PMC:7558333 / 12076-14677
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T30 | 503-508 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T31 | 751-756 | Body_part | denotes | serum | http://purl.org/sig/ont/fma/fma63083 |
| T32 | 935-952 | Body_part | denotes | respiratory tract | http://purl.org/sig/ont/fma/fma265130 |
| T33 | 1081-1089 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
| T34 | 1296-1301 | Body_part | denotes | serum | http://purl.org/sig/ont/fma/fma63083 |
| T35 | 1507-1515 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T20 | 503-508 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T21 | 751-756 | Body_part | denotes | serum | http://purl.obolibrary.org/obo/UBERON_0001977 |
| T22 | 935-952 | Body_part | denotes | respiratory tract | http://purl.obolibrary.org/obo/UBERON_0000065 |
| T23 | 1296-1301 | Body_part | denotes | serum | http://purl.obolibrary.org/obo/UBERON_0001977 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T58 | 270-272 | Disease | denotes | IA | http://purl.obolibrary.org/obo/MONDO_0000240 |
| T59 | 351-353 | Disease | denotes | IA | http://purl.obolibrary.org/obo/MONDO_0000240 |
| T60 | 1184-1186 | Disease | denotes | IA | http://purl.obolibrary.org/obo/MONDO_0000240 |
| T61 | 1243-1245 | Disease | denotes | IA | http://purl.obolibrary.org/obo/MONDO_0000240 |
| T62 | 1575-1577 | Disease | denotes | IA | http://purl.obolibrary.org/obo/MONDO_0000240 |
| T63 | 1618-1620 | Disease | denotes | IA | http://purl.obolibrary.org/obo/MONDO_0000240 |
| T64 | 1713-1721 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T65 | 1722-1731 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T66 | 1783-1796 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T67 | 1855-1868 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T68 | 1978-1987 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T69 | 2006-2008 | Disease | denotes | IA | http://purl.obolibrary.org/obo/MONDO_0000240 |
| T70 | 2116-2129 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T71 | 2197-2219 | Disease | denotes | invasive aspergillosis | http://purl.obolibrary.org/obo/MONDO_0000240 |
| T72 | 2206-2219 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T73 | 2270-2272 | Disease | denotes | IA | http://purl.obolibrary.org/obo/MONDO_0000240 |
| T74 | 2483-2485 | Disease | denotes | IA | http://purl.obolibrary.org/obo/MONDO_0000240 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T85 | 26-31 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | Tests |
| T86 | 118-120 | http://purl.obolibrary.org/obo/CLO_0053799 | denotes | 45 |
| T87 | 259-260 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T88 | 274-276 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 22 |
| T89 | 432-441 | http://purl.obolibrary.org/obo/UBERON_0001155 | denotes | colonized |
| T90 | 503-508 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T91 | 580-581 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T92 | 684-693 | http://purl.obolibrary.org/obo/UBERON_0001155 | denotes | colonized |
| T93 | 721-722 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T94 | 833-834 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T95 | 898-899 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T96 | 1018-1019 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T97 | 1028-1040 | http://purl.obolibrary.org/obo/UBERON_0001155 | denotes | colonization |
| T98 | 1090-1101 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing was |
| T99 | 1257-1258 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T100 | 1446-1447 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T101 | 1626-1638 | http://purl.obolibrary.org/obo/UBERON_0001155 | denotes | in colonized |
| T102 | 1955-1956 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T103 | 1989-2001 | http://purl.obolibrary.org/obo/UBERON_0001155 | denotes | colonization |
| T104 | 2141-2153 | http://purl.obolibrary.org/obo/UBERON_0001155 | denotes | in colonized |
| T105 | 2168-2170 | http://purl.obolibrary.org/obo/CLO_0050509 | denotes | 27 |
| T106 | 2250-2251 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T107 | 2338-2347 | http://purl.obolibrary.org/obo/UBERON_0001155 | denotes | colonized |
| T108 | 2416-2417 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T109 | 2545-2548 | http://purl.obolibrary.org/obo/CLO_0050509 | denotes | 2/7 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T5 | 589-607 | http://purl.obolibrary.org/obo/GO_0016046 | denotes | detection of fungi |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T13 | 735-737 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T14 | 1313-1315 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T96 | 0-4 | Sentence | denotes | 3.4. |
| T97 | 5-74 | Sentence | denotes | Relevance of Various Tests and Categorization of Patients and Outcome |
| T98 | 75-175 | Sentence | denotes | Table 6 presents the classification of the 45 patients using original or modified AspICU algorithms. |
| T99 | 176-293 | Sentence | denotes | It appears that using an AspICU algorithm, nine patients were considered as having a putative IA (22% of the cohort). |
| T100 | 294-527 | Sentence | denotes | When including PCR, the number of patients with putative IA would increase from 9 to 15 (33%) patients, while most patients might be only colonized because all presented compatible clinical signs and abnormal chest CT scan (Table 5). |
| T101 | 528-694 | Sentence | denotes | Regarding Aspergillus detection, eight patients had a single detection of fungi using culture and/or PCR in respiratory samples and thus were classified as colonized. |
| T102 | 695-857 | Sentence | denotes | One of these patients had a concomitant GM detection in serum (index = 0.551), was not treated and is still alive, thus was considered as a false positive result. |
| T103 | 858-996 | Sentence | denotes | Finally, seven (16%) patients presented a heavy burden of Aspergillus in the respiratory tract with repeated positive cultures and/or PCR. |
| T104 | 997-1140 | Sentence | denotes | In order to rule out a chronic colonization before the episode, an anti-Aspergillus antibody testing was performed and showed negative results. |
| T105 | 1141-1360 | Sentence | denotes | These patients were classified as putative IA, and three of them could even be considered as probable IA because of a positive biomarker of angioinvasion (serum PCR and/or GM) in agreement with EORTC/MSG classification. |
| T106 | 1361-1485 | Sentence | denotes | Interestingly, following these classification criteria, CT scan abnormalities showed a gradation according to patient group. |
| T107 | 1486-1751 | Sentence | denotes | Diffuse reticular or alveolar opacities were observed in patients classified as probable IA (Figure 2), nodules in half of putative IA, and in colonized patients, only non-specific and hard to interpret signs in the context of COVID-19 infection could be described. |
| T108 | 1752-2019 | Sentence | denotes | In addition, putative/probable aspergillosis patients appeared more severely ill than patients without aspergillosis, since SOFA score at day seven was significantly higher in this group (p = 0.01) with a continuum between no infection, colonization and IA (Table 5). |
| T109 | 2020-2231 | Sentence | denotes | Similarly, the mean ICU length of stay increased significantly from 12 days in patients without aspergillosis to 23 days in colonized patients, and 27 days in putative/probable invasive aspergillosis (p = 0.02). |
| T110 | 2232-2328 | Sentence | denotes | All patients with a putative/probable IA were treated either with voriconazole or isavuconazole. |
| T111 | 2329-2386 | Sentence | denotes | Only one colonized patient was treated with voriconazole. |
| T112 | 2387-2601 | Sentence | denotes | Six patients died; there was a trend towards higher mortality in the group of putative/probable IA compared to uninfected patients, although not significant (2/7; 28.6%) versus 4/30 (13.3%), respectively (Table 7). |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 245 | 54-62 | Species | denotes | Patients | Tax:9606 |
| 259 | 121-129 | Species | denotes | patients | Tax:9606 |
| 260 | 224-232 | Species | denotes | patients | Tax:9606 |
| 261 | 328-336 | Species | denotes | patients | Tax:9606 |
| 262 | 388-396 | Species | denotes | patients | Tax:9606 |
| 263 | 409-417 | Species | denotes | patients | Tax:9606 |
| 264 | 567-575 | Species | denotes | patients | Tax:9606 |
| 265 | 708-716 | Species | denotes | patients | Tax:9606 |
| 266 | 879-887 | Species | denotes | patients | Tax:9606 |
| 267 | 1147-1155 | Species | denotes | patients | Tax:9606 |
| 268 | 538-549 | Species | denotes | Aspergillus | Tax:746128 |
| 269 | 916-927 | Species | denotes | Aspergillus | Tax:746128 |
| 270 | 1069-1080 | Species | denotes | Aspergillus | Tax:746128 |
| 271 | 735-737 | Chemical | denotes | GM | MESH:C012990 |
| 277 | 1471-1478 | Species | denotes | patient | Tax:9606 |
| 278 | 1543-1551 | Species | denotes | patients | Tax:9606 |
| 279 | 1639-1647 | Species | denotes | patients | Tax:9606 |
| 280 | 1713-1721 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 281 | 1722-1731 | Disease | denotes | infection | MESH:D007239 |
| 300 | 1797-1805 | Species | denotes | patients | Tax:9606 |
| 301 | 1838-1846 | Species | denotes | patients | Tax:9606 |
| 302 | 2099-2107 | Species | denotes | patients | Tax:9606 |
| 303 | 2154-2162 | Species | denotes | patients | Tax:9606 |
| 304 | 2236-2244 | Species | denotes | patients | Tax:9606 |
| 305 | 2348-2355 | Species | denotes | patient | Tax:9606 |
| 306 | 2391-2399 | Species | denotes | patients | Tax:9606 |
| 307 | 2509-2517 | Species | denotes | patients | Tax:9606 |
| 308 | 2298-2310 | Chemical | denotes | voriconazole | MESH:D065819 |
| 309 | 2314-2327 | Chemical | denotes | isavuconazole | MESH:C508735 |
| 310 | 2373-2385 | Chemical | denotes | voriconazole | MESH:D065819 |
| 311 | 1783-1796 | Disease | denotes | aspergillosis | MESH:D001228 |
| 312 | 1855-1868 | Disease | denotes | aspergillosis | MESH:D001228 |
| 313 | 1978-1987 | Disease | denotes | infection | MESH:D007239 |
| 314 | 2116-2129 | Disease | denotes | aspergillosis | MESH:D001228 |
| 315 | 2197-2219 | Disease | denotes | invasive aspergillosis | MESH:D055744 |
| 316 | 2400-2404 | Disease | denotes | died | MESH:D003643 |
| 317 | 2439-2448 | Disease | denotes | mortality | MESH:D003643 |