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LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"173","span":{"begin":215,"end":220},"obj":"Species"},{"id":"174","span":{"begin":236,"end":253},"obj":"Species"},{"id":"175","span":{"begin":520,"end":525},"obj":"Species"},{"id":"176","span":{"begin":884,"end":889},"obj":"Species"},{"id":"177","span":{"begin":1093,"end":1098},"obj":"Species"},{"id":"178","span":{"begin":1319,"end":1324},"obj":"Species"},{"id":"179","span":{"begin":255,"end":259},"obj":"Species"},{"id":"180","span":{"begin":347,"end":351},"obj":"Species"},{"id":"181","span":{"begin":417,"end":421},"obj":"Species"},{"id":"182","span":{"begin":821,"end":825},"obj":"Species"},{"id":"183","span":{"begin":1246,"end":1255},"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":"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":277,"end":285},"obj":"Body_part"},{"id":"T23","span":{"begin":352,"end":359},"obj":"Body_part"},{"id":"T24","span":{"begin":433,"end":441},"obj":"Body_part"},{"id":"T25","span":{"begin":526,"end":533},"obj":"Body_part"},{"id":"T26","span":{"begin":558,"end":562},"obj":"Body_part"},{"id":"T27","span":{"begin":974,"end":982},"obj":"Body_part"},{"id":"T28","span":{"begin":1129,"end":1137},"obj":"Body_part"},{"id":"T29","span":{"begin":1272,"end":1279},"obj":"Body_part"},{"id":"T30","span":{"begin":1280,"end":1287},"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":"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":1246,"end":1255},"obj":"Disease"}],"attributes":[{"id":"A28","pred":"mondo_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"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":71,"end":72},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T46","span":{"begin":168,"end":173},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T47","span":{"begin":215,"end":220},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T48","span":{"begin":234,"end":235},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T49","span":{"begin":236,"end":241},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T50","span":{"begin":341,"end":342},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T51","span":{"begin":343,"end":346},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9596"},{"id":"T52","span":{"begin":372,"end":373},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T53","span":{"begin":520,"end":533},"obj":"http://purl.obolibrary.org/obo/PR_000029067"},{"id":"T54","span":{"begin":558,"end":562},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T55","span":{"begin":884,"end":889},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T56","span":{"begin":1093,"end":1098},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T57","span":{"begin":1169,"end":1170},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T58","span":{"begin":1319,"end":1324},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"}],"text":"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":"T41","span":{"begin":32,"end":1337},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"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."}