PMC:7417788 / 64374-66944
Annnotations
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1425 | 64-72 | CHEBI:28073;CHEBI:28073 | denotes | Chromium |
| T1426 | 114-122 | CHEBI:28073;CHEBI:28073 | denotes | chromium |
| T1427 | 346-354 | CHEBI:28073;CHEBI:28073 | denotes | Chromium |
| T1428 | 373-380 | CHEBI:33893;CHEBI:33893 | denotes | Reagent |
| T1429 | 919-923 | SO:0000704;GO:0010467 | denotes | gene |
| T1430 | 924-934 | GO:0010467 | denotes | expression |
| T1431 | 996-1006 | GO:0010467 | denotes | expression |
| T1432 | 1351-1358 | GO:0010467 | denotes | express |
| T1433 | 1359-1362 | PR:000008457 | denotes | HBB |
| T1434 | 1364-1368 | PR:000008856 | denotes | HBA1 |
| T1435 | 1404-1415 | SO:0000673 | denotes | transcripts |
| T1436 | 1441-1444 | CL:0000232 | denotes | RBC |
| T1437 | 1502-1512 | GO:0010467 | denotes | expressing |
| T1438 | 1513-1518 | SO:0000704 | denotes | genes |
| T1439 | 1566-1574 | SO:0001026 | denotes | genomics |
| T1440 | 2022-2027 | SO:0000704 | denotes | genes |
| T1441 | 2096-2108 | GO:0005739 | denotes | mitochondria |
| T1442 | 2119-2128 | GO:0005840 | denotes | ribosomes |
| T1443 | 2143-2148 | SO:0000704 | denotes | genes |
| T1444 | 2501-2506 | SO:0000704 | denotes | Genes |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T460 | 80-84 | Body_part | denotes | Cell | http://purl.org/sig/ont/fma/fma68646 |
| T461 | 239-243 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T462 | 303-307 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T463 | 308-311 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T464 | 362-366 | Body_part | denotes | Cell | http://purl.org/sig/ont/fma/fma68646 |
| T465 | 370-372 | Body_part | denotes | v2 | http://purl.org/sig/ont/fma/fma13443|http://purl.org/sig/ont/fma/fma68615 |
| T467 | 656-660 | Body_part | denotes | Cell | http://purl.org/sig/ont/fma/fma68646 |
| T468 | 805-809 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T469 | 810-813 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T470 | 919-923 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T471 | 991-995 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T472 | 1307-1311 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T473 | 1340-1345 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T474 | 1458-1462 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T475 | 1581-1585 | Body_part | denotes | Cell | http://purl.org/sig/ont/fma/fma68646 |
| T476 | 1769-1774 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T477 | 1786-1791 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T478 | 1803-1808 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T479 | 1898-1903 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T480 | 1915-1920 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T481 | 1932-1937 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T482 | 1950-1955 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T483 | 1968-1973 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T484 | 2119-2128 | Body_part | denotes | ribosomes | http://purl.org/sig/ont/fma/fma66867 |
| T485 | 2527-2531 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T138 | 2265-2268 | Disease | denotes | SNE | http://purl.obolibrary.org/obo/MONDO_0018859 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1088 | 80-84 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | Cell |
| T1089 | 239-243 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1090 | 303-307 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1091 | 362-366 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | Cell |
| T1092 | 656-660 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | Cell |
| T1093 | 805-809 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1094 | 919-923 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T1095 | 991-995 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1096 | 1095-1097 | http://purl.obolibrary.org/obo/CLO_0037161 | denotes | en |
| T1097 | 1307-1311 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1098 | 1340-1345 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1099 | 1441-1444 | http://purl.obolibrary.org/obo/CL_0000232 | denotes | RBC |
| T1100 | 1458-1462 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1101 | 1513-1518 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T1102 | 1519-1522 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T1103 | 1581-1585 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | Cell |
| T1104 | 1696-1701 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T1105 | 1717-1718 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T1106 | 1769-1774 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1107 | 1786-1791 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1108 | 1793-1795 | http://purl.obolibrary.org/obo/CLO_0001627 | denotes | AA |
| T1109 | 1803-1808 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1110 | 1870-1875 | http://purl.obolibrary.org/obo/CLO_0001294 | denotes | 3, 22 |
| T1111 | 1898-1903 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1112 | 1915-1920 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1113 | 1932-1937 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1114 | 1950-1955 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1115 | 1968-1973 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1116 | 2022-2027 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T1117 | 2143-2148 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T1118 | 2501-2506 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | Genes |
| T1119 | 2527-2531 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T66017 | 64-72 | Chemical | denotes | Chromium | http://purl.obolibrary.org/obo/CHEBI_28073 |
| T92241 | 114-122 | Chemical | denotes | chromium | http://purl.obolibrary.org/obo/CHEBI_28073 |
| T117 | 346-354 | Chemical | denotes | Chromium | http://purl.obolibrary.org/obo/CHEBI_28073 |
| T55021 | 1095-1097 | Chemical | denotes | en | http://purl.obolibrary.org/obo/CHEBI_30347 |
| T11829 | 1776-1778 | Chemical | denotes | YA | http://purl.obolibrary.org/obo/CHEBI_74879 |
| T87384 | 1793-1795 | Chemical | denotes | AA | http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816 |
| T1892 | 1905-1907 | Chemical | denotes | YH | http://purl.obolibrary.org/obo/CHEBI_73695 |
| T95792 | 1922-1924 | Chemical | denotes | AH | http://purl.obolibrary.org/obo/CHEBI_73771 |
| T124 | 2066-2069 | Chemical | denotes | PCA | http://purl.obolibrary.org/obo/CHEBI_36751|http://purl.obolibrary.org/obo/CHEBI_62248 |
| T52524 | 2110-2112 | Chemical | denotes | MT | http://purl.obolibrary.org/obo/CHEBI_73614 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T296 | 919-934 | http://purl.obolibrary.org/obo/GO_0010467 | denotes | gene expression |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T356 | 0-59 | Sentence | denotes | scRNA-seq data alignment, processing and sample aggregation |
| T357 | 60-295 | Sentence | denotes | The Chromium Single Cell 5′ Library (the 10x Genomics chromium platform Illumina NovaSeq6000), Gel Bead and Multiplex Kit, and Chip Kit (10x Genomics) were used to convert single-cell suspension samples to barcoded scRNA-seq libraries. |
| T358 | 296-444 | Sentence | denotes | Single-cell RNA libraries were prepared using the Chromium Single Cell 5′ v2 Reagent (10x Genomics, 120237) kit as per the manufacturer’s protocols. |
| T359 | 445-512 | Sentence | denotes | The quality of the libraries was checked using the FastQC software. |
| T360 | 513-643 | Sentence | denotes | Initial processing of the sequenced data was performed using CellRanger software (https://support.10xgenomics.com, version 3.1.0). |
| T361 | 644-827 | Sentence | denotes | The command Cell Ranger count in CellRanger Software Suite (10x Genomics) was used to demultiplex and barcode the sequences derived from the 10x Genomics single-cell RNA-seq platform. |
| T362 | 828-1132 | Sentence | denotes | The data was filtered, normalized, dimensionality was reduced, clustered, and differential gene expression analysis were performed after calculation of the single-cell expression matrix by CellRanger using Python (version 3.7.7) Scanpy (https://scanpy.readthedocs.io/en/stable/index.html, version 1.4.6). |
| T363 | 1133-1272 | Sentence | denotes | Data collection and the subsequent analyses were performed in an unsupervised manner, but not blinded to the conditions of the experiments. |
| T364 | 1273-1474 | Sentence | denotes | For quality control, the filtered cell population was mainly those cells that express HBB, HBA1, and several light and heavy chain transcripts, which identified as the RBC-contaminated cell population. |
| T365 | 1475-1620 | Sentence | denotes | Likewise, several clusters expressing genes has no significance (P ≥ 0.1, calculate by 10x genomics Loupe Cell Browser with it default algorithm. |
| T366 | 1621-1716 | Sentence | denotes | P values are adjusted using the Benjamini-Hochberg correction for multiple tests) were removed. |
| T367 | 1717-1858 | Sentence | denotes | A total of 16 libraries were sequenced, and 166,609 cells (YA 77,652 cells, AA 88,957 cells) were analyzed after quality control in cohort-1. |
| T368 | 1859-2017 | Sentence | denotes | For cohort-3, 22 libraries and 205,434 cells (YH 79,039 cells, AH 88,750 cells, YCR 19,533 cells, ACR 18,112 cells) were remained for the subsequent analysis. |
| T369 | 2018-2317 | Sentence | denotes | The genes used in principal component analysis (PCA) analysis have eliminated mitochondria (MT), and ribosomes (RPL and RPS) genes with 50 principal components, and then aligned together, followed by t-distributed stochastic neighbor embedding (t-SNE) are both used after the results of the aligned. |
| T370 | 2318-2500 | Sentence | denotes | And using the run_harmony function (in pyharmony package, version 1.0.7) and combat function (in Scanpy) methods to deal with batch effect issues if batch effect existing in dataset. |
| T371 | 2501-2570 | Sentence | denotes | Genes not detected in any cell were removed from subsequent analysis. |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 1445 | 178-181 | Gene | denotes | Kit | Gene:3815 |
| 1446 | 404-407 | Gene | denotes | kit | Gene:3815 |
| 1447 | 192-195 | Gene | denotes | Kit | Gene:3815 |
| 1448 | 64-72 | Chemical | denotes | Chromium | MESH:D002857 |
| 1449 | 114-122 | Chemical | denotes | chromium | MESH:D002857 |
| 1453 | 1359-1362 | Gene | denotes | HBB | Gene:3043 |
| 1454 | 1364-1368 | Gene | denotes | HBA1 | Gene:3039 |
| 1455 | 1922-1924 | Disease | denotes | AH | MESH:D007039 |