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LitCovid-sample-CHEBI

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T428","span":{"begin":152,"end":159},"obj":"Chemical"},{"id":"T429","span":{"begin":628,"end":640},"obj":"Chemical"},{"id":"T430","span":{"begin":726,"end":737},"obj":"Chemical"},{"id":"T431","span":{"begin":796,"end":806},"obj":"Chemical"}],"attributes":[{"id":"A428","pred":"chebi_id","subj":"T428","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A429","pred":"chebi_id","subj":"T429","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A430","pred":"chebi_id","subj":"T430","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A431","pred":"chebi_id","subj":"T431","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"}],"text":"The genomes of SARS-CoV as well as bat and pangolin coronavirus sequences reported to be closely related to SARS-CoV-2 were downloaded from NCBI. The S protein sequences from all of those genomes were aligned using EMBOSS needle v6.6.0 (Rice et al., 2000) via the EMBL-EBI provided web service (Madeira et al., 2019). Manual analysis was performed in the regions containing canonical N-glycosylation sequons (N-X-S/T). For further sequence analysis of SARS-CoV-2 S variants, the genomes of SARS-CoV-2 were downloaded from NCBI and GISAID and further processed using Biopython 1.76 to extract all sequences annotated as “surface glycoprotein” and to remove any incomplete sequence as well as any sequence containing unassigned amino acids. For sequence analysis of human ACE2 variants, the single nucleotide polymorphisms (SNPs) of ACE2 were extracted from the NCBI dbSNP database and filtered for missense mutation entries with a reported minor allele frequency. Manual analysis was performed on both SARS-CoV-2 S and human ACE2 variants to further examine the regions containing canonical N-glycosylation sequons (N-X-S/T). LibreOffice Writer and its macro capabilities was used to shade regions on the linear sequence of S and ACE2."}

LitCovid-sample-PD-NCBITaxon

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T163","span":{"begin":15,"end":23},"obj":"Species"},{"id":"T164","span":{"begin":35,"end":38},"obj":"Species"},{"id":"T165","span":{"begin":43,"end":63},"obj":"Species"},{"id":"T166","span":{"begin":108,"end":118},"obj":"Species"},{"id":"T167","span":{"begin":237,"end":241},"obj":"Species"},{"id":"T168","span":{"begin":452,"end":462},"obj":"Species"},{"id":"T169","span":{"begin":490,"end":500},"obj":"Species"},{"id":"T170","span":{"begin":764,"end":769},"obj":"Species"},{"id":"T171","span":{"begin":1001,"end":1011},"obj":"Species"},{"id":"T172","span":{"begin":1018,"end":1023},"obj":"Species"}],"attributes":[{"id":"A169","pred":"ncbi_taxonomy_id","subj":"T169","obj":"NCBItxid:2697049"},{"id":"A171","pred":"ncbi_taxonomy_id","subj":"T171","obj":"NCBItxid:2697049"},{"id":"A168","pred":"ncbi_taxonomy_id","subj":"T168","obj":"NCBItxid:2697049"},{"id":"A167","pred":"ncbi_taxonomy_id","subj":"T167","obj":"NCBItxid:4530"},{"id":"A170","pred":"ncbi_taxonomy_id","subj":"T170","obj":"NCBItxid:9606"},{"id":"A166","pred":"ncbi_taxonomy_id","subj":"T166","obj":"NCBItxid:2697049"},{"id":"A165","pred":"ncbi_taxonomy_id","subj":"T165","obj":"NCBItxid:2708335"},{"id":"A172","pred":"ncbi_taxonomy_id","subj":"T172","obj":"NCBItxid:9606"},{"id":"A164","pred":"ncbi_taxonomy_id","subj":"T164","obj":"NCBItxid:9397"},{"id":"A163","pred":"ncbi_taxonomy_id","subj":"T163","obj":"NCBItxid:694009"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"The genomes of SARS-CoV as well as bat and pangolin coronavirus sequences reported to be closely related to SARS-CoV-2 were downloaded from NCBI. The S protein sequences from all of those genomes were aligned using EMBOSS needle v6.6.0 (Rice et al., 2000) via the EMBL-EBI provided web service (Madeira et al., 2019). Manual analysis was performed in the regions containing canonical N-glycosylation sequons (N-X-S/T). For further sequence analysis of SARS-CoV-2 S variants, the genomes of SARS-CoV-2 were downloaded from NCBI and GISAID and further processed using Biopython 1.76 to extract all sequences annotated as “surface glycoprotein” and to remove any incomplete sequence as well as any sequence containing unassigned amino acids. For sequence analysis of human ACE2 variants, the single nucleotide polymorphisms (SNPs) of ACE2 were extracted from the NCBI dbSNP database and filtered for missense mutation entries with a reported minor allele frequency. Manual analysis was performed on both SARS-CoV-2 S and human ACE2 variants to further examine the regions containing canonical N-glycosylation sequons (N-X-S/T). LibreOffice Writer and its macro capabilities was used to shade regions on the linear sequence of S and ACE2."}

LitCovid-sample-sentences

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T421","span":{"begin":0,"end":145},"obj":"Sentence"},{"id":"T422","span":{"begin":146,"end":317},"obj":"Sentence"},{"id":"T423","span":{"begin":318,"end":418},"obj":"Sentence"},{"id":"T424","span":{"begin":419,"end":738},"obj":"Sentence"},{"id":"T425","span":{"begin":739,"end":962},"obj":"Sentence"},{"id":"T426","span":{"begin":963,"end":1124},"obj":"Sentence"},{"id":"T427","span":{"begin":1125,"end":1234},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The genomes of SARS-CoV as well as bat and pangolin coronavirus sequences reported to be closely related to SARS-CoV-2 were downloaded from NCBI. The S protein sequences from all of those genomes were aligned using EMBOSS needle v6.6.0 (Rice et al., 2000) via the EMBL-EBI provided web service (Madeira et al., 2019). Manual analysis was performed in the regions containing canonical N-glycosylation sequons (N-X-S/T). For further sequence analysis of SARS-CoV-2 S variants, the genomes of SARS-CoV-2 were downloaded from NCBI and GISAID and further processed using Biopython 1.76 to extract all sequences annotated as “surface glycoprotein” and to remove any incomplete sequence as well as any sequence containing unassigned amino acids. For sequence analysis of human ACE2 variants, the single nucleotide polymorphisms (SNPs) of ACE2 were extracted from the NCBI dbSNP database and filtered for missense mutation entries with a reported minor allele frequency. Manual analysis was performed on both SARS-CoV-2 S and human ACE2 variants to further examine the regions containing canonical N-glycosylation sequons (N-X-S/T). LibreOffice Writer and its macro capabilities was used to shade regions on the linear sequence of S and ACE2."}

LitCovid-sample-PD-MONDO

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T100","span":{"begin":15,"end":23},"obj":"Disease"},{"id":"T101","span":{"begin":108,"end":118},"obj":"Disease"},{"id":"T102","span":{"begin":452,"end":462},"obj":"Disease"},{"id":"T103","span":{"begin":490,"end":500},"obj":"Disease"},{"id":"T104","span":{"begin":1001,"end":1011},"obj":"Disease"}],"attributes":[{"id":"A100","pred":"mondo_id","subj":"T100","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A101","pred":"mondo_id","subj":"T101","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A102","pred":"mondo_id","subj":"T102","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A103","pred":"mondo_id","subj":"T103","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A104","pred":"mondo_id","subj":"T104","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"The genomes of SARS-CoV as well as bat and pangolin coronavirus sequences reported to be closely related to SARS-CoV-2 were downloaded from NCBI. The S protein sequences from all of those genomes were aligned using EMBOSS needle v6.6.0 (Rice et al., 2000) via the EMBL-EBI provided web service (Madeira et al., 2019). Manual analysis was performed in the regions containing canonical N-glycosylation sequons (N-X-S/T). For further sequence analysis of SARS-CoV-2 S variants, the genomes of SARS-CoV-2 were downloaded from NCBI and GISAID and further processed using Biopython 1.76 to extract all sequences annotated as “surface glycoprotein” and to remove any incomplete sequence as well as any sequence containing unassigned amino acids. For sequence analysis of human ACE2 variants, the single nucleotide polymorphisms (SNPs) of ACE2 were extracted from the NCBI dbSNP database and filtered for missense mutation entries with a reported minor allele frequency. Manual analysis was performed on both SARS-CoV-2 S and human ACE2 variants to further examine the regions containing canonical N-glycosylation sequons (N-X-S/T). LibreOffice Writer and its macro capabilities was used to shade regions on the linear sequence of S and ACE2."}

LitCovid-sample-UniProt

LitCovid-sample-PD-FMA

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T205","span":{"begin":4,"end":11},"obj":"Body_part"},{"id":"T206","span":{"begin":152,"end":159},"obj":"Body_part"},{"id":"T207","span":{"begin":188,"end":195},"obj":"Body_part"},{"id":"T208","span":{"begin":479,"end":486},"obj":"Body_part"},{"id":"T209","span":{"begin":628,"end":640},"obj":"Body_part"},{"id":"T210","span":{"begin":726,"end":737},"obj":"Body_part"},{"id":"T211","span":{"begin":796,"end":806},"obj":"Body_part"}],"attributes":[{"id":"A205","pred":"fma_id","subj":"T205","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A206","pred":"fma_id","subj":"T206","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A207","pred":"fma_id","subj":"T207","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A208","pred":"fma_id","subj":"T208","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A209","pred":"fma_id","subj":"T209","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A210","pred":"fma_id","subj":"T210","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A211","pred":"fma_id","subj":"T211","obj":"http://purl.org/sig/ont/fma/fma82740"}],"text":"The genomes of SARS-CoV as well as bat and pangolin coronavirus sequences reported to be closely related to SARS-CoV-2 were downloaded from NCBI. The S protein sequences from all of those genomes were aligned using EMBOSS needle v6.6.0 (Rice et al., 2000) via the EMBL-EBI provided web service (Madeira et al., 2019). Manual analysis was performed in the regions containing canonical N-glycosylation sequons (N-X-S/T). For further sequence analysis of SARS-CoV-2 S variants, the genomes of SARS-CoV-2 were downloaded from NCBI and GISAID and further processed using Biopython 1.76 to extract all sequences annotated as “surface glycoprotein” and to remove any incomplete sequence as well as any sequence containing unassigned amino acids. For sequence analysis of human ACE2 variants, the single nucleotide polymorphisms (SNPs) of ACE2 were extracted from the NCBI dbSNP database and filtered for missense mutation entries with a reported minor allele frequency. Manual analysis was performed on both SARS-CoV-2 S and human ACE2 variants to further examine the regions containing canonical N-glycosylation sequons (N-X-S/T). LibreOffice Writer and its macro capabilities was used to shade regions on the linear sequence of S and ACE2."}

LitCovid-sample-PD-GO-BP-0

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T130","span":{"begin":386,"end":399},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T131","span":{"begin":1092,"end":1105},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"The genomes of SARS-CoV as well as bat and pangolin coronavirus sequences reported to be closely related to SARS-CoV-2 were downloaded from NCBI. The S protein sequences from all of those genomes were aligned using EMBOSS needle v6.6.0 (Rice et al., 2000) via the EMBL-EBI provided web service (Madeira et al., 2019). Manual analysis was performed in the regions containing canonical N-glycosylation sequons (N-X-S/T). For further sequence analysis of SARS-CoV-2 S variants, the genomes of SARS-CoV-2 were downloaded from NCBI and GISAID and further processed using Biopython 1.76 to extract all sequences annotated as “surface glycoprotein” and to remove any incomplete sequence as well as any sequence containing unassigned amino acids. For sequence analysis of human ACE2 variants, the single nucleotide polymorphisms (SNPs) of ACE2 were extracted from the NCBI dbSNP database and filtered for missense mutation entries with a reported minor allele frequency. Manual analysis was performed on both SARS-CoV-2 S and human ACE2 variants to further examine the regions containing canonical N-glycosylation sequons (N-X-S/T). LibreOffice Writer and its macro capabilities was used to shade regions on the linear sequence of S and ACE2."}

LitCovid-sample-GO-BP

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T123","span":{"begin":386,"end":399},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T124","span":{"begin":1092,"end":1105},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"The genomes of SARS-CoV as well as bat and pangolin coronavirus sequences reported to be closely related to SARS-CoV-2 were downloaded from NCBI. The S protein sequences from all of those genomes were aligned using EMBOSS needle v6.6.0 (Rice et al., 2000) via the EMBL-EBI provided web service (Madeira et al., 2019). Manual analysis was performed in the regions containing canonical N-glycosylation sequons (N-X-S/T). For further sequence analysis of SARS-CoV-2 S variants, the genomes of SARS-CoV-2 were downloaded from NCBI and GISAID and further processed using Biopython 1.76 to extract all sequences annotated as “surface glycoprotein” and to remove any incomplete sequence as well as any sequence containing unassigned amino acids. For sequence analysis of human ACE2 variants, the single nucleotide polymorphisms (SNPs) of ACE2 were extracted from the NCBI dbSNP database and filtered for missense mutation entries with a reported minor allele frequency. Manual analysis was performed on both SARS-CoV-2 S and human ACE2 variants to further examine the regions containing canonical N-glycosylation sequons (N-X-S/T). LibreOffice Writer and its macro capabilities was used to shade regions on the linear sequence of S and ACE2."}

2_test

{"project":"2_test","denotations":[{"id":"32841605-10827456-19659563","span":{"begin":250,"end":254},"obj":"10827456"},{"id":"32841605-30976793-19659564","span":{"begin":311,"end":315},"obj":"30976793"}],"text":"The genomes of SARS-CoV as well as bat and pangolin coronavirus sequences reported to be closely related to SARS-CoV-2 were downloaded from NCBI. The S protein sequences from all of those genomes were aligned using EMBOSS needle v6.6.0 (Rice et al., 2000) via the EMBL-EBI provided web service (Madeira et al., 2019). Manual analysis was performed in the regions containing canonical N-glycosylation sequons (N-X-S/T). For further sequence analysis of SARS-CoV-2 S variants, the genomes of SARS-CoV-2 were downloaded from NCBI and GISAID and further processed using Biopython 1.76 to extract all sequences annotated as “surface glycoprotein” and to remove any incomplete sequence as well as any sequence containing unassigned amino acids. For sequence analysis of human ACE2 variants, the single nucleotide polymorphisms (SNPs) of ACE2 were extracted from the NCBI dbSNP database and filtered for missense mutation entries with a reported minor allele frequency. Manual analysis was performed on both SARS-CoV-2 S and human ACE2 variants to further examine the regions containing canonical N-glycosylation sequons (N-X-S/T). LibreOffice Writer and its macro capabilities was used to shade regions on the linear sequence of S and ACE2."}

PMC:7443692 / 62196-63430 JSONTXT

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PMC:7443692 / 62196-63430 JSON TXT