PMC:7354481 / 11561-15193 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7354481","sourcedb":"PMC","sourceid":"7354481","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7354481","text":"2. Material and Methods\n\n2.1. Genome Sequences\nThe SARS-CoV-2 genome sequences from China, Italy, Spain (Valencia), and those for MERS, SARS, OC43 and 229E were obtained from NCBI (GenBank: NC_045512.2, LC528232.1, MT066156.1, MT198652.2, KT225476.2, NC_004718.3, NC_006213.1, NC_002645.1, respectively). The SARS-CoV-2 genome sequences from England (hCoV-19/England/20136087804/2020|EPI_ISL_420910, no treatment) and Turkey (hCoV-19/Turkey/GLAB-CoV008/2020) were obtained from the China National Bioinformatics Center, GISAID database [23] (https://www.gisaid.org). In addition, a SARS-CoV-2 strain isolated from a Turkish patient, and infected to Vero E6 cells passage 4 sequence (hCoV-19/Turkey/ERAGEM-001/2020;) was used for alignment studies with the miRBase mature miRNA search tool.\n\n2.2. miR Prediction\nThe miRTarget and miRBase programmes were used to predict the similarities between the SARS-CoV-2 genome and human miRs; e-value \u003c10 and score \u003e70 were considered as significant. DianaTools miRPath V3 were then used to create heat maps for pathways affected by selected miRs, focusing on the microT-CDS version 5.0 database. The p value threshold was 0.05 and microT threshold was 0.8. Heatmap analysis was done with pathway intersection [24].\n\n2.3. Mutational Analysis of Potential miRNA Sites\nViral genome sequencing data was obtained from the GISAID database (https://www.gisaid.org), and analysed as multiple sequence alignments using the Clustal Omega at EBI (www.ebi.ac.uk/Tools/msa/clustalo/).\n\n2.4. Pathway Analysis\nBioproject data was obtained from PRJNA615032 bioproject trancriptome data, which includes lung biopsies from SARS-CoV-2-infected patients and healthy volunteers as well as mock and SARS-CoV-2-transfected NHEB and A549 cell lines. The data have been deposited with links to BioProject accession number PRJNA615032 in the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/). All the selected data were reanalysed at the Rosalind bioinformatics server. Data analysis was performed according to 1.5 fold change between untransfected and transfected cell lines in a data pool calculation for both cell lines at p \u003c 0.05 significance level. Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA, USA). Reads were trimmed using cutadapt [25]. Quality scores were assessed using FastQC [26]. Reads were aligned to the Homo sapiens genome built by GRCh38 using STAR [27]. Individual sample reads were quantified using HTseq [28] and normalized via relative log expression (RLE) using DESeq2 R library [29]. Read distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC [30]. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (partitioning around medoids) method using the fpc R library (https://cran.r-project.org/web/packages/fpc/index.html). Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library [31], was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro [32], NCBI [33], MSigDB [34,35], REACTOME [36], and WikiPathways [37]. Enrichment was calculated relative to a set of background genes relevant for the experiment.","divisions":[{"label":"title","span":{"begin":0,"end":23}},{"label":"sec","span":{"begin":25,"end":789}},{"label":"title","span":{"begin":25,"end":46}},{"label":"p","span":{"begin":47,"end":789}},{"label":"sec","span":{"begin":791,"end":1254}},{"label":"title","span":{"begin":791,"end":810}},{"label":"p","span":{"begin":811,"end":1254}},{"label":"sec","span":{"begin":1256,"end":1511}},{"label":"title","span":{"begin":1256,"end":1305}},{"label":"p","span":{"begin":1306,"end":1511}},{"label":"title","span":{"begin":1513,"end":1534}}],"tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T70","span":{"begin":30,"end":36},"obj":"Body_part"},{"id":"T71","span":{"begin":62,"end":68},"obj":"Body_part"},{"id":"T72","span":{"begin":320,"end":326},"obj":"Body_part"},{"id":"T73","span":{"begin":657,"end":662},"obj":"Body_part"},{"id":"T74","span":{"begin":909,"end":915},"obj":"Body_part"},{"id":"T75","span":{"begin":1009,"end":1011},"obj":"Body_part"},{"id":"T76","span":{"begin":1312,"end":1318},"obj":"Body_part"},{"id":"T77","span":{"begin":1626,"end":1630},"obj":"Body_part"},{"id":"T78","span":{"begin":1754,"end":1758},"obj":"Body_part"},{"id":"T79","span":{"begin":2097,"end":2101},"obj":"Body_part"},{"id":"T80","span":{"begin":2144,"end":2148},"obj":"Body_part"},{"id":"T81","span":{"begin":2470,"end":2476},"obj":"Body_part"},{"id":"T82","span":{"begin":3183,"end":3187},"obj":"Body_part"}],"attributes":[{"id":"A70","pred":"fma_id","subj":"T70","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A71","pred":"fma_id","subj":"T71","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A72","pred":"fma_id","subj":"T72","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A73","pred":"fma_id","subj":"T73","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A74","pred":"fma_id","subj":"T74","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A75","pred":"fma_id","subj":"T75","obj":"http://purl.org/sig/ont/fma/fma13442"},{"id":"A76","pred":"fma_id","subj":"T76","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A77","pred":"fma_id","subj":"T77","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A78","pred":"fma_id","subj":"T78","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A79","pred":"fma_id","subj":"T79","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A80","pred":"fma_id","subj":"T80","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A81","pred":"fma_id","subj":"T81","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A82","pred":"fma_id","subj":"T82","obj":"http://purl.org/sig/ont/fma/fma74402"},{"subj":"T70","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T71","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T72","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T73","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T74","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T75","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T76","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T77","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T78","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T79","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T80","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T81","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T82","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T12","span":{"begin":1626,"end":1630},"obj":"Body_part"}],"attributes":[{"id":"A12","pred":"uberon_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"subj":"T12","pred":"source","obj":"LitCovid-PD-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T47","span":{"begin":51,"end":59},"obj":"Disease"},{"id":"T48","span":{"begin":136,"end":140},"obj":"Disease"},{"id":"T49","span":{"begin":309,"end":317},"obj":"Disease"},{"id":"T50","span":{"begin":582,"end":590},"obj":"Disease"},{"id":"T51","span":{"begin":898,"end":906},"obj":"Disease"},{"id":"T52","span":{"begin":1645,"end":1653},"obj":"Disease"},{"id":"T53","span":{"begin":1717,"end":1725},"obj":"Disease"},{"id":"T54","span":{"begin":2499,"end":2503},"obj":"Disease"},{"id":"T55","span":{"begin":2720,"end":2723},"obj":"Disease"},{"id":"T57","span":{"begin":2984,"end":2987},"obj":"Disease"}],"attributes":[{"id":"A47","pred":"mondo_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A48","pred":"mondo_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A49","pred":"mondo_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A50","pred":"mondo_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A51","pred":"mondo_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A52","pred":"mondo_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A53","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A54","pred":"mondo_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/MONDO_0010408"},{"id":"A55","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0009532"},{"id":"A56","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0018881"},{"id":"A57","pred":"mondo_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/MONDO_0018959"},{"subj":"T47","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T48","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T49","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T50","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T51","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T52","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T53","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T54","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T55","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T57","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T108","span":{"begin":418,"end":424},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9005"},{"id":"T109","span":{"begin":434,"end":440},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9005"},{"id":"T110","span":{"begin":580,"end":581},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T111","span":{"begin":614,"end":615},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T112","span":{"begin":649,"end":662},"obj":"http://purl.obolibrary.org/obo/CLO_0051719"},{"id":"T113","span":{"begin":691,"end":697},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9005"},{"id":"T114","span":{"begin":920,"end":925},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T115","span":{"begin":1009,"end":1011},"obj":"http://purl.obolibrary.org/obo/CLO_0050428"},{"id":"T116","span":{"begin":1087,"end":1095},"obj":"http://purl.obolibrary.org/obo/CLO_0009985"},{"id":"T117","span":{"begin":1626,"end":1630},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T118","span":{"begin":1626,"end":1630},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T119","span":{"begin":1749,"end":1753},"obj":"http://purl.obolibrary.org/obo/CLO_0001601"},{"id":"T120","span":{"begin":1749,"end":1753},"obj":"http://purl.obolibrary.org/obo/CLO_0050025"},{"id":"T121","span":{"begin":1749,"end":1753},"obj":"http://purl.obolibrary.org/obo/CLO_0054264"},{"id":"T122","span":{"begin":1749,"end":1753},"obj":"http://purl.obolibrary.org/obo/CLO_0054265"},{"id":"T123","span":{"begin":1749,"end":1753},"obj":"http://purl.obolibrary.org/obo/CLO_0054266"},{"id":"T124","span":{"begin":1749,"end":1753},"obj":"http://purl.obolibrary.org/obo/CLO_0054267"},{"id":"T125","span":{"begin":1749,"end":1753},"obj":"http://purl.obolibrary.org/obo/CLO_0054268"},{"id":"T126","span":{"begin":1749,"end":1753},"obj":"http://purl.obolibrary.org/obo/CLO_0054269"},{"id":"T127","span":{"begin":1754,"end":1764},"obj":"http://purl.obolibrary.org/obo/CLO_0000031"},{"id":"T128","span":{"begin":2097,"end":2107},"obj":"http://purl.obolibrary.org/obo/CLO_0000031"},{"id":"T129","span":{"begin":2111,"end":2112},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T130","span":{"begin":2144,"end":2154},"obj":"http://purl.obolibrary.org/obo/CLO_0000031"},{"id":"T131","span":{"begin":2254,"end":2255},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T132","span":{"begin":2457,"end":2469},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T133","span":{"begin":2505,"end":2507},"obj":"http://purl.obolibrary.org/obo/CLO_0050509"},{"id":"T134","span":{"begin":2903,"end":2908},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T135","span":{"begin":2959,"end":2964},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T136","span":{"begin":3183,"end":3187},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T137","span":{"begin":3512,"end":3514},"obj":"http://purl.obolibrary.org/obo/CLO_0001313"},{"id":"T138","span":{"begin":3578,"end":3579},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T139","span":{"begin":3598,"end":3603},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"}],"attributes":[{"subj":"T108","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T109","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T110","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T111","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T112","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T113","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T114","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T115","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T116","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T117","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T118","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T119","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T120","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T121","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T122","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T123","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T124","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T125","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T126","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T127","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T128","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T129","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T130","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T131","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T132","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T133","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T134","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T135","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T136","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T137","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T138","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T139","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T20","span":{"begin":1518,"end":1525},"obj":"Chemical"},{"id":"T21","span":{"begin":2984,"end":2987},"obj":"Chemical"}],"attributes":[{"id":"A20","pred":"chebi_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/CHEBI_34922"},{"id":"A21","pred":"chebi_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/CHEBI_51135"},{"id":"A22","pred":"chebi_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/CHEBI_60882"},{"subj":"T20","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T21","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T72","span":{"begin":0,"end":2},"obj":"Sentence"},{"id":"T73","span":{"begin":3,"end":23},"obj":"Sentence"},{"id":"T74","span":{"begin":25,"end":29},"obj":"Sentence"},{"id":"T75","span":{"begin":30,"end":46},"obj":"Sentence"},{"id":"T76","span":{"begin":47,"end":304},"obj":"Sentence"},{"id":"T77","span":{"begin":305,"end":566},"obj":"Sentence"},{"id":"T78","span":{"begin":567,"end":789},"obj":"Sentence"},{"id":"T79","span":{"begin":791,"end":810},"obj":"Sentence"},{"id":"T80","span":{"begin":811,"end":989},"obj":"Sentence"},{"id":"T81","span":{"begin":990,"end":1135},"obj":"Sentence"},{"id":"T82","span":{"begin":1136,"end":1196},"obj":"Sentence"},{"id":"T83","span":{"begin":1197,"end":1254},"obj":"Sentence"},{"id":"T84","span":{"begin":1256,"end":1260},"obj":"Sentence"},{"id":"T85","span":{"begin":1261,"end":1305},"obj":"Sentence"},{"id":"T86","span":{"begin":1306,"end":1511},"obj":"Sentence"},{"id":"T87","span":{"begin":1513,"end":1517},"obj":"Sentence"},{"id":"T88","span":{"begin":1518,"end":1534},"obj":"Sentence"},{"id":"T89","span":{"begin":1535,"end":1765},"obj":"Sentence"},{"id":"T90","span":{"begin":1766,"end":1924},"obj":"Sentence"},{"id":"T91","span":{"begin":1925,"end":2001},"obj":"Sentence"},{"id":"T92","span":{"begin":2002,"end":2186},"obj":"Sentence"},{"id":"T93","span":{"begin":2187,"end":2342},"obj":"Sentence"},{"id":"T94","span":{"begin":2343,"end":2382},"obj":"Sentence"},{"id":"T95","span":{"begin":2383,"end":2430},"obj":"Sentence"},{"id":"T96","span":{"begin":2431,"end":2509},"obj":"Sentence"},{"id":"T97","span":{"begin":2510,"end":2644},"obj":"Sentence"},{"id":"T98","span":{"begin":2645,"end":2785},"obj":"Sentence"},{"id":"T99","span":{"begin":2786,"end":2888},"obj":"Sentence"},{"id":"T100","span":{"begin":2889,"end":3106},"obj":"Sentence"},{"id":"T101","span":{"begin":3107,"end":3237},"obj":"Sentence"},{"id":"T102","span":{"begin":3238,"end":3383},"obj":"Sentence"},{"id":"T103","span":{"begin":3384,"end":3539},"obj":"Sentence"},{"id":"T104","span":{"begin":3540,"end":3632},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T72","pred":"source","obj":"LitCovid-sentences"},{"subj":"T73","pred":"source","obj":"LitCovid-sentences"},{"subj":"T74","pred":"source","obj":"LitCovid-sentences"},{"subj":"T75","pred":"source","obj":"LitCovid-sentences"},{"subj":"T76","pred":"source","obj":"LitCovid-sentences"},{"subj":"T77","pred":"source","obj":"LitCovid-sentences"},{"subj":"T78","pred":"source","obj":"LitCovid-sentences"},{"subj":"T79","pred":"source","obj":"LitCovid-sentences"},{"subj":"T80","pred":"source","obj":"LitCovid-sentences"},{"subj":"T81","pred":"source","obj":"LitCovid-sentences"},{"subj":"T82","pred":"source","obj":"LitCovid-sentences"},{"subj":"T83","pred":"source","obj":"LitCovid-sentences"},{"subj":"T84","pred":"source","obj":"LitCovid-sentences"},{"subj":"T85","pred":"source","obj":"LitCovid-sentences"},{"subj":"T86","pred":"source","obj":"LitCovid-sentences"},{"subj":"T87","pred":"source","obj":"LitCovid-sentences"},{"subj":"T88","pred":"source","obj":"LitCovid-sentences"},{"subj":"T89","pred":"source","obj":"LitCovid-sentences"},{"subj":"T90","pred":"source","obj":"LitCovid-sentences"},{"subj":"T91","pred":"source","obj":"LitCovid-sentences"},{"subj":"T92","pred":"source","obj":"LitCovid-sentences"},{"subj":"T93","pred":"source","obj":"LitCovid-sentences"},{"subj":"T94","pred":"source","obj":"LitCovid-sentences"},{"subj":"T95","pred":"source","obj":"LitCovid-sentences"},{"subj":"T96","pred":"source","obj":"LitCovid-sentences"},{"subj":"T97","pred":"source","obj":"LitCovid-sentences"},{"subj":"T98","pred":"source","obj":"LitCovid-sentences"},{"subj":"T99","pred":"source","obj":"LitCovid-sentences"},{"subj":"T100","pred":"source","obj":"LitCovid-sentences"},{"subj":"T101","pred":"source","obj":"LitCovid-sentences"},{"subj":"T102","pred":"source","obj":"LitCovid-sentences"},{"subj":"T103","pred":"source","obj":"LitCovid-sentences"},{"subj":"T104","pred":"source","obj":"LitCovid-sentences"}]},{"project":"2_test","denotations":[{"id":"32512929-24935956-144200712","span":{"begin":537,"end":539},"obj":"24935956"},{"id":"32512929-28382917-144200713","span":{"begin":1250,"end":1252},"obj":"28382917"},{"id":"32512929-25977294-144200714","span":{"begin":2378,"end":2380},"obj":"25977294"},{"id":"32512929-23104886-144200715","span":{"begin":2563,"end":2565},"obj":"23104886"},{"id":"32512929-25260700-144200716","span":{"begin":2640,"end":2642},"obj":"25260700"},{"id":"32512929-25516281-144200717","span":{"begin":2781,"end":2783},"obj":"25516281"},{"id":"32512929-22743226-144200718","span":{"begin":3259,"end":3261},"obj":"22743226"},{"id":"32512929-30398656-144200719","span":{"begin":3481,"end":3483},"obj":"30398656"},{"id":"32512929-19854944-144200720","span":{"begin":3494,"end":3496},"obj":"19854944"},{"id":"32512929-29145629-144200721","span":{"begin":3535,"end":3537},"obj":"29145629"}],"attributes":[{"subj":"32512929-24935956-144200712","pred":"source","obj":"2_test"},{"subj":"32512929-28382917-144200713","pred":"source","obj":"2_test"},{"subj":"32512929-25977294-144200714","pred":"source","obj":"2_test"},{"subj":"32512929-23104886-144200715","pred":"source","obj":"2_test"},{"subj":"32512929-25260700-144200716","pred":"source","obj":"2_test"},{"subj":"32512929-25516281-144200717","pred":"source","obj":"2_test"},{"subj":"32512929-22743226-144200718","pred":"source","obj":"2_test"},{"subj":"32512929-30398656-144200719","pred":"source","obj":"2_test"},{"subj":"32512929-19854944-144200720","pred":"source","obj":"2_test"},{"subj":"32512929-29145629-144200721","pred":"source","obj":"2_test"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"199","span":{"begin":51,"end":61},"obj":"Species"},{"id":"200","span":{"begin":309,"end":319},"obj":"Species"},{"id":"201","span":{"begin":351,"end":358},"obj":"Species"},{"id":"202","span":{"begin":418,"end":424},"obj":"Species"},{"id":"203","span":{"begin":426,"end":433},"obj":"Species"},{"id":"204","span":{"begin":434,"end":440},"obj":"Species"},{"id":"205","span":{"begin":582,"end":592},"obj":"Species"},{"id":"206","span":{"begin":624,"end":631},"obj":"Species"},{"id":"207","span":{"begin":683,"end":690},"obj":"Species"},{"id":"208","span":{"begin":691,"end":697},"obj":"Species"},{"id":"209","span":{"begin":142,"end":146},"obj":"Species"},{"id":"210","span":{"begin":151,"end":155},"obj":"Species"},{"id":"211","span":{"begin":446,"end":449},"obj":"Species"},{"id":"212","span":{"begin":130,"end":134},"obj":"Disease"},{"id":"213","span":{"begin":637,"end":645},"obj":"Disease"},{"id":"216","span":{"begin":898,"end":908},"obj":"Species"},{"id":"217","span":{"begin":920,"end":925},"obj":"Species"},{"id":"219","span":{"begin":1471,"end":1474},"obj":"Gene"},{"id":"226","span":{"begin":2499,"end":2503},"obj":"Gene"},{"id":"227","span":{"begin":1665,"end":1673},"obj":"Species"},{"id":"228","span":{"begin":1717,"end":1727},"obj":"Species"},{"id":"229","span":{"begin":2457,"end":2469},"obj":"Species"},{"id":"230","span":{"begin":1645,"end":1664},"obj":"Disease"},{"id":"231","span":{"begin":1749,"end":1753},"obj":"CellLine"}],"attributes":[{"id":"A199","pred":"tao:has_database_id","subj":"199","obj":"Tax:2697049"},{"id":"A200","pred":"tao:has_database_id","subj":"200","obj":"Tax:2697049"},{"id":"A201","pred":"tao:has_database_id","subj":"201","obj":"Tax:2697049"},{"id":"A202","pred":"tao:has_database_id","subj":"202","obj":"Tax:9103"},{"id":"A203","pred":"tao:has_database_id","subj":"203","obj":"Tax:2697049"},{"id":"A204","pred":"tao:has_database_id","subj":"204","obj":"Tax:9103"},{"id":"A205","pred":"tao:has_database_id","subj":"205","obj":"Tax:2697049"},{"id":"A206","pred":"tao:has_database_id","subj":"206","obj":"Tax:9606"},{"id":"A207","pred":"tao:has_database_id","subj":"207","obj":"Tax:2697049"},{"id":"A208","pred":"tao:has_database_id","subj":"208","obj":"Tax:9103"},{"id":"A209","pred":"tao:has_database_id","subj":"209","obj":"Tax:31631"},{"id":"A210","pred":"tao:has_database_id","subj":"210","obj":"Tax:11137"},{"id":"A211","pred":"tao:has_database_id","subj":"211","obj":"Tax:11118"},{"id":"A212","pred":"tao:has_database_id","subj":"212","obj":"MESH:D018352"},{"id":"A213","pred":"tao:has_database_id","subj":"213","obj":"MESH:D007239"},{"id":"A216","pred":"tao:has_database_id","subj":"216","obj":"Tax:2697049"},{"id":"A217","pred":"tao:has_database_id","subj":"217","obj":"Tax:9606"},{"id":"A219","pred":"tao:has_database_id","subj":"219","obj":"Gene:6907"},{"id":"A226","pred":"tao:has_database_id","subj":"226","obj":"Gene:6770"},{"id":"A227","pred":"tao:has_database_id","subj":"227","obj":"Tax:9606"},{"id":"A228","pred":"tao:has_database_id","subj":"228","obj":"Tax:2697049"},{"id":"A229","pred":"tao:has_database_id","subj":"229","obj":"Tax:9606"},{"id":"A230","pred":"tao:has_database_id","subj":"230","obj":"MESH:C000657245"},{"id":"A231","pred":"tao:has_database_id","subj":"231","obj":"CVCL:0023"},{"subj":"199","pred":"source","obj":"LitCovid-PubTator"},{"subj":"200","pred":"source","obj":"LitCovid-PubTator"},{"subj":"201","pred":"source","obj":"LitCovid-PubTator"},{"subj":"202","pred":"source","obj":"LitCovid-PubTator"},{"subj":"203","pred":"source","obj":"LitCovid-PubTator"},{"subj":"204","pred":"source","obj":"LitCovid-PubTator"},{"subj":"205","pred":"source","obj":"LitCovid-PubTator"},{"subj":"206","pred":"source","obj":"LitCovid-PubTator"},{"subj":"207","pred":"source","obj":"LitCovid-PubTator"},{"subj":"208","pred":"source","obj":"LitCovid-PubTator"},{"subj":"209","pred":"source","obj":"LitCovid-PubTator"},{"subj":"210","pred":"source","obj":"LitCovid-PubTator"},{"subj":"211","pred":"source","obj":"LitCovid-PubTator"},{"subj":"212","pred":"source","obj":"LitCovid-PubTator"},{"subj":"213","pred":"source","obj":"LitCovid-PubTator"},{"subj":"216","pred":"source","obj":"LitCovid-PubTator"},{"subj":"217","pred":"source","obj":"LitCovid-PubTator"},{"subj":"219","pred":"source","obj":"LitCovid-PubTator"},{"subj":"226","pred":"source","obj":"LitCovid-PubTator"},{"subj":"227","pred":"source","obj":"LitCovid-PubTator"},{"subj":"228","pred":"source","obj":"LitCovid-PubTator"},{"subj":"229","pred":"source","obj":"LitCovid-PubTator"},{"subj":"230","pred":"source","obj":"LitCovid-PubTator"},{"subj":"231","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_"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#bdec93","default":true},{"id":"LitCovid-PD-UBERON","color":"#ec93d7"},{"id":"LitCovid-PD-MONDO","color":"#93ece6"},{"id":"LitCovid-PD-CLO","color":"#eccc93"},{"id":"LitCovid-PD-CHEBI","color":"#b293ec"},{"id":"LitCovid-sentences","color":"#93ec98"},{"id":"2_test","color":"#ec93a7"},{"id":"LitCovid-PubTator","color":"#93c1ec"}]}]}}