PMC:7306567 / 30257-32058
Annnotations
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 |