PMC:7565665 / 13983-15074 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T76","span":{"begin":418,"end":429},"obj":"Body_part"},{"id":"T77","span":{"begin":584,"end":604},"obj":"Body_part"},{"id":"T78","span":{"begin":817,"end":835},"obj":"Body_part"},{"id":"T79","span":{"begin":837,"end":840},"obj":"Body_part"},{"id":"T80","span":{"begin":930,"end":933},"obj":"Body_part"},{"id":"T81","span":{"begin":971,"end":975},"obj":"Body_part"},{"id":"T82","span":{"begin":1044,"end":1047},"obj":"Body_part"},{"id":"T83","span":{"begin":1071,"end":1075},"obj":"Body_part"}],"attributes":[{"id":"A76","pred":"fma_id","subj":"T76","obj":"http://purl.org/sig/ont/fma/fma62860"},{"id":"A77","pred":"fma_id","subj":"T77","obj":"http://purl.org/sig/ont/fma/fma83023"},{"id":"A78","pred":"fma_id","subj":"T78","obj":"http://purl.org/sig/ont/fma/fma82785"},{"id":"A79","pred":"fma_id","subj":"T79","obj":"http://purl.org/sig/ont/fma/fma82785"},{"id":"A80","pred":"fma_id","subj":"T80","obj":"http://purl.org/sig/ont/fma/fma82785"},{"id":"A81","pred":"fma_id","subj":"T81","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A82","pred":"fma_id","subj":"T82","obj":"http://purl.org/sig/ont/fma/fma82785"},{"id":"A83","pred":"fma_id","subj":"T83","obj":"http://purl.org/sig/ont/fma/fma7195"}],"text":"In the case of Streptococcus pneumoniae (S. pneumoniae), which is the most common pathogen causing community acquired pneumonia [76], studies have demonstrated that infection activates the autophagy pathway as part of the body’s immune response [77,78]. Recently, it has been shown that this induction of autophagy makes the clearance of S. pneumoniae infection more effective by enhancing the rate of phagocytosis by neutrophils [78], demonstrating that autophagy is necessary for an effective immune response in pneumonia. Studies have also exhibited the activation of autophagy in alveolar macrophages by Pseudomonas aeruginosa (P. aeruginosa) [5,79] and Klebsiella pneumoniae [46,79] to induce the degradation of these pathogens in phagolysosomes. Moreover, there has been evidence that autophagy is activated by lipopolysaccharide (LPS), which is a bacterial toxin on the outer membrane of Gram-negative bacteria. Typically, LPS can cause inflammation that leads to lung injury [80,81]; however, the activation of autophagy in response to LPS was shown to attenuate lung injury [82,83]."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T22","span":{"begin":971,"end":975},"obj":"Body_part"},{"id":"T23","span":{"begin":1071,"end":1075},"obj":"Body_part"}],"attributes":[{"id":"A22","pred":"uberon_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A23","pred":"uberon_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"}],"text":"In the case of Streptococcus pneumoniae (S. pneumoniae), which is the most common pathogen causing community acquired pneumonia [76], studies have demonstrated that infection activates the autophagy pathway as part of the body’s immune response [77,78]. Recently, it has been shown that this induction of autophagy makes the clearance of S. pneumoniae infection more effective by enhancing the rate of phagocytosis by neutrophils [78], demonstrating that autophagy is necessary for an effective immune response in pneumonia. Studies have also exhibited the activation of autophagy in alveolar macrophages by Pseudomonas aeruginosa (P. aeruginosa) [5,79] and Klebsiella pneumoniae [46,79] to induce the degradation of these pathogens in phagolysosomes. Moreover, there has been evidence that autophagy is activated by lipopolysaccharide (LPS), which is a bacterial toxin on the outer membrane of Gram-negative bacteria. Typically, LPS can cause inflammation that leads to lung injury [80,81]; however, the activation of autophagy in response to LPS was shown to attenuate lung injury [82,83]."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T127","span":{"begin":15,"end":39},"obj":"Disease"},{"id":"T128","span":{"begin":44,"end":54},"obj":"Disease"},{"id":"T129","span":{"begin":118,"end":127},"obj":"Disease"},{"id":"T130","span":{"begin":165,"end":174},"obj":"Disease"},{"id":"T131","span":{"begin":341,"end":351},"obj":"Disease"},{"id":"T132","span":{"begin":352,"end":361},"obj":"Disease"},{"id":"T133","span":{"begin":514,"end":523},"obj":"Disease"},{"id":"T134","span":{"begin":658,"end":679},"obj":"Disease"},{"id":"T135","span":{"begin":944,"end":956},"obj":"Disease"},{"id":"T136","span":{"begin":976,"end":982},"obj":"Disease"},{"id":"T137","span":{"begin":1076,"end":1082},"obj":"Disease"}],"attributes":[{"id":"A127","pred":"mondo_id","subj":"T127","obj":"http://purl.obolibrary.org/obo/MONDO_0005972"},{"id":"A128","pred":"mondo_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A129","pred":"mondo_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A130","pred":"mondo_id","subj":"T130","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A131","pred":"mondo_id","subj":"T131","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A132","pred":"mondo_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A133","pred":"mondo_id","subj":"T133","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A134","pred":"mondo_id","subj":"T134","obj":"http://purl.obolibrary.org/obo/MONDO_0030602"},{"id":"A135","pred":"mondo_id","subj":"T135","obj":"http://purl.obolibrary.org/obo/MONDO_0021166"},{"id":"A136","pred":"mondo_id","subj":"T136","obj":"http://purl.obolibrary.org/obo/MONDO_0021178"},{"id":"A137","pred":"mondo_id","subj":"T137","obj":"http://purl.obolibrary.org/obo/MONDO_0021178"}],"text":"In the case of Streptococcus pneumoniae (S. pneumoniae), which is the most common pathogen causing community acquired pneumonia [76], studies have demonstrated that infection activates the autophagy pathway as part of the body’s immune response [77,78]. Recently, it has been shown that this induction of autophagy makes the clearance of S. pneumoniae infection more effective by enhancing the rate of phagocytosis by neutrophils [78], demonstrating that autophagy is necessary for an effective immune response in pneumonia. Studies have also exhibited the activation of autophagy in alveolar macrophages by Pseudomonas aeruginosa (P. aeruginosa) [5,79] and Klebsiella pneumoniae [46,79] to induce the degradation of these pathogens in phagolysosomes. Moreover, there has been evidence that autophagy is activated by lipopolysaccharide (LPS), which is a bacterial toxin on the outer membrane of Gram-negative bacteria. Typically, LPS can cause inflammation that leads to lung injury [80,81]; however, the activation of autophagy in response to LPS was shown to attenuate lung injury [82,83]."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T162","span":{"begin":175,"end":184},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T163","span":{"begin":267,"end":270},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T164","span":{"begin":557,"end":567},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T165","span":{"begin":768,"end":771},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T166","span":{"begin":804,"end":813},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T167","span":{"begin":852,"end":853},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T168","span":{"begin":883,"end":891},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T169","span":{"begin":909,"end":917},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_2"},{"id":"T170","span":{"begin":971,"end":975},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T171","span":{"begin":971,"end":975},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T172","span":{"begin":1005,"end":1015},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T173","span":{"begin":1071,"end":1075},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T174","span":{"begin":1071,"end":1075},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"}],"text":"In the case of Streptococcus pneumoniae (S. pneumoniae), which is the most common pathogen causing community acquired pneumonia [76], studies have demonstrated that infection activates the autophagy pathway as part of the body’s immune response [77,78]. Recently, it has been shown that this induction of autophagy makes the clearance of S. pneumoniae infection more effective by enhancing the rate of phagocytosis by neutrophils [78], demonstrating that autophagy is necessary for an effective immune response in pneumonia. Studies have also exhibited the activation of autophagy in alveolar macrophages by Pseudomonas aeruginosa (P. aeruginosa) [5,79] and Klebsiella pneumoniae [46,79] to induce the degradation of these pathogens in phagolysosomes. Moreover, there has been evidence that autophagy is activated by lipopolysaccharide (LPS), which is a bacterial toxin on the outer membrane of Gram-negative bacteria. Typically, LPS can cause inflammation that leads to lung injury [80,81]; however, the activation of autophagy in response to LPS was shown to attenuate lung injury [82,83]."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T49","span":{"begin":817,"end":835},"obj":"Chemical"},{"id":"T50","span":{"begin":837,"end":840},"obj":"Chemical"},{"id":"T53","span":{"begin":864,"end":869},"obj":"Chemical"},{"id":"T54","span":{"begin":930,"end":933},"obj":"Chemical"},{"id":"T57","span":{"begin":1044,"end":1047},"obj":"Chemical"}],"attributes":[{"id":"A49","pred":"chebi_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/CHEBI_16412"},{"id":"A50","pred":"chebi_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/CHEBI_16412"},{"id":"A51","pred":"chebi_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/CHEBI_52603"},{"id":"A52","pred":"chebi_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/CHEBI_89981"},{"id":"A53","pred":"chebi_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/CHEBI_27026"},{"id":"A54","pred":"chebi_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/CHEBI_16412"},{"id":"A55","pred":"chebi_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/CHEBI_52603"},{"id":"A56","pred":"chebi_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/CHEBI_89981"},{"id":"A57","pred":"chebi_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/CHEBI_16412"},{"id":"A58","pred":"chebi_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/CHEBI_52603"},{"id":"A59","pred":"chebi_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/CHEBI_89981"}],"text":"In the case of Streptococcus pneumoniae (S. pneumoniae), which is the most common pathogen causing community acquired pneumonia [76], studies have demonstrated that infection activates the autophagy pathway as part of the body’s immune response [77,78]. Recently, it has been shown that this induction of autophagy makes the clearance of S. pneumoniae infection more effective by enhancing the rate of phagocytosis by neutrophils [78], demonstrating that autophagy is necessary for an effective immune response in pneumonia. Studies have also exhibited the activation of autophagy in alveolar macrophages by Pseudomonas aeruginosa (P. aeruginosa) [5,79] and Klebsiella pneumoniae [46,79] to induce the degradation of these pathogens in phagolysosomes. Moreover, there has been evidence that autophagy is activated by lipopolysaccharide (LPS), which is a bacterial toxin on the outer membrane of Gram-negative bacteria. Typically, LPS can cause inflammation that leads to lung injury [80,81]; however, the activation of autophagy in response to LPS was shown to attenuate lung injury [82,83]."}

{"project":"LitCovid-PubTator","denotations":[{"id":"356","span":{"begin":15,"end":39},"obj":"Species"},{"id":"357","span":{"begin":41,"end":54},"obj":"Species"},{"id":"358","span":{"begin":338,"end":351},"obj":"Species"},{"id":"359","span":{"begin":608,"end":630},"obj":"Species"},{"id":"360","span":{"begin":632,"end":645},"obj":"Species"},{"id":"361","span":{"begin":658,"end":679},"obj":"Species"},{"id":"362","span":{"begin":817,"end":835},"obj":"Chemical"},{"id":"363","span":{"begin":118,"end":127},"obj":"Disease"},{"id":"364","span":{"begin":165,"end":174},"obj":"Disease"},{"id":"365","span":{"begin":352,"end":361},"obj":"Disease"},{"id":"366","span":{"begin":514,"end":523},"obj":"Disease"},{"id":"367","span":{"begin":944,"end":956},"obj":"Disease"},{"id":"368","span":{"begin":971,"end":982},"obj":"Disease"},{"id":"369","span":{"begin":1071,"end":1082},"obj":"Disease"}],"attributes":[{"id":"A356","pred":"tao:has_database_id","subj":"356","obj":"Tax:1313"},{"id":"A357","pred":"tao:has_database_id","subj":"357","obj":"Tax:1313"},{"id":"A358","pred":"tao:has_database_id","subj":"358","obj":"Tax:1313"},{"id":"A359","pred":"tao:has_database_id","subj":"359","obj":"Tax:287"},{"id":"A360","pred":"tao:has_database_id","subj":"360","obj":"Tax:287"},{"id":"A361","pred":"tao:has_database_id","subj":"361","obj":"Tax:573"},{"id":"A362","pred":"tao:has_database_id","subj":"362","obj":"MESH:D008070"},{"id":"A363","pred":"tao:has_database_id","subj":"363","obj":"MESH:D011014"},{"id":"A364","pred":"tao:has_database_id","subj":"364","obj":"MESH:D007239"},{"id":"A365","pred":"tao:has_database_id","subj":"365","obj":"MESH:D007239"},{"id":"A366","pred":"tao:has_database_id","subj":"366","obj":"MESH:D011014"},{"id":"A367","pred":"tao:has_database_id","subj":"367","obj":"MESH:D007249"},{"id":"A368","pred":"tao:has_database_id","subj":"368","obj":"MESH:D055370"},{"id":"A369","pred":"tao:has_database_id","subj":"369","obj":"MESH:D055370"}],"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":"In the case of Streptococcus pneumoniae (S. pneumoniae), which is the most common pathogen causing community acquired pneumonia [76], studies have demonstrated that infection activates the autophagy pathway as part of the body’s immune response [77,78]. Recently, it has been shown that this induction of autophagy makes the clearance of S. pneumoniae infection more effective by enhancing the rate of phagocytosis by neutrophils [78], demonstrating that autophagy is necessary for an effective immune response in pneumonia. Studies have also exhibited the activation of autophagy in alveolar macrophages by Pseudomonas aeruginosa (P. aeruginosa) [5,79] and Klebsiella pneumoniae [46,79] to induce the degradation of these pathogens in phagolysosomes. Moreover, there has been evidence that autophagy is activated by lipopolysaccharide (LPS), which is a bacterial toxin on the outer membrane of Gram-negative bacteria. Typically, LPS can cause inflammation that leads to lung injury [80,81]; however, the activation of autophagy in response to LPS was shown to attenuate lung injury [82,83]."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T54","span":{"begin":29,"end":39},"obj":"Phenotype"},{"id":"T55","span":{"begin":44,"end":54},"obj":"Phenotype"},{"id":"T56","span":{"begin":118,"end":127},"obj":"Phenotype"},{"id":"T57","span":{"begin":341,"end":351},"obj":"Phenotype"},{"id":"T58","span":{"begin":514,"end":523},"obj":"Phenotype"},{"id":"T59","span":{"begin":669,"end":679},"obj":"Phenotype"}],"attributes":[{"id":"A54","pred":"hp_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A55","pred":"hp_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A56","pred":"hp_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A57","pred":"hp_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A58","pred":"hp_id","subj":"T58","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A59","pred":"hp_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"In the case of Streptococcus pneumoniae (S. pneumoniae), which is the most common pathogen causing community acquired pneumonia [76], studies have demonstrated that infection activates the autophagy pathway as part of the body’s immune response [77,78]. Recently, it has been shown that this induction of autophagy makes the clearance of S. pneumoniae infection more effective by enhancing the rate of phagocytosis by neutrophils [78], demonstrating that autophagy is necessary for an effective immune response in pneumonia. Studies have also exhibited the activation of autophagy in alveolar macrophages by Pseudomonas aeruginosa (P. aeruginosa) [5,79] and Klebsiella pneumoniae [46,79] to induce the degradation of these pathogens in phagolysosomes. Moreover, there has been evidence that autophagy is activated by lipopolysaccharide (LPS), which is a bacterial toxin on the outer membrane of Gram-negative bacteria. Typically, LPS can cause inflammation that leads to lung injury [80,81]; however, the activation of autophagy in response to LPS was shown to attenuate lung injury [82,83]."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T182","span":{"begin":189,"end":198},"obj":"http://purl.obolibrary.org/obo/GO_0016236"},{"id":"T183","span":{"begin":189,"end":198},"obj":"http://purl.obolibrary.org/obo/GO_0006914"},{"id":"T184","span":{"begin":229,"end":244},"obj":"http://purl.obolibrary.org/obo/GO_0006955"},{"id":"T185","span":{"begin":305,"end":314},"obj":"http://purl.obolibrary.org/obo/GO_0016236"},{"id":"T186","span":{"begin":305,"end":314},"obj":"http://purl.obolibrary.org/obo/GO_0006914"},{"id":"T187","span":{"begin":402,"end":414},"obj":"http://purl.obolibrary.org/obo/GO_0006909"},{"id":"T188","span":{"begin":455,"end":464},"obj":"http://purl.obolibrary.org/obo/GO_0016236"},{"id":"T189","span":{"begin":455,"end":464},"obj":"http://purl.obolibrary.org/obo/GO_0006914"},{"id":"T190","span":{"begin":495,"end":510},"obj":"http://purl.obolibrary.org/obo/GO_0006955"},{"id":"T191","span":{"begin":571,"end":580},"obj":"http://purl.obolibrary.org/obo/GO_0016236"},{"id":"T192","span":{"begin":571,"end":580},"obj":"http://purl.obolibrary.org/obo/GO_0006914"},{"id":"T193","span":{"begin":702,"end":713},"obj":"http://purl.obolibrary.org/obo/GO_0009056"},{"id":"T194","span":{"begin":791,"end":800},"obj":"http://purl.obolibrary.org/obo/GO_0016236"},{"id":"T195","span":{"begin":791,"end":800},"obj":"http://purl.obolibrary.org/obo/GO_0006914"},{"id":"T196","span":{"begin":944,"end":956},"obj":"http://purl.obolibrary.org/obo/GO_0006954"},{"id":"T197","span":{"begin":1019,"end":1028},"obj":"http://purl.obolibrary.org/obo/GO_0016236"},{"id":"T198","span":{"begin":1019,"end":1028},"obj":"http://purl.obolibrary.org/obo/GO_0006914"},{"id":"T199","span":{"begin":1032,"end":1047},"obj":"http://purl.obolibrary.org/obo/GO_0032496"}],"text":"In the case of Streptococcus pneumoniae (S. pneumoniae), which is the most common pathogen causing community acquired pneumonia [76], studies have demonstrated that infection activates the autophagy pathway as part of the body’s immune response [77,78]. Recently, it has been shown that this induction of autophagy makes the clearance of S. pneumoniae infection more effective by enhancing the rate of phagocytosis by neutrophils [78], demonstrating that autophagy is necessary for an effective immune response in pneumonia. Studies have also exhibited the activation of autophagy in alveolar macrophages by Pseudomonas aeruginosa (P. aeruginosa) [5,79] and Klebsiella pneumoniae [46,79] to induce the degradation of these pathogens in phagolysosomes. Moreover, there has been evidence that autophagy is activated by lipopolysaccharide (LPS), which is a bacterial toxin on the outer membrane of Gram-negative bacteria. Typically, LPS can cause inflammation that leads to lung injury [80,81]; however, the activation of autophagy in response to LPS was shown to attenuate lung injury [82,83]."}

{"project":"LitCovid-sentences","denotations":[{"id":"T68","span":{"begin":0,"end":253},"obj":"Sentence"},{"id":"T69","span":{"begin":254,"end":524},"obj":"Sentence"},{"id":"T70","span":{"begin":525,"end":751},"obj":"Sentence"},{"id":"T71","span":{"begin":752,"end":918},"obj":"Sentence"},{"id":"T72","span":{"begin":919,"end":1091},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In the case of Streptococcus pneumoniae (S. pneumoniae), which is the most common pathogen causing community acquired pneumonia [76], studies have demonstrated that infection activates the autophagy pathway as part of the body’s immune response [77,78]. Recently, it has been shown that this induction of autophagy makes the clearance of S. pneumoniae infection more effective by enhancing the rate of phagocytosis by neutrophils [78], demonstrating that autophagy is necessary for an effective immune response in pneumonia. Studies have also exhibited the activation of autophagy in alveolar macrophages by Pseudomonas aeruginosa (P. aeruginosa) [5,79] and Klebsiella pneumoniae [46,79] to induce the degradation of these pathogens in phagolysosomes. Moreover, there has been evidence that autophagy is activated by lipopolysaccharide (LPS), which is a bacterial toxin on the outer membrane of Gram-negative bacteria. Typically, LPS can cause inflammation that leads to lung injury [80,81]; however, the activation of autophagy in response to LPS was shown to attenuate lung injury [82,83]."}