PMC:7258756 / 8767-9640 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"155","span":{"begin":867,"end":871},"obj":"Gene"},{"id":"156","span":{"begin":32,"end":42},"obj":"Species"},{"id":"157","span":{"begin":748,"end":758},"obj":"Species"},{"id":"158","span":{"begin":835,"end":845},"obj":"Species"},{"id":"159","span":{"begin":515,"end":517},"obj":"Chemical"}],"attributes":[{"id":"A155","pred":"tao:has_database_id","subj":"155","obj":"Gene:6195"},{"id":"A156","pred":"tao:has_database_id","subj":"156","obj":"Tax:2697049"},{"id":"A157","pred":"tao:has_database_id","subj":"157","obj":"Tax:2697049"},{"id":"A158","pred":"tao:has_database_id","subj":"158","obj":"Tax:2697049"},{"id":"A159","pred":"tao:has_database_id","subj":"159","obj":"MESH:D009711"}],"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":"Full-length genome sequences of SARS-CoV-2 were downloaded from the GISAID database17 (Supplementary Table I (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm5.pdf)). Multiple sequence alignment was performed using the MEGA software version 7.018 with retrieved sequences from two of the three positive cases and the available GISAID sequences. A phylogenetic tree was generated using the neighbour joining method and the Kimura-2-parameter as the nucleotide (nt) substitution model with 1000 bootstrap replications as implemented in MEGA software18. Per cent nucleotide divergence and amino acid (aa) divergence were calculated using the p-distance method18. Mutations specific to the Indian SARS-CoV-2 viruses were identified by comparing the coding regions with respect to the SARS-CoV-2, Wuhan, China (Wuhan hu-1)."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T38","span":{"begin":12,"end":18},"obj":"Body_part"},{"id":"T39","span":{"begin":503,"end":513},"obj":"Body_part"},{"id":"T40","span":{"begin":515,"end":517},"obj":"Body_part"},{"id":"T41","span":{"begin":615,"end":625},"obj":"Body_part"},{"id":"T42","span":{"begin":641,"end":651},"obj":"Body_part"},{"id":"T43","span":{"begin":653,"end":655},"obj":"Body_part"}],"attributes":[{"id":"A38","pred":"fma_id","subj":"T38","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A39","pred":"fma_id","subj":"T39","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A41","pred":"fma_id","subj":"T41","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A42","pred":"fma_id","subj":"T42","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A43","pred":"fma_id","subj":"T43","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"Full-length genome sequences of SARS-CoV-2 were downloaded from the GISAID database17 (Supplementary Table I (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm5.pdf)). Multiple sequence alignment was performed using the MEGA software version 7.018 with retrieved sequences from two of the three positive cases and the available GISAID sequences. A phylogenetic tree was generated using the neighbour joining method and the Kimura-2-parameter as the nucleotide (nt) substitution model with 1000 bootstrap replications as implemented in MEGA software18. Per cent nucleotide divergence and amino acid (aa) divergence were calculated using the p-distance method18. Mutations specific to the Indian SARS-CoV-2 viruses were identified by comparing the coding regions with respect to the SARS-CoV-2, Wuhan, China (Wuhan hu-1)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T83","span":{"begin":32,"end":40},"obj":"Disease"},{"id":"T84","span":{"begin":32,"end":36},"obj":"Disease"},{"id":"T85","span":{"begin":748,"end":756},"obj":"Disease"},{"id":"T86","span":{"begin":748,"end":752},"obj":"Disease"},{"id":"T87","span":{"begin":835,"end":843},"obj":"Disease"},{"id":"T88","span":{"begin":835,"end":839},"obj":"Disease"}],"attributes":[{"id":"A83","pred":"mondo_id","subj":"T83","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A84","pred":"mondo_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A85","pred":"mondo_id","subj":"T85","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A86","pred":"mondo_id","subj":"T86","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A87","pred":"mondo_id","subj":"T87","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A88","pred":"mondo_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Full-length genome sequences of SARS-CoV-2 were downloaded from the GISAID database17 (Supplementary Table I (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm5.pdf)). Multiple sequence alignment was performed using the MEGA software version 7.018 with retrieved sequences from two of the three positive cases and the available GISAID sequences. A phylogenetic tree was generated using the neighbour joining method and the Kimura-2-parameter as the nucleotide (nt) substitution model with 1000 bootstrap replications as implemented in MEGA software18. Per cent nucleotide divergence and amino acid (aa) divergence were calculated using the p-distance method18. Mutations specific to the Indian SARS-CoV-2 viruses were identified by comparing the coding regions with respect to the SARS-CoV-2, Wuhan, China (Wuhan hu-1)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T71","span":{"begin":400,"end":401},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T72","span":{"begin":606,"end":609},"obj":"http://purl.obolibrary.org/obo/CLO_0008190"},{"id":"T73","span":{"begin":653,"end":655},"obj":"http://purl.obolibrary.org/obo/CLO_0001627"},{"id":"T74","span":{"begin":759,"end":766},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"}],"text":"Full-length genome sequences of SARS-CoV-2 were downloaded from the GISAID database17 (Supplementary Table I (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm5.pdf)). Multiple sequence alignment was performed using the MEGA software version 7.018 with retrieved sequences from two of the three positive cases and the available GISAID sequences. A phylogenetic tree was generated using the neighbour joining method and the Kimura-2-parameter as the nucleotide (nt) substitution model with 1000 bootstrap replications as implemented in MEGA software18. Per cent nucleotide divergence and amino acid (aa) divergence were calculated using the p-distance method18. Mutations specific to the Indian SARS-CoV-2 viruses were identified by comparing the coding regions with respect to the SARS-CoV-2, Wuhan, China (Wuhan hu-1)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T18","span":{"begin":274,"end":278},"obj":"Chemical"},{"id":"T19","span":{"begin":503,"end":513},"obj":"Chemical"},{"id":"T20","span":{"begin":515,"end":517},"obj":"Chemical"},{"id":"T21","span":{"begin":589,"end":593},"obj":"Chemical"},{"id":"T22","span":{"begin":615,"end":625},"obj":"Chemical"},{"id":"T23","span":{"begin":641,"end":651},"obj":"Chemical"},{"id":"T24","span":{"begin":641,"end":646},"obj":"Chemical"},{"id":"T25","span":{"begin":647,"end":651},"obj":"Chemical"},{"id":"T26","span":{"begin":653,"end":655},"obj":"Chemical"}],"attributes":[{"id":"A18","pred":"chebi_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/CHEBI_6617"},{"id":"A19","pred":"chebi_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A20","pred":"chebi_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A21","pred":"chebi_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/CHEBI_6617"},{"id":"A22","pred":"chebi_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A23","pred":"chebi_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A24","pred":"chebi_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A25","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A26","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"}],"text":"Full-length genome sequences of SARS-CoV-2 were downloaded from the GISAID database17 (Supplementary Table I (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm5.pdf)). Multiple sequence alignment was performed using the MEGA software version 7.018 with retrieved sequences from two of the three positive cases and the available GISAID sequences. A phylogenetic tree was generated using the neighbour joining method and the Kimura-2-parameter as the nucleotide (nt) substitution model with 1000 bootstrap replications as implemented in MEGA software18. Per cent nucleotide divergence and amino acid (aa) divergence were calculated using the p-distance method18. Mutations specific to the Indian SARS-CoV-2 viruses were identified by comparing the coding regions with respect to the SARS-CoV-2, Wuhan, China (Wuhan hu-1)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T70","span":{"begin":0,"end":221},"obj":"Sentence"},{"id":"T71","span":{"begin":222,"end":399},"obj":"Sentence"},{"id":"T72","span":{"begin":400,"end":605},"obj":"Sentence"},{"id":"T73","span":{"begin":606,"end":714},"obj":"Sentence"},{"id":"T74","span":{"begin":715,"end":873},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Full-length genome sequences of SARS-CoV-2 were downloaded from the GISAID database17 (Supplementary Table I (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm5.pdf)). Multiple sequence alignment was performed using the MEGA software version 7.018 with retrieved sequences from two of the three positive cases and the available GISAID sequences. A phylogenetic tree was generated using the neighbour joining method and the Kimura-2-parameter as the nucleotide (nt) substitution model with 1000 bootstrap replications as implemented in MEGA software18. Per cent nucleotide divergence and amino acid (aa) divergence were calculated using the p-distance method18. Mutations specific to the Indian SARS-CoV-2 viruses were identified by comparing the coding regions with respect to the SARS-CoV-2, Wuhan, China (Wuhan hu-1)."}

{"project":"2_test","denotations":[{"id":"32242873-31565258-47036565","span":{"begin":83,"end":85},"obj":"31565258"},{"id":"32242873-27004904-47036566","span":{"begin":298,"end":301},"obj":"27004904"},{"id":"32242873-27004904-47036567","span":{"begin":602,"end":604},"obj":"27004904"},{"id":"32242873-27004904-47036568","span":{"begin":711,"end":713},"obj":"27004904"},{"id":"T62421","span":{"begin":83,"end":85},"obj":"31565258"},{"id":"T79581","span":{"begin":298,"end":301},"obj":"27004904"},{"id":"T13164","span":{"begin":602,"end":604},"obj":"27004904"},{"id":"T93390","span":{"begin":711,"end":713},"obj":"27004904"}],"text":"Full-length genome sequences of SARS-CoV-2 were downloaded from the GISAID database17 (Supplementary Table I (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm5.pdf)). Multiple sequence alignment was performed using the MEGA software version 7.018 with retrieved sequences from two of the three positive cases and the available GISAID sequences. A phylogenetic tree was generated using the neighbour joining method and the Kimura-2-parameter as the nucleotide (nt) substitution model with 1000 bootstrap replications as implemented in MEGA software18. Per cent nucleotide divergence and amino acid (aa) divergence were calculated using the p-distance method18. Mutations specific to the Indian SARS-CoV-2 viruses were identified by comparing the coding regions with respect to the SARS-CoV-2, Wuhan, China (Wuhan hu-1)."}