PMC:7354481 / 13096-15193
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T77 | 91-95 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T78 | 219-223 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T79 | 562-566 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T80 | 609-613 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T81 | 935-941 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T82 | 1648-1652 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T12 | 91-95 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T52 | 110-118 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T53 | 182-190 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T54 | 964-968 | Disease | denotes | STAR | http://purl.obolibrary.org/obo/MONDO_0010408 |
| T55 | 1185-1188 | Disease | denotes | MDS | http://purl.obolibrary.org/obo/MONDO_0009532|http://purl.obolibrary.org/obo/MONDO_0018881 |
| T57 | 1449-1452 | Disease | denotes | PAM | http://purl.obolibrary.org/obo/MONDO_0018959 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T117 | 91-95 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T118 | 91-95 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T119 | 214-218 | http://purl.obolibrary.org/obo/CLO_0001601 | denotes | A549 |
| T120 | 214-218 | http://purl.obolibrary.org/obo/CLO_0050025 | denotes | A549 |
| T121 | 214-218 | http://purl.obolibrary.org/obo/CLO_0054264 | denotes | A549 |
| T122 | 214-218 | http://purl.obolibrary.org/obo/CLO_0054265 | denotes | A549 |
| T123 | 214-218 | http://purl.obolibrary.org/obo/CLO_0054266 | denotes | A549 |
| T124 | 214-218 | http://purl.obolibrary.org/obo/CLO_0054267 | denotes | A549 |
| T125 | 214-218 | http://purl.obolibrary.org/obo/CLO_0054268 | denotes | A549 |
| T126 | 214-218 | http://purl.obolibrary.org/obo/CLO_0054269 | denotes | A549 |
| T127 | 219-229 | http://purl.obolibrary.org/obo/CLO_0000031 | denotes | cell lines |
| T128 | 562-572 | http://purl.obolibrary.org/obo/CLO_0000031 | denotes | cell lines |
| T129 | 576-577 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T130 | 609-619 | http://purl.obolibrary.org/obo/CLO_0000031 | denotes | cell lines |
| T131 | 719-720 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T132 | 922-934 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | Homo sapiens |
| T133 | 970-972 | http://purl.obolibrary.org/obo/CLO_0050509 | denotes | 27 |
| T134 | 1368-1373 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T135 | 1424-1429 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T136 | 1648-1652 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T137 | 1977-1979 | http://purl.obolibrary.org/obo/CLO_0001313 | denotes | 36 |
| T138 | 2043-2044 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T139 | 2063-2068 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T21 | 1449-1452 | Chemical | denotes | PAM | http://purl.obolibrary.org/obo/CHEBI_51135|http://purl.obolibrary.org/obo/CHEBI_60882 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T89 | 0-230 | Sentence | denotes | Bioproject 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. |
| T90 | 231-389 | Sentence | denotes | The data have been deposited with links to BioProject accession number PRJNA615032 in the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/). |
| T91 | 390-466 | Sentence | denotes | All the selected data were reanalysed at the Rosalind bioinformatics server. |
| T92 | 467-651 | Sentence | denotes | 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 < 0.05 significance level. |
| T93 | 652-807 | Sentence | denotes | Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA, USA). |
| T94 | 808-847 | Sentence | denotes | Reads were trimmed using cutadapt [25]. |
| T95 | 848-895 | Sentence | denotes | Quality scores were assessed using FastQC [26]. |
| T96 | 896-974 | Sentence | denotes | Reads were aligned to the Homo sapiens genome built by GRCh38 using STAR [27]. |
| T97 | 975-1109 | Sentence | denotes | Individual sample reads were quantified using HTseq [28] and normalized via relative log expression (RLE) using DESeq2 R library [29]. |
| T98 | 1110-1250 | Sentence | denotes | Read distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC [30]. |
| T99 | 1251-1353 | Sentence | denotes | DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. |
| T100 | 1354-1571 | Sentence | denotes | 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). |
| T101 | 1572-1702 | Sentence | denotes | Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. |
| T102 | 1703-1848 | Sentence | denotes | The topGO R library [31], was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. |
| T103 | 1849-2004 | Sentence | denotes | Several database sources were referenced for enrichment analysis, including Interpro [32], NCBI [33], MSigDB [34,35], REACTOME [36], and WikiPathways [37]. |
| T104 | 2005-2097 | Sentence | denotes | Enrichment was calculated relative to a set of background genes relevant for the experiment. |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32512929-25977294-144200714 | 843-845 | 25977294 | denotes | 25 |
| 32512929-23104886-144200715 | 1028-1030 | 23104886 | denotes | 28 |
| 32512929-25260700-144200716 | 1105-1107 | 25260700 | denotes | 29 |
| 32512929-25516281-144200717 | 1246-1248 | 25516281 | denotes | 30 |
| 32512929-22743226-144200718 | 1724-1726 | 22743226 | denotes | 31 |
| 32512929-30398656-144200719 | 1946-1948 | 30398656 | denotes | 33 |
| 32512929-19854944-144200720 | 1959-1961 | 19854944 | denotes | 34 |
| 32512929-29145629-144200721 | 2000-2002 | 29145629 | denotes | 37 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 226 | 964-968 | Gene | denotes | STAR | Gene:6770 |
| 227 | 130-138 | Species | denotes | patients | Tax:9606 |
| 228 | 182-192 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 229 | 922-934 | Species | denotes | Homo sapiens | Tax:9606 |
| 230 | 110-129 | Disease | denotes | SARS-CoV-2-infected | MESH:C000657245 |
| 231 | 214-218 | CellLine | denotes | A549 | CVCL:0023 |