PMC:7558333 / 22322-23910 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T50","span":{"begin":438,"end":443},"obj":"Body_part"},{"id":"T51","span":{"begin":1174,"end":1182},"obj":"Body_part"},{"id":"T52","span":{"begin":1458,"end":1463},"obj":"Body_part"}],"attributes":[{"id":"A50","pred":"fma_id","subj":"T50","obj":"http://purl.org/sig/ont/fma/fma9670"},{"id":"A51","pred":"fma_id","subj":"T51","obj":"http://purl.org/sig/ont/fma/fma62871"},{"id":"A52","pred":"fma_id","subj":"T52","obj":"http://purl.org/sig/ont/fma/fma9670"}],"text":"Classification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology"}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T35","span":{"begin":438,"end":443},"obj":"Body_part"},{"id":"T36","span":{"begin":1458,"end":1463},"obj":"Body_part"}],"attributes":[{"id":"A35","pred":"uberon_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"A36","pred":"uberon_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"}],"text":"Classification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology"}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T126","span":{"begin":477,"end":479},"obj":"Disease"},{"id":"T127","span":{"begin":1421,"end":1423},"obj":"Disease"},{"id":"T128","span":{"begin":1440,"end":1442},"obj":"Disease"},{"id":"T129","span":{"begin":1511,"end":1513},"obj":"Disease"}],"attributes":[{"id":"A126","pred":"mondo_id","subj":"T126","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"},{"id":"A127","pred":"mondo_id","subj":"T127","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"},{"id":"A128","pred":"mondo_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"},{"id":"A129","pred":"mondo_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"}],"text":"Classification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology"}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T160","span":{"begin":192,"end":204},"obj":"http://purl.obolibrary.org/obo/UBERON_0001155"},{"id":"T161","span":{"begin":413,"end":414},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T162","span":{"begin":438,"end":443},"obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"T163","span":{"begin":438,"end":443},"obj":"http://www.ebi.ac.uk/efo/EFO_0000296"},{"id":"T164","span":{"begin":1183,"end":1190},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T165","span":{"begin":1458,"end":1463},"obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"T166","span":{"begin":1458,"end":1463},"obj":"http://www.ebi.ac.uk/efo/EFO_0000296"}],"text":"Classification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology"}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T19","span":{"begin":1475,"end":1477},"obj":"GlycoEpitope"}],"attributes":[{"id":"A19","pred":"glyco_epitope_db_id","subj":"T19","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"Classification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology"}

{"project":"LitCovid-sentences","denotations":[{"id":"T159","span":{"begin":0,"end":177},"obj":"Sentence"},{"id":"T160","span":{"begin":178,"end":453},"obj":"Sentence"},{"id":"T161","span":{"begin":454,"end":500},"obj":"Sentence"},{"id":"T162","span":{"begin":501,"end":503},"obj":"Sentence"},{"id":"T163","span":{"begin":504,"end":557},"obj":"Sentence"},{"id":"T164","span":{"begin":558,"end":586},"obj":"Sentence"},{"id":"T165","span":{"begin":587,"end":644},"obj":"Sentence"},{"id":"T166","span":{"begin":645,"end":669},"obj":"Sentence"},{"id":"T167","span":{"begin":670,"end":778},"obj":"Sentence"},{"id":"T168","span":{"begin":779,"end":781},"obj":"Sentence"},{"id":"T169","span":{"begin":782,"end":839},"obj":"Sentence"},{"id":"T170","span":{"begin":840,"end":868},"obj":"Sentence"},{"id":"T171","span":{"begin":869,"end":926},"obj":"Sentence"},{"id":"T172","span":{"begin":927,"end":951},"obj":"Sentence"},{"id":"T173","span":{"begin":952,"end":1064},"obj":"Sentence"},{"id":"T174","span":{"begin":1065,"end":1067},"obj":"Sentence"},{"id":"T175","span":{"begin":1068,"end":1193},"obj":"Sentence"},{"id":"T176","span":{"begin":1194,"end":1222},"obj":"Sentence"},{"id":"T177","span":{"begin":1223,"end":1280},"obj":"Sentence"},{"id":"T178","span":{"begin":1281,"end":1305},"obj":"Sentence"},{"id":"T179","span":{"begin":1306,"end":1397},"obj":"Sentence"},{"id":"T180","span":{"begin":1398,"end":1489},"obj":"Sentence"},{"id":"T181","span":{"begin":1490,"end":1588},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Classification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology"}

{"project":"LitCovid-PubTator","denotations":[{"id":"562","span":{"begin":206,"end":217},"obj":"Species"},{"id":"563","span":{"begin":264,"end":275},"obj":"Species"},{"id":"564","span":{"begin":326,"end":337},"obj":"Species"},{"id":"565","span":{"begin":504,"end":515},"obj":"Species"},{"id":"566","span":{"begin":687,"end":698},"obj":"Species"},{"id":"567","span":{"begin":782,"end":793},"obj":"Species"},{"id":"568","span":{"begin":969,"end":980},"obj":"Species"},{"id":"569","span":{"begin":1068,"end":1079},"obj":"Species"},{"id":"570","span":{"begin":1162,"end":1173},"obj":"Species"},{"id":"571","span":{"begin":1323,"end":1334},"obj":"Species"}],"attributes":[{"id":"A562","pred":"tao:has_database_id","subj":"562","obj":"Tax:746128"},{"id":"A563","pred":"tao:has_database_id","subj":"563","obj":"Tax:746128"},{"id":"A564","pred":"tao:has_database_id","subj":"564","obj":"Tax:746128"},{"id":"A565","pred":"tao:has_database_id","subj":"565","obj":"Tax:746128"},{"id":"A566","pred":"tao:has_database_id","subj":"566","obj":"Tax:746128"},{"id":"A567","pred":"tao:has_database_id","subj":"567","obj":"Tax:746128"},{"id":"A568","pred":"tao:has_database_id","subj":"568","obj":"Tax:746128"},{"id":"A569","pred":"tao:has_database_id","subj":"569","obj":"Tax:746128"},{"id":"A570","pred":"tao:has_database_id","subj":"570","obj":"Tax:746128"},{"id":"A571","pred":"tao:has_database_id","subj":"571","obj":"Tax:746128"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Classification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology"}