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LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"97","span":{"begin":26,"end":29},"obj":"Gene"},{"id":"104","span":{"begin":81,"end":91},"obj":"Species"},{"id":"105","span":{"begin":111,"end":133},"obj":"Species"},{"id":"106","span":{"begin":364,"end":368},"obj":"Species"},{"id":"107","span":{"begin":370,"end":378},"obj":"Species"},{"id":"108","span":{"begin":383,"end":391},"obj":"Species"},{"id":"109","span":{"begin":467,"end":477},"obj":"Species"},{"id":"113","span":{"begin":575,"end":585},"obj":"Species"},{"id":"114","span":{"begin":614,"end":622},"obj":"Species"},{"id":"115","span":{"begin":701,"end":711},"obj":"Species"},{"id":"119","span":{"begin":844,"end":854},"obj":"Species"},{"id":"120","span":{"begin":859,"end":867},"obj":"Species"},{"id":"121","span":{"begin":1004,"end":1008},"obj":"Species"}],"attributes":[{"id":"A97","pred":"tao:has_database_id","subj":"97","obj":"Gene:6700"},{"id":"A104","pred":"tao:has_database_id","subj":"104","obj":"Tax:2697049"},{"id":"A105","pred":"tao:has_database_id","subj":"105","obj":"Tax:2697049"},{"id":"A106","pred":"tao:has_database_id","subj":"106","obj":"Tax:11118"},{"id":"A107","pred":"tao:has_database_id","subj":"107","obj":"Tax:694009"},{"id":"A108","pred":"tao:has_database_id","subj":"108","obj":"Tax:1335626"},{"id":"A109","pred":"tao:has_database_id","subj":"109","obj":"Tax:2697049"},{"id":"A113","pred":"tao:has_database_id","subj":"113","obj":"Tax:2697049"},{"id":"A114","pred":"tao:has_database_id","subj":"114","obj":"Tax:694009"},{"id":"A115","pred":"tao:has_database_id","subj":"115","obj":"Tax:2697049"},{"id":"A119","pred":"tao:has_database_id","subj":"119","obj":"Tax:2697049"},{"id":"A120","pred":"tao:has_database_id","subj":"120","obj":"Tax:694009"},{"id":"A121","pred":"tao:has_database_id","subj":"121","obj":"Tax:11118"}],"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":"2. Materials and Methods\n\n2.1. Data Collection\nThe complete genomic sequences of SARS-CoV-2 were obtained from 2019 Novel Coronavirus Resource (2019nCoVR) [12] and two databases, including the National Center for Biotechnology Information (NCBI) [13] and Global Initiative on Sharing All Influenza Data (GISAID) [14]. The DNA sequences of two other representative CoVs (SARS-CoV and MERS-CoV) were included for comparative analysis. The genomic information of latest SARS-CoV-2 strains is shown in Table S1.\n\n2.2. Homology Analysis\nThe amino acid sequences of 28 proteins in SARS-CoV-2 were compared with those of SARS-CoV to analyze protein homology by using NCBI Blastp [15]. Proteins from SARS and SARS-CoV-2 were treated as homologous: identity value ≥ 65%, query coverage ≥ 95%.\n\n2.3. Phylogenetic Analysis\nComparative genomic analyses of SARS-CoV-2 and SARS-CoV were performed by zpicture for the global comparison [16]. Multiple sequence alignment and the construction of phylogenetic trees of 38 CoVs were conducted using MEGA7 [17]. The evolutionary distances were calculated using the Maximum Composite Likelihood method [18]."}

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T8","span":{"begin":322,"end":325},"obj":"Body_part"},{"id":"T9","span":{"begin":536,"end":546},"obj":"Body_part"},{"id":"T10","span":{"begin":563,"end":571},"obj":"Body_part"},{"id":"T11","span":{"begin":634,"end":641},"obj":"Body_part"},{"id":"T12","span":{"begin":678,"end":686},"obj":"Body_part"}],"attributes":[{"id":"A8","pred":"fma_id","subj":"T8","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A9","pred":"fma_id","subj":"T9","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A10","pred":"fma_id","subj":"T10","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A11","pred":"fma_id","subj":"T11","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A12","pred":"fma_id","subj":"T12","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"2. Materials and Methods\n\n2.1. Data Collection\nThe complete genomic sequences of SARS-CoV-2 were obtained from 2019 Novel Coronavirus Resource (2019nCoVR) [12] and two databases, including the National Center for Biotechnology Information (NCBI) [13] and Global Initiative on Sharing All Influenza Data (GISAID) [14]. The DNA sequences of two other representative CoVs (SARS-CoV and MERS-CoV) were included for comparative analysis. The genomic information of latest SARS-CoV-2 strains is shown in Table S1.\n\n2.2. Homology Analysis\nThe amino acid sequences of 28 proteins in SARS-CoV-2 were compared with those of SARS-CoV to analyze protein homology by using NCBI Blastp [15]. Proteins from SARS and SARS-CoV-2 were treated as homologous: identity value ≥ 65%, query coverage ≥ 95%.\n\n2.3. Phylogenetic Analysis\nComparative genomic analyses of SARS-CoV-2 and SARS-CoV were performed by zpicture for the global comparison [16]. Multiple sequence alignment and the construction of phylogenetic trees of 38 CoVs were conducted using MEGA7 [17]. The evolutionary distances were calculated using the Maximum Composite Likelihood method [18]."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T41","span":{"begin":504,"end":506},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T42","span":{"begin":1132,"end":1134},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"}],"text":"2. Materials and Methods\n\n2.1. Data Collection\nThe complete genomic sequences of SARS-CoV-2 were obtained from 2019 Novel Coronavirus Resource (2019nCoVR) [12] and two databases, including the National Center for Biotechnology Information (NCBI) [13] and Global Initiative on Sharing All Influenza Data (GISAID) [14]. The DNA sequences of two other representative CoVs (SARS-CoV and MERS-CoV) were included for comparative analysis. The genomic information of latest SARS-CoV-2 strains is shown in Table S1.\n\n2.2. Homology Analysis\nThe amino acid sequences of 28 proteins in SARS-CoV-2 were compared with those of SARS-CoV to analyze protein homology by using NCBI Blastp [15]. Proteins from SARS and SARS-CoV-2 were treated as homologous: identity value ≥ 65%, query coverage ≥ 95%.\n\n2.3. Phylogenetic Analysis\nComparative genomic analyses of SARS-CoV-2 and SARS-CoV were performed by zpicture for the global comparison [16]. Multiple sequence alignment and the construction of phylogenetic trees of 38 CoVs were conducted using MEGA7 [17]. The evolutionary distances were calculated using the Maximum Composite Likelihood method [18]."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T4","span":{"begin":322,"end":325},"obj":"Chemical"},{"id":"T5","span":{"begin":536,"end":546},"obj":"Chemical"},{"id":"T6","span":{"begin":536,"end":541},"obj":"Chemical"},{"id":"T7","span":{"begin":542,"end":546},"obj":"Chemical"},{"id":"T8","span":{"begin":563,"end":571},"obj":"Chemical"},{"id":"T9","span":{"begin":634,"end":641},"obj":"Chemical"}],"attributes":[{"id":"A4","pred":"chebi_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A5","pred":"chebi_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A6","pred":"chebi_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A7","pred":"chebi_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A8","pred":"chebi_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A9","pred":"chebi_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"2. Materials and Methods\n\n2.1. Data Collection\nThe complete genomic sequences of SARS-CoV-2 were obtained from 2019 Novel Coronavirus Resource (2019nCoVR) [12] and two databases, including the National Center for Biotechnology Information (NCBI) [13] and Global Initiative on Sharing All Influenza Data (GISAID) [14]. The DNA sequences of two other representative CoVs (SARS-CoV and MERS-CoV) were included for comparative analysis. The genomic information of latest SARS-CoV-2 strains is shown in Table S1.\n\n2.2. Homology Analysis\nThe amino acid sequences of 28 proteins in SARS-CoV-2 were compared with those of SARS-CoV to analyze protein homology by using NCBI Blastp [15]. Proteins from SARS and SARS-CoV-2 were treated as homologous: identity value ≥ 65%, query coverage ≥ 95%.\n\n2.3. Phylogenetic Analysis\nComparative genomic analyses of SARS-CoV-2 and SARS-CoV were performed by zpicture for the global comparison [16]. Multiple sequence alignment and the construction of phylogenetic trees of 38 CoVs were conducted using MEGA7 [17]. The evolutionary distances were calculated using the Maximum Composite Likelihood method [18]."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T22","span":{"begin":0,"end":2},"obj":"Sentence"},{"id":"T23","span":{"begin":3,"end":24},"obj":"Sentence"},{"id":"T24","span":{"begin":26,"end":30},"obj":"Sentence"},{"id":"T25","span":{"begin":31,"end":46},"obj":"Sentence"},{"id":"T26","span":{"begin":47,"end":317},"obj":"Sentence"},{"id":"T27","span":{"begin":318,"end":432},"obj":"Sentence"},{"id":"T28","span":{"begin":433,"end":507},"obj":"Sentence"},{"id":"T29","span":{"begin":509,"end":513},"obj":"Sentence"},{"id":"T30","span":{"begin":514,"end":531},"obj":"Sentence"},{"id":"T31","span":{"begin":532,"end":677},"obj":"Sentence"},{"id":"T32","span":{"begin":678,"end":783},"obj":"Sentence"},{"id":"T33","span":{"begin":785,"end":789},"obj":"Sentence"},{"id":"T34","span":{"begin":790,"end":811},"obj":"Sentence"},{"id":"T35","span":{"begin":812,"end":926},"obj":"Sentence"},{"id":"T36","span":{"begin":927,"end":1041},"obj":"Sentence"},{"id":"T37","span":{"begin":1042,"end":1136},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2. Materials and Methods\n\n2.1. Data Collection\nThe complete genomic sequences of SARS-CoV-2 were obtained from 2019 Novel Coronavirus Resource (2019nCoVR) [12] and two databases, including the National Center for Biotechnology Information (NCBI) [13] and Global Initiative on Sharing All Influenza Data (GISAID) [14]. The DNA sequences of two other representative CoVs (SARS-CoV and MERS-CoV) were included for comparative analysis. The genomic information of latest SARS-CoV-2 strains is shown in Table S1.\n\n2.2. Homology Analysis\nThe amino acid sequences of 28 proteins in SARS-CoV-2 were compared with those of SARS-CoV to analyze protein homology by using NCBI Blastp [15]. Proteins from SARS and SARS-CoV-2 were treated as homologous: identity value ≥ 65%, query coverage ≥ 95%.\n\n2.3. Phylogenetic Analysis\nComparative genomic analyses of SARS-CoV-2 and SARS-CoV were performed by zpicture for the global comparison [16]. Multiple sequence alignment and the construction of phylogenetic trees of 38 CoVs were conducted using MEGA7 [17]. The evolutionary distances were calculated using the Maximum Composite Likelihood method [18]."}

2_test

{"project":"2_test","denotations":[{"id":"32098422-27004904-144406950","span":{"begin":1037,"end":1039},"obj":"27004904"},{"id":"32098422-15258291-144406951","span":{"begin":1132,"end":1134},"obj":"15258291"}],"text":"2. Materials and Methods\n\n2.1. Data Collection\nThe complete genomic sequences of SARS-CoV-2 were obtained from 2019 Novel Coronavirus Resource (2019nCoVR) [12] and two databases, including the National Center for Biotechnology Information (NCBI) [13] and Global Initiative on Sharing All Influenza Data (GISAID) [14]. The DNA sequences of two other representative CoVs (SARS-CoV and MERS-CoV) were included for comparative analysis. The genomic information of latest SARS-CoV-2 strains is shown in Table S1.\n\n2.2. Homology Analysis\nThe amino acid sequences of 28 proteins in SARS-CoV-2 were compared with those of SARS-CoV to analyze protein homology by using NCBI Blastp [15]. Proteins from SARS and SARS-CoV-2 were treated as homologous: identity value ≥ 65%, query coverage ≥ 95%.\n\n2.3. Phylogenetic Analysis\nComparative genomic analyses of SARS-CoV-2 and SARS-CoV were performed by zpicture for the global comparison [16]. Multiple sequence alignment and the construction of phylogenetic trees of 38 CoVs were conducted using MEGA7 [17]. The evolutionary distances were calculated using the Maximum Composite Likelihood method [18]."}