PMC:7306567 / 13143-14109 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T16","span":{"begin":231,"end":236},"obj":"Body_part"},{"id":"T17","span":{"begin":268,"end":274},"obj":"Body_part"}],"attributes":[{"id":"A16","pred":"fma_id","subj":"T16","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma312401"}],"text":"If a patient is admitted to the ICU and has influenza with pulmonary infiltrates, the diagnosis of IAPA should be considered and further investigation performed as appropriate. Ideally, this would include in order of invasiveness, serum GM testing, fungal cultures of sputum and/or tracheal aspirate, pulmonary CT, bronchoscopy to visualize the large airways and obtain BAL fluid for GM testing and fungal and bacterial cultures. Testing is most appropriate in patients who are on mechanical ventilation, but the diagnostic strategy is less clear in patients not intubated. As up to 50% of patients may present with tracheobronchitis, the presence of plaques and ulceration might be considered for inclusion in the definition of IPA [35]. Policies for taking biopsies of lesions seen on bronchoscopy may vary, mainly because of concerns about the risk of bleeding with biopsy in ICU patients. The use of a flexible brush may also be sufficient to make the diagnosis."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T14","span":{"begin":231,"end":236},"obj":"Body_part"},{"id":"T15","span":{"begin":268,"end":274},"obj":"Body_part"}],"attributes":[{"id":"A14","pred":"uberon_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A15","pred":"uberon_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/UBERON_0007311"}],"text":"If a patient is admitted to the ICU and has influenza with pulmonary infiltrates, the diagnosis of IAPA should be considered and further investigation performed as appropriate. Ideally, this would include in order of invasiveness, serum GM testing, fungal cultures of sputum and/or tracheal aspirate, pulmonary CT, bronchoscopy to visualize the large airways and obtain BAL fluid for GM testing and fungal and bacterial cultures. Testing is most appropriate in patients who are on mechanical ventilation, but the diagnostic strategy is less clear in patients not intubated. As up to 50% of patients may present with tracheobronchitis, the presence of plaques and ulceration might be considered for inclusion in the definition of IPA [35]. Policies for taking biopsies of lesions seen on bronchoscopy may vary, mainly because of concerns about the risk of bleeding with biopsy in ICU patients. The use of a flexible brush may also be sufficient to make the diagnosis."}

{"project":"LitCovid-PubTator","denotations":[{"id":"131","span":{"begin":237,"end":239},"obj":"Chemical"},{"id":"132","span":{"begin":384,"end":386},"obj":"Chemical"},{"id":"133","span":{"begin":59,"end":80},"obj":"Disease"},{"id":"134","span":{"begin":616,"end":633},"obj":"Disease"},{"id":"135","span":{"begin":855,"end":863},"obj":"Disease"}],"attributes":[{"id":"A131","pred":"tao:has_database_id","subj":"131","obj":"MESH:C012990"},{"id":"A132","pred":"tao:has_database_id","subj":"132","obj":"MESH:C012990"},{"id":"A133","pred":"tao:has_database_id","subj":"133","obj":"MESH:D017254"},{"id":"A135","pred":"tao:has_database_id","subj":"135","obj":"MESH:D006470"}],"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":"If a patient is admitted to the ICU and has influenza with pulmonary infiltrates, the diagnosis of IAPA should be considered and further investigation performed as appropriate. Ideally, this would include in order of invasiveness, serum GM testing, fungal cultures of sputum and/or tracheal aspirate, pulmonary CT, bronchoscopy to visualize the large airways and obtain BAL fluid for GM testing and fungal and bacterial cultures. Testing is most appropriate in patients who are on mechanical ventilation, but the diagnostic strategy is less clear in patients not intubated. As up to 50% of patients may present with tracheobronchitis, the presence of plaques and ulceration might be considered for inclusion in the definition of IPA [35]. Policies for taking biopsies of lesions seen on bronchoscopy may vary, mainly because of concerns about the risk of bleeding with biopsy in ICU patients. The use of a flexible brush may also be sufficient to make the diagnosis."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T67","span":{"begin":44,"end":53},"obj":"Disease"},{"id":"T68","span":{"begin":616,"end":633},"obj":"Disease"},{"id":"T69","span":{"begin":663,"end":673},"obj":"Disease"}],"attributes":[{"id":"A67","pred":"mondo_id","subj":"T67","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A68","pred":"mondo_id","subj":"T68","obj":"http://purl.obolibrary.org/obo/MONDO_0021925"},{"id":"A69","pred":"mondo_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/MONDO_0043839"}],"text":"If a patient is admitted to the ICU and has influenza with pulmonary infiltrates, the diagnosis of IAPA should be considered and further investigation performed as appropriate. Ideally, this would include in order of invasiveness, serum GM testing, fungal cultures of sputum and/or tracheal aspirate, pulmonary CT, bronchoscopy to visualize the large airways and obtain BAL fluid for GM testing and fungal and bacterial cultures. Testing is most appropriate in patients who are on mechanical ventilation, but the diagnostic strategy is less clear in patients not intubated. As up to 50% of patients may present with tracheobronchitis, the presence of plaques and ulceration might be considered for inclusion in the definition of IPA [35]. Policies for taking biopsies of lesions seen on bronchoscopy may vary, mainly because of concerns about the risk of bleeding with biopsy in ICU patients. The use of a flexible brush may also be sufficient to make the diagnosis."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T81","span":{"begin":3,"end":4},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T82","span":{"begin":40,"end":43},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T83","span":{"begin":240,"end":247},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T84","span":{"begin":351,"end":358},"obj":"http://purl.obolibrary.org/obo/UBERON_0001005"},{"id":"T85","span":{"begin":387,"end":394},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T86","span":{"begin":430,"end":440},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T87","span":{"begin":734,"end":736},"obj":"http://purl.obolibrary.org/obo/CLO_0001000"},{"id":"T88","span":{"begin":904,"end":905},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"If a patient is admitted to the ICU and has influenza with pulmonary infiltrates, the diagnosis of IAPA should be considered and further investigation performed as appropriate. Ideally, this would include in order of invasiveness, serum GM testing, fungal cultures of sputum and/or tracheal aspirate, pulmonary CT, bronchoscopy to visualize the large airways and obtain BAL fluid for GM testing and fungal and bacterial cultures. Testing is most appropriate in patients who are on mechanical ventilation, but the diagnostic strategy is less clear in patients not intubated. As up to 50% of patients may present with tracheobronchitis, the presence of plaques and ulceration might be considered for inclusion in the definition of IPA [35]. Policies for taking biopsies of lesions seen on bronchoscopy may vary, mainly because of concerns about the risk of bleeding with biopsy in ICU patients. The use of a flexible brush may also be sufficient to make the diagnosis."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T74","span":{"begin":237,"end":239},"obj":"Chemical"},{"id":"T76","span":{"begin":370,"end":373},"obj":"Chemical"},{"id":"T77","span":{"begin":384,"end":386},"obj":"Chemical"},{"id":"T79","span":{"begin":729,"end":732},"obj":"Chemical"}],"attributes":[{"id":"A74","pred":"chebi_id","subj":"T74","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A75","pred":"chebi_id","subj":"T74","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A76","pred":"chebi_id","subj":"T76","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A77","pred":"chebi_id","subj":"T77","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A78","pred":"chebi_id","subj":"T77","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A79","pred":"chebi_id","subj":"T79","obj":"http://purl.obolibrary.org/obo/CHEBI_17824"},{"id":"A80","pred":"chebi_id","subj":"T79","obj":"http://purl.obolibrary.org/obo/CHEBI_30802"}],"text":"If a patient is admitted to the ICU and has influenza with pulmonary infiltrates, the diagnosis of IAPA should be considered and further investigation performed as appropriate. Ideally, this would include in order of invasiveness, serum GM testing, fungal cultures of sputum and/or tracheal aspirate, pulmonary CT, bronchoscopy to visualize the large airways and obtain BAL fluid for GM testing and fungal and bacterial cultures. Testing is most appropriate in patients who are on mechanical ventilation, but the diagnostic strategy is less clear in patients not intubated. As up to 50% of patients may present with tracheobronchitis, the presence of plaques and ulceration might be considered for inclusion in the definition of IPA [35]. Policies for taking biopsies of lesions seen on bronchoscopy may vary, mainly because of concerns about the risk of bleeding with biopsy in ICU patients. The use of a flexible brush may also be sufficient to make the diagnosis."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T9","span":{"begin":237,"end":239},"obj":"GlycoEpitope"},{"id":"T10","span":{"begin":384,"end":386},"obj":"GlycoEpitope"}],"attributes":[{"id":"A9","pred":"glyco_epitope_db_id","subj":"T9","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A10","pred":"glyco_epitope_db_id","subj":"T10","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"If a patient is admitted to the ICU and has influenza with pulmonary infiltrates, the diagnosis of IAPA should be considered and further investigation performed as appropriate. Ideally, this would include in order of invasiveness, serum GM testing, fungal cultures of sputum and/or tracheal aspirate, pulmonary CT, bronchoscopy to visualize the large airways and obtain BAL fluid for GM testing and fungal and bacterial cultures. Testing is most appropriate in patients who are on mechanical ventilation, but the diagnostic strategy is less clear in patients not intubated. As up to 50% of patients may present with tracheobronchitis, the presence of plaques and ulceration might be considered for inclusion in the definition of IPA [35]. Policies for taking biopsies of lesions seen on bronchoscopy may vary, mainly because of concerns about the risk of bleeding with biopsy in ICU patients. The use of a flexible brush may also be sufficient to make the diagnosis."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T21","span":{"begin":59,"end":80},"obj":"Phenotype"},{"id":"T22","span":{"begin":729,"end":732},"obj":"Phenotype"}],"attributes":[{"id":"A21","pred":"hp_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/HP_0002113"},{"id":"A22","pred":"hp_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/HP_0020103"}],"text":"If a patient is admitted to the ICU and has influenza with pulmonary infiltrates, the diagnosis of IAPA should be considered and further investigation performed as appropriate. Ideally, this would include in order of invasiveness, serum GM testing, fungal cultures of sputum and/or tracheal aspirate, pulmonary CT, bronchoscopy to visualize the large airways and obtain BAL fluid for GM testing and fungal and bacterial cultures. Testing is most appropriate in patients who are on mechanical ventilation, but the diagnostic strategy is less clear in patients not intubated. As up to 50% of patients may present with tracheobronchitis, the presence of plaques and ulceration might be considered for inclusion in the definition of IPA [35]. Policies for taking biopsies of lesions seen on bronchoscopy may vary, mainly because of concerns about the risk of bleeding with biopsy in ICU patients. The use of a flexible brush may also be sufficient to make the diagnosis."}

{"project":"LitCovid-sentences","denotations":[{"id":"T85","span":{"begin":0,"end":176},"obj":"Sentence"},{"id":"T86","span":{"begin":177,"end":429},"obj":"Sentence"},{"id":"T87","span":{"begin":430,"end":573},"obj":"Sentence"},{"id":"T88","span":{"begin":574,"end":738},"obj":"Sentence"},{"id":"T89","span":{"begin":739,"end":892},"obj":"Sentence"},{"id":"T90","span":{"begin":893,"end":966},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"If a patient is admitted to the ICU and has influenza with pulmonary infiltrates, the diagnosis of IAPA should be considered and further investigation performed as appropriate. Ideally, this would include in order of invasiveness, serum GM testing, fungal cultures of sputum and/or tracheal aspirate, pulmonary CT, bronchoscopy to visualize the large airways and obtain BAL fluid for GM testing and fungal and bacterial cultures. Testing is most appropriate in patients who are on mechanical ventilation, but the diagnostic strategy is less clear in patients not intubated. As up to 50% of patients may present with tracheobronchitis, the presence of plaques and ulceration might be considered for inclusion in the definition of IPA [35]. Policies for taking biopsies of lesions seen on bronchoscopy may vary, mainly because of concerns about the risk of bleeding with biopsy in ICU patients. The use of a flexible brush may also be sufficient to make the diagnosis."}

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T96","span":{"begin":59,"end":68},"obj":"UBERON:0002048"},{"id":"T97","span":{"begin":231,"end":236},"obj":"UBERON:0001977"},{"id":"T98","span":{"begin":249,"end":255},"obj":"NCBITaxon:4751"},{"id":"T99","span":{"begin":268,"end":274},"obj":"UBERON:0007311"},{"id":"T100","span":{"begin":282,"end":290},"obj":"UBERON:0003126"},{"id":"T101","span":{"begin":301,"end":310},"obj":"UBERON:0002048"},{"id":"T102","span":{"begin":351,"end":358},"obj":"UBERON:0001005"},{"id":"T103","span":{"begin":374,"end":379},"obj":"UBERON:0006314"},{"id":"T104","span":{"begin":399,"end":405},"obj":"NCBITaxon:4751"},{"id":"T105","span":{"begin":410,"end":419},"obj":"NCBITaxon:2"},{"id":"T106","span":{"begin":616,"end":633},"obj":"UBERON:0007196"},{"id":"T56564","span":{"begin":59,"end":68},"obj":"UBERON:0002048"},{"id":"T93733","span":{"begin":231,"end":236},"obj":"UBERON:0001977"},{"id":"T7027","span":{"begin":249,"end":255},"obj":"NCBITaxon:4751"},{"id":"T1997","span":{"begin":268,"end":274},"obj":"UBERON:0007311"},{"id":"T25508","span":{"begin":282,"end":290},"obj":"UBERON:0003126"},{"id":"T27731","span":{"begin":301,"end":310},"obj":"UBERON:0002048"},{"id":"T66249","span":{"begin":351,"end":358},"obj":"UBERON:0001005"},{"id":"T68615","span":{"begin":374,"end":379},"obj":"UBERON:0006314"},{"id":"T43239","span":{"begin":399,"end":405},"obj":"NCBITaxon:4751"},{"id":"T51425","span":{"begin":410,"end":419},"obj":"NCBITaxon:2"},{"id":"T29952","span":{"begin":616,"end":633},"obj":"UBERON:0007196"}],"text":"If a patient is admitted to the ICU and has influenza with pulmonary infiltrates, the diagnosis of IAPA should be considered and further investigation performed as appropriate. Ideally, this would include in order of invasiveness, serum GM testing, fungal cultures of sputum and/or tracheal aspirate, pulmonary CT, bronchoscopy to visualize the large airways and obtain BAL fluid for GM testing and fungal and bacterial cultures. Testing is most appropriate in patients who are on mechanical ventilation, but the diagnostic strategy is less clear in patients not intubated. As up to 50% of patients may present with tracheobronchitis, the presence of plaques and ulceration might be considered for inclusion in the definition of IPA [35]. Policies for taking biopsies of lesions seen on bronchoscopy may vary, mainly because of concerns about the risk of bleeding with biopsy in ICU patients. The use of a flexible brush may also be sufficient to make the diagnosis."}

{"project":"2_test","denotations":[{"id":"32572532-27365388-47963428","span":{"begin":734,"end":736},"obj":"27365388"},{"id":"T9256","span":{"begin":734,"end":736},"obj":"27365388"}],"text":"If a patient is admitted to the ICU and has influenza with pulmonary infiltrates, the diagnosis of IAPA should be considered and further investigation performed as appropriate. Ideally, this would include in order of invasiveness, serum GM testing, fungal cultures of sputum and/or tracheal aspirate, pulmonary CT, bronchoscopy to visualize the large airways and obtain BAL fluid for GM testing and fungal and bacterial cultures. Testing is most appropriate in patients who are on mechanical ventilation, but the diagnostic strategy is less clear in patients not intubated. As up to 50% of patients may present with tracheobronchitis, the presence of plaques and ulceration might be considered for inclusion in the definition of IPA [35]. Policies for taking biopsies of lesions seen on bronchoscopy may vary, mainly because of concerns about the risk of bleeding with biopsy in ICU patients. The use of a flexible brush may also be sufficient to make the diagnosis."}