PMC:7033720 / 6737-7229 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7033720","sourcedb":"PMC","sourceid":"7033720","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7033720","text":"Phylogenetic and recombination analyses\nReference sequences associated with CoVs were downloaded from GenBank and aligned using mafft program. Phylogenetic trees (both amino acid and nucleotide alignment) were reconstructed using the maximum likelihood method in PhyML 3.0 [7], employing a best fit substitution model and a SPR branch swapping algorithm. Recombination event were discovered from phylogenetic analyses and confirmed with similarity plot implemented in the Simplot program [8].","divisions":[{"label":"title","span":{"begin":0,"end":39}}],"tracks":[{"project":"LitCovid-PubTator","denotations":[{"id":"86","span":{"begin":324,"end":327},"obj":"Gene"},{"id":"87","span":{"begin":76,"end":80},"obj":"Species"}],"attributes":[{"id":"A86","pred":"tao:has_database_id","subj":"86","obj":"Gene:6697"},{"id":"A87","pred":"tao:has_database_id","subj":"87","obj":"Tax:11118"},{"subj":"86","pred":"source","obj":"LitCovid-PubTator"},{"subj":"87","pred":"source","obj":"LitCovid-PubTator"}],"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_"}]},{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T40","span":{"begin":168,"end":178},"obj":"Body_part"},{"id":"T41","span":{"begin":183,"end":193},"obj":"Body_part"}],"attributes":[{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A41","pred":"fma_id","subj":"T41","obj":"http://purl.org/sig/ont/fma/fma82740"},{"subj":"T40","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T41","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T50","span":{"begin":288,"end":289},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T51","span":{"begin":322,"end":323},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"attributes":[{"subj":"T50","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T51","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T11","span":{"begin":168,"end":178},"obj":"Chemical"},{"id":"T12","span":{"begin":168,"end":173},"obj":"Chemical"},{"id":"T13","span":{"begin":174,"end":178},"obj":"Chemical"},{"id":"T14","span":{"begin":183,"end":193},"obj":"Chemical"}],"attributes":[{"id":"A11","pred":"chebi_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A12","pred":"chebi_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A13","pred":"chebi_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A14","pred":"chebi_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"subj":"T11","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T12","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T13","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T14","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T61","span":{"begin":0,"end":39},"obj":"Sentence"},{"id":"T62","span":{"begin":40,"end":142},"obj":"Sentence"},{"id":"T63","span":{"begin":143,"end":354},"obj":"Sentence"},{"id":"T64","span":{"begin":355,"end":492},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T61","pred":"source","obj":"LitCovid-sentences"},{"subj":"T62","pred":"source","obj":"LitCovid-sentences"},{"subj":"T63","pred":"source","obj":"LitCovid-sentences"},{"subj":"T64","pred":"source","obj":"LitCovid-sentences"}]},{"project":"MyTest","denotations":[{"id":"32020836-20525638-27792007","span":{"begin":274,"end":275},"obj":"20525638"},{"id":"32020836-9847317-27792008","span":{"begin":489,"end":490},"obj":"9847317"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"attributes":[{"subj":"32020836-20525638-27792007","pred":"source","obj":"MyTest"},{"subj":"32020836-9847317-27792008","pred":"source","obj":"MyTest"}]},{"project":"2_test","denotations":[{"id":"32020836-20525638-27792007","span":{"begin":274,"end":275},"obj":"20525638"},{"id":"32020836-9847317-27792008","span":{"begin":489,"end":490},"obj":"9847317"}],"attributes":[{"subj":"32020836-20525638-27792007","pred":"source","obj":"2_test"},{"subj":"32020836-9847317-27792008","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PubTator","color":"#a4ec93","default":true},{"id":"LitCovid-PD-FMA-UBERON","color":"#ec93be"},{"id":"LitCovid-PD-CLO","color":"#93d8ec"},{"id":"LitCovid-PD-CHEBI","color":"#ece693"},{"id":"LitCovid-sentences","color":"#cc93ec"},{"id":"MyTest","color":"#93ecb2"},{"id":"2_test","color":"#ec9893"}]}]}}