PMC:7033720 / 5289-6148 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"81","span":{"begin":230,"end":235},"obj":"Species"},{"id":"82","span":{"begin":293,"end":298},"obj":"Species"},{"id":"83","span":{"begin":315,"end":320},"obj":"Species"}],"attributes":[{"id":"A81","pred":"tao:has_database_id","subj":"81","obj":"Tax:9606"},{"id":"A82","pred":"tao:has_database_id","subj":"82","obj":"Tax:9606"},{"id":"A83","pred":"tao:has_database_id","subj":"83","obj":"Tax:9606"}],"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":"To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline was carried out on sequenced data. Briefly, reads containing adaptor sequences and low-complex regions were removed from the dataset. Human reads were also removed by mapping against the reference human genome. All non-human and non-repeat sequence reads were then compared to a reference virus database (downloaded from https://ftp.ncbi.nih.gov/blast/db/ref_viruses_rep_genomes.tar.gz) and the non-redundant protein database (nr) using blastn and diamond blastx programs [4], respectively. Taxonomy lineage information was obtained for each blast hits by matching the accession number with the taxonomy database, which was subsequently used to identify reads of virus origin. Bacterial pathogen identification was carried out by using the Metaphlan2 program [5]."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T34","span":{"begin":299,"end":305},"obj":"Body_part"},{"id":"T35","span":{"begin":505,"end":512},"obj":"Body_part"}],"attributes":[{"id":"A34","pred":"fma_id","subj":"T34","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline was carried out on sequenced data. Briefly, reads containing adaptor sequences and low-complex regions were removed from the dataset. Human reads were also removed by mapping against the reference human genome. All non-human and non-repeat sequence reads were then compared to a reference virus database (downloaded from https://ftp.ncbi.nih.gov/blast/db/ref_viruses_rep_genomes.tar.gz) and the non-redundant protein database (nr) using blastn and diamond blastx programs [4], respectively. Taxonomy lineage information was obtained for each blast hits by matching the accession number with the taxonomy database, which was subsequently used to identify reads of virus origin. Bacterial pathogen identification was carried out by using the Metaphlan2 program [5]."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T38","span":{"begin":66,"end":67},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T39","span":{"begin":230,"end":235},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T40","span":{"begin":293,"end":298},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T41","span":{"begin":315,"end":320},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T42","span":{"begin":373,"end":374},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T43","span":{"begin":385,"end":390},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T44","span":{"begin":448,"end":450},"obj":"http://purl.obolibrary.org/obo/CLO_0002709"},{"id":"T45","span":{"begin":759,"end":764},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"}],"text":"To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline was carried out on sequenced data. Briefly, reads containing adaptor sequences and low-complex regions were removed from the dataset. Human reads were also removed by mapping against the reference human genome. All non-human and non-repeat sequence reads were then compared to a reference virus database (downloaded from https://ftp.ncbi.nih.gov/blast/db/ref_viruses_rep_genomes.tar.gz) and the non-redundant protein database (nr) using blastn and diamond blastx programs [4], respectively. Taxonomy lineage information was obtained for each blast hits by matching the accession number with the taxonomy database, which was subsequently used to identify reads of virus origin. Bacterial pathogen identification was carried out by using the Metaphlan2 program [5]."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T9","span":{"begin":505,"end":512},"obj":"Chemical"},{"id":"T10","span":{"begin":544,"end":551},"obj":"Chemical"}],"attributes":[{"id":"A9","pred":"chebi_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A10","pred":"chebi_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/CHEBI_33417"}],"text":"To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline was carried out on sequenced data. Briefly, reads containing adaptor sequences and low-complex regions were removed from the dataset. Human reads were also removed by mapping against the reference human genome. All non-human and non-repeat sequence reads were then compared to a reference virus database (downloaded from https://ftp.ncbi.nih.gov/blast/db/ref_viruses_rep_genomes.tar.gz) and the non-redundant protein database (nr) using blastn and diamond blastx programs [4], respectively. Taxonomy lineage information was obtained for each blast hits by matching the accession number with the taxonomy database, which was subsequently used to identify reads of virus origin. Bacterial pathogen identification was carried out by using the Metaphlan2 program [5]."}

{"project":"LitCovid-sentences","denotations":[{"id":"T51","span":{"begin":0,"end":130},"obj":"Sentence"},{"id":"T52","span":{"begin":131,"end":229},"obj":"Sentence"},{"id":"T53","span":{"begin":230,"end":306},"obj":"Sentence"},{"id":"T54","span":{"begin":307,"end":586},"obj":"Sentence"},{"id":"T55","span":{"begin":587,"end":772},"obj":"Sentence"},{"id":"T56","span":{"begin":773,"end":859},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline was carried out on sequenced data. Briefly, reads containing adaptor sequences and low-complex regions were removed from the dataset. Human reads were also removed by mapping against the reference human genome. All non-human and non-repeat sequence reads were then compared to a reference virus database (downloaded from https://ftp.ncbi.nih.gov/blast/db/ref_viruses_rep_genomes.tar.gz) and the non-redundant protein database (nr) using blastn and diamond blastx programs [4], respectively. Taxonomy lineage information was obtained for each blast hits by matching the accession number with the taxonomy database, which was subsequently used to identify reads of virus origin. Bacterial pathogen identification was carried out by using the Metaphlan2 program [5]."}

{"project":"MyTest","denotations":[{"id":"32020836-25402007-27792004","span":{"begin":569,"end":570},"obj":"25402007"},{"id":"32020836-26418763-27792005","span":{"begin":856,"end":857},"obj":"26418763"}],"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/"}],"text":"To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline was carried out on sequenced data. Briefly, reads containing adaptor sequences and low-complex regions were removed from the dataset. Human reads were also removed by mapping against the reference human genome. All non-human and non-repeat sequence reads were then compared to a reference virus database (downloaded from https://ftp.ncbi.nih.gov/blast/db/ref_viruses_rep_genomes.tar.gz) and the non-redundant protein database (nr) using blastn and diamond blastx programs [4], respectively. Taxonomy lineage information was obtained for each blast hits by matching the accession number with the taxonomy database, which was subsequently used to identify reads of virus origin. Bacterial pathogen identification was carried out by using the Metaphlan2 program [5]."}

{"project":"2_test","denotations":[{"id":"32020836-25402007-27792004","span":{"begin":569,"end":570},"obj":"25402007"},{"id":"32020836-26418763-27792005","span":{"begin":856,"end":857},"obj":"26418763"}],"text":"To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline was carried out on sequenced data. Briefly, reads containing adaptor sequences and low-complex regions were removed from the dataset. Human reads were also removed by mapping against the reference human genome. All non-human and non-repeat sequence reads were then compared to a reference virus database (downloaded from https://ftp.ncbi.nih.gov/blast/db/ref_viruses_rep_genomes.tar.gz) and the non-redundant protein database (nr) using blastn and diamond blastx programs [4], respectively. Taxonomy lineage information was obtained for each blast hits by matching the accession number with the taxonomy database, which was subsequently used to identify reads of virus origin. Bacterial pathogen identification was carried out by using the Metaphlan2 program [5]."}