PMC:7247521 / 7007-7790 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"120","span":{"begin":72,"end":75},"obj":"Disease"},{"id":"121","span":{"begin":199,"end":201},"obj":"Disease"},{"id":"122","span":{"begin":247,"end":251},"obj":"Disease"},{"id":"123","span":{"begin":505,"end":509},"obj":"Disease"}],"attributes":[{"id":"A121","pred":"tao:has_database_id","subj":"121","obj":"MESH:D009765"}],"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":"2.1 Data preparation\nCompounds of the main herb in formula MSXG, SGMH, XCH, WLS and Others were searched in TCMSP [13], and screened based on drug-likeness (DL) ≥0.18 [14] and oral bioavailability (OB) ≥30 % [15]. Then, the corresponding Pubchem CIDs of the compounds were retrieved from the Pubchem database [16]. Finally, BATMAN-TCM [17], an bioinformatics analysis tool for studying TCM’s molecular mechanisms, was used to identify potential target genes of the active components (uploaded by Pubchem CIDs). To make the results more credible, we set the cutoff score ≥ 30 as the standard. Finally, to discovery the co-differentially presented targets in the five formulae, we conducted pan-formula analysis using Venn diagrams (http://bioinformatics.psb.ugent.be/webtools/Venn/)."}

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T84","span":{"begin":143,"end":147},"obj":"CHEBI:23888;CHEBI:23888"},{"id":"T85","span":{"begin":259,"end":268},"obj":"CHEBI:36357;CHEBI:36357"},{"id":"T86","span":{"begin":453,"end":458},"obj":"SO:0001867"}],"text":"2.1 Data preparation\nCompounds of the main herb in formula MSXG, SGMH, XCH, WLS and Others were searched in TCMSP [13], and screened based on drug-likeness (DL) ≥0.18 [14] and oral bioavailability (OB) ≥30 % [15]. Then, the corresponding Pubchem CIDs of the compounds were retrieved from the Pubchem database [16]. Finally, BATMAN-TCM [17], an bioinformatics analysis tool for studying TCM’s molecular mechanisms, was used to identify potential target genes of the active components (uploaded by Pubchem CIDs). To make the results more credible, we set the cutoff score ≥ 30 as the standard. Finally, to discovery the co-differentially presented targets in the five formulae, we conducted pan-formula analysis using Venn diagrams (http://bioinformatics.psb.ugent.be/webtools/Venn/)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T53","span":{"begin":204,"end":212},"obj":"http://purl.obolibrary.org/obo/CLO_0001279"},{"id":"T54","span":{"begin":453,"end":458},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T55","span":{"begin":466,"end":472},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T56","span":{"begin":690,"end":693},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9596"}],"text":"2.1 Data preparation\nCompounds of the main herb in formula MSXG, SGMH, XCH, WLS and Others were searched in TCMSP [13], and screened based on drug-likeness (DL) ≥0.18 [14] and oral bioavailability (OB) ≥30 % [15]. Then, the corresponding Pubchem CIDs of the compounds were retrieved from the Pubchem database [16]. Finally, BATMAN-TCM [17], an bioinformatics analysis tool for studying TCM’s molecular mechanisms, was used to identify potential target genes of the active components (uploaded by Pubchem CIDs). To make the results more credible, we set the cutoff score ≥ 30 as the standard. Finally, to discovery the co-differentially presented targets in the five formulae, we conducted pan-formula analysis using Venn diagrams (http://bioinformatics.psb.ugent.be/webtools/Venn/)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T25","span":{"begin":143,"end":147},"obj":"Chemical"},{"id":"T26","span":{"begin":158,"end":160},"obj":"Chemical"},{"id":"T27","span":{"begin":332,"end":335},"obj":"Chemical"}],"attributes":[{"id":"A25","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_23888"},{"id":"A26","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_68596"},{"id":"A27","pred":"chebi_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/CHEBI_145500"}],"text":"2.1 Data preparation\nCompounds of the main herb in formula MSXG, SGMH, XCH, WLS and Others were searched in TCMSP [13], and screened based on drug-likeness (DL) ≥0.18 [14] and oral bioavailability (OB) ≥30 % [15]. Then, the corresponding Pubchem CIDs of the compounds were retrieved from the Pubchem database [16]. Finally, BATMAN-TCM [17], an bioinformatics analysis tool for studying TCM’s molecular mechanisms, was used to identify potential target genes of the active components (uploaded by Pubchem CIDs). To make the results more credible, we set the cutoff score ≥ 30 as the standard. Finally, to discovery the co-differentially presented targets in the five formulae, we conducted pan-formula analysis using Venn diagrams (http://bioinformatics.psb.ugent.be/webtools/Venn/)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T44","span":{"begin":0,"end":21},"obj":"Sentence"},{"id":"T45","span":{"begin":22,"end":214},"obj":"Sentence"},{"id":"T46","span":{"begin":215,"end":315},"obj":"Sentence"},{"id":"T47","span":{"begin":316,"end":511},"obj":"Sentence"},{"id":"T48","span":{"begin":512,"end":592},"obj":"Sentence"},{"id":"T49","span":{"begin":593,"end":783},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.1 Data preparation\nCompounds of the main herb in formula MSXG, SGMH, XCH, WLS and Others were searched in TCMSP [13], and screened based on drug-likeness (DL) ≥0.18 [14] and oral bioavailability (OB) ≥30 % [15]. Then, the corresponding Pubchem CIDs of the compounds were retrieved from the Pubchem database [16]. Finally, BATMAN-TCM [17], an bioinformatics analysis tool for studying TCM’s molecular mechanisms, was used to identify potential target genes of the active components (uploaded by Pubchem CIDs). To make the results more credible, we set the cutoff score ≥ 30 as the standard. Finally, to discovery the co-differentially presented targets in the five formulae, we conducted pan-formula analysis using Venn diagrams (http://bioinformatics.psb.ugent.be/webtools/Venn/)."}

{"project":"2_test","denotations":[{"id":"32554251-24735618-6393492","span":{"begin":116,"end":118},"obj":"24735618"},{"id":"32554251-17033281-6393493","span":{"begin":169,"end":171},"obj":"17033281"},{"id":"32554251-22837674-6393494","span":{"begin":210,"end":212},"obj":"22837674"},{"id":"32554251-26400175-6393495","span":{"begin":311,"end":313},"obj":"26400175"},{"id":"32554251-26879404-6393496","span":{"begin":337,"end":339},"obj":"26879404"}],"text":"2.1 Data preparation\nCompounds of the main herb in formula MSXG, SGMH, XCH, WLS and Others were searched in TCMSP [13], and screened based on drug-likeness (DL) ≥0.18 [14] and oral bioavailability (OB) ≥30 % [15]. Then, the corresponding Pubchem CIDs of the compounds were retrieved from the Pubchem database [16]. Finally, BATMAN-TCM [17], an bioinformatics analysis tool for studying TCM’s molecular mechanisms, was used to identify potential target genes of the active components (uploaded by Pubchem CIDs). To make the results more credible, we set the cutoff score ≥ 30 as the standard. Finally, to discovery the co-differentially presented targets in the five formulae, we conducted pan-formula analysis using Venn diagrams (http://bioinformatics.psb.ugent.be/webtools/Venn/)."}