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PMC:7306567 / 30257-32058 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T46 312-321 Body_part denotes chemokine http://purl.org/sig/ont/fma/fma241981
T47 332-340 Body_part denotes monocyte http://purl.org/sig/ont/fma/fma62864
T48 356-367 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T49 405-409 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T50 465-469 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T51 500-504 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T52 525-543 Body_part denotes type 2 pneumocytes http://purl.org/sig/ont/fma/fma62501
T53 557-562 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T54 1187-1192 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T55 1218-1223 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T41 465-469 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T42 1187-1192 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T43 1218-1223 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
282 237-255 Disease denotes SARS-2003-infected MESH:D045169
283 275-307 Disease denotes corticosteroids [61] Lymphopenia MESH:D008231
284 771-826 Disease denotes Fungal infection Invasive Aspergillus tracheobronchitis MESH:D000072742
285 858-896 Disease denotes Invasive Aspergillus tracheobronchitis MESH:D001228
286 1253-1261 Disease denotes COVID-19 MESH:C000657245
287 1280-1300 Disease denotes Secondary infections MESH:D060085
288 1484-1493 Disease denotes mortality MESH:D003643
289 1606-1614 Disease denotes COVID-19 MESH:C000657245
290 1653-1662 Disease denotes mortality MESH:D003643
291 1676-1684 Disease denotes COVID-19 MESH:C000657245
292 1772-1781 Disease denotes mortality MESH:D003643
293 1792-1800 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T145 55-59 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T146 72-76 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T147 237-241 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T148 296-307 Disease denotes Lymphopenia http://purl.obolibrary.org/obo/MONDO_0003783
T149 771-787 Disease denotes Fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T150 778-787 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T151 809-826 Disease denotes tracheobronchitis http://purl.obolibrary.org/obo/MONDO_0021925
T152 879-896 Disease denotes tracheobronchitis http://purl.obolibrary.org/obo/MONDO_0021925
T153 1029-1033 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T154 1253-1261 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T155 1290-1303 Disease denotes infections In http://purl.obolibrary.org/obo/MONDO_0005550
T156 1363-1373 Disease denotes pneumoniae http://purl.obolibrary.org/obo/MONDO_0005249
T157 1527-1536 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T158 1574-1578 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T159 1606-1614 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T160 1623-1627 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T161 1676-1684 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T162 1693-1697 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T163 1792-1800 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T201 332-340 http://purl.obolibrary.org/obo/CL_0000576 denotes monocyte
T202 399-404 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T203 405-409 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T204 445-455 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T205 465-469 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T206 465-469 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T207 487-494 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airways
T208 500-504 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T209 557-562 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T210 734-737 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T211 1494-1496 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T212 197-211 Chemical denotes corticosteroid http://purl.obolibrary.org/obo/CHEBI_50858
T213 220-223 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T215 275-290 Chemical denotes corticosteroids http://purl.obolibrary.org/obo/CHEBI_50858
T216 424-436 Chemical denotes sialic acids http://purl.obolibrary.org/obo/CHEBI_26667
T217 431-436 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T218 608-613 Chemical denotes NADPH http://purl.obolibrary.org/obo/CHEBI_16474|http://purl.obolibrary.org/obo/CHEBI_57783
T220 684-694 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T221 1080-1083 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T222 1084-1086 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T224 1111-1114 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T225 1115-1117 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T227 1193-1195 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T229 1224-1226 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 1084-1086 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T30 1115-1117 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T31 1193-1195 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T32 1224-1226 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T41 220-223 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T42 296-307 Phenotype denotes Lymphopenia http://purl.obolibrary.org/obo/HP_0001888
T43 1363-1373 Phenotype denotes pneumoniae http://purl.obolibrary.org/obo/HP_0002090

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T218 0-59 Sentence denotes Table 2 Comparison between characteristics of IAPA and CAPA
T219 60-76 Sentence denotes Factor IAPA CAPA
T220 77-175 Sentence denotes Host/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]
T221 176-295 Sentence denotes IAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]
T222 296-398 Sentence denotes Lymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]
T223 399-567 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 568-770 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 771-922 Sentence denotes Fungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]
T226 923-1055 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 1056-1186 Sentence denotes Aspergillus diagnostics BAL GM positive in > 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]
T228 1187-1279 Sentence denotes Serum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]
T229 1280-1479 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 1480-1801 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 146-150 GO:0018995 denotes host
T289 197-211 CHEBI:50858;CHEBI:50858 denotes corticosteroid
T290 237-241 SP_10 denotes SARS
T291 275-290 CHEBI:50858;CHEBI:50858 denotes corticosteroids
T292 332-340 CL:0000576 denotes monocyte
T293 349-353 PR:000007437 denotes FCN1
T294 356-367 CL:0000235 denotes macrophages
T295 424-430 CHEBI:30563;CHEBI:30563 denotes sialic
T296 431-436 CHEBI:41865;CHEBI:41865 denotes acids
T297 445-455 UBERON:0000483 denotes epithelial
T298 456-461 UBERON:0000115 denotes layer
T299 465-469 UBERON:0002048 denotes lung
T300 487-494 UBERON:0001005 denotes airways
T301 500-510 GO:0035376 denotes Cell entry
T302 519-523 PR:000003622;G_3;PG_10 denotes ACE2
T303 525-543 CL:0002063 denotes type 2 pneumocytes
T304 548-562 CL:0000064 denotes ciliated cells
T305 575-585 GO:0065007 denotes modulation
T306 608-629 GO:0043020 denotes NADPH oxidase complex
T307 700-707 GO:0006952 denotes defense
T308 809-826 UBERON:0007196 denotes tracheobronchitis
T309 1187-1192 UBERON:0001977 denotes Serum
T310 1218-1223 UBERON:0001977 denotes Serum
T311 1253-1261 SP_7 denotes COVID-19
T312 1360-1362 NCBITaxon:4896 denotes S.
T313 1363-1373 NCBITaxon:31031 denotes pneumoniae
T314 1375-1386 NCBITaxon:286 denotes Pseudomonas
T315 1387-1397 NCBITaxon:8296 denotes aeruginosa
T316 1402-1403 NCBITaxon:4932 denotes S
T317 1403-1404 NCBITaxon:4896 denotes .
T318 1606-1614 SP_7 denotes COVID-19
T319 1676-1684 SP_7 denotes COVID-19
T320 1792-1800 SP_7 denotes COVID-19
T342 1360-1362 NCBITaxon:4896 denotes S.
T23407 1363-1373 NCBITaxon:31031 denotes pneumoniae
T35842 1375-1386 NCBITaxon:286 denotes Pseudomonas
T24939 1387-1397 NCBITaxon:8296 denotes aeruginosa
T27555 1402-1403 NCBITaxon:4932 denotes S
T55957 1403-1404 NCBITaxon:4896 denotes .
T31088 1606-1614 SP_7 denotes COVID-19
T66943 1676-1684 SP_7 denotes COVID-19
T66351 1792-1800 SP_7 denotes COVID-19

2_test

Id Subject Object Predicate Lexical cue
32572532-30076119-47963455 126-127 30076119 denotes 9
32572532-32339350-47963456 172-174 32339350 denotes 60
32572532-22895826-47963457 217-218 22895826 denotes 7
32572532-12890854-47963458 292-294 12890854 denotes 61
32572532-16554799-47963459 496-498 16554799 denotes 63
32572532-24563256-47963460 631-633 24563256 denotes 65
32572532-22895826-47963461 853-854 22895826 denotes 7
32572532-28387526-47963461 853-854 28387526 denotes 7
32572532-30076119-47963461 853-854 30076119 denotes 7
32572532-32339350-47963462 919-921 32339350 denotes 60
32572532-22895826-47963463 986-987 22895826 denotes 7
32572532-28387526-47963463 986-987 28387526 denotes 7
32572532-30076119-47963463 986-987 30076119 denotes 7
32572532-22895826-47963464 1106-1107 22895826 denotes 7
32572532-28387526-47963464 1106-1107 28387526 denotes 7
32572532-30076119-47963464 1106-1107 30076119 denotes 7
32572532-32339350-47963465 1183-1185 32339350 denotes 60
32572532-22895826-47963466 1213-1214 22895826 denotes 7
32572532-28387526-47963466 1213-1214 28387526 denotes 7
32572532-30076119-47963466 1213-1214 30076119 denotes 7
32572532-32339350-47963467 1276-1278 32339350 denotes 60
32572532-27709265-47963468 1413-1415 27709265 denotes 66
32572532-31986264-47963469 1476-1478 31986264 denotes 67
32572532-30076119-47963470 1564-1565 30076119 denotes 9
T1239 126-127 30076119 denotes 9
T11993 172-174 32339350 denotes 60
T58330 217-218 22895826 denotes 7
T34258 292-294 12890854 denotes 61
T40916 496-498 16554799 denotes 63
T49447 631-633 24563256 denotes 65
T76577 853-854 22895826 denotes 7
T1286 853-854 28387526 denotes 7
T13233 853-854 30076119 denotes 7
T5897 919-921 32339350 denotes 60
T37794 986-987 22895826 denotes 7
T50031 986-987 28387526 denotes 7
T83601 986-987 30076119 denotes 7
T28555 1106-1107 22895826 denotes 7
T74628 1106-1107 28387526 denotes 7
T70095 1106-1107 30076119 denotes 7
T97225 1183-1185 32339350 denotes 60
T50555 1213-1214 22895826 denotes 7
T89999 1213-1214 28387526 denotes 7
T65385 1213-1214 30076119 denotes 7
T41608 1276-1278 32339350 denotes 60
T66653 1413-1415 27709265 denotes 66
T99520 1476-1478 31986264 denotes 67
T87804 1564-1565 30076119 denotes 9