405-409 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T42 1127-1132 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T43 1158-1163 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
282 177-195 Disease denotes SARS-2003-infected MESH:D045169
283 215-247 Disease denotes corticosteroids [61] Lymphopenia MESH:D008231
284 711-766 Disease denotes Fungal infection Invasive Aspergillus tracheobronchitis MESH:D000072742
285 798-836 Disease denotes Invasive Aspergillus tracheobronchitis MESH:D001228
286 1193-1201 Disease denotes COVID-19 MESH:C000657245
287 1220-1240 Disease denotes Secondary infections MESH:D060085
288 1424-1433 Disease denotes mortality MESH:D003643
289 1546-1554 Disease denotes COVID-19 MESH:C000657245
290 1593-1602 Disease denotes mortality MESH:D003643
291 1616-1624 Disease denotes COVID-19 MESH:C000657245
292 1712-1721 Disease denotes mortality MESH:D003643
293 1732-1740 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T146 12-16 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T147 177-181 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T148 236-247 Disease denotes Lymphopenia http://purl.obolibrary.org/obo/MONDO_0003783
T149 711-727 Disease denotes Fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T150 718-727 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T151 749-766 Disease denotes tracheobronchitis http://purl.obolibrary.org/obo/MONDO_0021925
T152 819-836 Disease denotes tracheobronchitis http://purl.obolibrary.org/obo/MONDO_0021925
T153 969-973 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T154 1193-1201 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T155 1230-1243 Disease denotes infections In http://purl.obolibrary.org/obo/MONDO_0005550
T156 1303-1313 Disease denotes pneumoniae http://purl.obolibrary.org/obo/MONDO_0005249
T157 1467-1476 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T158 1514-1518 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T159 1546-1554 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T160 1563-1567 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T161 1616-1624 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T162 1633-1637 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T163 1732-1740 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T201 272-280 http://purl.obolibrary.org/obo/CL_0000576 denotes monocyte
T202 339-344 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T203 345-349 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T204 385-395 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T205 405-409 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T206 405-409 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T207 427-434 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airways
T208 440-444 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T209 497-502 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T210 674-677 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T211 1434-1436 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T212 137-151 Chemical denotes corticosteroid http://purl.obolibrary.org/obo/CHEBI_50858
T213 160-163 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T215 215-230 Chemical denotes corticosteroids http://purl.obolibrary.org/obo/CHEBI_50858
T216 364-376 Chemical denotes sialic acids http://purl.obolibrary.org/obo/CHEBI_26667
T217 371-376 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T218 548-553 Chemical denotes NADPH http://purl.obolibrary.org/obo/CHEBI_16474|http://purl.obolibrary.org/obo/CHEBI_57783
T220 624-634 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T221 1020-1023 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T222 1024-1026 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T224 1051-1054 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T225 1055-1057 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T227 1133-1135 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T229 1164-1166 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T29 1024-1026 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T30 1055-1057 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T31 1133-1135 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T32 1164-1166 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T41 160-163 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T42 236-247 Phenotype denotes Lymphopenia http://purl.obolibrary.org/obo/HP_0001888
T43 1303-1313 Phenotype denotes pneumoniae http://purl.obolibrary.org/obo/HP_0002090

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T219 0-16 Sentence denotes Factor IAPA CAPA
T220 17-115 Sentence denotes Host/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]
T221 116-235 Sentence denotes IAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]
T222 236-338 Sentence denotes Lymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]
T223 339-507 Sentence denotes Virus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]
T224 508-710 Sentence denotes Immune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet
T225 711-862 Sentence denotes Fungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]
T226 863-995 Sentence denotes Median time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]
T227 996-1126 Sentence denotes Aspergillus diagnostics BAL GM positive in > 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]
T228 1127-1219 Sentence denotes Serum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]
T229 1220-1419 Sentence denotes Secondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]
T230 1420-1741 Sentence denotes ICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p < 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T288 86-90 GO:0018995 denotes host
T289 137-151 CHEBI:50858;CHEBI:50858 denotes corticosteroid
T290 177-181 SP_10 denotes SARS
T291 215-230 CHEBI:50858;CHEBI:50858 denotes corticosteroids
T292 272-280 CL:0000576 denotes monocyte
T293 289-293 PR:000007437 denotes FCN1
T294 296-307 CL:0000235 denotes macrophages
T295 364-370 CHEBI:30563;CHEBI:30563 denotes sialic
T296 371-376 CHEBI:41865;CHEBI:41865 denotes acids
T297 385-395 UBERON:0000483 denotes epithelial
T298 396-401 UBERON:0000115 denotes layer
T299 405-409 UBERON:0002048 denotes lung
T300 427-434 UBERON:0001005 denotes airways
T301 440-450 GO:0035376 denotes Cell entry
T302 459-463 PR:000003622;G_3;PG_10 denotes ACE2
T303 465-483 CL:0002063 denotes type 2 pneumocytes
T304 488-502 CL:0000064 denotes ciliated cells
T305 515-525 GO:0065007 denotes modulation
T306 548-569 GO:0043020 denotes NADPH oxidase complex
T307 640-647 GO:0006952 denotes defense
T308 749-766 UBERON:0007196 denotes tracheobronchitis
T309 1127-1132 UBERON:0001977 denotes Serum
T310 1158-1163 UBERON:0001977 denotes Serum
T311 1193-1201 SP_7 denotes COVID-19
T312 1300-1302 NCBITaxon:4896 denotes S.
T313 1303-1313 NCBITaxon:31031 denotes pneumoniae
T314 1315-1326 NCBITaxon:286 denotes Pseudomonas
T315 1327-1337 NCBITaxon:8296 denotes aeruginosa
T316 1342-1343 NCBITaxon:4932 denotes S
T317 1343-1344 NCBITaxon:4896 denotes .
T318 1546-1554 SP_7 denotes COVID-19
T319 1616-1624 SP_7 denotes COVID-19
T320 1732-1740 SP_7 denotes COVID-19
T342 1300-1302 NCBITaxon:4896 denotes S.
T23407 1303-1313 NCBITaxon:31031 denotes pneumoniae
T35842 1315-1326 NCBITaxon:286 denotes Pseudomonas
T24939 1327-1337 NCBITaxon:8296 denotes aeruginosa
T27555 1342-1343 NCBITaxon:4932 denotes S
T55957 1343-1344 NCBITaxon:4896 denotes .
T31088 1546-1554 SP_7 denotes COVID-19
T66943 1616-1624 SP_7 denotes COVID-19
T66351 1732-1740 SP_7 denotes COVID-19

2_test

Id Subject Object Predicate Lexical cue
32572532-30076119-47963455 66-67 30076119 denotes 9
32572532-32339350-47963456 112-114 32339350 denotes 60
32572532-22895826-47963457 157-158 22895826 denotes 7
32572532-12890854-47963458 232-234 12890854 denotes 61
32572532-16554799-47963459 436-438 16554799 denotes 63
32572532-24563256-47963460 571-573 24563256 denotes 65
32572532-22895826-47963461 793-794 22895826 denotes 7
32572532-28387526-47963461 793-794 28387526 denotes 7
32572532-30076119-47963461 793-794 30076119 denotes 7
32572532-32339350-47963462 859-861 32339350 denotes 60
32572532-22895826-47963463 926-927 22895826 denotes 7
32572532-28387526-47963463 926-927 28387526 denotes 7
32572532-30076119-47963463 926-927 30076119 denotes 7
32572532-22895826-47963464 1046-1047 22895826 denotes 7
32572532-28387526-47963464 1046-1047 28387526 denotes 7
32572532-30076119-47963464 1046-1047 30076119 denotes 7
32572532-32339350-47963465 1123-1125 32339350 denotes 60
32572532-22895826-47963466 1153-1154 22895826 denotes 7
32572532-28387526-47963466 1153-1154 28387526 denotes 7
32572532-30076119-47963466 1153-1154 30076119 denotes 7
32572532-32339350-47963467 1216-1218 32339350 denotes 60
32572532-27709265-47963468 1353-1355 27709265 denotes 66
32572532-31986264-47963469 1416-1418 31986264 denotes 67
32572532-30076119-47963470 1504-1505 30076119 denotes 9
T1239 66-67 30076119 denotes 9
T11993 112-114 32339350 denotes 60
T58330 157-158 22895826 denotes 7
T34258 232-234 12890854 denotes 61
T40916 436-438 16554799 denotes 63
T49447 571-573 24563256 denotes 65
T76577 793-794 22895826 denotes 7
T1286 793-794 28387526 denotes 7
T13233 793-794 30076119 denotes 7
T5897 859-861 32339350 denotes 60
T37794 926-927 22895826 denotes 7
T50031 926-927 28387526 denotes 7
T83601 926-927 30076119 denotes 7
T28555 1046-1047 22895826 denotes 7
T74628 1046-1047 28387526 denotes 7
T70095 1046-1047 30076119 denotes 7
T97225 1123-1125 32339350 denotes 60
T50555 1153-1154 22895826 denotes 7
T89999 1153-1154 28387526 denotes 7
T65385 1153-1154 30076119 denotes 7
T41608 1216-1218 32339350 denotes 60
T66653 1353-1355 27709265 denotes 66
T99520 1416-1418 31986264 denotes 67
T87804 1504-1505 30076119 denotes 9