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LitCovid-sample-CHEBI

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T168","span":{"begin":504,"end":514},"obj":"Chemical"},{"id":"T169","span":{"begin":1125,"end":1135},"obj":"Chemical"},{"id":"T170","span":{"begin":1293,"end":1296},"obj":"Chemical"}],"attributes":[{"id":"A168","pred":"chebi_id","subj":"T168","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A169","pred":"chebi_id","subj":"T169","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A170","pred":"chebi_id","subj":"T170","obj":"http://purl.obolibrary.org/obo/CHEBI_16857"},{"id":"A171","pred":"chebi_id","subj":"T170","obj":"http://purl.obolibrary.org/obo/CHEBI_30013"}],"text":"3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

LitCovid-sample-PD-NCBITaxon

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T71","span":{"begin":39,"end":49},"obj":"Species"},{"id":"T72","span":{"begin":304,"end":314},"obj":"Species"},{"id":"T73","span":{"begin":355,"end":365},"obj":"Species"},{"id":"T74","span":{"begin":638,"end":648},"obj":"Species"},{"id":"T75","span":{"begin":733,"end":743},"obj":"Species"},{"id":"T76","span":{"begin":947,"end":957},"obj":"Species"},{"id":"T77","span":{"begin":1190,"end":1200},"obj":"Species"}],"attributes":[{"id":"A71","pred":"ncbi_taxonomy_id","subj":"T71","obj":"NCBItxid:2697049"},{"id":"A72","pred":"ncbi_taxonomy_id","subj":"T72","obj":"NCBItxid:2697049"},{"id":"A73","pred":"ncbi_taxonomy_id","subj":"T73","obj":"NCBItxid:2697049"},{"id":"A74","pred":"ncbi_taxonomy_id","subj":"T74","obj":"NCBItxid:2697049"},{"id":"A75","pred":"ncbi_taxonomy_id","subj":"T75","obj":"NCBItxid:2697049"},{"id":"A76","pred":"ncbi_taxonomy_id","subj":"T76","obj":"NCBItxid:2697049"},{"id":"A77","pred":"ncbi_taxonomy_id","subj":"T77","obj":"NCBItxid:2697049"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

LitCovid-sample-sentences

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T145","span":{"begin":142,"end":334},"obj":"Sentence"},{"id":"T146","span":{"begin":335,"end":442},"obj":"Sentence"},{"id":"T147","span":{"begin":443,"end":524},"obj":"Sentence"},{"id":"T148","span":{"begin":525,"end":728},"obj":"Sentence"},{"id":"T149","span":{"begin":729,"end":942},"obj":"Sentence"},{"id":"T150","span":{"begin":943,"end":1059},"obj":"Sentence"},{"id":"T151","span":{"begin":1060,"end":1185},"obj":"Sentence"},{"id":"T152","span":{"begin":1186,"end":1357},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

LitCovid-sample-PD-MONDO

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T50","span":{"begin":39,"end":49},"obj":"Disease"},{"id":"T51","span":{"begin":304,"end":314},"obj":"Disease"},{"id":"T52","span":{"begin":355,"end":365},"obj":"Disease"},{"id":"T53","span":{"begin":638,"end":648},"obj":"Disease"},{"id":"T54","span":{"begin":733,"end":743},"obj":"Disease"},{"id":"T55","span":{"begin":947,"end":957},"obj":"Disease"},{"id":"T56","span":{"begin":1190,"end":1200},"obj":"Disease"}],"attributes":[{"id":"A50","pred":"mondo_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A51","pred":"mondo_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A52","pred":"mondo_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A53","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A54","pred":"mondo_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A55","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A56","pred":"mondo_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

LitCovid-sample-PD-IDO

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T83","span":{"begin":722,"end":727},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"}],"text":"3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

LitCovid-sample-PD-FMA

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T89","span":{"begin":504,"end":514},"obj":"Body_part"},{"id":"T90","span":{"begin":1125,"end":1135},"obj":"Body_part"}],"attributes":[{"id":"A89","pred":"fma_id","subj":"T89","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A90","pred":"fma_id","subj":"T90","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

LitCovid-sample-PD-MAT

{"project":"LitCovid-sample-PD-MAT","denotations":[{"id":"T5","span":{"begin":665,"end":674},"obj":"http://purl.obolibrary.org/obo/MAT_0000491"}],"text":"3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

LitCovid-sample-PD-GO-BP-0

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T63","span":{"begin":708,"end":721},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T64","span":{"begin":1312,"end":1325},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

LitCovid-sample-GO-BP

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T59","span":{"begin":708,"end":721},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T60","span":{"begin":1312,"end":1325},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

LitCovid-sample-Glycan

PMC:7443692 / 25589-26946 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7443692 / 25589-26946 JSON TXT