PMC:7253482 / 15384-16383 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"556","span":{"begin":541,"end":544},"obj":"Species"},{"id":"557","span":{"begin":736,"end":745},"obj":"Species"},{"id":"558","span":{"begin":94,"end":96},"obj":"Chemical"},{"id":"559","span":{"begin":97,"end":99},"obj":"Chemical"},{"id":"560","span":{"begin":170,"end":172},"obj":"Chemical"},{"id":"561","span":{"begin":173,"end":175},"obj":"Chemical"},{"id":"562","span":{"begin":227,"end":229},"obj":"Chemical"},{"id":"563","span":{"begin":230,"end":232},"obj":"Chemical"},{"id":"564","span":{"begin":343,"end":345},"obj":"Chemical"},{"id":"565","span":{"begin":346,"end":348},"obj":"Chemical"},{"id":"566","span":{"begin":710,"end":716},"obj":"Chemical"},{"id":"567","span":{"begin":885,"end":892},"obj":"Chemical"},{"id":"568","span":{"begin":213,"end":217},"obj":"Disease"},{"id":"569","span":{"begin":321,"end":325},"obj":"Disease"},{"id":"570","span":{"begin":727,"end":731},"obj":"Disease"},{"id":"571","span":{"begin":841,"end":845},"obj":"Disease"}],"attributes":[{"id":"A556","pred":"tao:has_database_id","subj":"556","obj":"Tax:11118"},{"id":"A557","pred":"tao:has_database_id","subj":"557","obj":"Tax:1335626"},{"id":"A558","pred":"tao:has_database_id","subj":"558","obj":"MESH:C022306"},{"id":"A559","pred":"tao:has_database_id","subj":"559","obj":"MESH:D003903"},{"id":"A560","pred":"tao:has_database_id","subj":"560","obj":"MESH:C022306"},{"id":"A561","pred":"tao:has_database_id","subj":"561","obj":"MESH:D003903"},{"id":"A562","pred":"tao:has_database_id","subj":"562","obj":"MESH:C022306"},{"id":"A563","pred":"tao:has_database_id","subj":"563","obj":"MESH:D003903"},{"id":"A564","pred":"tao:has_database_id","subj":"564","obj":"MESH:C022306"},{"id":"A565","pred":"tao:has_database_id","subj":"565","obj":"MESH:D003903"},{"id":"A566","pred":"tao:has_database_id","subj":"566","obj":"MESH:D011134"},{"id":"A567","pred":"tao:has_database_id","subj":"567","obj":"MESH:D011134"},{"id":"A568","pred":"tao:has_database_id","subj":"568","obj":"MESH:D045169"},{"id":"A569","pred":"tao:has_database_id","subj":"569","obj":"MESH:D018352"},{"id":"A570","pred":"tao:has_database_id","subj":"570","obj":"MESH:D045169"},{"id":"A571","pred":"tao:has_database_id","subj":"571","obj":"MESH:D018352"}],"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":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T93","span":{"begin":63,"end":73},"obj":"Body_part"},{"id":"T94","span":{"begin":443,"end":453},"obj":"Body_part"},{"id":"T95","span":{"begin":547,"end":555},"obj":"Body_part"},{"id":"T96","span":{"begin":613,"end":620},"obj":"Body_part"},{"id":"T97","span":{"begin":785,"end":795},"obj":"Body_part"},{"id":"T98","span":{"begin":848,"end":856},"obj":"Body_part"}],"attributes":[{"id":"A93","pred":"fma_id","subj":"T93","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A94","pred":"fma_id","subj":"T94","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A95","pred":"fma_id","subj":"T95","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A96","pred":"fma_id","subj":"T96","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A97","pred":"fma_id","subj":"T97","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A98","pred":"fma_id","subj":"T98","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T55","span":{"begin":213,"end":217},"obj":"Disease"},{"id":"T56","span":{"begin":727,"end":731},"obj":"Disease"}],"attributes":[{"id":"A55","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A56","pred":"mondo_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T93","span":{"begin":330,"end":331},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T94","span":{"begin":399,"end":400},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T95","span":{"begin":562,"end":564},"obj":"http://purl.obolibrary.org/obo/CLO_0001387"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T176","span":{"begin":63,"end":73},"obj":"Chemical"},{"id":"T177","span":{"begin":94,"end":96},"obj":"Chemical"},{"id":"T178","span":{"begin":170,"end":172},"obj":"Chemical"},{"id":"T179","span":{"begin":227,"end":229},"obj":"Chemical"},{"id":"T180","span":{"begin":343,"end":345},"obj":"Chemical"},{"id":"T181","span":{"begin":443,"end":448},"obj":"Chemical"},{"id":"T182","span":{"begin":449,"end":453},"obj":"Chemical"},{"id":"T183","span":{"begin":547,"end":555},"obj":"Chemical"},{"id":"T184","span":{"begin":613,"end":620},"obj":"Chemical"},{"id":"T185","span":{"begin":785,"end":790},"obj":"Chemical"},{"id":"T186","span":{"begin":791,"end":795},"obj":"Chemical"},{"id":"T187","span":{"begin":848,"end":856},"obj":"Chemical"},{"id":"T188","span":{"begin":885,"end":892},"obj":"Chemical"}],"attributes":[{"id":"A176","pred":"chebi_id","subj":"T176","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A177","pred":"chebi_id","subj":"T177","obj":"http://purl.obolibrary.org/obo/CHEBI_33793"},{"id":"A178","pred":"chebi_id","subj":"T178","obj":"http://purl.obolibrary.org/obo/CHEBI_33793"},{"id":"A179","pred":"chebi_id","subj":"T179","obj":"http://purl.obolibrary.org/obo/CHEBI_33793"},{"id":"A180","pred":"chebi_id","subj":"T180","obj":"http://purl.obolibrary.org/obo/CHEBI_33793"},{"id":"A181","pred":"chebi_id","subj":"T181","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A182","pred":"chebi_id","subj":"T182","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A183","pred":"chebi_id","subj":"T183","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A184","pred":"chebi_id","subj":"T184","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A185","pred":"chebi_id","subj":"T185","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A186","pred":"chebi_id","subj":"T186","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A187","pred":"chebi_id","subj":"T187","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A188","pred":"chebi_id","subj":"T188","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T42","span":{"begin":38,"end":48},"obj":"http://www.geneontology.org/formats/oboInOwl#Synonym"},{"id":"T43","span":{"begin":52,"end":62},"obj":"http://www.geneontology.org/formats/oboInOwl#Synonym"},{"id":"T44","span":{"begin":438,"end":442},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T45","span":{"begin":968,"end":981},"obj":"http://purl.obolibrary.org/obo/BFO_0000034"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-sample-Enju","denotations":[{"id":"T69499","span":{"begin":0,"end":8},"obj":"NN"},{"id":"T65163","span":{"begin":9,"end":11},"obj":"IN"},{"id":"T23395","span":{"begin":12,"end":15},"obj":"DT"},{"id":"T78947","span":{"begin":16,"end":24},"obj":"JJ"},{"id":"T61369","span":{"begin":25,"end":30},"obj":"NN"},{"id":"T85886","span":{"begin":31,"end":33},"obj":"IN"},{"id":"T53309","span":{"begin":34,"end":48},"obj":"JJ"},{"id":"T78726","span":{"begin":49,"end":51},"obj":"TO"},{"id":"T13118","span":{"begin":52,"end":62},"obj":"JJ"},{"id":"T63573","span":{"begin":63,"end":73},"obj":"NN"},{"id":"T72369","span":{"begin":74,"end":87},"obj":"NNS"},{"id":"T18378","span":{"begin":88,"end":89},"obj":"-LRB-"},{"id":"T58404","span":{"begin":89,"end":93},"obj":"FW"},{"id":"T58779","span":{"begin":94,"end":99},"obj":"NN"},{"id":"T10324","span":{"begin":100,"end":106},"obj":"NNS"},{"id":"T30580","span":{"begin":106,"end":107},"obj":"-RRB-"},{"id":"T83087","span":{"begin":108,"end":116},"obj":"VBD"},{"id":"T2494","span":{"begin":117,"end":121},"obj":"IN"},{"id":"T4328","span":{"begin":122,"end":129},"obj":"VBN"},{"id":"T12652","span":{"begin":130,"end":138},"obj":"NNS"},{"id":"T92287","span":{"begin":139,"end":148},"obj":"VBD"},{"id":"T88501","span":{"begin":149,"end":162},"obj":"RB"},{"id":"T11718","span":{"begin":163,"end":169},"obj":"JJR"},{"id":"T86795","span":{"begin":170,"end":175},"obj":"NN"},{"id":"T59603","span":{"begin":176,"end":182},"obj":"NNS"},{"id":"T7211","span":{"begin":183,"end":184},"obj":"-LRB-"},{"id":"T4769","span":{"begin":184,"end":191},"obj":"NN"},{"id":"T47239","span":{"begin":191,"end":192},"obj":"-RRB-"},{"id":"T90969","span":{"begin":194,"end":200},"obj":"VBN"},{"id":"T92849","span":{"begin":201,"end":209},"obj":"NNS"},{"id":"T78244","span":{"begin":210,"end":212},"obj":"IN"},{"id":"T54331","span":{"begin":213,"end":217},"obj":"NNS"},{"id":"T42940","span":{"begin":218,"end":221},"obj":"VBD"},{"id":"T56294","span":{"begin":222,"end":226},"obj":"JJ"},{"id":"T46802","span":{"begin":227,"end":232},"obj":"NN"},{"id":"T64331","span":{"begin":233,"end":239},"obj":"NNS"},{"id":"T35591","span":{"begin":240,"end":242},"obj":"IN"},{"id":"T4586","span":{"begin":243,"end":247},"obj":"CD"},{"id":"T68155","span":{"begin":248,"end":256},"obj":"VBN"},{"id":"T78948","span":{"begin":257,"end":261},"obj":"IN"},{"id":"T78585","span":{"begin":262,"end":266},"obj":"CD"},{"id":"T27968","span":{"begin":267,"end":270},"obj":"IN"},{"id":"T96310","span":{"begin":271,"end":278},"obj":"VBN"},{"id":"T43288","span":{"begin":279,"end":286},"obj":"NNS"},{"id":"T92960","span":{"begin":288,"end":296},"obj":"RB"},{"id":"T14475","span":{"begin":296,"end":297},"obj":"-COMMA-"},{"id":"T32298","span":{"begin":298,"end":301},"obj":"DT"},{"id":"T12634","span":{"begin":302,"end":308},"obj":"VBN"},{"id":"T80500","span":{"begin":309,"end":317},"obj":"NNS"},{"id":"T77635","span":{"begin":318,"end":320},"obj":"IN"},{"id":"T24392","span":{"begin":321,"end":325},"obj":"NNS"},{"id":"T2961","span":{"begin":326,"end":329},"obj":"VBD"},{"id":"T6521","span":{"begin":330,"end":331},"obj":"DT"},{"id":"T8471","span":{"begin":332,"end":342},"obj":"VBN"},{"id":"T37460","span":{"begin":343,"end":348},"obj":"NN"},{"id":"T55408","span":{"begin":349,"end":354},"obj":"NN"},{"id":"T45120","span":{"begin":355,"end":357},"obj":"IN"},{"id":"T23381","span":{"begin":358,"end":362},"obj":"CD"},{"id":"T30445","span":{"begin":363,"end":371},"obj":"VBN"},{"id":"T55016","span":{"begin":372,"end":376},"obj":"IN"},{"id":"T1385","span":{"begin":377,"end":384},"obj":"VBN"},{"id":"T65828","span":{"begin":385,"end":393},"obj":"NNS"},{"id":"T35353","span":{"begin":394,"end":398},"obj":"IN"},{"id":"T91154","span":{"begin":399,"end":400},"obj":"DT"},{"id":"T26380","span":{"begin":401,"end":406},"obj":"NN"},{"id":"T92544","span":{"begin":407,"end":409},"obj":"IN"},{"id":"T79406","span":{"begin":410,"end":414},"obj":"CD"},{"id":"T92418","span":{"begin":416,"end":427},"obj":"RB"},{"id":"T91452","span":{"begin":427,"end":428},"obj":"-COMMA-"},{"id":"T84302","span":{"begin":429,"end":433},"obj":"WRB"},{"id":"T74584","span":{"begin":434,"end":442},"obj":"JJ"},{"id":"T76352","span":{"begin":443,"end":453},"obj":"JJ"},{"id":"T98451","span":{"begin":454,"end":465},"obj":"NNS"},{"id":"T72837","span":{"begin":466,"end":470},"obj":"VBD"},{"id":"T54724","span":{"begin":471,"end":477},"obj":"VBN"},{"id":"T45778","span":{"begin":478,"end":482},"obj":"IN"},{"id":"T98923","span":{"begin":483,"end":486},"obj":"DT"},{"id":"T59533","span":{"begin":487,"end":492},"obj":"RB"},{"id":"T25862","span":{"begin":493,"end":505},"obj":"VBN"},{"id":"T32515","span":{"begin":506,"end":516},"obj":"JJ"},{"id":"T94405","span":{"begin":517,"end":522},"obj":"NN"},{"id":"T76643","span":{"begin":523,"end":525},"obj":"IN"},{"id":"T13755","span":{"begin":526,"end":529},"obj":"DT"},{"id":"T14482","span":{"begin":530,"end":540},"obj":"JJ"},{"id":"T65032","span":{"begin":541,"end":544},"obj":"NN"},{"id":"T12704","span":{"begin":545,"end":546},"obj":"NN"},{"id":"T70323","span":{"begin":547,"end":555},"obj":"NNS"},{"id":"T33888","span":{"begin":556,"end":557},"obj":"-LRB-"},{"id":"T60190","span":{"begin":557,"end":564},"obj":"NN"},{"id":"T27628","span":{"begin":564,"end":565},"obj":"-RRB-"},{"id":"T87038","span":{"begin":565,"end":566},"obj":"-COMMA-"},{"id":"T49843","span":{"begin":567,"end":575},"obj":"NNS"},{"id":"T77547","span":{"begin":576,"end":578},"obj":"IN"},{"id":"T63244","span":{"begin":579,"end":588},"obj":"NNS"},{"id":"T5765","span":{"begin":589,"end":593},"obj":"VBD"},{"id":"T8574","span":{"begin":594,"end":605},"obj":"VBN"},{"id":"T21020","span":{"begin":606,"end":608},"obj":"IN"},{"id":"T89986","span":{"begin":609,"end":612},"obj":"DT"},{"id":"T65568","span":{"begin":613,"end":620},"obj":"NN"},{"id":"T63130","span":{"begin":621,"end":628},"obj":"NN"},{"id":"T96535","span":{"begin":629,"end":639},"obj":"IN"},{"id":"T21467","span":{"begin":640,"end":643},"obj":"DT"},{"id":"T66745","span":{"begin":644,"end":650},"obj":"NN"},{"id":"T45284","span":{"begin":651,"end":660},"obj":"VBG"},{"id":"T17381","span":{"begin":661,"end":670},"obj":"JJ"},{"id":"T55156","span":{"begin":671,"end":686},"obj":"NNS"},{"id":"T13067","span":{"begin":687,"end":697},"obj":"VBG"},{"id":"T40910","span":{"begin":698,"end":705},"obj":"IN"},{"id":"T14483","span":{"begin":706,"end":709},"obj":"DT"},{"id":"T31354","span":{"begin":846,"end":847},"obj":"NN"},{"id":"T92070","span":{"begin":848,"end":856},"obj":"NNS"},{"id":"T5507","span":{"begin":857,"end":861},"obj":"WDT"},{"id":"T19099","span":{"begin":862,"end":870},"obj":"VBP"},{"id":"T77842","span":{"begin":871,"end":875},"obj":"RB"},{"id":"T99218","span":{"begin":876,"end":880},"obj":"IN"},{"id":"T68020","span":{"begin":881,"end":884},"obj":"DT"},{"id":"T87267","span":{"begin":885,"end":892},"obj":"NNS"},{"id":"T55216","span":{"begin":894,"end":896},"obj":"PRP"},{"id":"T15548","span":{"begin":897,"end":902},"obj":"MD"},{"id":"T19328","span":{"begin":903,"end":910},"obj":"VB"},{"id":"T29556","span":{"begin":710,"end":716},"obj":"NN"},{"id":"T94871","span":{"begin":717,"end":723},"obj":"NN"},{"id":"T71413","span":{"begin":724,"end":726},"obj":"IN"},{"id":"T81413","span":{"begin":727,"end":731},"obj":"NNS"},{"id":"T68523","span":{"begin":732,"end":735},"obj":"CC"},{"id":"T70297","span":{"begin":736,"end":740},"obj":"NNP"},{"id":"T12679","span":{"begin":741,"end":745},"obj":"NNP"},{"id":"T87216","span":{"begin":747,"end":749},"obj":"PRP"},{"id":"T15902","span":{"begin":750,"end":752},"obj":"VBZ"},{"id":"T6523","span":{"begin":753,"end":764},"obj":"JJ"},{"id":"T19232","span":{"begin":765,"end":767},"obj":"TO"},{"id":"T97839","span":{"begin":768,"end":772},"obj":"VB"},{"id":"T99309","span":{"begin":773,"end":776},"obj":"DT"},{"id":"T40498","span":{"begin":777,"end":781},"obj":"NN"},{"id":"T81866","span":{"begin":782,"end":784},"obj":"IN"},{"id":"T9331","span":{"begin":785,"end":795},"obj":"JJ"},{"id":"T44303","span":{"begin":796,"end":805},"obj":"NN"},{"id":"T83531","span":{"begin":806,"end":808},"obj":"IN"},{"id":"T76133","span":{"begin":809,"end":812},"obj":"DT"},{"id":"T29918","span":{"begin":813,"end":829},"obj":"JJ"},{"id":"T15412","span":{"begin":830,"end":837},"obj":"NNS"},{"id":"T38048","span":{"begin":838,"end":840},"obj":"IN"},{"id":"T48648","span":{"begin":841,"end":845},"obj":"NNS"},{"id":"T73414","span":{"begin":911,"end":915},"obj":"IN"},{"id":"T39503","span":{"begin":916,"end":920},"obj":"DT"},{"id":"T1176","span":{"begin":921,"end":924},"obj":"MD"},{"id":"T73192","span":{"begin":925,"end":931},"obj":"VB"},{"id":"T18164","span":{"begin":932,"end":936},"obj":"IN"},{"id":"T59646","span":{"begin":937,"end":940},"obj":"DT"},{"id":"T56626","span":{"begin":941,"end":950},"obj":"JJ"},{"id":"T77011","span":{"begin":951,"end":967},"obj":"JJ"},{"id":"T13068","span":{"begin":968,"end":981},"obj":"NN"},{"id":"T25400","span":{"begin":982,"end":984},"obj":"IN"},{"id":"T95940","span":{"begin":985,"end":990},"obj":"DT"},{"id":"T4558","span":{"begin":991,"end":998},"obj":"NNS"}],"relations":[{"id":"R34568","pred":"arg1Of","subj":"T69499","obj":"T65163"},{"id":"R57790","pred":"arg2Of","subj":"T61369","obj":"T65163"},{"id":"R44708","pred":"arg1Of","subj":"T61369","obj":"T23395"},{"id":"R35799","pred":"arg1Of","subj":"T61369","obj":"T78947"},{"id":"R71053","pred":"arg1Of","subj":"T61369","obj":"T85886"},{"id":"R48201","pred":"arg2Of","subj":"T72369","obj":"T85886"},{"id":"R88738","pred":"arg1Of","subj":"T13118","obj":"T53309"},{"id":"R93094","pred":"arg1Of","subj":"T13118","obj":"T78726"},{"id":"R15619","pred":"arg1Of","subj":"T72369","obj":"T13118"},{"id":"R7301","pred":"arg1Of","subj":"T72369","obj":"T63573"},{"id":"R64002","pred":"arg1Of","subj":"T72369","obj":"T18378"},{"id":"R11093","pred":"arg2Of","subj":"T10324","obj":"T18378"},{"id":"R88392","pred":"arg3Of","subj":"T30580","obj":"T18378"},{"id":"R93551","pred":"arg1Of","subj":"T10324","obj":"T58404"},{"id":"R6860","pred":"arg1Of","subj":"T10324","obj":"T58779"},{"id":"R16925","pred":"arg1Of","subj":"T69499","obj":"T83087"},{"id":"R88573","pred":"arg2Of","subj":"T92287","obj":"T83087"},{"id":"R18139","pred":"arg1Of","subj":"T92287","obj":"T2494"},{"id":"R58586","pred":"arg2Of","subj":"T12652","obj":"T4328"},{"id":"R49381","pred":"arg1Of","subj":"T12652","obj":"T92287"},{"id":"R70296","pred":"arg2Of","subj":"T59603","obj":"T92287"},{"id":"R97765","pred":"arg1Of","subj":"T11718","obj":"T88501"},{"id":"R56320","pred":"arg1Of","subj":"T59603","obj":"T11718"},{"id":"R34279","pred":"arg1Of","subj":"T59603","obj":"T86795"},{"id":"R13531","pred":"arg1Of","subj":"T59603","obj":"T7211"},{"id":"R2422","pred":"arg2Of","subj":"T4769","obj":"T7211"},{"id":"R45689","pred":"arg3Of","subj":"T47239","obj":"T7211"},{"id":"R37083","pred":"arg2Of","subj":"T92849","obj":"T90969"},{"id":"R38632","pred":"arg1Of","subj":"T92849","obj":"T78244"},{"id":"R45550","pred":"arg2Of","subj":"T54331","obj":"T78244"},{"id":"R78533","pred":"arg1Of","subj":"T92849","obj":"T42940"},{"id":"R64905","pred":"arg2Of","subj":"T64331","obj":"T42940"},{"id":"R7575","pred":"arg1Of","subj":"T64331","obj":"T56294"},{"id":"R3248","pred":"arg1Of","subj":"T64331","obj":"T46802"},{"id":"R16314","pred":"arg1Of","subj":"T64331","obj":"T35591"},{"id":"R34905","pred":"arg2Of","subj":"T4586","obj":"T35591"},{"id":"R48342","pred":"arg1Of","subj":"T64331","obj":"T68155"},{"id":"R50174","pred":"arg2Of","subj":"T78948","obj":"T68155"},{"id":"R94531","pred":"arg2Of","subj":"T78585","obj":"T78948"},{"id":"R68081","pred":"arg1Of","subj":"T78585","obj":"T27968"},{"id":"R39372","pred":"arg2Of","subj":"T43288","obj":"T27968"},{"id":"R11468","pred":"arg2Of","subj":"T43288","obj":"T96310"},{"id":"R24616","pred":"arg1Of","subj":"T2961","obj":"T92960"},{"id":"R68851","pred":"arg1Of","subj":"T2961","obj":"T14475"},{"id":"R23393","pred":"arg1Of","subj":"T80500","obj":"T32298"},{"id":"R73701","pred":"arg2Of","subj":"T80500","obj":"T12634"},{"id":"R77783","pred":"arg1Of","subj":"T80500","obj":"T77635"},{"id":"R5916","pred":"arg2Of","subj":"T24392","obj":"T77635"},{"id":"R36158","pred":"arg1Of","subj":"T80500","obj":"T2961"},{"id":"R40924","pred":"arg2Of","subj":"T55408","obj":"T2961"},{"id":"R22467","pred":"arg1Of","subj":"T55408","obj":"T6521"},{"id":"R31129","pred":"arg2Of","subj":"T55408","obj":"T8471"},{"id":"R44924","pred":"arg1Of","subj":"T55408","obj":"T37460"},{"id":"R96796","pred":"arg1Of","subj":"T55408","obj":"T45120"},{"id":"R69300","pred":"arg2Of","subj":"T23381","obj":"T45120"},{"id":"R90166","pred":"arg1Of","subj":"T2961","obj":"T30445"},{"id":"R30304","pred":"arg2Of","subj":"T55016","obj":"T30445"},{"id":"R12429","pred":"arg2Of","subj":"T65828","obj":"T55016"},{"id":"R1617","pred":"arg2Of","subj":"T65828","obj":"T1385"},{"id":"R52562","pred":"arg1Of","subj":"T65828","obj":"T35353"},{"id":"R41359","pred":"arg2Of","subj":"T26380","obj":"T35353"},{"id":"R58840","pred":"arg1Of","subj":"T26380","obj":"T91154"},{"id":"R3337","pred":"arg1Of","subj":"T26380","obj":"T92544"},{"id":"R58419","pred":"arg2Of","subj":"T79406","obj":"T92544"},{"id":"R63445","pred":"arg1Of","subj":"T8574","obj":"T92418"},{"id":"R94598","pred":"arg1Of","subj":"T8574","obj":"T91452"},{"id":"R44950","pred":"arg1Of","subj":"T8574","obj":"T84302"},{"id":"R49097","pred":"arg2Of","subj":"T54724","obj":"T84302"},{"id":"R15450","pred":"arg1Of","subj":"T98451","obj":"T74584"},{"id":"R66839","pred":"arg1Of","subj":"T98451","obj":"T76352"},{"id":"R15217","pred":"arg1Of","subj":"T98451","obj":"T72837"},{"id":"R77763","pred":"arg2Of","subj":"T54724","obj":"T72837"},{"id":"R37654","pred":"arg2Of","subj":"T98451","obj":"T54724"},{"id":"R36115","pred":"arg1Of","subj":"T54724","obj":"T45778"},{"id":"R3433","pred":"arg2Of","subj":"T94405","obj":"T45778"},{"id":"R53298","pred":"arg1Of","subj":"T94405","obj":"T98923"},{"id":"R43272","pred":"arg1Of","subj":"T25862","obj":"T59533"},{"id":"R50247","pred":"arg1Of","subj":"T94405","obj":"T25862"},{"id":"R26701","pred":"arg1Of","subj":"T94405","obj":"T32515"},{"id":"R74679","pred":"arg1Of","subj":"T94405","obj":"T76643"},{"id":"R51542","pred":"arg2Of","subj":"T70323","obj":"T76643"},{"id":"R2173","pred":"arg1Of","subj":"T70323","obj":"T13755"},{"id":"R85398","pred":"arg1Of","subj":"T70323","obj":"T14482"},{"id":"R51942","pred":"arg1Of","subj":"T70323","obj":"T65032"},{"id":"R5341","pred":"arg1Of","subj":"T70323","obj":"T12704"},{"id":"R68632","pred":"arg1Of","subj":"T70323","obj":"T33888"},{"id":"R28101","pred":"arg2Of","subj":"T60190","obj":"T33888"},{"id":"R79333","pred":"arg3Of","subj":"T27628","obj":"T33888"},{"id":"R50373","pred":"arg1Of","subj":"T8574","obj":"T87038"},{"id":"R78452","pred":"arg1Of","subj":"T49843","obj":"T77547"},{"id":"R70051","pred":"arg2Of","subj":"T63244","obj":"T77547"},{"id":"R86243","pred":"arg1Of","subj":"T49843","obj":"T5765"},{"id":"R62080","pred":"arg2Of","subj":"T8574","obj":"T5765"},{"id":"R36037","pred":"arg2Of","subj":"T49843","obj":"T8574"},{"id":"R69989","pred":"arg1Of","subj":"T8574","obj":"T21020"},{"id":"R21042","pred":"arg2Of","subj":"T63130","obj":"T21020"},{"id":"R99168","pred":"arg1Of","subj":"T63130","obj":"T89986"},{"id":"R84573","pred":"arg1Of","subj":"T63130","obj":"T65568"},{"id":"R18040","pred":"arg1Of","subj":"T8574","obj":"T96535"},{"id":"R83519","pred":"arg2Of","subj":"T66745","obj":"T96535"},{"id":"R40238","pred":"arg1Of","subj":"T66745","obj":"T21467"},{"id":"R11527","pred":"arg1Of","subj":"T66745","obj":"T45284"},{"id":"R26362","pred":"arg2Of","subj":"T55156","obj":"T45284"},{"id":"R13176","pred":"arg1Of","subj":"T55156","obj":"T17381"},{"id":"R81127","pred":"arg1Of","subj":"T55156","obj":"T13067"},{"id":"R91880","pred":"arg1Of","subj":"T13067","obj":"T40910"},{"id":"R25217","pred":"arg2Of","subj":"T94871","obj":"T40910"},{"id":"R32001","pred":"arg1Of","subj":"T94871","obj":"T14483"},{"id":"R4994","pred":"arg1Of","subj":"T94871","obj":"T29556"},{"id":"R90788","pred":"arg1Of","subj":"T94871","obj":"T71413"},{"id":"R72986","pred":"arg2Of","subj":"T68523","obj":"T71413"},{"id":"R8907","pred":"arg1Of","subj":"T81413","obj":"T68523"},{"id":"R79279","pred":"arg2Of","subj":"T12679","obj":"T68523"},{"id":"R85917","pred":"arg1Of","subj":"T12679","obj":"T70297"},{"id":"R32448","pred":"arg1Of","subj":"T97839","obj":"T87216"},{"id":"R64157","pred":"arg1Of","subj":"T97839","obj":"T15902"},{"id":"R45114","pred":"arg2Of","subj":"T6523","obj":"T15902"},{"id":"R15047","pred":"arg1Of","subj":"T97839","obj":"T6523"},{"id":"R54914","pred":"arg1Of","subj":"T97839","obj":"T19232"},{"id":"R93413","pred":"arg2Of","subj":"T40498","obj":"T97839"},{"id":"R52293","pred":"arg1Of","subj":"T40498","obj":"T99309"},{"id":"R68351","pred":"arg1Of","subj":"T40498","obj":"T81866"},{"id":"R25896","pred":"arg2Of","subj":"T44303","obj":"T81866"},{"id":"R99374","pred":"arg1Of","subj":"T44303","obj":"T9331"},{"id":"R59233","pred":"arg1Of","subj":"T40498","obj":"T83531"},{"id":"R54761","pred":"arg2Of","subj":"T15412","obj":"T83531"},{"id":"R30100","pred":"arg1Of","subj":"T15412","obj":"T76133"},{"id":"R78903","pred":"arg1Of","subj":"T15412","obj":"T29918"},{"id":"R28428","pred":"arg1Of","subj":"T15412","obj":"T38048"},{"id":"R47308","pred":"arg2Of","subj":"T92070","obj":"T38048"},{"id":"R6622","pred":"arg1Of","subj":"T92070","obj":"T48648"},{"id":"R35155","pred":"arg1Of","subj":"T92070","obj":"T31354"},{"id":"R48312","pred":"arg1Of","subj":"T15412","obj":"T5507"},{"id":"R78066","pred":"arg1Of","subj":"T15412","obj":"T19099"},{"id":"R50475","pred":"arg1Of","subj":"T19099","obj":"T77842"},{"id":"R20046","pred":"arg1Of","subj":"T77842","obj":"T99218"},{"id":"R97244","pred":"arg2Of","subj":"T87267","obj":"T99218"},{"id":"R41837","pred":"arg1Of","subj":"T87267","obj":"T68020"},{"id":"R75268","pred":"arg1Of","subj":"T55216","obj":"T15548"},{"id":"R87991","pred":"arg2Of","subj":"T19328","obj":"T15548"},{"id":"R19742","pred":"arg1Of","subj":"T55216","obj":"T19328"},{"id":"R78169","pred":"arg2Of","subj":"T73192","obj":"T19328"},{"id":"R66651","pred":"arg1Of","subj":"T73192","obj":"T73414"},{"id":"R91245","pred":"arg1Of","subj":"T39503","obj":"T1176"},{"id":"R29477","pred":"arg2Of","subj":"T73192","obj":"T1176"},{"id":"R12670","pred":"arg1Of","subj":"T39503","obj":"T73192"},{"id":"R29370","pred":"arg1Of","subj":"T73192","obj":"T18164"},{"id":"R47689","pred":"arg2Of","subj":"T13068","obj":"T18164"},{"id":"R40679","pred":"arg1Of","subj":"T13068","obj":"T59646"},{"id":"R43019","pred":"arg1Of","subj":"T13068","obj":"T56626"},{"id":"R94313","pred":"arg1Of","subj":"T13068","obj":"T77011"},{"id":"R21921","pred":"arg1Of","subj":"T13068","obj":"T25400"},{"id":"R46751","pred":"arg2Of","subj":"T4558","obj":"T25400"},{"id":"R54397","pred":"arg1Of","subj":"T4558","obj":"T95940"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T92","span":{"begin":63,"end":73},"obj":"Body_part"},{"id":"T93","span":{"begin":443,"end":453},"obj":"Body_part"},{"id":"T94","span":{"begin":547,"end":555},"obj":"Body_part"},{"id":"T95","span":{"begin":613,"end":620},"obj":"Body_part"},{"id":"T96","span":{"begin":785,"end":795},"obj":"Body_part"},{"id":"T97","span":{"begin":848,"end":856},"obj":"Body_part"}],"attributes":[{"id":"A94","pred":"fma_id","subj":"T94","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A95","pred":"fma_id","subj":"T95","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A97","pred":"fma_id","subj":"T97","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A92","pred":"fma_id","subj":"T92","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A93","pred":"fma_id","subj":"T93","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A96","pred":"fma_id","subj":"T96","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T128","span":{"begin":63,"end":73},"obj":"Chemical"},{"id":"T129","span":{"begin":443,"end":448},"obj":"Chemical"},{"id":"T130","span":{"begin":547,"end":555},"obj":"Chemical"},{"id":"T131","span":{"begin":613,"end":620},"obj":"Chemical"},{"id":"T132","span":{"begin":785,"end":790},"obj":"Chemical"},{"id":"T133","span":{"begin":848,"end":856},"obj":"Chemical"},{"id":"T134","span":{"begin":885,"end":892},"obj":"Chemical"}],"attributes":[{"id":"A132","pred":"chebi_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A134","pred":"chebi_id","subj":"T134","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A131","pred":"chebi_id","subj":"T131","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A128","pred":"chebi_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A130","pred":"chebi_id","subj":"T130","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A133","pred":"chebi_id","subj":"T133","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A129","pred":"chebi_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T104","span":{"begin":213,"end":217},"obj":"Species"},{"id":"T105","span":{"begin":321,"end":325},"obj":"Species"},{"id":"T106","span":{"begin":727,"end":731},"obj":"Species"},{"id":"T107","span":{"begin":736,"end":740},"obj":"Species"},{"id":"T108","span":{"begin":841,"end":845},"obj":"Species"}],"attributes":[{"id":"A107","pred":"ncbi_taxonomy_id","subj":"T107","obj":"NCBItxid:1335626"},{"id":"A108","pred":"ncbi_taxonomy_id","subj":"T108","obj":"NCBItxid:1335626"},{"id":"A104","pred":"ncbi_taxonomy_id","subj":"T104","obj":"NCBItxid:694009"},{"id":"A105","pred":"ncbi_taxonomy_id","subj":"T105","obj":"NCBItxid:1335626"},{"id":"A106","pred":"ncbi_taxonomy_id","subj":"T106","obj":"NCBItxid:694009"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T90","span":{"begin":0,"end":193},"obj":"Sentence"},{"id":"T91","span":{"begin":194,"end":287},"obj":"Sentence"},{"id":"T92","span":{"begin":288,"end":415},"obj":"Sentence"},{"id":"T93","span":{"begin":416,"end":746},"obj":"Sentence"},{"id":"T94","span":{"begin":747,"end":893},"obj":"Sentence"},{"id":"T95","span":{"begin":894,"end":999},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T50","span":{"begin":213,"end":217},"obj":"Disease"},{"id":"T51","span":{"begin":727,"end":731},"obj":"Disease"}],"attributes":[{"id":"A51","pred":"mondo_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A50","pred":"mondo_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-sample-Pubtator","denotations":[{"id":"558","span":{"begin":94,"end":96},"obj":"Chemical"},{"id":"559","span":{"begin":97,"end":99},"obj":"Chemical"},{"id":"560","span":{"begin":170,"end":172},"obj":"Chemical"},{"id":"561","span":{"begin":173,"end":175},"obj":"Chemical"},{"id":"568","span":{"begin":213,"end":217},"obj":"Disease"},{"id":"562","span":{"begin":227,"end":229},"obj":"Chemical"},{"id":"563","span":{"begin":230,"end":232},"obj":"Chemical"},{"id":"569","span":{"begin":321,"end":325},"obj":"Disease"},{"id":"564","span":{"begin":343,"end":345},"obj":"Chemical"},{"id":"565","span":{"begin":346,"end":348},"obj":"Chemical"},{"id":"556","span":{"begin":541,"end":544},"obj":"Species"},{"id":"566","span":{"begin":710,"end":716},"obj":"Chemical"},{"id":"570","span":{"begin":727,"end":731},"obj":"Disease"},{"id":"557","span":{"begin":736,"end":745},"obj":"Species"},{"id":"571","span":{"begin":841,"end":845},"obj":"Disease"},{"id":"567","span":{"begin":885,"end":892},"obj":"Chemical"}],"attributes":[{"id":"A561","pred":"pubann:denotes","subj":"561","obj":"MESH:D003903"},{"id":"A556","pred":"pubann:denotes","subj":"556","obj":"Tax:11118"},{"id":"A564","pred":"pubann:denotes","subj":"564","obj":"MESH:C022306"},{"id":"A565","pred":"pubann:denotes","subj":"565","obj":"MESH:D003903"},{"id":"A571","pred":"pubann:denotes","subj":"571","obj":"MESH:D018352"},{"id":"A562","pred":"pubann:denotes","subj":"562","obj":"MESH:C022306"},{"id":"A557","pred":"pubann:denotes","subj":"557","obj":"Tax:1335626"},{"id":"A569","pred":"pubann:denotes","subj":"569","obj":"MESH:D018352"},{"id":"A568","pred":"pubann:denotes","subj":"568","obj":"MESH:D045169"},{"id":"A570","pred":"pubann:denotes","subj":"570","obj":"MESH:D045169"},{"id":"A559","pred":"pubann:denotes","subj":"559","obj":"MESH:D003903"},{"id":"A567","pred":"pubann:denotes","subj":"567","obj":"MESH:D011134"},{"id":"A560","pred":"pubann:denotes","subj":"560","obj":"MESH:C022306"},{"id":"A566","pred":"pubann:denotes","subj":"566","obj":"MESH:D011134"},{"id":"A563","pred":"pubann:denotes","subj":"563","obj":"MESH:D003903"},{"id":"A558","pred":"pubann:denotes","subj":"558","obj":"MESH:C022306"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-sample-UniProt","denotations":[{"id":"T3703","span":{"begin":545,"end":555},"obj":"Protein"},{"id":"T3736","span":{"begin":846,"end":856},"obj":"Protein"}],"attributes":[{"id":"A3703","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9UIP0"},{"id":"A3704","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9UIN9"},{"id":"A3705","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9UIN8"},{"id":"A3706","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9UIN7"},{"id":"A3707","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9UIN6"},{"id":"A3708","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9UBH8"},{"id":"A3709","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9NRH8"},{"id":"A3710","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9NRH7"},{"id":"A3711","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9NRH6"},{"id":"A3712","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9NRH5"},{"id":"A3713","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9NRH4"},{"id":"A3714","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9NPG5"},{"id":"A3715","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9NPE0"},{"id":"A3716","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q9NP52"},{"id":"A3717","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q95IF9"},{"id":"A3718","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q8N5P3"},{"id":"A3719","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q8IZU6"},{"id":"A3720","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q8IZU5"},{"id":"A3721","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q8IZU4"},{"id":"A3722","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q86Z04"},{"id":"A3723","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q7YR44"},{"id":"A3724","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q7LA71"},{"id":"A3725","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q7LA70"},{"id":"A3726","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q5STD2"},{"id":"A3727","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q5SQ85"},{"id":"A3728","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q1XI16"},{"id":"A3729","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q1XI12"},{"id":"A3730","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/Q15517"},{"id":"A3731","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/O43509"},{"id":"A3732","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/O19084"},{"id":"A3733","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/B0UYZ7"},{"id":"A3734","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/B0S7V2"},{"id":"A3735","pred":"uniprot_id","subj":"T3703","obj":"https://www.uniprot.org/uniprot/A5A6L9"},{"id":"A3736","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9UIP0"},{"id":"A3737","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9UIN9"},{"id":"A3738","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9UIN8"},{"id":"A3739","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9UIN7"},{"id":"A3740","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9UIN6"},{"id":"A3741","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9UBH8"},{"id":"A3742","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9NRH8"},{"id":"A3743","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9NRH7"},{"id":"A3744","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9NRH6"},{"id":"A3745","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9NRH5"},{"id":"A3746","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9NRH4"},{"id":"A3747","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9NPG5"},{"id":"A3748","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9NPE0"},{"id":"A3749","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q9NP52"},{"id":"A3750","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q95IF9"},{"id":"A3751","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q8N5P3"},{"id":"A3752","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q8IZU6"},{"id":"A3753","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q8IZU5"},{"id":"A3754","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q8IZU4"},{"id":"A3755","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q86Z04"},{"id":"A3756","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q7YR44"},{"id":"A3757","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q7LA71"},{"id":"A3758","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q7LA70"},{"id":"A3759","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q5STD2"},{"id":"A3760","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q5SQ85"},{"id":"A3761","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q1XI16"},{"id":"A3762","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q1XI12"},{"id":"A3763","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/Q15517"},{"id":"A3764","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/O43509"},{"id":"A3765","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/O19084"},{"id":"A3766","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/B0UYZ7"},{"id":"A3767","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/B0S7V2"},{"id":"A3768","pred":"uniprot_id","subj":"T3736","obj":"https://www.uniprot.org/uniprot/A5A6L9"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}

{"project":"LitCovid-sentences","denotations":[{"id":"T90","span":{"begin":0,"end":193},"obj":"Sentence"},{"id":"T91","span":{"begin":194,"end":287},"obj":"Sentence"},{"id":"T92","span":{"begin":288,"end":415},"obj":"Sentence"},{"id":"T93","span":{"begin":416,"end":746},"obj":"Sentence"},{"id":"T94","span":{"begin":747,"end":893},"obj":"Sentence"},{"id":"T95","span":{"begin":894,"end":999},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Analysis of the relative ratio of non-synonymous to synonymous nucleotide substitutions (i.e. dN/dS ratios) revealed that exposed residues exhibited significantly higher dN/dS values (Fig. 4b). Buried residues on SARS had mean dN/dS ratios of 0.31 compared with 2.82 for exposed resides. Likewise, the buried residues on MERS had a calculated dN/dS ratio of 0.10 compared with exposed residues with a value of 0.45. Furthermore, when per-site amino-acid diversities were mapped onto the fully glycosylated structural model of the respective CoV S proteins (Fig. 4c), hotspots of mutations were highlighted on the protein surface throughout the trimer revealing extensive vulnerabilities permeating through the glycan shield of SARS and MERS CoVs. It is interesting to note the lack of amino-acid diversity on the receptor-binding domains of MERS S proteins that protrude away from the glycans. We would suggest that this may result from the intrinsic receptor-binding functionality of these domains."}