PMC:7199903 / 6390-7139 JSON TXT

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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T42","span":{"begin":132,"end":144},"obj":"Body_part"},{"id":"T43","span":{"begin":196,"end":209},"obj":"Body_part"},{"id":"T44","span":{"begin":260,"end":273},"obj":"Body_part"}],"attributes":[{"id":"A42","pred":"fma_id","subj":"T42","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A43","pred":"fma_id","subj":"T43","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A44","pred":"fma_id","subj":"T44","obj":"http://purl.org/sig/ont/fma/fma82784"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T32","span":{"begin":48,"end":56},"obj":"Disease"}],"attributes":[{"id":"A32","pred":"mondo_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T47","span":{"begin":223,"end":224},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T48","span":{"begin":384,"end":386},"obj":"http://purl.obolibrary.org/obo/CLO_0050507"},{"id":"T49","span":{"begin":734,"end":736},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T50","span":{"begin":746,"end":748},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T51","span":{"begin":746,"end":748},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T69","span":{"begin":132,"end":144},"obj":"Chemical"},{"id":"T70","span":{"begin":196,"end":209},"obj":"Chemical"},{"id":"T71","span":{"begin":260,"end":273},"obj":"Chemical"},{"id":"T72","span":{"begin":746,"end":748},"obj":"Chemical"}],"attributes":[{"id":"A69","pred":"chebi_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/CHEBI_24396"},{"id":"A70","pred":"chebi_id","subj":"T70","obj":"http://purl.obolibrary.org/obo/CHEBI_24396"},{"id":"A71","pred":"chebi_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/CHEBI_24396"},{"id":"A72","pred":"chebi_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-sample-PD-IDO

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T32","span":{"begin":17,"end":21},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T33","span":{"begin":403,"end":408},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T34","span":{"begin":466,"end":470},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-sample-Enju

LitCovid-sample-PD-FMA

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T42","span":{"begin":132,"end":144},"obj":"Body_part"},{"id":"T43","span":{"begin":196,"end":209},"obj":"Body_part"},{"id":"T44","span":{"begin":260,"end":273},"obj":"Body_part"}],"attributes":[{"id":"A42","pred":"fma_id","subj":"T42","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A43","pred":"fma_id","subj":"T43","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A44","pred":"fma_id","subj":"T44","obj":"http://purl.org/sig/ont/fma/fma82784"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-sample-CHEBI

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T51","span":{"begin":132,"end":144},"obj":"Chemical"},{"id":"T52","span":{"begin":196,"end":209},"obj":"Chemical"},{"id":"T53","span":{"begin":260,"end":273},"obj":"Chemical"}],"attributes":[{"id":"A51","pred":"chebi_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/CHEBI_24396"},{"id":"A52","pred":"chebi_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/CHEBI_24396"},{"id":"A53","pred":"chebi_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/CHEBI_24396"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-sample-PD-NCBITaxon

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T29","span":{"begin":48,"end":58},"obj":"Species"}],"attributes":[{"id":"A29","pred":"ncbi_taxonomy_id","subj":"T29","obj":"NCBItxid:2697049"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-sample-sentences

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T45","span":{"begin":0,"end":153},"obj":"Sentence"},{"id":"T46","span":{"begin":154,"end":255},"obj":"Sentence"},{"id":"T47","span":{"begin":256,"end":418},"obj":"Sentence"},{"id":"T48","span":{"begin":419,"end":631},"obj":"Sentence"},{"id":"T49","span":{"begin":632,"end":749},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-sample-PD-MONDO

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T28","span":{"begin":48,"end":58},"obj":"Disease"}],"attributes":[{"id":"A28","pred":"mondo_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-sample-Pubtator

{"project":"LitCovid-sample-Pubtator","denotations":[{"id":"201","span":{"begin":97,"end":113},"obj":"Gene"},{"id":"202","span":{"begin":59,"end":60},"obj":"Gene"},{"id":"203","span":{"begin":48,"end":58},"obj":"Species"},{"id":"204","span":{"begin":196,"end":209},"obj":"Chemical"},{"id":"205","span":{"begin":232,"end":247},"obj":"Chemical"},{"id":"206","span":{"begin":260,"end":273},"obj":"Chemical"},{"id":"207","span":{"begin":340,"end":346},"obj":"Chemical"},{"id":"208","span":{"begin":387,"end":402},"obj":"Chemical"},{"id":"209","span":{"begin":495,"end":501},"obj":"Chemical"},{"id":"210","span":{"begin":518,"end":530},"obj":"Chemical"},{"id":"211","span":{"begin":691,"end":697},"obj":"Chemical"}],"attributes":[{"id":"A206","pred":"pubann:denotes","subj":"206","obj":"MESH:D006020"},{"id":"A204","pred":"pubann:denotes","subj":"204","obj":"MESH:D006020"},{"id":"A207","pred":"pubann:denotes","subj":"207","obj":"MESH:D011134"},{"id":"A203","pred":"pubann:denotes","subj":"203","obj":"Tax:2697049"},{"id":"A209","pred":"pubann:denotes","subj":"209","obj":"MESH:D011134"},{"id":"A202","pred":"pubann:denotes","subj":"202","obj":"Gene:43740568"},{"id":"A211","pred":"pubann:denotes","subj":"211","obj":"MESH:D011134"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-sample-UniProt

LitCovid-sample-PD-GO-BP-0

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T25","span":{"begin":31,"end":44},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T26","span":{"begin":581,"end":594},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T27","span":{"begin":618,"end":630},"obj":"http://purl.obolibrary.org/obo/GO_0036065"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-sample-GO-BP

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T23","span":{"begin":31,"end":44},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T24","span":{"begin":581,"end":594},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T25","span":{"begin":618,"end":630},"obj":"http://purl.obolibrary.org/obo/GO_0036065"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T26","span":{"begin":31,"end":44},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T27","span":{"begin":581,"end":594},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T28","span":{"begin":618,"end":630},"obj":"http://purl.obolibrary.org/obo/GO_0036065"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T45","span":{"begin":0,"end":153},"obj":"Sentence"},{"id":"T46","span":{"begin":154,"end":255},"obj":"Sentence"},{"id":"T47","span":{"begin":256,"end":418},"obj":"Sentence"},{"id":"T48","span":{"begin":419,"end":631},"obj":"Sentence"},{"id":"T49","span":{"begin":632,"end":749},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"201","span":{"begin":97,"end":113},"obj":"Gene"},{"id":"202","span":{"begin":59,"end":60},"obj":"Gene"},{"id":"203","span":{"begin":48,"end":58},"obj":"Species"},{"id":"204","span":{"begin":196,"end":209},"obj":"Chemical"},{"id":"205","span":{"begin":232,"end":247},"obj":"Chemical"},{"id":"206","span":{"begin":260,"end":273},"obj":"Chemical"},{"id":"207","span":{"begin":340,"end":346},"obj":"Chemical"},{"id":"208","span":{"begin":387,"end":402},"obj":"Chemical"},{"id":"209","span":{"begin":495,"end":501},"obj":"Chemical"},{"id":"210","span":{"begin":518,"end":530},"obj":"Chemical"},{"id":"211","span":{"begin":691,"end":697},"obj":"Chemical"}],"attributes":[{"id":"A202","pred":"tao:has_database_id","subj":"202","obj":"Gene:43740568"},{"id":"A203","pred":"tao:has_database_id","subj":"203","obj":"Tax:2697049"},{"id":"A204","pred":"tao:has_database_id","subj":"204","obj":"MESH:D006020"},{"id":"A206","pred":"tao:has_database_id","subj":"206","obj":"MESH:D006020"},{"id":"A207","pred":"tao:has_database_id","subj":"207","obj":"MESH:D011134"},{"id":"A209","pred":"tao:has_database_id","subj":"209","obj":"MESH:D011134"},{"id":"A211","pred":"tao:has_database_id","subj":"211","obj":"MESH:D011134"}],"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":"To determine the site-specific glycosylation of SARS-CoV-2 S, we used trypsin, chymotrypsin, and α-lytic protease to generate three glycopeptide samples. These proteases were selected to generate glycopeptides that contain a single N-linked glycan sequon. The glycopeptides were analyzed by liquid chromatography–mass spectrometry, and the glycan compositions were determined for all 22 N-linked glycan sites (Fig. 2). To convey the main processing features at each site, the abundances of each glycan are summed into oligomannose-type, hybrid-type, and categories of complex-type glycosylation based on branching and fucosylation. The detailed, expanded graphs showing the diverse range of glycan compositions are presented in table S1 and fig. S2."}

PMC:7199903 / 6390-7139 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7199903 / 6390-7139 JSON TXT