PMC:7252096 / 113300-114988 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T113 70-76 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T114 230-236 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T115 271-276 Body_part denotes joint http://purl.org/sig/ont/fma/fma7490
T116 277-283 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T117 838-841 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T118 995-999 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T119 1004-1008 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T120 1292-1297 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T121 1469-1480 Body_part denotes Pneumocytes http://purl.org/sig/ont/fma/fma62499
T122 1607-1612 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T123 1614-1619 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T175 51-52 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T176 120-125 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T177 126-131 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T178 142-147 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T179 224-229 http://purl.obolibrary.org/obo/CLO_0007836 denotes mouse
T180 271-276 http://purl.obolibrary.org/obo/UBERON_0000982 denotes joint
T181 271-276 http://purl.obolibrary.org/obo/UBERON_0004905 denotes joint
T182 425-430 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T183 521-526 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T184 794-798 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T185 991-999 http://purl.obolibrary.org/obo/CLO_0008190 denotes per cell
T186 1004-1008 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T187 1051-1056 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T188 1170-1175 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T189 1192-1197 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T190 1267-1272 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T191 1292-1297 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T192 1391-1396 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T193 1575-1576 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T194 1607-1612 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T195 1614-1619 http://purl.obolibrary.org/obo/GO_0005623 denotes Cells

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T7 466-476 http://purl.obolibrary.org/obo/GO_0006351 denotes transcript
T8 1004-1014 http://purl.obolibrary.org/obo/GO_0007049 denotes cell cycle

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T812 0-132 Sentence denotes Libraries corresponding to 14 mice were aligned to a custom reference genome encompassing both murine (mm10) and herpes virus genes:
T813 133-237 Sentence denotes 84 known genes from MHV68 were retrieved from NCBI (NCBI: txid33708) and added to the mm10 mouse genome.
T814 238-397 Sentence denotes Reads were aligned to the custom joint genome and processed according to the Drop-Seq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq).
T815 398-542 Sentence denotes Barcodes with < 200 unique genes, > 20,000 UMI counts, and > 30% of transcript counts derived from mitochondrially encoded genes were discarded.
T816 543-800 Sentence denotes Data analysis was performed using the Scanpy Package following the common procedure, the expression matrices were normalized using scran’s size factor based approach and log transformed via scanpy’s pp.log1p() function (Lun et al., 2016, Wolf et al., 2018).
T817 801-986 Sentence denotes SoupX was utilized to reduce ambient RNA bias, using default parameters with pCut set to 0.3, and was applied to each sample before merging the count matrices (Young and Behjati, 2020).
T818 987-1034 Sentence denotes UMI per cell and cell cycle were regressed out.
T819 1035-1273 Sentence denotes Highly variable genes were selected by running pp.highly_variable_genes() for each sample separately, returning the top 4,000 variable genes per sample, and genes identified in variable in > 5 samples were retained, yielding 14,305 genes.
T820 1274-1461 Sentence denotes Next, only Epcam+ cells were considered, principal components (PCs) were calculated using only the selected variable genes, and 6 PCs were used to perform unsupervised Louvain clustering.
T821 1462-1613 Sentence denotes Type I Pneumocytes were excluded from this analysis based on uniformly negative expression of Ace2, resulting in a final dataset subset of 5,558 cells.
T822 1614-1688 Sentence denotes Cells were identified as infected if at least one viral read was detected.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2783 1285-1290 Gene denotes Epcam Gene:4072
2784 1556-1560 Gene denotes Ace2 Gene:59272
2785 30-34 Species denotes mice Tax:10090
2786 95-101 Species denotes murine Tax:10090
2787 153-158 Species denotes MHV68 Tax:1440122
2788 224-229 Species denotes mouse Tax:10090
2789 1639-1647 Disease denotes infected MESH:D007239

2_test

Id Subject Object Predicate Lexical cue
32413319-27909575-20790583 775-779 27909575 denotes 2016
32413319-29409532-20790584 794-798 29409532 denotes 2018