PMC:7321036 / 112432-113455
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T43 | 139-142 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T44 | 175-179 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T45 | 180-184 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T46 | 797-801 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T47 | 849-854 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T32 | 175-179 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T392 | 26-34 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T393 | 37-46 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T394 | 829-837 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T97 | 169-174 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T98 | 175-179 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T99 | 175-179 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T100 | 180-190 | http://purl.obolibrary.org/obo/CLO_0000031 | denotes | cell lines |
| T101 | 196-197 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T102 | 263-264 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T103 | 299-300 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T104 | 393-394 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T105 | 505-506 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T106 | 508-509 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T107 | 541-551 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activities |
| T108 | 665-673 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activity |
| T109 | 797-801 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T110 | 849-854 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T50023 | 76-78 | Chemical | denotes | TF | http://purl.obolibrary.org/obo/CHEBI_74862 |
| T82567 | 323-325 | Chemical | denotes | TF | http://purl.obolibrary.org/obo/CHEBI_74862 |
| T37072 | 352-354 | Chemical | denotes | TF | http://purl.obolibrary.org/obo/CHEBI_74862 |
| T63761 | 538-540 | Chemical | denotes | TF | http://purl.obolibrary.org/obo/CHEBI_74862 |
| T25789 | 662-664 | Chemical | denotes | TF | http://purl.obolibrary.org/obo/CHEBI_74862 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T34 | 54-74 | http://purl.obolibrary.org/obo/GO_0000981 | denotes | Transcription Factor |
| T35 | 54-67 | http://purl.obolibrary.org/obo/GO_0006351 | denotes | Transcription |
| T36 | 76-78 | http://purl.obolibrary.org/obo/GO_0000981 | denotes | TF |
| T37 | 323-325 | http://purl.obolibrary.org/obo/GO_0000981 | denotes | TF |
| T38 | 352-354 | http://purl.obolibrary.org/obo/GO_0000981 | denotes | TF |
| T39 | 538-540 | http://purl.obolibrary.org/obo/GO_0000981 | denotes | TF |
| T40 | 662-664 | http://purl.obolibrary.org/obo/GO_0000981 | denotes | TF |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 2362 | 169-174 | Species | denotes | human | Tax:9606 |
| 2363 | 614-619 | Species | denotes | VIPER | Tax:31156 |
| 2364 | 695-700 | Species | denotes | VIPER | Tax:31156 |
| 2365 | 903-908 | Species | denotes | VIPER | Tax:31156 |
| 2366 | 26-46 | Disease | denotes | SARS-CoV-2 infection | MESH:C000657245 |
| 2367 | 829-848 | Disease | denotes | SARS-CoV-2 infected | MESH:C000657245 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T956 | 0-250 | Sentence | denotes | To evaluate the effect of SARS-CoV-2 infection at the Transcription Factor (TF) level, we applied DoRothEA (Garcia-Alonso et al., 2019) to RNA-seq datasets of different human lung cell lines from a recent study (GSE147507) (Blanco-Melo et al., 2020). |
| T957 | 251-346 | Sentence | denotes | DoRothEA is a comprehensive resource containing a curated collection of TF-target interactions. |
| T958 | 347-455 | Sentence | denotes | Each TF-target interaction is associated with a confidence level based on the number of supporting evidence. |
| T959 | 456-653 | Sentence | denotes | Here we selected the most reliable interactions (A, B, and C levels) and computed TF activities based on the normalized expression of their targets using the VIPER algorithm (Alvarez et al., 2016). |
| T960 | 654-892 | Sentence | denotes | For the TF activity enrichment analysis, VIPER was executed with the Wald statistic resulting from the differential expression analysis at the gene level between controls and SARS-CoV-2 infected cells using the DESeq2 package (Love et al. |
| T961 | 893-899 | Sentence | denotes | 2014). |
| T962 | 900-1023 | Sentence | denotes | In VIPER, we set the eset.filter parameter to FALSE and consider five as the minimum number of targets allowed per regulon. |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32645325-31340985-20773123 | 130-134 | 31340985 | denotes | 2019 |
| 32645325-32416070-20773124 | 244-248 | 32416070 | denotes | 2020 |
| 32645325-27322546-20773125 | 647-651 | 27322546 | denotes | 2016 |
| 32645325-25516281-20773126 | 893-897 | 25516281 | denotes | 2014 |