PMC:7033720 / 3314-7229 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":"Materials and methods\n\nEthics statement\nThis study was approved by the Ethics Committee of the Zhongnan Hospital of Wuhan University. The mNGS analyses of BALF samples were performed on existing samples collected during standard diagnostic tests, posing no extra burden to patients.\n\nSequence of events\n2nd January 2020. Obtained BALF samples from two patients with unusual pneumonia.\n3rd January 2020. Performed SARS-specific RT-PCR assay, yielded partial RdRp fragment, and revealed potential pathogen.\n4th January 2020. Extended RdRp fragments and obtained more genome fragments, and started mNGS RNA library preparation\n5th January 2020. Completed mNGS RNA library preparation.\n6th January 2020. Started mNGS sequencing on Miseq platform.\n7th January 2020. Received sequencing data, started pathogen identification pipeline, obtained virus genome, corrected the genome end with mapping, identified 2019-nCoV as sole pathogen, and the final CoV genome was 29,881 nt.\n8th January 2020. Performed genome comparisons and evolutionary analyses.\nSince 3rd January 2020, instant progress reports have been sent to Chinese Center for Disease Control and Prevention (CDC), keeping pace with every advancement we made in pathogen identification and characterization.\n\nLibrary preparation and sequencing\nTotal RNA extracted from BALF samples (collected on 2nd January 2020) were subject to metagenomic next-generation sequencing (mNGS) testing. The concentration of RNA samples were low (\u003c0.5 ng/ul) based on measurement by Qubit RNA HS Assay Kit (Thermo Fisher Scientific), and therefore the library preparation was performed with Trio RNA-Seq kit (NuGEN Technologies, USA) which targeted low concentration RNA samples and contained AnyDeplete probe that removes human ribosomal RNA. The resulting libraries were subject to 150 bp pair-end sequencing with an Illumina Miseq platform. The sequencing results were obtained in less than 24 h.\n\nPathogen discovery and characterization\nTo 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].\nReads were also assembled de novo using Megahit [6], with the virus genome identified based on the blast procedure described above. To validate the assembled genome sequences, reads were subsequently mapped to the genomes and a majority consensus sequences were determined for each sample. Minor variation calling was performed after mapping using Genious software package, with a minimum coverage set to 20 and minimum variant frequency set to 0.05. In addition to mapping, the virus genomes were also confirmed with Sanger sequencing using primers designed based on the NGS sequences.\n\nPhylogenetic 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":21}},{"label":"sec","span":{"begin":23,"end":282}},{"label":"title","span":{"begin":23,"end":39}},{"label":"p","span":{"begin":40,"end":282}},{"label":"sec","span":{"begin":284,"end":1260}},{"label":"title","span":{"begin":284,"end":302}},{"label":"p","span":{"begin":303,"end":384}},{"label":"p","span":{"begin":385,"end":504}},{"label":"p","span":{"begin":505,"end":623}},{"label":"p","span":{"begin":624,"end":681}},{"label":"p","span":{"begin":682,"end":742}},{"label":"p","span":{"begin":743,"end":969}},{"label":"p","span":{"begin":970,"end":1043}},{"label":"p","span":{"begin":1044,"end":1260}},{"label":"sec","span":{"begin":1262,"end":1933}},{"label":"title","span":{"begin":1262,"end":1296}},{"label":"p","span":{"begin":1297,"end":1933}},{"label":"sec","span":{"begin":1935,"end":3421}},{"label":"title","span":{"begin":1935,"end":1974}},{"label":"p","span":{"begin":1975,"end":2834}},{"label":"p","span":{"begin":2835,"end":3421}},{"label":"title","span":{"begin":3423,"end":3462}}],"tracks":[{"project":"LitCovid-PubTator","denotations":[{"id":"65","span":{"begin":273,"end":281},"obj":"Species"},{"id":"68","span":{"begin":352,"end":360},"obj":"Species"},{"id":"69","span":{"begin":374,"end":383},"obj":"Disease"},{"id":"72","span":{"begin":902,"end":911},"obj":"Species"},{"id":"73","span":{"begin":944,"end":947},"obj":"Species"},{"id":"76","span":{"begin":1625,"end":1629},"obj":"Gene"},{"id":"77","span":{"begin":1757,"end":1762},"obj":"Species"},{"id":"81","span":{"begin":2205,"end":2210},"obj":"Species"},{"id":"82","span":{"begin":2268,"end":2273},"obj":"Species"},{"id":"83","span":{"begin":2290,"end":2295},"obj":"Species"},{"id":"86","span":{"begin":3747,"end":3750},"obj":"Gene"},{"id":"87","span":{"begin":3499,"end":3503},"obj":"Species"}],"attributes":[{"id":"A65","pred":"tao:has_database_id","subj":"65","obj":"Tax:9606"},{"id":"A68","pred":"tao:has_database_id","subj":"68","obj":"Tax:9606"},{"id":"A69","pred":"tao:has_database_id","subj":"69","obj":"MESH:D011014"},{"id":"A72","pred":"tao:has_database_id","subj":"72","obj":"Tax:2697049"},{"id":"A73","pred":"tao:has_database_id","subj":"73","obj":"Tax:11118"},{"id":"A76","pred":"tao:has_database_id","subj":"76","obj":"Gene:7204"},{"id":"A77","pred":"tao:has_database_id","subj":"77","obj":"Tax:9606"},{"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"},{"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":"65","pred":"source","obj":"LitCovid-PubTator"},{"subj":"68","pred":"source","obj":"LitCovid-PubTator"},{"subj":"69","pred":"source","obj":"LitCovid-PubTator"},{"subj":"72","pred":"source","obj":"LitCovid-PubTator"},{"subj":"73","pred":"source","obj":"LitCovid-PubTator"},{"subj":"76","pred":"source","obj":"LitCovid-PubTator"},{"subj":"77","pred":"source","obj":"LitCovid-PubTator"},{"subj":"81","pred":"source","obj":"LitCovid-PubTator"},{"subj":"82","pred":"source","obj":"LitCovid-PubTator"},{"subj":"83","pred":"source","obj":"LitCovid-PubTator"},{"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":"T19","span":{"begin":565,"end":571},"obj":"Body_part"},{"id":"T20","span":{"begin":600,"end":603},"obj":"Body_part"},{"id":"T21","span":{"begin":657,"end":660},"obj":"Body_part"},{"id":"T22","span":{"begin":844,"end":850},"obj":"Body_part"},{"id":"T23","span":{"begin":866,"end":872},"obj":"Body_part"},{"id":"T24","span":{"begin":915,"end":919},"obj":"Body_part"},{"id":"T25","span":{"begin":948,"end":954},"obj":"Body_part"},{"id":"T26","span":{"begin":998,"end":1004},"obj":"Body_part"},{"id":"T27","span":{"begin":1303,"end":1306},"obj":"Body_part"},{"id":"T28","span":{"begin":1459,"end":1462},"obj":"Body_part"},{"id":"T29","span":{"begin":1523,"end":1526},"obj":"Body_part"},{"id":"T30","span":{"begin":1630,"end":1633},"obj":"Body_part"},{"id":"T31","span":{"begin":1701,"end":1704},"obj":"Body_part"},{"id":"T32","span":{"begin":1763,"end":1776},"obj":"Body_part"},{"id":"T33","span":{"begin":1773,"end":1776},"obj":"Body_part"},{"id":"T34","span":{"begin":2274,"end":2280},"obj":"Body_part"},{"id":"T35","span":{"begin":2480,"end":2487},"obj":"Body_part"},{"id":"T36","span":{"begin":2903,"end":2909},"obj":"Body_part"},{"id":"T37","span":{"begin":2993,"end":2999},"obj":"Body_part"},{"id":"T38","span":{"begin":3049,"end":3056},"obj":"Body_part"},{"id":"T39","span":{"begin":3320,"end":3327},"obj":"Body_part"},{"id":"T40","span":{"begin":3591,"end":3601},"obj":"Body_part"},{"id":"T41","span":{"begin":3606,"end":3616},"obj":"Body_part"}],"attributes":[{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A20","pred":"fma_id","subj":"T20","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A21","pred":"fma_id","subj":"T21","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A22","pred":"fma_id","subj":"T22","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A23","pred":"fma_id","subj":"T23","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A24","pred":"fma_id","subj":"T24","obj":"http://purl.org/sig/ont/fma/fma25000"},{"id":"A25","pred":"fma_id","subj":"T25","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A26","pred":"fma_id","subj":"T26","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A27","pred":"fma_id","subj":"T27","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A28","pred":"fma_id","subj":"T28","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A29","pred":"fma_id","subj":"T29","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A30","pred":"fma_id","subj":"T30","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A31","pred":"fma_id","subj":"T31","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A32","pred":"fma_id","subj":"T32","obj":"http://purl.org/sig/ont/fma/fma67118"},{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma67095"},{"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"},{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A37","pred":"fma_id","subj":"T37","obj":"http://purl.org/sig/ont/fma/fma84116"},{"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/fma84116"},{"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":"T19","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T20","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T21","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T22","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T23","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T24","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T25","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T26","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T27","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T28","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T29","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T30","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T31","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T32","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T33","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T34","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T35","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T36","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T37","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T38","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T39","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T40","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T41","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T7","span":{"begin":374,"end":383},"obj":"Disease"},{"id":"T8","span":{"begin":413,"end":417},"obj":"Disease"}],"attributes":[{"id":"A7","pred":"mondo_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A8","pred":"mondo_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"subj":"T7","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T8","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T33","span":{"begin":240,"end":245},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T34","span":{"begin":838,"end":843},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T35","span":{"begin":1162,"end":1165},"obj":"http://purl.obolibrary.org/obo/CL_0000990"},{"id":"T36","span":{"begin":1429,"end":1436},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T37","span":{"begin":1757,"end":1762},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T38","span":{"begin":2041,"end":2042},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T39","span":{"begin":2205,"end":2210},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T40","span":{"begin":2268,"end":2273},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T41","span":{"begin":2290,"end":2295},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T42","span":{"begin":2348,"end":2349},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T43","span":{"begin":2360,"end":2365},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T44","span":{"begin":2423,"end":2425},"obj":"http://purl.obolibrary.org/obo/CLO_0002709"},{"id":"T45","span":{"begin":2734,"end":2739},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T46","span":{"begin":2897,"end":2902},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T47","span":{"begin":3061,"end":3062},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T48","span":{"begin":3214,"end":3215},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T49","span":{"begin":3314,"end":3319},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T50","span":{"begin":3711,"end":3712},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T51","span":{"begin":3745,"end":3746},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"attributes":[{"subj":"T33","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T34","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T35","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T36","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T37","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T38","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T39","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T40","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T41","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T42","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T43","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T44","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T45","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T46","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T47","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T48","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T49","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T50","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T51","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T6","span":{"begin":1527,"end":1529},"obj":"Chemical"},{"id":"T7","span":{"begin":1738,"end":1743},"obj":"Chemical"},{"id":"T8","span":{"begin":1763,"end":1776},"obj":"Chemical"},{"id":"T9","span":{"begin":2480,"end":2487},"obj":"Chemical"},{"id":"T10","span":{"begin":2519,"end":2526},"obj":"Chemical"},{"id":"T11","span":{"begin":3591,"end":3601},"obj":"Chemical"},{"id":"T12","span":{"begin":3591,"end":3596},"obj":"Chemical"},{"id":"T13","span":{"begin":3597,"end":3601},"obj":"Chemical"},{"id":"T14","span":{"begin":3606,"end":3616},"obj":"Chemical"}],"attributes":[{"id":"A6","pred":"chebi_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/CHEBI_74056"},{"id":"A7","pred":"chebi_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/CHEBI_50406"},{"id":"A8","pred":"chebi_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/CHEBI_18111"},{"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"},{"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":"T6","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T7","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T8","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T9","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T10","pred":"source","obj":"LitCovid-PD-CHEBI"},{"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-PD-HP","denotations":[{"id":"T6","span":{"begin":374,"end":383},"obj":"Phenotype"}],"attributes":[{"id":"A6","pred":"hp_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"subj":"T6","pred":"source","obj":"LitCovid-PD-HP"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T25","span":{"begin":0,"end":21},"obj":"Sentence"},{"id":"T26","span":{"begin":23,"end":39},"obj":"Sentence"},{"id":"T27","span":{"begin":40,"end":133},"obj":"Sentence"},{"id":"T28","span":{"begin":134,"end":282},"obj":"Sentence"},{"id":"T29","span":{"begin":284,"end":302},"obj":"Sentence"},{"id":"T30","span":{"begin":303,"end":320},"obj":"Sentence"},{"id":"T31","span":{"begin":321,"end":384},"obj":"Sentence"},{"id":"T32","span":{"begin":385,"end":402},"obj":"Sentence"},{"id":"T33","span":{"begin":403,"end":504},"obj":"Sentence"},{"id":"T34","span":{"begin":505,"end":522},"obj":"Sentence"},{"id":"T35","span":{"begin":523,"end":623},"obj":"Sentence"},{"id":"T36","span":{"begin":624,"end":641},"obj":"Sentence"},{"id":"T37","span":{"begin":642,"end":681},"obj":"Sentence"},{"id":"T38","span":{"begin":682,"end":699},"obj":"Sentence"},{"id":"T39","span":{"begin":700,"end":742},"obj":"Sentence"},{"id":"T40","span":{"begin":743,"end":760},"obj":"Sentence"},{"id":"T41","span":{"begin":761,"end":969},"obj":"Sentence"},{"id":"T42","span":{"begin":970,"end":987},"obj":"Sentence"},{"id":"T43","span":{"begin":988,"end":1043},"obj":"Sentence"},{"id":"T44","span":{"begin":1044,"end":1260},"obj":"Sentence"},{"id":"T45","span":{"begin":1262,"end":1296},"obj":"Sentence"},{"id":"T46","span":{"begin":1297,"end":1437},"obj":"Sentence"},{"id":"T47","span":{"begin":1438,"end":1777},"obj":"Sentence"},{"id":"T48","span":{"begin":1778,"end":1877},"obj":"Sentence"},{"id":"T49","span":{"begin":1878,"end":1933},"obj":"Sentence"},{"id":"T50","span":{"begin":1935,"end":1974},"obj":"Sentence"},{"id":"T51","span":{"begin":1975,"end":2105},"obj":"Sentence"},{"id":"T52","span":{"begin":2106,"end":2204},"obj":"Sentence"},{"id":"T53","span":{"begin":2205,"end":2281},"obj":"Sentence"},{"id":"T54","span":{"begin":2282,"end":2561},"obj":"Sentence"},{"id":"T55","span":{"begin":2562,"end":2747},"obj":"Sentence"},{"id":"T56","span":{"begin":2748,"end":2834},"obj":"Sentence"},{"id":"T57","span":{"begin":2835,"end":2966},"obj":"Sentence"},{"id":"T58","span":{"begin":2967,"end":3124},"obj":"Sentence"},{"id":"T59","span":{"begin":3125,"end":3285},"obj":"Sentence"},{"id":"T60","span":{"begin":3286,"end":3421},"obj":"Sentence"},{"id":"T61","span":{"begin":3423,"end":3462},"obj":"Sentence"},{"id":"T62","span":{"begin":3463,"end":3565},"obj":"Sentence"},{"id":"T63","span":{"begin":3566,"end":3777},"obj":"Sentence"},{"id":"T64","span":{"begin":3778,"end":3915},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T25","pred":"source","obj":"LitCovid-sentences"},{"subj":"T26","pred":"source","obj":"LitCovid-sentences"},{"subj":"T27","pred":"source","obj":"LitCovid-sentences"},{"subj":"T28","pred":"source","obj":"LitCovid-sentences"},{"subj":"T29","pred":"source","obj":"LitCovid-sentences"},{"subj":"T30","pred":"source","obj":"LitCovid-sentences"},{"subj":"T31","pred":"source","obj":"LitCovid-sentences"},{"subj":"T32","pred":"source","obj":"LitCovid-sentences"},{"subj":"T33","pred":"source","obj":"LitCovid-sentences"},{"subj":"T34","pred":"source","obj":"LitCovid-sentences"},{"subj":"T35","pred":"source","obj":"LitCovid-sentences"},{"subj":"T36","pred":"source","obj":"LitCovid-sentences"},{"subj":"T37","pred":"source","obj":"LitCovid-sentences"},{"subj":"T38","pred":"source","obj":"LitCovid-sentences"},{"subj":"T39","pred":"source","obj":"LitCovid-sentences"},{"subj":"T40","pred":"source","obj":"LitCovid-sentences"},{"subj":"T41","pred":"source","obj":"LitCovid-sentences"},{"subj":"T42","pred":"source","obj":"LitCovid-sentences"},{"subj":"T43","pred":"source","obj":"LitCovid-sentences"},{"subj":"T44","pred":"source","obj":"LitCovid-sentences"},{"subj":"T45","pred":"source","obj":"LitCovid-sentences"},{"subj":"T46","pred":"source","obj":"LitCovid-sentences"},{"subj":"T47","pred":"source","obj":"LitCovid-sentences"},{"subj":"T48","pred":"source","obj":"LitCovid-sentences"},{"subj":"T49","pred":"source","obj":"LitCovid-sentences"},{"subj":"T50","pred":"source","obj":"LitCovid-sentences"},{"subj":"T51","pred":"source","obj":"LitCovid-sentences"},{"subj":"T52","pred":"source","obj":"LitCovid-sentences"},{"subj":"T53","pred":"source","obj":"LitCovid-sentences"},{"subj":"T54","pred":"source","obj":"LitCovid-sentences"},{"subj":"T55","pred":"source","obj":"LitCovid-sentences"},{"subj":"T56","pred":"source","obj":"LitCovid-sentences"},{"subj":"T57","pred":"source","obj":"LitCovid-sentences"},{"subj":"T58","pred":"source","obj":"LitCovid-sentences"},{"subj":"T59","pred":"source","obj":"LitCovid-sentences"},{"subj":"T60","pred":"source","obj":"LitCovid-sentences"},{"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":"32020836-25402007-27792004","span":{"begin":2544,"end":2545},"obj":"25402007"},{"id":"32020836-26418763-27792005","span":{"begin":2831,"end":2832},"obj":"26418763"},{"id":"32020836-25609793-27792006","span":{"begin":2884,"end":2885},"obj":"25609793"},{"id":"32020836-20525638-27792007","span":{"begin":3697,"end":3698},"obj":"20525638"},{"id":"32020836-9847317-27792008","span":{"begin":3912,"end":3913},"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":"32020836-25402007-27792004","pred":"source","obj":"MyTest"},{"subj":"32020836-26418763-27792005","pred":"source","obj":"MyTest"},{"subj":"32020836-25609793-27792006","pred":"source","obj":"MyTest"},{"subj":"32020836-20525638-27792007","pred":"source","obj":"MyTest"},{"subj":"32020836-9847317-27792008","pred":"source","obj":"MyTest"}]},{"project":"2_test","denotations":[{"id":"32020836-25402007-27792004","span":{"begin":2544,"end":2545},"obj":"25402007"},{"id":"32020836-26418763-27792005","span":{"begin":2831,"end":2832},"obj":"26418763"},{"id":"32020836-25609793-27792006","span":{"begin":2884,"end":2885},"obj":"25609793"},{"id":"32020836-20525638-27792007","span":{"begin":3697,"end":3698},"obj":"20525638"},{"id":"32020836-9847317-27792008","span":{"begin":3912,"end":3913},"obj":"9847317"}],"attributes":[{"subj":"32020836-25402007-27792004","pred":"source","obj":"2_test"},{"subj":"32020836-26418763-27792005","pred":"source","obj":"2_test"},{"subj":"32020836-25609793-27792006","pred":"source","obj":"2_test"},{"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":"#93ecbf","default":true},{"id":"LitCovid-PD-FMA-UBERON","color":"#eca593"},{"id":"LitCovid-PD-MONDO","color":"#939aec"},{"id":"LitCovid-PD-CLO","color":"#b4ec93"},{"id":"LitCovid-PD-CHEBI","color":"#ec93ce"},{"id":"LitCovid-PD-HP","color":"#93e8ec"},{"id":"LitCovid-sentences","color":"#ecd593"},{"id":"MyTest","color":"#bb93ec"},{"id":"2_test","color":"#93eca1"}]}]}}