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LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"173","span":{"begin":222,"end":227},"obj":"Species"},{"id":"174","span":{"begin":243,"end":260},"obj":"Species"},{"id":"175","span":{"begin":527,"end":532},"obj":"Species"},{"id":"176","span":{"begin":891,"end":896},"obj":"Species"},{"id":"177","span":{"begin":1100,"end":1105},"obj":"Species"},{"id":"178","span":{"begin":1326,"end":1331},"obj":"Species"},{"id":"179","span":{"begin":262,"end":266},"obj":"Species"},{"id":"180","span":{"begin":354,"end":358},"obj":"Species"},{"id":"181","span":{"begin":424,"end":428},"obj":"Species"},{"id":"182","span":{"begin":828,"end":832},"obj":"Species"},{"id":"183","span":{"begin":1253,"end":1262},"obj":"Disease"}],"attributes":[{"id":"A173","pred":"tao:has_database_id","subj":"173","obj":"Tax:9606"},{"id":"A174","pred":"tao:has_database_id","subj":"174","obj":"Tax:694448"},{"id":"A175","pred":"tao:has_database_id","subj":"175","obj":"Tax:9606"},{"id":"A176","pred":"tao:has_database_id","subj":"176","obj":"Tax:9606"},{"id":"A177","pred":"tao:has_database_id","subj":"177","obj":"Tax:9606"},{"id":"A178","pred":"tao:has_database_id","subj":"178","obj":"Tax:9606"},{"id":"A179","pred":"tao:has_database_id","subj":"179","obj":"Tax:694448"},{"id":"A180","pred":"tao:has_database_id","subj":"180","obj":"Tax:694448"},{"id":"A181","pred":"tao:has_database_id","subj":"181","obj":"Tax:694448"},{"id":"A182","pred":"tao:has_database_id","subj":"182","obj":"Tax:694448"},{"id":"A183","pred":"tao:has_database_id","subj":"183","obj":"MESH:D007239"}],"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":"Fig. 1 Overall workflow of this study.\nOur network-based methodology combines a systems pharmacology-based network medicine platform that quantifies the interplay between the virus–host interactome and drug targets in the human PPI network. a Human coronavirus (HCoV)-associated host proteins were collected from literatures and pooled to generate a pan-HCoV protein subnetwork. b Network proximity between drug targets and HCoV-associated proteins was calculated to screen for candidate repurposable drugs for HCoVs under the human protein interactome model. c, d Gene set enrichment analysis was utilized to validate the network-based prediction. e Top candidates were further prioritized for drug combinations using network-based method captured by the “Complementary Exposure” pattern: the targets of the drugs both hit the HCoV–host subnetwork, but target separate neighborhoods in the human interactome network. f Overall hypothesis of the network-based methodology: (i) the proteins that functionally associate with HCoVs are localized in the corresponding subnetwork within the comprehensive human interactome network; and (ii) proteins that serve as drug targets for a specific disease may also be suitable drug targets for potential antiviral infection owing to common protein–protein interactions elucidated by the human interactome."}

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T22","span":{"begin":284,"end":292},"obj":"Body_part"},{"id":"T23","span":{"begin":359,"end":366},"obj":"Body_part"},{"id":"T24","span":{"begin":440,"end":448},"obj":"Body_part"},{"id":"T25","span":{"begin":533,"end":540},"obj":"Body_part"},{"id":"T26","span":{"begin":565,"end":569},"obj":"Body_part"},{"id":"T27","span":{"begin":981,"end":989},"obj":"Body_part"},{"id":"T28","span":{"begin":1136,"end":1144},"obj":"Body_part"},{"id":"T29","span":{"begin":1279,"end":1286},"obj":"Body_part"},{"id":"T30","span":{"begin":1287,"end":1294},"obj":"Body_part"}],"attributes":[{"id":"A22","pred":"fma_id","subj":"T22","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A23","pred":"fma_id","subj":"T23","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A24","pred":"fma_id","subj":"T24","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A25","pred":"fma_id","subj":"T25","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A26","pred":"fma_id","subj":"T26","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A27","pred":"fma_id","subj":"T27","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A28","pred":"fma_id","subj":"T28","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A29","pred":"fma_id","subj":"T29","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A30","pred":"fma_id","subj":"T30","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Fig. 1 Overall workflow of this study.\nOur network-based methodology combines a systems pharmacology-based network medicine platform that quantifies the interplay between the virus–host interactome and drug targets in the human PPI network. a Human coronavirus (HCoV)-associated host proteins were collected from literatures and pooled to generate a pan-HCoV protein subnetwork. b Network proximity between drug targets and HCoV-associated proteins was calculated to screen for candidate repurposable drugs for HCoVs under the human protein interactome model. c, d Gene set enrichment analysis was utilized to validate the network-based prediction. e Top candidates were further prioritized for drug combinations using network-based method captured by the “Complementary Exposure” pattern: the targets of the drugs both hit the HCoV–host subnetwork, but target separate neighborhoods in the human interactome network. f Overall hypothesis of the network-based methodology: (i) the proteins that functionally associate with HCoVs are localized in the corresponding subnetwork within the comprehensive human interactome network; and (ii) proteins that serve as drug targets for a specific disease may also be suitable drug targets for potential antiviral infection owing to common protein–protein interactions elucidated by the human interactome."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T28","span":{"begin":1253,"end":1262},"obj":"Disease"}],"attributes":[{"id":"A28","pred":"mondo_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"Fig. 1 Overall workflow of this study.\nOur network-based methodology combines a systems pharmacology-based network medicine platform that quantifies the interplay between the virus–host interactome and drug targets in the human PPI network. a Human coronavirus (HCoV)-associated host proteins were collected from literatures and pooled to generate a pan-HCoV protein subnetwork. b Network proximity between drug targets and HCoV-associated proteins was calculated to screen for candidate repurposable drugs for HCoVs under the human protein interactome model. c, d Gene set enrichment analysis was utilized to validate the network-based prediction. e Top candidates were further prioritized for drug combinations using network-based method captured by the “Complementary Exposure” pattern: the targets of the drugs both hit the HCoV–host subnetwork, but target separate neighborhoods in the human interactome network. f Overall hypothesis of the network-based methodology: (i) the proteins that functionally associate with HCoVs are localized in the corresponding subnetwork within the comprehensive human interactome network; and (ii) proteins that serve as drug targets for a specific disease may also be suitable drug targets for potential antiviral infection owing to common protein–protein interactions elucidated by the human interactome."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T45","span":{"begin":78,"end":79},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T46","span":{"begin":175,"end":180},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T47","span":{"begin":222,"end":227},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T48","span":{"begin":241,"end":242},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T49","span":{"begin":243,"end":248},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T50","span":{"begin":348,"end":349},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T51","span":{"begin":350,"end":353},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9596"},{"id":"T52","span":{"begin":379,"end":380},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T53","span":{"begin":527,"end":540},"obj":"http://purl.obolibrary.org/obo/PR_000029067"},{"id":"T54","span":{"begin":565,"end":569},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T55","span":{"begin":891,"end":896},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T56","span":{"begin":1100,"end":1105},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T57","span":{"begin":1176,"end":1177},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T58","span":{"begin":1326,"end":1331},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"}],"text":"Fig. 1 Overall workflow of this study.\nOur network-based methodology combines a systems pharmacology-based network medicine platform that quantifies the interplay between the virus–host interactome and drug targets in the human PPI network. a Human coronavirus (HCoV)-associated host proteins were collected from literatures and pooled to generate a pan-HCoV protein subnetwork. b Network proximity between drug targets and HCoV-associated proteins was calculated to screen for candidate repurposable drugs for HCoVs under the human protein interactome model. c, d Gene set enrichment analysis was utilized to validate the network-based prediction. e Top candidates were further prioritized for drug combinations using network-based method captured by the “Complementary Exposure” pattern: the targets of the drugs both hit the HCoV–host subnetwork, but target separate neighborhoods in the human interactome network. f Overall hypothesis of the network-based methodology: (i) the proteins that functionally associate with HCoVs are localized in the corresponding subnetwork within the comprehensive human interactome network; and (ii) proteins that serve as drug targets for a specific disease may also be suitable drug targets for potential antiviral infection owing to common protein–protein interactions elucidated by the human interactome."}

LitCovid-PD-CHEBI

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T40","span":{"begin":0,"end":38},"obj":"Sentence"},{"id":"T41","span":{"begin":39,"end":1344},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Fig. 1 Overall workflow of this study.\nOur network-based methodology combines a systems pharmacology-based network medicine platform that quantifies the interplay between the virus–host interactome and drug targets in the human PPI network. a Human coronavirus (HCoV)-associated host proteins were collected from literatures and pooled to generate a pan-HCoV protein subnetwork. b Network proximity between drug targets and HCoV-associated proteins was calculated to screen for candidate repurposable drugs for HCoVs under the human protein interactome model. c, d Gene set enrichment analysis was utilized to validate the network-based prediction. e Top candidates were further prioritized for drug combinations using network-based method captured by the “Complementary Exposure” pattern: the targets of the drugs both hit the HCoV–host subnetwork, but target separate neighborhoods in the human interactome network. f Overall hypothesis of the network-based methodology: (i) the proteins that functionally associate with HCoVs are localized in the corresponding subnetwork within the comprehensive human interactome network; and (ii) proteins that serve as drug targets for a specific disease may also be suitable drug targets for potential antiviral infection owing to common protein–protein interactions elucidated by the human interactome."}