PMC:7558333 / 16875-18597
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T38 | 259-264 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T39 | 688-692 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T40 | 789-794 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T41 | 1197-1205 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
| T42 | 1399-1404 | Body_part | denotes | serum | http://purl.org/sig/ont/fma/fma63083 |
| T43 | 1412-1417 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T44 | 1550-1558 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T26 | 259-264 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T27 | 789-794 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T28 | 1399-1404 | Body_part | denotes | serum | http://purl.obolibrary.org/obo/UBERON_0001977 |
| T29 | 1412-1417 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T98 | 160-162 | Disease | denotes | IA | http://purl.obolibrary.org/obo/MONDO_0000240 |
| T99 | 1609-1629 | Disease | denotes | respiratory diseases | http://purl.obolibrary.org/obo/MONDO_0005087 |
| T100 | 1685-1698 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T101 | 1711-1713 | Disease | denotes | IA | http://purl.obolibrary.org/obo/MONDO_0000240 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T121 | 17-18 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T122 | 176-177 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T123 | 196-197 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T124 | 259-264 | http://purl.obolibrary.org/obo/UBERON_0000178 | denotes | blood |
| T125 | 259-264 | http://www.ebi.ac.uk/efo/EFO_0000296 | denotes | blood |
| T126 | 514-515 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T127 | 588-590 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T128 | 688-692 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T129 | 789-794 | http://purl.obolibrary.org/obo/UBERON_0000178 | denotes | blood |
| T130 | 789-794 | http://www.ebi.ac.uk/efo/EFO_0000296 | denotes | blood |
| T131 | 1206-1213 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T132 | 1238-1250 | http://purl.obolibrary.org/obo/UBERON_0001155 | denotes | colonization |
| T133 | 1290-1302 | http://purl.obolibrary.org/obo/UBERON_0001155 | denotes | colonization |
| T134 | 1412-1417 | http://purl.obolibrary.org/obo/UBERON_0000178 | denotes | blood |
| T135 | 1412-1417 | http://www.ebi.ac.uk/efo/EFO_0000296 | denotes | blood |
| T136 | 1559-1566 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T137 | 1644-1645 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T15 | 310-312 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T16 | 773-775 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T17 | 1405-1407 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T18 | 1580-1582 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T125 | 0-351 | Sentence | denotes | In order to have a well-balanced patient management, limiting unnecessary and costly antifungal treatments while not neglecting the life-threatening feature of IA, we included A. fumigatus PCR as a monitoring tool for fungal detection in both respiratory and blood samples in addition to classical culture and GM approaches but with some restrictions. |
| T126 | 352-432 | Sentence | denotes | As expected, PCR allowed detecting Aspergillus in much more respiratory samples. |
| T127 | 433-592 | Sentence | denotes | We previously showed that PCR improved the detection of Aspergillus in BAL, with a particular added value in ICU patients compared to hematology patients [11]. |
| T128 | 593-744 | Sentence | denotes | Furthermore, PCR using in-house but also marketed kits is also capable of identifying specific gene mutations associated with azole resistance [11,24]. |
| T129 | 745-874 | Sentence | denotes | Besides, the sensitivity of GM detection in blood is less sensitive in ICU than for patients with hematological malignancies [5]. |
| T130 | 875-1015 | Sentence | denotes | Here, the higher sensitivity of Aspergillus detection also incites us to adopt modified criteria for case definition to gain in specificity. |
| T131 | 1016-1477 | Sentence | denotes | Two major changes were introduced to modify the granularity of the classification: (i) the first one is to combine Aspergillus detection in respiratory samples and anti-Aspergillus antibody testing, to distinguish chronic colonization (positive serology) from acute massive colonization (negative serology) and (ii) the second is to introduce of obvious biomarkers of angioinvasion (serum GM and blood PCR), similar to those of the EORTC/MSG classification [2]. |
| T132 | 1478-1722 | Sentence | denotes | Of note, the combination of positive culture, positive anti-Aspergillus antibody testing and positive GM in the context of chronic respiratory diseases characterized a transition step from chronic pulmonary aspergillosis to probable IA [25,26]. |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 403 | 33-40 | Species | denotes | patient | Tax:9606 |
| 404 | 176-188 | Species | denotes | A. fumigatus | Tax:746128 |
| 405 | 546-554 | Species | denotes | patients | Tax:9606 |
| 406 | 578-586 | Species | denotes | patients | Tax:9606 |
| 407 | 829-837 | Species | denotes | patients | Tax:9606 |
| 408 | 387-398 | Species | denotes | Aspergillus | Tax:746128 |
| 409 | 489-500 | Species | denotes | Aspergillus | Tax:746128 |
| 410 | 907-918 | Species | denotes | Aspergillus | Tax:746128 |
| 411 | 1131-1142 | Species | denotes | Aspergillus | Tax:746128 |
| 412 | 1185-1196 | Species | denotes | Aspergillus | Tax:746128 |
| 413 | 1538-1549 | Species | denotes | Aspergillus | Tax:746128 |
| 414 | 310-312 | Chemical | denotes | GM | MESH:C012990 |
| 415 | 719-724 | Chemical | denotes | azole | MESH:D001393 |
| 416 | 773-775 | Chemical | denotes | GM | MESH:C012990 |
| 417 | 1405-1407 | Chemical | denotes | GM | MESH:C012990 |
| 418 | 1580-1582 | Chemical | denotes | GM | MESH:C012990 |
| 419 | 843-869 | Disease | denotes | hematological malignancies | MESH:D019337 |
| 420 | 1609-1629 | Disease | denotes | respiratory diseases | MESH:D012140 |
| 421 | 1675-1698 | Disease | denotes | pulmonary aspergillosis | MESH:D055732 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32664423-29248586-60101711 | 588-590 | 29248586 | denotes | 11 |
| 32664423-29248586-60101712 | 737-739 | 29248586 | denotes | 11 |
| 32664423-25903571-60101713 | 740-742 | 25903571 | denotes | 24 |
| 32664423-17906086-60101714 | 1715-1717 | 17906086 | denotes | 25 |
| 32664423-26699723-60101715 | 1718-1720 | 26699723 | denotes | 26 |